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Data analysis guidelines for single‑cell RNA‑seq in biomedical studies and clinical applications

Military Medical research 2023年第4期10卷 529-553页

作者： Min Su Tao Pan Qiu‑Zhen Chen Wei‑Wei Zhou Yi Gong Gang Xu Huan‑Yu Yan Si Li Qiao‑Zhen Shi Ya Zhang Xiao He Chun‑Jie Jiang Shi‑Cai Fan Xia Li Murray J.Cairns Xi Wang Yong‑Sheng Li State Key Laboratory of Reproductive Medicine Nanjing Medical UniversityNanjing 211166China College of Biomedical Information and Engineering the First Affiliated Hospital of Hainan Medical UniversityHainan Medical UniversityHaikou 571199HainanChina College of Bioinformatics Science and Technology Harbin Medical UniversityHarbin 150081HeilongjiangChina Department of Immunology Nanjing Medical UniversityNanjing 211166China Department of Laboratory Medicine Women and Children’s Hospital of Chongqing Medical UniversityChongqing 401174China Baylor College of Medicine HoustonTX 77030USA Shenzhen Institute for Advanced Study University of Electronic Science and Technology of ChinaShenzhen 518110GuangdongChina School of Biomedical Sciences and Pharmacy Faculty of Health and Medicinethe University of NewcastleUniversity DriveCallaghanNSW 2308Australia Precision Medicine Research Program Hunter Medical Research InstituteNew Lambton HeightsNSW 2305Australia

The application of single-cell RNA sequencing(scRNA-seq)in biomedical research has advanced our understanding of the pathogenesis of disease and provided valuable insights into new diagnostic and therapeutic *** the expansion of capacity for high-throughput scRNA-seq,including clinical samples,the analysis of these huge volumes of data has become a daunting prospect for researchers entering this ***,we review the workflow for typical scRNA-seq data analysis,covering raw data processing and quality control,basic data analysis applicable for almost all scRNA-seq data sets,and advanced data analysis that should be tailored to specific scientific *** summarizing the current methods for each analysis step,we also provide an online repository of software and wrapped-up scripts to support the *** and caveats are pointed out for some specific analysis tasks and *** hope this resource will be helpful to researchers engaging with scRNA-seq,in particular for emerging clinical applications.

关键词： Single-cell RNA-sequencing(scRNA-seq) Data analysis Biomedical research Clinical applications

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Investigating the impact of metal ion variations in terephthalate metal–organic frameworks on the organic solvent nanofiltration performance of mixed matrix membranes

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Journal of Membrane science 2024年 700卷

作者： Ajebe, Eyasu Gebrie Hu, Chien Chieh Lugito, Graecia Hu, Chun-Po Hung, Wei-Song Lee, Kueir-Rarn Lai, Juin-Yih Graduate Institute of Applied Science and Technology Advanced Membrane Materials Research Center National Taiwan University of Science and Technology Taipei Taiwan Chemical Engineering Study Program Faculty of Industrial Technology Institut Teknologi Bandung West Java Indonesia Nanyang Technological University 1 Cleantech Loop Singapore R&D Center for Membrane Technology Chung Yuan University Chungli Taoyuan Taiwan Department of Chemical Engineering and Materials Science Yuan Ze University Chungli Taoyuan Taiwan

Nano-fillers integrated into mixed matrix membranes (MMMs) present promising alternatives for organic solvent nanofiltration (OSN). In this work, our objective is to enhance OSN performance by incorporating terephthalate metal-organic frameworks (M-BDC, where M = Zr or Cu) into a P84 matrix to fabricate M-BDC/P84 composite MMMs. This work focuses on the influence of metal cluster variation on particle size, pore size distribution, and specific surface area of M-BDC, while systematically investigating the impact of M-BDC addition on OSN performance and underlying separation mechanisms. The synthesized membranes underwent comprehensive characterization using SEM, XRD, ATR-FTIR, contact angle, zeta potential, and thermogravimetric analysis. Significantly, all MMMs exhibited superior permeance and methyl blue (MB) rejection compared to P84 membranes. This enhancement is attributed to the improved interfacial contact between M-BDC and P84, as well as their effective dispersion within the membrane matrix. Interestingly, comparative analysis between Cu-BDC/P84 and Zr-BDC/P84 MMMs revealed the latter's superior permeance, attributed to its larger pore size and surface area. The resulting MMMs demonstrated outstanding MB rejection (>96.7%) with ethanol permeance of 21.5 and 19.0 LMH/Bar for Zr-BDC/P84 and Cu-BDC/P84 MMMs, respectively. Furthermore, the stable performance of M-BDC-based MMMs during prolonged MB/ethanol operation underscores their potential significance in the field of OSN, providing valuable insights for future membrane design and application. © 2024 Elsevier B.V.

