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Benchmarking Algorithms for Gene Set Scoring of Single-cell ATAC-seq Data

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GENOMICS PROTEOMICS & BIOINFORMATICS 2024年第2期22卷 qzae014页

作者： Wang, Xi Lian, Qiwei Dong, Haoyu Xu, Shuo Su, Yaru Wu, Xiaohui Soochow Univ Suzhou Med Coll Pasteurien Coll Suzhou 215000 Peoples R China Xiamen Univ Dept Automat Xiamen 361005 Peoples R China Fuzhou Univ Coll Math & Comp Sci Fuzhou 350116 Peoples R China

Gene set scoring (GSS) has been routinely conducted for gene expression analysis of bulk or single-cell RNA sequencing (RNA-seq) data, which helps to decipher single-cell heterogeneity and cell type-specific variability by incorporating prior knowledge from functional gene sets. Single-cell assay for transposase accessible chromatin using sequencing (scATAC-seq) is a powerful technique for interrogating single-cell chromatin-based gene regulation, and genes or gene sets with dynamic regulatory potentials can be regarded as cell type-specific markers as if in single-cell RNA-seq (scRNA-seq). However, there are few GSS tools specifically designed for scATAC-seq, and the applicability and performance of RNA-seq GSS tools on scATAC-seq data remain to be investigated. Here, we systematically benchmarked ten GSS tools, including four bulk RNA-seq tools, five scRNA-seq tools, and one scATAC-seq method. First, using matched scATAC-seq and scRNA-seq datasets, we found that the performance of GSS tools on scATAC-seq data was comparable to that on scRNA-seq, suggesting their applicability to scATAC-seq. Then, the performance of different GSS tools was extensively evaluated using up to ten scATAC-seq datasets. Moreover, we evaluated the impact of gene activity conversion, dropout imputation, and gene set collections on the results of GSS. Results show that dropout imputation can significantly promote the performance of almost all GSS tools, while the impact of gene activity conversion methods or gene set collections on GSS performance is more dependent on GSS tools or datasets. Finally, we provided practical guidelines for choosing appropriate preprocessing methods and GSS tools in different application scenarios.

关键词： Single-cell ATAC-seq Gene set scoring Pathway analysis Single-cell RNA-seq Benchmark CHROMATIN ACCESSIBILITY RNA-SEQ REVEALS

New approach to measuring topological phase transitions utilizing Floquet technology

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CHINESE PHYSICS B 2024年第9期33卷 282-288页

作者： Yang, Xue-Ying Wu, Wei Chen, Ping-Xing Natl Univ Def Technol Coll Sci Changsha 410073 Peoples R China

The Floquet technique provides a novel anomalous topological phase for non-equilibrium phase transitions. Based on the high symmetry of the quantum anomalous Hall model, the findings suggest a one-to-one correspondence between the average spin texture and the Floquet quasi-energy spectrum. A new approach is proposed to directly measure the quasi-energy spectrum, replacing previous measurements of the average spin texture. Finally, we proposed a reliable experimental scheme based on ion trap platforms. This scheme markedly reduces the measurement workload, improves the measurement fidelity, and is applicable to multiple platforms such as cold atoms and nuclear magnetic resonance.

关键词： topological phase transition Floquet technique ion trap 03.65.Vf 42.50.Dv 37.10.Ty

Pressure generation under deformation in a large-volume press

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CHINESE PHYSICS B 2024年第9期33卷 622-626页

作者： Wang, Saisai Zhao, Xinyu Hu, Kuo Feng, Bingtao Hou, Xuyuan Zhang, Yiming Liu, Shucheng Shang, Yuchen Liu, Zhaodong Yao, Mingguang Liu, Bingbing Jilin Univ Coll Phys State Key Lab Superhard Mat Synerget Extreme Condit User Facil Changchun 130012 Peoples R China Jilin Univ Coll Earth Sci Changchun 130012 Peoples R China

Deformation can change the transition pathway of materials under high pressure, thus significantly affects physical and chemical properties of matters. However, accurate pressure calibration under deformation is challenging and thereby causes relatively large pressure uncertainties in deformation experiments, resulting in the synthesis of complex multiphase materials. Here, pressure generations of three types of deformation assemblies were well calibrated in a Walker-type large-volume press (LVP) by electrical resistance measurements combined with finite element simulations (FESs). Hard Al2O3 or diamond pistons in shear and uniaxial deformation assemblies significantly increase the efficiency of pressure generation compared with the conventional quasi-hydrostatic assembly. The uniaxial deformation assembly using flat diamond pistons possesses the highest efficiency in these deformation assemblies. This finding is further confirmed by stress distribution analysis based on FESs. With this deformation assembly, we found shear can effectively promote the transformation of C60 into diamond under high pressure and realized the synthesis of phase-pure diamond at relatively moderate pressure and temperature conditions. The present developed techniques will help improve pressure efficiencies in LVP and explore the new physical and chemical properties of materials under deformation in both science and technology.

