Article
Mathematical & Computational Biology
Lou E. Whitehead, Oliver Sailer, Miles D. Witham, James M. S. Wason
Summary: Basket trials are a novel clinical trial design that investigate a single intervention in multiple patient subgroups called baskets. They have advantages of reduced sample sizes, increased efficiency, and reduced costs compared to separate trials. Primarily used in Phase II oncology settings, basket trials could also be beneficial in other areas with shared biological mechanisms, like chronic aging-related diseases.
STATISTICS IN MEDICINE
(2023)
Article
Pharmacology & Pharmacy
Shufang Liu, Kentaro Takeda, Alan Rong
Summary: The phase II basket trial in oncology is a novel design that evaluates the treatment effects of a targeted anticancer agent in multiple cancer types simultaneously. The proposed two-stage adaptive biomarker basket (ABB) design selects biomarker-positive (BM+) subjects who are most sensitive to the treatment and assesses early efficacy and futility using pre-defined interim analyses. Extensive simulation studies demonstrate the superior performance of the ABB design in estimating the biomarker cutoff and selecting BM+ subjects.
PHARMACEUTICAL STATISTICS
(2023)
Article
Mathematical & Computational Biology
Kentaro Takeda, Shufang Liu, Alan Rong
Summary: The basket trial is a novel clinical trial design that evaluates the effectiveness of a treatment in multiple cancer types simultaneously. By incorporating additional classifiers like biomarkers, the treatment effects can be categorized more accurately among different baskets. The constrained hierarchical Bayesian model for latent subgroups (CHBM-LS) allows adaptive information borrowing across baskets by identifying latent subgroups, ultimately improving the handling of heterogeneous treatment effects in basket trials.
STATISTICS IN MEDICINE
(2022)
Article
Biochemical Research Methods
Shaima Belhechmi, Gwenael Le Teuff, Riccardo De Bin, Federico Rotolo, Stefan Michiels
Summary: This study aimed to find a compromise between the need for sparse model selection and the hierarchical constraint of biomarker-treatment interactions in high-dimensional data. Two weighting approaches and a group exponential Lasso method were proposed and compared with alternative methods. The results showed that the adaptive Lasso and group exponential Lasso methods outperformed their competitors in favoring the hierarchical constraint.
BMC BIOINFORMATICS
(2023)
Article
Health Care Sciences & Services
Valentin Vinnat, Djillali Annane, Sylvie Chevret
Summary: Precision medicine is changing healthcare by addressing patient variability and the need for innovative methods. In this study, a Bayesian sequential scheme was introduced to evaluate therapeutic interventions in an intensive care unit setting. By using a zero-inflated truncated Poisson model, the complexity of the data was efficiently addressed.
JOURNAL OF PERSONALIZED MEDICINE
(2023)
Article
Statistics & Probability
Luke O. Ouma, Michael J. Grayling, James M. S. Wason, Haiyan Zheng
Summary: Basket trials are innovative precision medicine clinical trial designs that evaluate a single targeted therapy across multiple diseases. By borrowing information, considering the comparability of treatment effects and outcomes between subtrials, substantial gains can be achieved. Different modeling strategies perform differently in various situations and may lead to different conclusions in the analysis of real data.
JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES C-APPLIED STATISTICS
(2022)
Article
Mathematics, Interdisciplinary Applications
Peter F. Thall
Summary: Adaptive enrichment designs for clinical trials have various functions such as identifying patient subgroups, selecting or comparing treatments based on interim data, or changing entry criteria; the structure of these designs depends on goals, patient heterogeneity, treatment effects, and practical constraints; this article covers basic concepts and different types of enrichment, with numerical examples for qualitative different cases involving treatment-biomarker interactions.
ANNUAL REVIEW OF STATISTICS AND ITS APPLICATION, VOL 8, 2021
(2021)
Article
Mathematical & Computational Biology
Yilin Liu, Michael Kane, Denise Esserman, Ondrej Blaha, Daniel Zelterman, Wei Wei
Summary: The paper proposes an information borrowing strategy for the design and monitoring of phase II basket trials based on the local multisource exchangeability assumption between baskets. The proposed method is able to maintain the family-wise type I error rate at a reasonable level and has desirable basket-wise power.
