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2024 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2024

作者： Lai, Xin Yang, Xiaohai Wang, Jiayin Zhu, Xiaoyan liu, Yuqian liu, Ruoyu Wang, xuwen Wang, Shenjie Xi'an Jiaotong University School of Computer Science and Technology Xi'an China

ISBN: (纸本)9798350386226

In genome-wide association studies (GWAS) and candidate gene studies (CGS), appropriate multiple testing correction methods can effectively address linkage disequilibrium (LD) blocks and are crucial for controlling the family-wise error rate (FWER) while ensuring the reliability of results. In our recent research, we observed that when the number of independent effective Single Nucleotide Polymorphisms (SNPs) is relatively small, existing multiple testing correction methods struggle to effectively control the FWER at 0.05 and lack robustness. This study proposes an enhanced method that builds upon the Moskvina and Schmidt approach by incorporating additional SNP correlation information, allowing for precise control of the FWER at 0.05 with limited independent effective SNPs. We also leverage Monte Carlo integration on a GPU to accelerate the computation of significance thresholds. Our method was evaluated through both simulation studies and real genotype datasets, demonstrating superior performance and robustness compared to existing methods. © 2024 IEEE.

关键词： Genome

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Ru(II)-base d aggregation-induce d emission (AIE) agents with efficient 1 O2 generation, photo-catalytic NADH oxidation and anticancer activity

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CHINESE CHEMICAL LETTERS 2025年第5期36卷

作者： Xu, Yunli Da, xuwen Wang, Lei Peng, Yatong Zhou, Wanpeng liu, Xiulian Wu, Yao Wang, Wentao Wang, Xuesong Zhou, Qianxiong Chinese Acad Sci Tech Inst Phys & Chem Key Lab Photochem Convers & Optoelect Mat Beijing 100190 Peoples R China Univ Chinese Acad Sci Beijing 100049 Peoples R China Univ Chinese Acad Sci Wenzhou Inst Wenzhou 325000 Peoples R China

Photodynamic therapy (PDT) has received much attention in recent years. However, traditional photosensitizers (PSs) applied in PDT usually suffer from aggregation-caused quenching (ACQ) effect in H2 O, single and inefficient photochemical mechanism of action (MoA), poor cancer targeting ability, etc . In this work, two novel Ru(II)-based aggregation-induced emission (AIE) agents (Ru1 and Ru2) were developed. Both complexes exhibited long triplet excited lifetimes and nearly 100 % singlet oxygen quantum yields in H2 O. In addition, Ru1 and Ru2 displayed potent photo-catalytic reduced nicotinamide adenine dinucleotide (NADH) oxidation activity with turnover frequency (TOF) values of about 1779 and 20 0 0 h-1 , respectively. Therefore, both Ru1 and Ru2 showed efficient PDT activity towards a series of cancer cells. Moreover, Ru2 was further loaded in bovine serum albumin (BSA) to enhance the tumor targeting ability in vivo , and the obtained Ru2@BSA could selectively accumulate in tumor tissues and effectively inhibit tumor growth on a 4T1 tumor-bearing mouse model. So far as we know, this work represents the first report about Ru(II) AIE agents that possess high singlet oxygen quantum yields and also potent photocatalytic NADH oxidation activity, and may provide new ideas for rational design of novel PSs with efficient PDT activity. (c) 2025 Published by Elsevier B.V. on behalf of Chinese Chemical Society and Institute of Materia Medica, Chinese Academy of Medical Sciences.

关键词： Ru(II) complexes Aggregation-induced emission Photo-catalytic NADH oxidation Photodynamic therapy Turnover frequency

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Decoupling of the Confused Complex in Oxidation of 3,3′,5,5′-Tetramethylbenzidine for the Reliable Chromogenic Bioassay

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ANALYTICAL CHEMISTRY 2023年第44期95卷 16407-16417页

作者： Zhu, Caixia Yang, Hong Cao, xuwen Hong, Qing Xu, Yuan Wang, Kaiyuan Shen, Yanfei liu, Songqin Zhang, Yuanjian Southeast Univ Sch Chem & Chem Engn Med Sch Jiangsu Engn Lab Smart Carbon Rich Mat & DevicesJ Nanjing Peoples R China

Regulation of the reaction pathways is a perennial theme in the field of chemistry. As a typical chromogenic substrate, 3,3 ',5,5 '-tetramethylbenzidine (TMB) generally undertakes one-electron oxidation, but the product (TMBox1) is essentially a confused complex and is unstable, which significantly hampers the clinic chromogenic bioassays for more than 50 years. Herein, we report that sodium dodecyl sulfate (SDS)-based micelles could drive the direct two-electron oxidation of TMB to the final stable TMBox2. Rather than activation of H2O2 oxidant in the one-electron TMB oxidation by common natural peroxidase, activation of the TMB substrate by SDS micelles decoupled the thermodynamically favorable complex between TMBox2 with unreacted TMB, leading to an unusual direct two-electron oxidation pathway. Mechanism studies demonstrated that the complementary spatial and electrostatic isolation effects, caused by the confined hydrophobic cavities and negatively charged outer surfaces of SDS micelles, were crucial. Further cascading with glucose oxidase, as a proof-of-concept application, allowed glucose to be more reliably measured, even in a broader range of concentrations without any conventional strong acid termination.