关键词： shear/uniaxial deformation pressure calibration finite element simulations large-volume press high pressure 81.40.Lm 07.35.+k 62.50.-p 81.40.Vw SIMPLE SHEAR DEFORMATION DISLOCATION MOBILITY SEISMIC ANISOTROPY TEMPERATURE OLIVINE DIA ACTIVATION CARBON PHASE

Alternate disinfection approaches or raise disinfectant dosages for sewage treatment plants to address the COVID-19 pandemic? From disinfection efficiency, DBP formation, and toxicity perspectives

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FRONTIERS OF ENVIRONMENTAL SCIENCE & ENGINEERING 2024年第9期18卷 115-0页

作者： Liao, Xiaobin Liu, Xinyue He, Yueyun Tang, Xueping Xia, Ruanjunjie Huang, Yongjun Li, Wenhua Zou, Jing Zhou, Zhenming Zhuang, Mazhan Huaqiao Univ Inst Municipal & Environm Engn Coll Civil Engn Xiamen 361021 Peoples R China Xiamen Inst Environm Sci Xiamen 361021 Peoples R China Huaqiao Univ Coll Biomed Sci Xiamen 361021 Peoples R China

During the COVID-19 pandemic, most sewage treatment plants increased disinfectant dosages to inactivate pathogenic viruses and microorganisms more effectively. However, this approach also led to the production of more disinfection by-products (DBPs). To ensure both disinfection efficiency and a reduction in DBP formation, new disinfection protocols are required. In this study, the disinfection efficiency, DBP amounts, and toxicity changes resulting from ozone (O3), ultraviolet (UV), chlorine (Cl2), and their combined processes were examined. The results demonstrated that the O3/UV/Cl2 combination achieved the highest disinfection efficiency. Chlorination produced the most DBPs, whereas UV treatment reduced the formation of trihalomethane (THM), halogenated ketones (HKs), haloacetic acids (HAA), dichloroacetonitrile (DCAN) and N-nitrosodimethylamine (NDMA) by 45.9%, 52.6%, 82.0%, 67.95%, and 47%, respectively. O-3 also significantly reduced their production by 99.1%, 91.1%, 99.5%, 100%, and 35%. Intracellular organic matter (IOM) was identified as the primary DBP precursors, producing 2.94 times more DBPs than extracellular organic matter (EOM). The increased DBP formation during chlorination was attributed to IOM leakage and cell membrane damage, which was verified using scanning electron microscopy (SEM). The toxicities of DBPs were evaluated for six disinfection methods, revealing inconsistent results. The overall toxicities were assessed using zebrafish embryo experiments. Both evaluations indicated that chlorination alone was the least favorable method. In addition, the toxicities followed a sequence: Cl-2 approximate to O-3/Cl-2 > O-3 > O-3/UV/Cl-2 > UV > UV/Cl-2. These findings can serve as a reference for sewage treatment plants in selecting appropriate disinfection methods to manage the COVID-19 epidemic from comprehensive perspective.

关键词： Sewage bacteria Disinfection by-products Toxicity Ozonation UV Chlorination BY-PRODUCT FORMATION WASTE-WATER DEGRADATION UV CHLORINATION INACTIVATION UV/CHLORINE BACTERIA OZONE SUBSTANCES

Orbital angular momentum conversion of acoustic vortex beams via planar lattice coupling

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CHINESE PHYSICS B 2024年第9期33卷 413-420页

作者： Han, Qingbang Liu, Zhipeng Yin, Cheng Wu, Simeng Luo, Yinlong Yang, Zixin Pan, Xiuyang Wang, Yiqiu Kan, Xuefen Zhang, Yuqiu Yu, Qiang Wu, Jian Hohai Univ Coll Informat Sci & Engn Changzhou 213200 Peoples R China Natl Univ Def Technol Coll Adv Interdisciplinary Studies Nanhu Laser Lab Changsha 410073 Peoples R China Chinese Acad Sci Suzhou Inst Nanotech & Nanob i Lab Suzhou 215123 Peoples R China Jiangsu Shipping coll Sch Transportat Engn Nantong 226010 Peoples R China

Orbital angular momentum (OAM) conversion is critical in understanding interactions between a structural sound field and a planar lattice. Herein, we explore the evolution of a monochromatic acoustic vortex beam (AVB) that is scattered by a phononic crystal (PnC) or a correlated random lattice. The phenomenon is ascribed to the enhanced orbit-orbit angular momentum coupling induced by the band structure. By modifying the coupling condition, accurate and continuous micro-manipulation of AVBs can be achieved, including the transverse/lateral gravity shift, the dynamics of the phase singularities, and the spatial distribution of acoustic pressure, etc. This research provides insight to the inhomogeneous coupling of AVBs with both propagating Bloch waves and localized Anderson modes, and may facilitate development of novel OAM-based acoustic devices for active sound field manipulation.

