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Cas12a 1

抗血清 1

核酸侧流免疫分析 1

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水产养殖 1

田间检测 1

疫苗 1

病原菌 1

稻瘟菌小麦致病型 1

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spp., foodborne pathogens threatening neonates and infants

Qiming CHEN, Yang ZHU, Zhen QIN, Yongjun QIU, Liming ZHAO

《农业科学与工程前沿（英文）》 2018年 第5卷 第3期   页码 330-339 doi: 10.15302/J-FASE-2018208

摘要：

Cronobacter spp. (formerly Enterobacter sakazakii) are special foodborne pathogens. Cronobacter infection can cause necrotizing enterocolitis, sepsis and meningitis in all age groups, especially neonates and infants, with a high fatality of up to 80%, although the infection is rare. Outbreaks of Cronobacter infection are epidemiologically proven to be associated with contaminated powdered infant formula (PIF). Cronobacter spp. can resist dry environments and survive for a long period in food with low water activity. Therefore, Cronobacter spp. have become serious pathogens of neonates and infants, as well as in the dairy industry. In this review, we present the taxonomy, pathogenesis, resistance, detection and control of Cronobacter spp.

关键词： Cronobacter spp.     desiccation resistance     pathogen control     pathogen detection     powdered infant formula    

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Systems understanding of plant–pathogen interactions through genome-wide protein–protein interaction

Hong LI,Ziding ZHANG

《农业科学与工程前沿（英文）》 2016年 第3卷 第2期   页码 102-112 doi: 10.15302/J-FASE-2016100

摘要： Plants are frequently affected by pathogen infections. To effectively defend against such infections, two major modes of innate immunity have evolved in plants; pathogen-associated molecular pattern-triggered immunity and effector-triggered immunity. Although the molecular components as well as the corresponding pathways involved in these two processes have been identified, many aspects of the molecular mechanisms of the plant immune system remain elusive. Recently, the rapid development of omics techniques (e.g., genomics, proteomics and transcriptomics) has provided a great opportunity to explore plant–pathogen interactions from a systems perspective and studies on protein–protein interactions (PPIs) between plants and pathogens have been carried out and characterized at the network level. In this review, we introduce experimental and computational identification methods of PPIs, popular PPI network analysis approaches, and existing bioinformatics resources/tools related to PPIs. Then, we focus on reviewing the progress in genome-wide PPI networks related to plant–pathogen interactions, including pathogen-centric PPI networks, plant-centric PPI networks and interspecies PPI networks between plants and pathogens. We anticipate genome-wide PPI network analysis will provide a clearer understanding of plant–pathogen interactions and will offer some new opportunities for crop protection and improvement.

关键词： plant–pathogen interactions     systems biology     omics     plant immunity     protein–protein interaction     network    

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Extracellular Vesicles in Pathogenic Infection, Transmission, and Immunity

Junyao Xiong,Usama Ashraf,Jing Ye,Shengbo Cao,

《工程（英文）》 doi: 10.1016/j.eng.2024.06.011

摘要： Extracellular vesicles (EVs) are secreted by cells and widely exist in body fluids, serving as an essential vehicle of intercellular communication. In recent years, EVs have gained significant attention owing to their ability to carry nucleic acids, lipids, and proteins of host and pathogen origins. A distinct composition of EVs during pathogenic infection contributes to mediating pathogenic infection, transmission, and immunity to target cells. Therefore, studying the role of EVs in pathogenic infection is crucial for understanding pathogen-host interactions and developing new anti-pathogenic therapies. This review offers an overview of current knowledge of EVs in the context of infection, transmission, and immunity to pathogens. Harnessing EVs’ biology during pathogenic infection may lay a foundation for the mitigation of pathogenic infection and associated disease outcomes.

关键词： Extracellular vesicles     Pathogen     Infection     Transmission     Immunity    

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Locally enhanced electric field treatment (LEEFT) for water disinfection