关键词： Organometallics

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High-performance UV polarization sensitive photodetector for a graphene(2D)/GaN(3D) junction with a non-centrosymmetric electric field

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Photonics research 2025年第6期13卷 1544-1553页

作者： Can Zou Qing Liu Lu Zhang Xiao Tang Xiaohang Li Shuti Li Fangliang Gao Guangdong Engineering Research Center of Optoelectronic Functional Materials and Devices School of Electronic Science and Engineering (School of Microelectronics) South China Normal University Guangzhou 510631 China Advanced Semiconductor Laboratory Electrical and Computer Engineering Program CEMSE Division King Abdullah University of Science and Technology Thuwal 239556900 Saudi Arabia e-mail: lishuti@*** e-mail: gaofl@m.***

This study pioneers a high-performance UV polarization-sensitive photodetector by ingeniously integrating non-centrosymmetric metal nanostructures into a graphene ( Gr ) / Al 2 O 3 / GaN heterojunction. Unlike conventional approaches constrained by graphene’s intrinsic isotropy or complex nanoscale patterning, our design introduces asymmetric metal architectures (E-/T-type) to artificially create directional anisotropy. These structures generate plasmon-enhanced localized electric fields that selectively amplify photogenerated carrier momentum under polarized UV light (325 nm), synergized with Fowler-Nordheim tunneling (FNT) across an atomically thin Al 2 O 3 barrier. The result is a breakthrough in performance: a record anisotropy ratio of 115.5 (E-type, − 2 V ) and exceptional responsivity (97.7 A/W), surpassing existing graphene-based detectors by over an order of magnitude. Crucially, by systematically modulating metal geometry and density, we demonstrate a universal platform adaptable to diverse 2D/3D systems. This study provides a valuable reference for developing and practically applying photodetectors with higher anisotropy than ultraviolet polarization sensitivity.

关键词： Chemical vapor deposition Metals Nanostructures Quantum efficiency Surface plasmon resonance X-ray diffraction

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Designing a Novel Low-Density, High-Strength Ti27.5zr26.5nb25.5ta8.5al12 Refractory High-Entropy Alloy for High-Temperature Applications

SSRN

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SSRN 2024年

作者： Naseer, Hashim Wang, Yangwei Bao, Jiawei Khan, Muhammad Abubaker Afifi, Mohamed A. School of Materials Science and Engineering Beijing Institute of Technology Beijing100081 China Tangshan Research Institute Beijing Institute of Technology Tangshan063000 China Beijing Advanced Innovation Center for Materials Genome Engineering School of Materials Science and Engineering University of Science and Technology Beijing Beijing100083 China Mechanical Engineering Program School of Engineering and Applied Sciences Nile University Giza12677 Egypt

This study introduces a novel Refractory High-Entropy Alloy (RHEA) with the composition Ti27.5Zr26.5Nb25.5Ta8.5Al12, designed for high-temperature structural applications while addressing the limitations of traditional nickel-based superalloys. The alloy was synthesized using vacuum arc melting and characterized through comprehensive experimental methods including X-ray diffraction (XRD), scanning electron microscopy (SEM) with energy dispersive spectroscopy (EDS), and transmission electron microscopy (TEM). This RHEA demonstrated exceptional mechanical properties, achieving a yield strength of 1356 MPa and a specific yield strength of 197.3 MPa·g⁻¹·cm³ at room temperature, with notable ductility (compressive strain >50%) across a wide temperature range up to 1000°C. The microstructural analysis revealed a two-phase BCC/B2 nanodomain structure that contributes significantly to its strength and ductility. This structure was further refined through controlled thermomechanical treatments, eliminating the need for additional heat treatment. The findings suggest that the Ti27.5Zr26.5Nb25.5Ta8.5Al12 RHEA holds great potential as a low-density, high-performance material for demanding environments, offering a viable alternative to heavier superalloys. © 2024, The Authors. All rights reserved.