关键词： Carbohydrates Micelles Oxidation Oxidation reactions Reaction products

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An Improved Design of Atomic-Beam Fluorescence Collector 37

An Improved Design of Atomic-Beam Fluorescence Collector

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37th European Frequency and Time Forum, EFTF 2024

作者： Hu, xuwen Sun, Fuyu Li, Chao liu, Jie Li, Xiaofeng Zhang, Shougang National Time Service Center Chinese Academy of Sciences Xi'an China Chinese Academy of Sciences Key Laboratory of Time Reference and Applications Xi'an China

ISBN: (纸本)9798350354270

Efficient fluorescence detection is crucial in the field of precision spectral analysis. This paper presents an improved design of an atomic-beam fluorescence collector that utilizes the convergence characteristics of ellipsoidal surfaces and the reflection characteristics of spherical surfaces. It calculates the parameter relationship for achieving full-angle fluorescence collection. The study fine-tunes the structural parameters and simulates the fluorescence collection efficiency and losses under different conditions when emitting from a non-ideal point light source. The improved fluorescence collector captures photons with nearly 4n solid angle coverage, allowing photons to be reflected at most twice before reaching the photo detector, thereby increasing collection efficiency. This improved collector can be used in various fields for detecting weak fluorescence signals. © 2024 IEEE.

关键词： Fluorescence microscopy

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基于四方对称光源透射光谱的脐橙可溶性固形物检测

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农业工程学报 2019年第10期35卷 267-273页

作者：宋杰李光林杨晓东张信刘旭文西南大学工程技术学院

提高利用可见-近红外(Vis-NIR)透射光谱检测脐橙内部物质含量的准确性在生产实际中具有重要意义。该研究利用特制的可见-近红外透射光谱测量装置采集了199个福本脐橙果蒂向上、水平、向下3种位置的透射光谱,比较了多元散射校正(multivar... 详细信息

提高利用可见-近红外(Vis-NIR)透射光谱检测脐橙内部物质含量的准确性在生产实际中具有重要意义。该研究利用特制的可见-近红外透射光谱测量装置采集了199个福本脐橙果蒂向上、水平、向下3种位置的透射光谱,比较了多元散射校正(multivariate scattering correction,MSC)、标准正态变量变换(standard normal variate transformation,SNV)、一阶导数和二阶导数预处理的效果,并采用效果最好的一阶导数对透射光谱进行预处理。在此基础上,结合后向区间偏最小二乘法(backward interval partial least squares,BiPLS)优选特征波段,竞争性自适应重加权采样(competitive adaptive re-weightedsampling,CARS)挑选特征变量建立了基于果蒂向上、水平、向下3种位置各自的透射光谱以及3种位置的平均光谱和加权光谱的可溶性固形物(soluble solid content,SSC)的偏最小二乘(partial least squares,PLS)模型。在果蒂向上、水平、向下3种位置各自的透射光谱建立的PLS模型中,基于果蒂水平位置透射光谱的PLS模型最优,校正相关系数为0.914,校正均方根误差为0.380,预测相关系数为0.924,预测均方根误差为0.404。基于果蒂向上、水平、向下3种位置平均透射光谱和加权透射光谱建立的PLS模型均取得了较好的预测结果,预测相关系数均大于0.91,预测均方根误差均小于0.43。该研究可以为脐橙内部物质含量在线检测装备的研制提供参考。

关键词：果实光谱分析模型脐橙四方对称光源透射可溶性固形物

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RMComBat: A Batch Effect Correction Algorithm for Repeated Measurement Sequencing Data to Prevent Overcorrection

RMComBat: A Batch Effect Correction Algorithm for Repeated M...