Jianfeng Zhou, Ting Wang, Cecilia Yu, Xing Xie

《环境科学与工程前沿（英文）》 2020年 第14卷 第5期 doi: 10.1007/s11783-020-1253-x

摘要： • Nanowire-assisted LEEFT is applied for water disinfection with low voltages. • LEEFT inactivates bacteria by disrupting cell membrane through electroporation. • Multiple electrodes and device configurations have been developed for LEEFT. • The LEEFT is low-cost, highly efficient, and produces no DBPs. • The LEEFT can potentially be applicable for water disinfection at all scales. Water disinfection is a critical step in water and wastewater treatment. The most widely used chlorination suffers from the formation of carcinogenic disinfection by-products (DBPs) while alternative methods (e.g., UV, O3, and membrane filtration) are limited by microbial regrowth, no residual disinfectant, and high operation cost. Here, a nanowire-enabled disinfection method, locally enhanced electric field treatment (LEEFT), is introduced with advantages of no chemical addition, no DBP formation, low energy consumption, and efficient microbial inactivation. Attributed to the lightning rod effect, the electric field near the tip area of the nanowires on the electrode is significantly enhanced to inactivate microbes, even though a small external voltage (usually<5 V) is applied. In this review, after emphasizing the significance of water disinfection, the theory of the LEEFT is explained. Subsequently, the recent development of the LEEFT technology on electrode materials and device configurations are summarized. The disinfection performance is analyzed, with respect to the operating parameters, universality against different microorganisms, electrode durability, and energy consumption. The studies on the inactivation mechanisms during the LEEFT are also reviewed. Lastly, the challenges and future research of LEEFT disinfection are discussed.

关键词： Water treatment     Nanotechnology     Pathogen inactivation     Electroporation     Nanowire     Chemical-free    

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PathogenTrack and Yeskit: tools for identifying intracellular pathogens from single-cell RNA-sequencing datasets as illustrated by application to COVID-19

《医学前沿（英文）》 2022年 第16卷 第2期   页码 251-262 doi: 10.1007/s11684-021-0915-9

摘要： Pathogenic microbes can induce cellular dysfunction, immune response, and cause infectious disease and other diseases including cancers. However, the cellular distributions of pathogens and their impact on host cells remain rarely explored due to the limited methods. Taking advantage of single-cell RNA-sequencing (scRNA-seq) analysis, we can assess the transcriptomic features at the single-cell level. Still, the tools used to interpret pathogens (such as viruses, bacteria, and fungi) at the single-cell level remain to be explored. Here, we introduced PathogenTrack, a python-based computational pipeline that uses unmapped scRNA-seq data to identify intracellular pathogens at the single-cell level. In addition, we established an R package named Yeskit to import, integrate, analyze, and interpret pathogen abundance and transcriptomic features in host cells. Robustness of these tools has been tested on various real and simulated scRNA-seq datasets. PathogenTrack is competitive to the state-of-the-art tools such as Viral-Track, and the first tools for identifying bacteria at the single-cell level. Using the raw data of bronchoalveolar lavage fluid samples (BALF) from COVID-19 patients in the SRA database, we found the SARS-CoV-2 virus exists in multiple cell types including epithelial cells and macrophages. SARS-CoV-2-positive neutrophils showed increased expression of genes related to type I interferon pathway and antigen presenting module. Additionally, we observed the Haemophilus parahaemolyticus in some macrophage and epithelial cells, indicating a co-infection of the bacterium in some severe cases of COVID-19. The PathogenTrack pipeline and the Yeskit package are publicly available at GitHub.

关键词： scRNA-seq     intracellular pathogen     microbe     COVID-19     SARS-CoV-2    

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Clinical manifestations and pathogen characteristics in children admitted for suspected COVID-19

Xiaofang Cai, Hanlan Jiang, Simin Zhang, Shengying Xia, Wenhui Du, Yaoling Ma, Tao Yu, Wenbin Li

《医学前沿（英文）》 2020年 第14卷 第6期   页码 776-785 doi: 10.1007/s11684-020-0820-7

摘要： Coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has spread around the world. However, approaches to distinguish COVID-19 from pneumonia caused by other pathogens have not yet been reported. We retrospectively analyzed the clinical data of 97 children with probable COVID-19. A total of 13 (13.4%) patients were confirmed positive for SARS-CoV-2 infection by nucleic acid RT-PCR testing, and 41 (42.3%) patients were found to be infected with other pathogens. Notably, no pathogen was detected in 43 (44.3%) patients. Among all patients, 25 (25.8%) had familial cluster exposure history, and 52 (53.6%) had one or more coexisting conditions. Fifteen (15.5%) patients were admitted or transferred to the PICU. In the 11 confirmed COVID-19 cases, 5 (45.5%) and 7 (63.6%) were positive for IgM and IgG against SARS-CoV-2, respectively. In 22 patients with suspected COVID-19, 1 (4.5%) was positive for IgG but negative for IgM. The most frequently detected pathogen was (29, 29.9%). One patient with confirmed COVID 19 died. Our results strongly indicated that the detection of asymptomatic COVID 19 or coexisting conditions must be strengthened in pediatric patients. These cases may be difficult to diagnose as COVID-19 unless etiologic analysis is conducted. A serologic test can be a useful adjunctive diagnostic tool in cases where SARS-CoV-2 infection is highly suspected but the nucleic acid test is negative.