关键词： acoustic vortex beam phononic crystal Anderson localization Imbert-Fedorov effect 43.40.+s 43.20.+g 46.40.-f 46.40.Cd

A Path Planning Algorithm Based on Improved RRT Sampling Region

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CMC-COMPUTERS MATERIALS & CONTINUA 2024年第3期80卷 4303-4323页

作者： Jiang, Xiangkui Wang, Zihao Dong, Chao Xian Univ Posts & Telecommun Coll Automat Xian 710121 Peoples R China

For the problem of slow search and tortuous paths in the Rapidly Exploring Random Tree (RRT) algorithm, a feedback-biased sampling RRT, called FS-RRT, is proposed based on RRT. Firstly, to improve the sampling efficiency of RRT to shorten the search time, the search area of the random tree is restricted to improve the sampling efficiency. Secondly, to obtain better information about obstacles to shorten the path length, a feedback-biased sampling strategy is used instead of the traditional random sampling, the collision of the expanding node with an obstacle generates feedback information so that the next expanding node avoids expanding within a specific angle range. Thirdly, this paper proposes using the inverse optimization strategy to remove redundancy points from the initial path, making the path shorter and more accurate. Finally, to satisfy the smooth operation of the robot in practice, auxiliary points are used to optimize the cubic Bezier curve to avoid path-crossing obstacles when using the Bezier curve optimization. The experimental results demonstrate that, compared to the traditional RRT algorithm, the proposed FS-RRT algorithm performs favorably against mainstream algorithms regarding running time, number of search iterations, and path length. Moreover, the improved algorithm also performs well in a narrow obstacle environment, and its effectiveness is further confirmed by experimental verification.

关键词： RRT inversive optimization path planning feedback bias sampling mobile robots ASTERISK

Characteristics and mechanism of Ni2+and Cd2+adsorption by recovered perlite from agar extraction residue

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CHINESE JOURNAL OF CHEMICAL ENGINEERING 2024年第8期72卷 141-152页

作者： Wang, Juan Zhu, Yanbing Jiang, Zedong Du, Xiping Zheng, Mingjing Li, Lijun Ni, Hui Wang, Yuanpeng Li, Zhipeng Li, Qingbiao Jimei Univ Coll Ocean Food & Biol Engn Xiamen 361021 Peoples R China Fujian Prov Key Lab Food Microbiol & Enzyme Engn Xiamen 361021 Peoples R China Res Ctr Food Biotechnol Xiamen City Xiamen 361021 Peoples R China Xiamen Ocean Vocat coll Xiamen 361012 Peoples R China Xiamen Univ Coll Chem & Chem Engn Xiamen 361021 Peoples R China

Ni2+ and Cd2+ in wastewater accumulated through the ecological chain and could jeopardize human health. Adsorption of Ni2+ and Cd2+ from wastewater using recovered perlite was an important way to solve the problem of resource utilization of solid waste from agar production. Our previous study confirmed that recovered perlite from agar extraction residue had better pore size and specific surface area than commercial perlite. However, the adsorption efficiency and adsorption mechanism of recovered perlite were the main factors limiting its adsorption application. The adsorption process of Ni2+ and Cd2+ by recovered perlite in aqueous solution was described by the pseudo-second-order kinetic equation, and the relevant adsorption mechanism was mainly chemisorption. Compared with commercial perlite, the adsorption removal rate of Ni2+ and Cd2+ by enzymatic recovered perlite could reach 92.9% and 89.2%, respectively, and were improved by 12.63% and 13.03%. Langmuir isothermal adsorption model could better describe the isothermal adsorption process of recovered perlite on heavy metal Ni2+ and Cd2+, and the relevant adsorption mechanism was mainly monolayer adsorption. The X-ray photoelectron spectroscopy (XPS) results indicated that the decrease of Si-O Si2+ hydroxyl coordination bond and the increase of C-Si bond might make the binding effect of recovered perlite with heavy metals stronger. The competitive adsorption of Ni2+ and Cd2+ by recovered perlite was still dominated by chemisorption and monolayer adsorption. This study was expected to provide a theoretical basis and technical support for the removal of Ni2+ and Cd2+ from wastewater using recovered perlite from seaweed residue. (c) 2024 The Chemical Industry and Engineering Society of China, and Chemical Industry Press Co., Ltd. All rights are reserved, including those for text and data mining, AI training, and similar technologies.