关键词： Scanning electron microscopy

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Biological methane production coupled with sulfur oxidation in a microbial electrosynthesis system without organic substrates

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Journal of Environmental sciences 2022年第6期34卷 68-78页

作者： Ha T.T.Dinh Hiromi Kambara Shuji Matsushita Yoshiteru Aoi Tomonori Kindaichi Noriatsu Ozaki Akiyoshi Ohashi Department of Civil and Environmental Engineering Graduate School of Advanced Science and EngineeringHiroshima University1-4-1KagamiyamaHigashihiroshimaHiroshima 739-8527Japan Faculty of Environment Ho Chi Minh City University of Natural Resources and Environment236 Le Van Sy1 WardTan Binh DistrictHo Chi Minh CityViet Nam Agricultural Technology Research Center Hiroshima Prefectural Technology Research Institute6869HaraHachihonmatsuHigashihiroshimaHiroshima 739-0151Japan Program of Biotechnology Graduate School of Integrated Sciences for LifeHiroshima University1-3-1KagamiyamaHigashihiroshimaHiroshima 739-8530Japan

Methane is produced in a microbial electrosynthesis system(MES) without organic substrates. However, a relatively high applied voltage is required for the bioelectrical *** this study, we demonstrated that electrotrophic methane production at the biocathode was achieved even at a very low voltage of 0.1 V in an MES, in which abiotic HS-oxidized to SO_(4)^(2-) at the anodic carbon-cloth surface coated with platinum powder. In addition, microbial community analysis revealed the most probable pathway for methane production from electrons. First, electrotrophic H_(2) was produced by syntrophic bacteria, such as Syntrophorhabdus, Syntrophobacter, Syntrophus, Leptolinea, and Aminicenantales, with the direct acceptance of electrons at the biocathode. Subsequently, most of the produced H_(2) was converted to acetate by homoacetogens, such as Clostridium and Spirochaeta 2. In conclusion,the majority of the methane was indirectly produced by a large population of acetoclastic methanogens, namely Methanosaeta, via acetate. Further, hydrogenotrophic methanogens,including Methanobacterium and Methanolinea, produced methane via H_(2).

关键词： Bioelectricity Homoacetogens Methane production Microbial electrosynthesis system Sulfur oxidation

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Synergetic effects of multiple junction and surface hydroxyl in Cu/CuO/Cu2O/TiO2 heterostructures towards highly efficient photocatalysts for hydrogen generation

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Materials science for Energy Technologies 2025年 8卷 131-142页

作者： Subagyo, Riki Anindika, Garcelina Rizky Aufkani, Afif Akmal Zhang, Lei Ardhyananta, Hosta Burhan, R.Y. Perry Nugraheni, Zjahra Vianita Akhlus, Syafsir Bahruji, Hasliza Prasetyoko, Didik Wellia, Diana Vanda Ivansyah, Atthar Luqman Arramel Kusumawati, Yuly Department of Chemistry Faculty of Science and Analytic Data Institut Teknologi Sepuluh Nopember Surabaya60111 Indonesia Center of Excellence Applied Physics and Chemistry Nano Center Indonesia Jl PUSPIPTEK South Tangerang Banten15314 Indonesia Department of Physics National University of Singapore Singapore117551 Singapore Department of Materials and Metallurgical Engineering Faculty of Industrial Technology and Systems Engineering Institut Teknologi Sepuluh Nopember Surabaya60111 Indonesia Centre of Advanced Material and Energy Science Universiti Brunei Darussalam Jalan Tungku Link BE 1410 Brunei Department of Chemistry Faculty of Mathematics and Natural Sciences Universitas Andalas Padang25163 Indonesia Master Program in Computational Science Faculty of Mathematics and Natural Science Institut Teknologi Bandung Jalan Ganesha No. 10 Bandung40132 Indonesia Instrumentation and Computational Physics Research Group Department of Physics Faculty of Mathematics and Natural Sciences Institut Teknologi Bandung Jalan Ganesha No.10 West Java Bandung40132 Indonesia

The implementation of titanium dioxide (TiO2) as a photocatalyst material in hydrogen (H2) evolution reaction (HER) has embarked renewed interest in the past decade. Rapid electron-hole pairs recombination and wide band gap of a photo-sensitive material of TiO2 are detrimental toward the targeted catalytical reaction. In this study, we present the rational design, fabrication, photocatalytic performance of TiO2-Cu/CuO/Cu2O heterostructures (CuTi) using viable chemical reduction method. The Z-scheme and S-scheme are succesfully generated across the TiO2/CuO/Cu2O interfaces, while the Schottky junction arises on the Cu perimeters. This is evidenced from the blue shifted about 0.3 eV of Cu 2p core level determined by using X-ray photoemission spectroscopy (XPS), in combination with the formation of inverse V-shape of the Mott-Schottky plots. In addition, we find that Cu/CuO/Cu2O facilitates photon absorption range up to the visible region. The multiple heterojunction and the large number of OHsurface enhanced charge carrier transfer are associated to the suppression of photoluminescence (PL) intensity, high surface hydroxyl (OHsurface) density in CuTi probed by XPS, and fast electron transfer based on the electrochemical measurements. The presence of OHsurface inhibits the recombination of electron. A significant H2 photogeneration rate enhancement is achieved when an optimized 5 wt% Cu/CuO/Cu2O concentration is used on TiO2 to achieve 7,157.19 μmol·g−1 (1,789.30 μmol·g−1·h−1). Based on this finding, zero emission energy innitiative could be materialized under multiple heterojunctions in photocatalytic process is beneficial for enhancing the H2 production. © 2025 The Authors

关键词： Titanium dioxide

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Experimentation of Integrating Roadmapping and Sci-Fi Prototyping Methods

Experimentation of Integrating Roadmapping and Sci-Fi Protot...