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2024 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2024

作者： liu, Yuqian Wei, Zhaoxing Wang, Jiayin Zhu, Xiaoyan liu, Ruoyu Wang, xuwen Wang, Shenjie Lai, Xin Xi'an Jiaotong University School of Computer Science and Technology Xi'an China Second Affiliated Hospital Xi'an Jiaotong University Department of Respiratory and Critical Care Medicine Xi'an China

ISBN: (纸本)9798350386226

Batch effects, caused by non-biological variations such as differences in laboratory conditions, reagent lots, or personnel, are a substantial source of noise in gene expression data. Accurately correcting these effects is crucial for valid biological inferences. However, the majority of existing batch effect correction algorithms are prone to overcorrection, where biologically meaningful signals are mistakenly identified as noise, especially in repeated measurement studies where time is confounded with batch. The failure to accurately distinguish between batch-related and biologically relevant variation leads to a loss of critical biological information. This paper presents RMComBat, an enhancement of the widely-used ComBat framework, which addresses this limitation by replacing the general linear model with a linear mixed-effects model. RMComBat incorporates subject-specific random intercepts to correct for sample correlation and enhance the preservation of biological signals. We tested RMComBat and several popular algorithms on simulated and real repeated measurement gene expression datasets, evaluating their performance through visual inspections and quantitative metrics. Results indicate that although most algorithms can reduce batch effects, they often do so at the cost of removing true biological signals. RMComBat demonstrates superior performance in preventing overcorrection, providing a more balanced and biologically informative correction in repeated measurement studies, so making it a valuable tool for improving the accuracy of gene expression analyses. © 2024 IEEE.

关键词： Gene expression

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Multi-Objective Policy Monitoring Method for Epidemic Control

Multi-Objective Policy Monitoring Method for Epidemic Contro...

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2024 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2024

作者： Lai, Xin Fan, Rundong liu, Ruoyu Wang, Jiayin Zhu, Xiaoyan liu, Yuqian Wang, xuwen Wang, Shenjie Xi'an Jiaotong University School of Computer Science and Technology Xi'an China

ISBN: (纸本)9798350386226

In the face of emerging infectious diseases such as COVID-19, timely government intervention is crucial, as swift policy actions can effectively prevent greater losses. However, policymakers often need to balance multiple conflicting objectives. The lack of high-quality data and suitable analytical tools poses significant challenges for policy evaluation, especially in multi-objective decision-making, where accurately assessing the impact of interventions becomes even more difficult. To address this issue, this paper proposes a real-time data-driven policy monitoring method for dynamically tracking the effects of policy interventions. We introduce a new non-parametric one-sided test control chart, leveraging the interpretability and ease of implementation of control charts to monitor risk levels across various policies. Experimental results demonstrate the effectiveness of this method in policy monitoring. © 2024 IEEE.

关键词： COVID-19

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Fatty Infiltration of Multifidus Muscles: An Easily Overlooked Risk Factor for the Severity of Osteoporotic Vertebral Fractures

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ORTHOPAEDIC SURGERY 2024年第3期16卷 585-593页

作者： Xu, Wuyan liu, Xiaowen Wu, Li Liang, Shaohua Zhang, Ye Huang, Junbing Zeng, xuwen Li, Siming Xu, Fan Xiong, Yuchao Jinan Univ Dept Radiol Guangzhou Red Cross Hosp Guangzhou Peoples R China Jinan Univ Dept Orthoped Guangzhou Red Cross Hosp Guangzhou Peoples R China Jinan Univ Clin Med Coll 2 Shenzhen Peoples R China Jinan Univ Guangzhou Red Cross Hosp Dept Radiol Guangzhou 510220 Peoples R China

ObjectivesOsteoporotic vertebral fractures (OVFs) are a critical public health concern requiring urgent attention, and severe OVFs impose substantial health and economic burdens on patients and society. Analysis of the risk factors for severe OVF is imperative to actively prevent the occurrence of this degenerative disorder. This study aimed to investigate the risk factors associated with the severity of OVF, with a specific focus on changes in the paraspinal *** total of 281 patients with a first-time single-level acute OVF between January 2016 and January 2023 were enrolled in the study. Clinical and radiological data were collected and analyzed. The cross-sectional area (CSA) and degree of fatty infiltration (FI) of the paraspinal muscles, including the multifidus muscles (MFMs), erector spinae muscles (ESMs), and psoas major muscles (PSMs), were measured by magnetic resonance imaging (MRI) of the L4/5 intervertebral discs. According to the classification system of osteoporotic fractures (OF classification) and recommended treatment plan, OVFs were divided into a low-grade OF group and a high-grade OF group. Univariate and multivariate logistic regression analyse s were performed to identify risk factors associated with the severity of ***-eight patients were included in the low-grade OF group, and 183 patients were included in the high-grade OF group. Univariate analysis revealed a significantly higher incidence of a high degree of FI of MFMs (OR = 1.71, p = 0.002) and ESMs (OR = 1.56, p = 0.021) in the high-grade OF group. Further multivariate logistic regression analysis demonstrated that a high degree of FI of the MFMs (OR = 1.71, p = 0.002) is an independent risk factor for the severity of *** high degree of FI of the MFMs was identified as an independent risk factor for the severity of OVF. Decreasing the degree of FI in the MFMs might lower the incidence of the severity of OVF, potentially reducing the necessity for s