STATISTICS IN MEDICINE
(2022)
Article
Pharmacology & Pharmacy
Chian Chen, Chin-Fu Hsiao
Summary: Basket trials in cancer research evaluate the effects of a single drug targeting a specific genetic variant across multiple cancer cohorts. Heterogeneity in treatment efficacy among these cohorts poses a challenge to the exchangeability assumption in Bayesian hierarchical modeling, which is commonly used in modern basket trial designs. This study provides recommendations for selecting prior distributions for scale parameters in adaptive basket trials using Bayesian hierarchical modeling, and evaluates the performance of the design through simulation studies on statistical power and type I error rates. Our research contributes to the understanding of the properties of Bayesian basket trial designs.
PHARMACEUTICAL STATISTICS
(2023)
Article
Mathematical & Computational Biology
Lauren Kanapka, Anastasia Ivanova
Summary: A basket trial is designed to speed up the drug development process by evaluating a new therapy in multiple populations within the same clinical trial. This paper proposes a frequentist approach to dynamic borrowing for basket trials using adaptive lasso. Simulation studies show that adaptive lasso can achieve similar power and type 1 error as existing Bayesian methods, while being easier to implement and faster. The proposed approach is flexible and can be extended to basket trials with any number of treatment arms and any type of endpoint.
STATISTICS IN MEDICINE
(2023)
Article
Mathematical & Computational Biology
Matthew A. Psioda, Jiawei Xu, Qi Jiang, Chunlei Ke, Zhao Yang, Joseph G. Ibrahim
Summary: This article introduces a Bayesian adaptive design methodology for oncology basket trials with binary endpoints, which provides more accurate estimation of response rates for individual baskets. Compared to existing methods, this approach better handles differences in activity across baskets and performs favorably in terms of computational feasibility and accuracy.
Review
Oncology
Alyson Haslam, Timothee Olivier, Jordan Tuia, Vinay Prasad
Summary: The utilization of basket trials in oncology has increased, but the overall response rate is low and varies widely depending on tumor type and genetic biomarker. It is unknown if the increasing options for less-common tumor types in basket trials have translated into patient benefit. There is also no strong correlation between the number of participants in each tumor basket and the incidence of the respective tumor.
Article
Health Care Sciences & Services
Xin Chen, Jingyi Zhang, Liyun Jiang, Fangrong Yan
Summary: This study proposes a statistical tool called 'IBIS' to identify biomarker-based subgroups and applies it to the enrichment design framework. IBIS consists of three main elements: subgroup division, efficacy evaluation, and subgroup identification. The proposed IBIS has superior and robust characteristics compared with traditional methods in terms of subgroup identification and population enrichment. Simulation studies demonstrate the accuracy and precision of IBIS in terms of estimation performance.
BMC MEDICAL RESEARCH METHODOLOGY
(2023)
Article
Mathematical & Computational Biology
Haiyan Zheng, James M. S. Wason
Summary: Basket trials have emerged as a new efficient approach in oncology for evaluating new treatments across multiple patient subgroups simultaneously. This article expands on the key ideas and applies them to disease areas beyond oncology. It introduces a robust Bayesian methodology for randomized, placebo-controlled basket trials with a continuous endpoint, allowing for borrowing of information across subtrials with similar treatment effects. The proposed methodology is evaluated through simulations and demonstrates advantages over other Bayesian analysis models in terms of identifying the most commensurate source of information and gauging the degree of borrowing from specific subtrials. Numerical results indicate that the methodology can improve the precision of estimates and potentially enhance the statistical power for hypothesis testing.
Article
Mathematical & Computational Biology
Haiyan Zheng, Michael J. Grayling, Pavel Mozgunov, Thomas Jaki, James M. S. Wason
Summary: Basket trials are increasingly used for evaluating new treatments in different patient subgroups. This paper proposes a Bayesian approach to determine sample size in basket trials, allowing information borrowing between similar subsets. The proposed approach yields comparable sample sizes for circumstances of no borrowing, and significantly reduces sample size when borrowing is enabled between commensurate subtrials. Examples and simulation studies demonstrate the feasibility and effectiveness of the proposed methodology.
Article
Otorhinolaryngology
Yangyang Zheng, Hongming Xu, Xiaoyan Li
Summary: This study retrospectively reviewed 49 pediatric patients with subglottic stenosis and found that endoscopic balloon dilatation can be safe and effective in the treatment of subglottic stenosis in children. However, for patients with more severe cases (grade IV), open surgery should be considered.