关键词： Agar extraction residue Recovered perlite Heavy metal ion Adsorption property HEAVY-METAL IONS AQUEOUS-SOLUTIONS EXPANDED PERLITE DOPED CARBON ADSORPTION REMOVAL ELECTROCOAGULATION COMPOSITES KINETICS FEATURES

The stretchable perovskite-based alternating current electroluminescence for human-device interaction

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SCIENCE BULLETIN 2024年第18期69卷 2807-2810页

作者： Zhu, Wenjuan Chen, Bing Peng, Dengfeng Nanjing Univ Posts & Telecommun Coll Elect & Opt Engn Nanjing 210023 Peoples R China Nanjing Univ Posts & Telecommun Coll Flexible Elect Future Technol Nanjing 210023 Peoples R China Shenzhen Univ Minist Educ & Guangdong Prov Coll Phys & Optoelect Engn Key Lab Optoelect Devices & Syst Shenzhen 518060 Peoples R China

In the ever-evolving landscape of flexible electronics and wearable technologies,the pursuit of advanced interactive systems that seamlessly integrate with the human body has become a paramount endeavor[1].This drive stems from the increasing demand for wearable devices that not only offer sophisticated functionalities but also provide comfort and aesthetic appeal when worn directly on the human skin[2].Central to this innovation trend are wearable displays,the visual interfaces that bridge the gap between users and the vast expanse of digital *** traditional rigid and flat displays,the next-generation wearable displays are boasting foldability and stretchability,as well as an innate ability to conform to the dynamic contours of human skin,thereby revolutionizing the way we interact with contemporary science and technology[3].

关键词： stretch thereby interaction

Heterosis Analysis in Endogenous Substances in Root Bleeding Sap of Sorghum

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PHYTON-INTERNATIONAL JOURNAL OF EXPERIMENTAL BOTANY 2024年第8期93卷 1963-1980页

作者： Zhao, Renjie Li, Yueqiao Xu, Chen Zhang, Zhian Zhou, Ziyang Zhou, Yihan Qi, Zexin Jilin Agr Univ Coll Agr Changchun 130118 Peoples R China Jilin Acad Agr Sci Changchun 130033 Peoples R China Jilin Engn Vocat coll Siping 136001 Peoples R China

Despite hybrid dominance contributing to the genetic improvement of crops, little is known about heterosis and inheritance patterns of endogenous substances in sorghum (Sorghum bicolor (L.) Moench) root bleeding sap. In this study, six sterile and six restorer lines of sorghum and 36 hybrid sorghum combinations formulated as incomplete double-row crosses were selected as test materials, and heterosis, combining ability, heritability, and their interrelationships of root bleeding sap endogenous substances in different hybrid sorghum combinations and their parents were investigated. The results showed that the root bleeding sap of the F1 generation of hybrid sorghum had a high heterosis in both soluble sugar content and amino acid content at the flowering stage, and the average high-parent heterosis was 129.34% and 74.57%, respectively. Indole-3-acetic acid (IAA), cytokinins (CTK), gibberellic acid (GA3), abscisic acid (ABA), soluble sugar, amino acid, and root bleeding intensity were mainly affected by non-additive genetic effects of the genes. Soluble protein was affected by additive genetic effects of the genes and had a high narrow heritability (75.50%), which could be selected at low generations in breeding. The combining ability analyses showed that the sterile lines 521A and 170A, and the restorer lines Ji318R and 0-30 were promising parents with high general combining ability. Correlation analysis showed that all endogenous substances of root bleeding sap were positively correlated with the sum of parental general combining ability (GCA) at highly significant levels, and IAA, CTK, GA3, ABA, soluble sugar, amino acid, and root bleeding intensity were positively correlated with male GCA at significant or highly significant levels. Therefore, the GCA of the restorer lines root bleeding sap endogenous material or the sum of both parents' GCA can be used to predict the performance of wounding endogenous material in the F1 generation of hybrid sorghum. Overall, this

关键词： Sorghum heterosis root bleeding sap combining ability heritability COMBINING ABILITY GROWTH TRANSFORMATION TOLERANCE MATURITY TRAITS SYSTEM YIELD