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Portland International Conference on Management of Engineering and technology (PICMET)

作者： Miwa Nishinaka Kunio Shirahada Yusuke Kishita Dohjin Miyamoto Hirotaka Osawa Sachiko Kiyokawa Hideaki Takeda The Graduate School of Management Kagawa University Takamatsu Kagawa Japan School of Knowledge Science Transformative Knowledge Management Research Area Japan Advanced Institute of Science and Technology (JAIST) Nomi Ishikawa Japan Department of Precision Engineering The University of Tokyo Tokyo Japan Communication in Science and Technology Education and Research Program Hokkaido University Sapporo Japan Faculty of Science and Technology Keio University Yokohama Kanagawa Japan Graduate School of Education The University of Tokyo Tokyo Japan National Institute of Informatics Tokyo Japan

ISBN: (数字)9781890843458

ISBN: (纸本)9798350369137

In 2023, we proposed a hypothetical knowledge management framework that incorporates science fiction prototyping (SFP) into the traditional roadmapping (RM) method to make RM more innovative and create a future beyond what we can currently imagine. Our main objective is to create a new organizational knowledge co-creation method for generating innovative ideas by incorporating humanistic factors utilizing SFP into RM. In the current article, we present the exploratory study we conducted to examine the hypothetical framework. Experimental workshops were held in November 2023 to compare the integrated method, in which SFP is applied to RM, with the original RM method. We followed a crossover design in the workshops and analyzed the results qualitatively and quantitatively following the perspectives proposed in the hypothetical framework. The qualitative analysis revealed successful integration regarding diverse and broader perspectives. The quantitative analysis utilizing Wilcoxon signed rank tests showed that the scores of the integrated method were significantly higher than those of RM for variables evaluating the effectiveness of the integration, while not for variables related to participants' feelings and satisfaction with the workshops, and sustainability. These findings indicate that the integration was successful in terms of its effectiveness as a method, while participants' subjective feelings toward the workshops were not different in both methods. As for sustainability, which requires a long-term perspective, no apparent differences were observed in these short-term workshops.

关键词： Statistical analysis Conferences Knowledge management Sustainable development Creativity

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Novel ruthenium-based catalysts with atomic dispersion for oxygen evolution reaction in water electrolysis

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Materials Today Chemistry 2024年 35卷

作者： Liao, Kuo-Wei Chen, Hsueh-Yu Wei, Wen-Hui Chen, Guan-Cheng Yamanaka, Ichiro Liu, Bo-Tau Hong, Ting-Fu Chiang, Tai-Chin Huang, Hsin-Chih Wang, Chen-Hao Department of Materials Science and Engineering National Taiwan University of Science and Technology Taipei106335 Taiwan Department of Chemical Science and Engineering School of Materials and Chemical Technology Tokyo Institute of Technology Meguro-ku Tokyo152-8552 Japan Department of Chemical and Materials Engineering National Yunlin University of Science and Technology Yunlin640301 Taiwan Department of Materials Engineering National Pingtung University of Science and Technology Pingtung912301 Taiwan Global Development Engineering Program National Taiwan University of Science and Technology Taipei106335 Taiwan Advanced Manufacturing Research Center National Taiwan University of Science and Technology Taipei106335 Taiwan

This study introduces a method for fabricating ultra-high-performance catalysts designed for the oxygen evolution reaction (OER), employing a combination of ball-milling, autoclave heat treatment procedures, and a two-step heat treatment approach. This method produces catalysts characterized by an atomic dispersion of ruthenium on nitrogen-doped carbon sheets (Ru–O/N–C–NH3). The Ru–O/N–C–NH3 catalyst exhibits exceptional OER activity in alkaline conditions, achieving a mass activity of 16842 A g−1Ru at 1.52 V, and a minimal overpotential of 290 mV at a current density of 10 mA cm−2. Moreover, this catalyst demonstrates enduring stability, showing no significant decay after a 100-h stability test in anion exchange membrane water electrolysis (AEMWE), with a mass activity approximating 62000 A g−1PGM. This is nearly three orders of magnitude greater than the AEMWE that utilizes commercial IrO2 as an anode. The atomic dispersion and the Ru–O/N bonding of the catalyst are substantiated to contribute to the notable enhancement in OER activity. © 2023 Elsevier Ltd