关键词： Fatty Infiltration Osteoporosis Multifidus Muscles Osteoporotic Vertebral Fracture

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Collaborative Morphological and Electrical Regulation of High-Mobility Conjugated Polymers via a Multifunctional Polymeric Additive

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MACROMOLECULES 2024年第22期57卷 10792-10801页

作者： Xu, Chenhui An, Chuanbin Gao, Mengyuan Zhang, xuwen He, Chunyong Dong, Weijia Wang, Tianzuo liu, Yuqian Deng, Yunfeng Ye, Long Han, Yang Geng, Yanhou Tianjin Univ Sch Mat Sci & Engn Tianjin Key Lab Mol Optoelect Sci Key Lab Organ Integrated CircuitsMinist Educ Tianjin 300072 Peoples R China Trina Solar State Key Lab Photovolta Sci & Technol Changzhou 213031 Peoples R China Joint Sch Natl Univ Singapore & Tianjin Univ Fuzhou 350207 Peoples R China China Spallat Neutron Source CSNS Spallat Neutron Source Sci Ctr Dongguan 523803 Peoples R China

Morphological and electrical control over conjugated polymers has a great potential for the fabrication of high-performance organic thin-film transistors (OTFTs). Herein, we employed a multifunctional polymeric additive, namely, PBTTT-b-HTPB, to optimize the molecular packing order of an isoindigo-based model polymer (IIDSiC8) and simultaneously regulate the minority carriers for boosted transport properties in OTFTs via facile solution processing. By detailed comparative study, we demonstrated that PBTTT-b-HTPB remarkably improved the crystallinity of IIDSiC8 by forming elongated fibers with higher molecular order in a thin film, which originated from the larger size ordered solution aggregates due to the presence of the insulating block. On the other hand, the p-type conjugated block of PBTTT worked as a hole trapping center, resulting in significantly increased electron density, reduced off-current, and optimal n-type performance. Benefiting from the collaborative morphological and electrical regulation, IIDSiC8/PBTTT-b-HTPB films displayed well-aligned ordered morphology and a high electron mobility up close to 7 cm2 V-1 s-1 together with an on/off ratio of 106 in bar-coated OTFTs. The high electron mobility is among the top performance values reported for isoindigo-based polymers. Our work has achieved simultaneous optimization of film microstructures and carrier transport characteristics of polymer semiconductors, providing opportunities for the production of OTFT devices with a superior performance.

关键词： Conjugated polymers

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PEcnv: accurate and efficient detection of copy number variations of various lengths

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BRIEFINGS IN BIOINFORMATICS 2022年第5期23卷 bbac375-bbac375页

作者： Wang, xuwen Xu, Ying liu, Ruoyu Lai, Xin liu, Yuqian Wang, Shenjie Zhang, Xuanping Wang, Jiayin Xi An Jiao Tong Univ Sch Comp Sci & Technol Xian Peoples R China Xi An Jiao Tong Univ Sch Comp Sci & Technol Med Informat Xian Peoples R China

Copy number variation (CNV) is a class of key biomarkers in many complex traits and diseases. Detecting CNV from sequencing data is a substantial bioinformatics problem and a standard requirement in clinical practice. Although many proposed CNV detection approaches exist, the core statistical model at their foundation is weakened by two critical computational issues: (i) identifying the optimal setting on the sliding window and (ii) correcting for bias and noise. We designed a statistical process model to overcome these limitations by calculating regional read depths via an exponentially weighted moving average strategy. A one-run detection of CNVs of various lengths is then achieved by a dynamic sliding window, whose size is self-adopted according to the weighted averages. We also designed a novel bias/noise reduction model, accompanied by the moving average, which can handle complicated patterns and extend training data. This model, called PEcnv, accurately detects CNVs ranging from kb-scale to chromosome-arm level. The model performance was validated with simulation samples and real samples. Comparative analysis showed that PEcnv outperforms current popular approaches. Notably, PEcnv provided considerable advantages in detecting small CNVs (1 kb-1 Mb) in panel sequencing data. Thus, PEcnv fills the gap left by existing methods focusing on large CNVs. PEcnv may have broad applications in clinical testing where panel sequencing is the dominant strategy.

关键词： genomics sequencing data analysis variant detection copy number variation (CNV) exponentially weighted moving average clinical panel sequencing

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