EUROPEAN ARCHIVES OF OTO-RHINO-LARYNGOLOGY
(2023)
Article
Chemistry, Applied
Yinxiao Zhang, Chi Zhang, Shuya Zhu, Jingyi Wang, He Li, Xinqi Liu
Summary: This study identified and analyzed digested soybean peptides (dPEP) utilized by L. rhamnosus Lra05 after 36 hours. The findings showed that L. rhamnosus Lra05 preferentially utilizes hydrophobic peptides with three to five amino acid residues and hydrophilic peptides with more than five residues. Moreover, they tend to use peptides with proline at penultimate C-terminal position or arginine at ultimate C-terminal position. Fraction 1 (F1) and fraction 7 (F7) obtained from dPEP exhibited the strongest growth and metabolism promoting effects, and their characteristics were similar to dPEP. These results provide a theoretical basis for the application of soybean peptides as potential prebiotics.
Review
Oncology
Yunshan Li, Feihan Gu, Yaodong He, Junwei Xiang, Xu Huang, Yuanyin Wang, Ran Chen
Summary: Adenoid cystic carcinoma (ACC) is a rare tumor that usually occurs in the salivary glands, accounting for 1% of all head and neck cancers. Studies have found an association between miRNAs and ACC, and miRNAs are becoming reliable biomarkers for disease detection.
INTERNATIONAL JOURNAL OF ONCOLOGY
(2023)
Article
Chemistry, Physical
Xiao-Gang Wang, Tucker Carrington Jr
Summary: Due to the ubiquity and importance of water, water dimer has been extensively studied. Despite the challenges of computing the (ro-)vibrational spectrum of water dimer, a variational approach using a product contracted basis is used in this study. The full G(16) symmetry of water dimer is exploited, and the results are compared with experimental data. The study reveals surprising findings regarding tunneling splittings and vibrational shifts, and differences with previous approaches.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Biochemistry & Molecular Biology
Hua Cheng, Ziyan Guo, Xiaoyu Zhang, Xiao-Jin Wang, Zizhang Li, Wen -Wen Huo, Hong-Cheng Zhong, Xiao-Jian Li, Xiang -Wen Wu, Wen-Hao Li, Zhuo-Wen Chen, Tian -Chi Wu, Xiang-Feng Gan, Bei-Long Zhong, Vassily A. Lyubetsky, Leonid Yu Rusin, Junnan Yang, Qiyi Zhao, Qing-Dong Cao, Jian-Rong Yang
Summary: Multiple primary lung cancer (MPLC) is a common subtype of lung cancer, and the lesions of a single MPLC patient show functional similarities that may reflect evolutionary convergence. However, whole-exome sequencing and evolutionary tree reconstruction reveal that cancer driver gene mutations occur early in the evolution, suggesting evolutionary contingency rather than adaptive convergence. The genetic diversity within a tumor is lower than the diversity between tumors from the same MPLC patient. These findings suggest that personalized therapies should be designed and delivered on a per-lesion basis to account for the genetic diversity among different tumors in an MPLC patient.
JOURNAL OF GENETICS AND GENOMICS
(2023)
Article
Chemistry, Physical
Kaihui Ji, Yanan Liu, Yinghua Luo, Xue Zhang, Yufan Bai, Hailong Yue, Pengtao Ma, Jingyang Niu, Jingping Wang
Summary: The development of high-efficiency photocatalysts is of vital importance in solving the problems of low efficiency and harsh conditions in organic oxidation reactions. This study successfully synthesized a novel hybrid polyoxometalate crystal, RuCd-SiW, which showed excellent photocatalytic activity for the selective oxidation of thioanisole under visible light irradiation.
JOURNAL OF PHYSICAL CHEMISTRY C
(2023)
Article
Engineering, Mechanical
Jie Hong, Zhefu Yang, Yongfeng Wang, Ronghui Cheng, Yanhong Ma
Summary: This paper investigates the combination resonances of bolted rotor systems with asymmetric preloads under multi-frequency excitation and proposes a new breathing model. Theoretical and experimental studies demonstrate that combination resonances could occur in practical dual rotor systems near specific frequencies.
MECHANICAL SYSTEMS AND SIGNAL PROCESSING
(2023)
Article
Chemistry, Multidisciplinary
Jie Tang, Chong Liu, Chenyu Zhu, Keju Sun, He Wang, Wen Yin, Chuting Xu, Yang Li, Weiguo Wang, Li Wang, Renan Wu, Chao Liu, Jiahui Huang
Summary: By controlling the reduction speed, we synthesized a unique copper nanocluster with strong cuprophilic interaction and revealed the key steps in the nucleation process.