关键词： coronavirus disease 2019     pediatrics     emergency     retrospective investigation     severe acute respiratory syndrome coronavirus 2    

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Composition, dispersion, and health risks of bioaerosols in wastewater treatment plants: A review

Yunping Han, Lin Li, Ying Wang, Jiawei Ma, Pengyu Li, Chao Han, Junxin Liu

《环境科学与工程前沿（英文）》 2021年 第15卷 第3期 doi: 10.1007/s11783-020-1330-1

摘要： Abstract • Bioaerosols are produced in the process of wastewater biological treatment. • The concentration of bioaerosol indoor is higher than outdoor. • Bioaerosols contain large amounts of potentially pathogenic biomass and chemicals. • Inhalation is the main route of exposure of bioaerosol. • Both the workers and the surrounding residents will be affected by the bioaerosol. Bioaerosols are defined as airborne particles (0.05–100 mm in size) of biological origin. They are considered potentially harmful to human health as they can contain pathogens such as bacteria, fungi, and viruses. This review summarizes the most recent research on the health risks of bioaerosols emitted from wastewater treatment plants (WWTPs) in order to improve the control of such bioaerosols. The concentration and size distribution of WWTP bioaerosols; their major emission sources, composition, and health risks; and considerations for future research are discussed. The major themes and findings in the literature are as follows: the major emission sources of WWTP bioaerosols include screen rooms, sludge-dewatering rooms, and aeration tanks; the bioaerosol concentrations in screen and sludge-dewatering rooms are higher than those outdoors. WWTP bioaerosols contain a variety of potentially pathogenic bacteria, fungi, antibiotic resistance genes, viruses, endotoxins, and toxic metal(loid)s. These potentially pathogenic substances spread with the bioaerosols, thereby posing health risks to workers and residents in and around the WWTP. Inhalation has been identified as the main exposure route, and children are at a higher risk of this than adults. Future studies should identify emerging contaminants, establish health risk assessments, and develop prevention and control systems.

关键词： Wastewater treatment plant     Bioaerosols     Pathogen     Dispersion     Risk assessment    

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Pathogen evolution, prevention/control strategy and clinical features of COVID-19: experiences from China

《医学前沿（英文）》 2023年 第17卷 第6期   页码 1030-1046 doi: 10.1007/s11684-023-1043-5

摘要： Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was reported at the end of 2019 as a worldwide health concern causing a pandemic of unusual viral pneumonia and many other organ damages, which was defined by the World Health Organization as coronavirus disease 2019 (COVID-19). The pandemic is considered a significant threat to global public health till now. In this review, we have summarized the lessons learnt during the emergence and spread of SARS-CoV-2, including its prototype and variants. The overall clinical features of variants of concern (VOC), heterogeneity in the clinical manifestations, radiology and pathology of COVID-19 patients are also discussed, along with advances in therapeutic agents.

关键词： coronavirus disease 2019     SARS-CoV-2     epidemiology     clinical features    

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Effect of the ultraviolet/chlorine process on microbial community structure, typical pathogens, and antibiotic resistance genes in reclaimed water

《环境科学与工程前沿（英文）》 2022年 第16卷 第8期 doi: 10.1007/s11783-022-1521-z

摘要：

• UV/chlorine can effectively remove VBNC pathogens, ARGs and MGEs in reclaimed water.

关键词： UV/chlorine process     Pathogen     Antibiotic resistance genes     High-throughput qPCR     Reclaimed water    

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海水养殖细菌性病害检测方法研究进展

肖婧凡,王玥,张元兴,雷霁霖

《中国工程科学》 2014年 第16卷 第9期   页码 10-15

摘要：

随着我国水产养殖业的不断发展，各种病害问题日益突出。细菌性病害在所有病害中占到相当大的比例，因此其检测方法的开发在水产养殖病害发现、防治、无公害水产品生产及卫生质量检验中均具有重要意义。本文对近年来国内外主要海水养殖细菌性病害检测方法的研究情况进行综述，介绍了主要细菌性病害的各种检测方法的原理、应用及其研究进展，为我国今后建立水产养殖细菌性病害检测方法标准及推动相应检测产品的商品化提供参考。