关键词： Ruthenium

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Mo-terminated edges in two-dimensional molybdenum disulfide for site-specific hydrolysis and DNA cleavage

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Materials Today 2025年 86卷 162-171页

作者： Wang, Cong Wu, Menghan Li, Muqing Zhao, Yingcan Zhao, Mingchuang Zhang, Yunhao Bai, Yichao Gao, Jianxiang Wang, Xiaoxia Tian, Xilin Zhang, Han Chang, Liang Zou, Xiaolong Liu, Bilu Kang, Feiyu Terrones, Mauricio Lei, Yu Institute of Materials Research Shenzhen Key Laboratory of Advanced Layered Materials for Value-added Applications Guangdong Provincial Key Laboratory of Thermal Management Engineering and Materials & Center of Double Helix Tsinghua Shenzhen International Graduate School Tsinghua University Shenzhen518055 China Institute of Materials Research & Shenzhen Geim Graphene Center Shenzhen Key Laboratory of Advanced Layered Materials for Value-added Applications Tsinghua-Berkeley Shenzhen Institute and Tsinghua Shenzhen International Graduate School Tsinghua University Shenzhen518055 China Environmental Science Program Department of Life Sciences Beijing Normal University-Hong Kong Baptist University United International College Guangdong519087 China Tsinghua Shenzhen International Graduate School Tsinghua University Shenzhen518055 China Department of Physics Department of Chemistry Department of Materials Sciences Center for 2-Dimensional and Layered Materials The Pennsylvania State University University ParkPA16802 United States International Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of Education Institute of Microscale Optoelectronics Shenzhen University Shenzhen518060 China

The hydrolysis of DNA serves as the foundational principle for gene engineering that enable precise gene cleavage at the molecular level. This process typically occurs in biological nucleases, which exhibit nucleobase-selective and catalytic hydrolysis capabilities rarely replicated in abiotic nanomaterials. Here, we demonstrate that molybdenum-terminated (Mo-terminated) edges of molybdenum disulfide (MoS2) possess the unique ability to abstract a proton (H+) from water molecules, thereby facilitating catalytic hydrolysis reactions that cleave the phosphodiester bonds in DNA through the action of hydroxide ions. The enhanced proton absorption at Mo-terminated edges of MoS2 significantly reduces the activation energy required for the DNA hydrolysis reaction. Furthermore, the favorable interaction between the Mo-terminated edges and thymine nucleobases promotes both charge transfer and P-O bond cleavage, enabling targeted DNA hydrolysis at 'TTTTTTT' sequences under dark conditions. This discovery underscores the potential of MoS2 as a stable, efficient nanosystem for precise genetic editing, heralding advanced applications in the field of gene engineering. © 2025 The Author(s)

关键词： Activation energy

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Heat transfer between occupied and unoccupied zone in large space building with floor-level side wall air-supply system

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建筑模拟（英文版） 2020年第6期13卷 1221-1233页

作者： Xinqi Yang Haidong Wang Chunxiao Su Xin Wang Yi Wang School of Environment and Architecture University of Shanghai for Science and Technology Shanghai 200093 China Advanced Study Program National Center for Atmospheric Research Boulder CO USA Research Applications Laboratory National Center for Atmospheric Research Boulder CO USA

The air supply terminal located at the floor level attached to side-wall is widely used in large space buildings, leading to potential energy saving as well as significant vertical thermal stratification. The cooling load calculation of such system is challenging, especially the calculation of the load gained from unoccupied zone. This paper adopts experiment and computational fluid dynamics (CFD) methods to study the heat transfer upward and downward across the stratified surface in large space building with floor-level side wall air-supply system. Five experimental cases with different heat source power and exhaust airflow ratios are performed to study their effects on the indoor thermal environment. We investigate the same cases in CFD and verify the result of vertical temperature distribution and cooling load components. As a critical parameter in evaluating the thermal stratification environment of large space building, the inter-zonal heat transfer coefficient Cb is emphatically discussed. By comparing the Cb value obtained through the two methods, the accuracy of the microscopic method is verified by the heat balance method. The results show that the Cb value is mainly affected by the zonal division and air distribution, but less prominently by exhaust airflow ratio and heat source in the occupied zone.

关键词： large space building thermal stratification CFD simulation floor level air supply inter-zonal heat transfer coefficient

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