Article
Physics, Fluids & Plasmas
Sizhe Duan, Xiaogang Wang, Huishan Cai, Ding Li
Summary: The nonlinear interaction between the m/n = 2/1 beta-induced Alfvén eigenmode (BAE) and the m/n = 2/1 tearing mode (TM) was studied in the HL-2A experiment using the hybrid kinetic-magnetohydrodynamic code M3D-K. Results showed that the nonlinear growth of TM can lead to gradient buildup on the magnetic island (MI) edge, triggering the destabilization of the linearly-stable BAE. The triggered BAE, along with TM, redistributes energetic particles and causes inward motion of the BAE mode structure, resulting in a delay effect on the MI's saturation. Furthermore, the mode coupling of BAE and TM generates a high-frequency axisymmetric m/n = 0/0 "breathing" mode, causing synchronized periodic oscillation of MI width in agreement with experimental observations.
Article
Astronomy & Astrophysics
Jing-jing Wang, Meng Guo, Lin-qiao Jiang, Bin Zhang
Summary: Two sets of CCD photometric observations were obtained for contact binary TU Boo in 2020 and 2021. The new light curves revealed that the heights of maximum were almost equal, which is different from previous studies. These distortions indicate past activity of the components, but stability in recent years. The symmetric multi-color light curves in 2020 and 2021 are important for understanding the configuration and evolution of this system.
RESEARCH IN ASTRONOMY AND ASTROPHYSICS
(2023)
Article
Clinical Neurology
Huihui Liu, Jing Jing, Anxin Wang, Qin Xu, Xia Meng, Hao Li, Zixiao Li, Yongjun Wang
Summary: This study compared the risk of stroke recurrence and the responses to dual antiplatelets with ticagrelor-aspirin versus clopidogrel-aspirin between patients with posterior circulation infarct (PCI) and those with anterior circulation infarct (ACI). The study found that the risk of stroke recurrence was similar between PCI and ACI patients, and ticagrelor-aspirin was superior to clopidogrel-aspirin in reducing the risk of stroke in both PCI and ACI patients within 90 days.
Article
Materials Science, Multidisciplinary
Meng-Ting Jiang, Qian Yang, Jian-Long Xu, Yu Yuan, Jing-Yue Zhang, Ya-Nan Zhong, Xu Gao, Sui-Dong Wang
Summary: Monolithically integrated pixels with stacked PbS colloidal quantum dot (CQD) photodiodes and organic blocking diodes are developed for short-wavelength infrared (SWIR) crossbar imaging arrays. These pixels exhibit normally-OFF behavior due to hole blocking under zero and forward biases. This monolithic integration effectively suppresses electrical crosstalk and reduces standby power consumption, resulting in a high-performance visible-SWIR imaging sensor.
ADVANCED OPTICAL MATERIALS
(2023)
Article
Geosciences, Multidisciplinary
Tinghui Yang, Nannan Yu, Tianren Yang, Tao Hong
Summary: In this study, the concept of social recovery is proposed and a comprehensive perspective on how a city's socioeconomic characteristics affect its social recovery is developed. The results indicate that cities with larger populations, a higher proportion of GDP in the secondary industry, higher road density, or more adequate medical resources tend to recover socially better. Furthermore, these municipal characteristics have significant spatial spillover effects.
INTERNATIONAL JOURNAL OF DISASTER RISK REDUCTION
(2023)
Review
Psychiatry
Wenhao Zong, Xiaowen Lu, Guijun Dong, Li Zhang, Kefeng Li
Summary: Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by stereotyped behaviors, impaired social and communication skills, and synaptic deficits. Exercise intervention has been shown to improve ASD symptoms by regulating synaptic plasticity, but the underlying molecular mechanisms are still unclear. This review highlights the synaptic structural alterations in ASD and the beneficial effects of exercise intervention on ASD symptoms. Moreover, it explores the possible molecular mechanisms of exercise intervention in improving ASD symptoms through regulating synaptic plasticity, which may contribute to optimizing exercise intervention strategies for ASD rehabilitation in the future.
FRONTIERS IN PSYCHIATRY
(2023)
Article
Cell Biology
Wenping Hu, Xinyue Wang, Yazhen Bi, Jingjing Bao, Mingyu Shang, Li Zhang
Summary: This study aims to reveal the molecular mechanism underlying sheep embryonic skeletal muscle development through transcriptome data analysis and molecular biology confirmation. miRNA-mediated competitive endogenous RNA networks were constructed, and three miRNAs and three genes related to muscle development were identified. The regulatory relationship between miR-410-5p and the TEAD1 gene in sheep embryonic myoblasts was validated, providing a reference and molecular basis for understanding the molecular mechanism of embryonic muscle development.