关键词： 水产养殖     细菌性病害     检测方法    

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鲆鲽类主要病原菌抗血清的制备及应用

甘玲玲,王蔚芳,高淳仁,雷霁霖

《中国工程科学》 2014年 第16卷 第9期   页码 21-25

摘要：

用甲醛灭活8 种鲆鲽类主要病原菌，鳗弧菌(Vibrio anguillarum)、创伤弧菌(Vibrio vulnificus)、哈维弧菌(Vibrio harveyi)、溶藻弧菌(Vibrio alginolyticus)、嗜水气单胞菌(Aeromonas hydrophila)、豚鼠气单胞菌(Aeromonas caviae)、迟缓爱德华菌(Edwardsiella tarda)、鮰爱德华菌(Edwardsiella ictaluri)，制备成灭活疫苗后肌肉注射大菱鲆获得各病原菌抗血清。结果显示，抗鳗弧菌血清、抗哈维弧菌血清、抗豚鼠气单胞菌血清、抗鮰爱德华菌效价为1:6 400，抗创伤弧菌血清、抗溶藻弧菌血清、抗嗜水气单胞菌血清效价为1:12 800，抗迟缓爱德华菌血清效价为1:102 400。应用ELISA分析各抗血清与8 种病原菌及迟缓爱德华菌蛋白的免疫交叉反应，结果显示，各病原菌与其本身的抗血清反应最为强烈，而与其他抗血清间有程度不等的交叉反应；菌蛋白与其相应的菌抗血清反应最为强烈，与其他病原菌抗血清反应较弱。本研究所制备的病原菌抗血清效价较高，且具有特异性，可应用于鲆鲽类病原菌的检测。

关键词： 鲆鲽类     疫苗     抗血清     病原菌    

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New insights in the battle between wheat and

Chunlei TANG,Xiaojie WANG,Yulin CHENG,Minjie LIU,Mengxin ZHAO,Jinping WEI,Zhensheng KANG

《农业科学与工程前沿（英文）》 2015年 第2卷 第2期   页码 101-114 doi: 10.15302/J-FASE-2015068

摘要： Wheat stripe rust caused by f. sp. ( ) poses a great threat to wheat production worldwide. The rapid change in virulence of leads to a loss of resistance in currently resistant wheat cultivars, which results in frequent disease epidemics. Therefore, a major focus is currently placed on investigating the molecular mechanisms underlying this rapid variation of pathogenicity and coevolving wheat resistance. Limited by the lack of a system for stable transformation of and the difficulties in wheat transformation, it is not easy to generate deeper insights into the wheat- interaction using established genetic methods. Nevertheless, considerable effort has been made to unravel the wheat- interaction and significant progress is being made. Histology and cytology have revealed basic details of infection strategies and defense responses during wheat- interactions, identified cellular components involved in wheat- interactions, and have helped to elucidate their role in the infection process or in plant defense responses. Transcriptome and genome sequencing has revealed the molecular features and dynamics of the wheat- pathosystem. Extensive molecular analyses have led to the identification of major components in the wheat resistance response and in virulence. Studies of wheat- interactions have now entered a new phase in which cellular and molecular approaches are being used. This review focuses on the cellular biology of wheat- interactions and integrates the emerging data from molecular analyses with the histocytological observations.

关键词： wheat     strip rust     Puccinia striiformis f. sp. tritici     host defense     pathogen virulence     biotrophic fungus    

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GWPD: a multifunctional platform to unravel biological risk factors in global engineered water systems

Aijie Wang,Fang Huang,Wenxiu Wang,Yanmei Zhao,Yiyi Su,Zelin Lei,Rui Gao,Yu Tao,Jun Wei,Haoyi Cheng,Jinsong Liang,Bin Liang,Jianhua Guo,Jiping Jiang,Lu Fan,Shu-Hong Gao,

《工程（英文）》 doi: 10.1016/j.eng.2024.04.022

摘要： Engineered water systems such as wastewater treatment plants (WWTPs) are potential reservoirs of various biological risk factors (BRFs), including pathogens, antibiotic resistance genes (ARGs), and virulence factors (VFs). Currently, a BRF database relevant to engineered water systems on a global geographic scale is lacking. Here, we present the Global Wastewater Pathogen Database (GWPD, http://gwpd.hitsz.edu.cn), an online database that provides information on the diversity, abundance, and distribution of BRFs from 1302 metagenome samples obtained from 186 cities, 68 countries, and six continents. We sorted these samples into six types: sewer networks, influent, anoxic activated sludge, oxic activated sludge, effluent, and receiving/natural waters. In total, 476 pathogens, 442 ARGs, and 246 VFs were identified. As a multifunctional database, GWPD provides an interactive visualization of these BRFs in a world map, an information retrieval interface, and an online one-click service for BRF annotation from metagenome sequencing data. GWPD is built on a web service framework, which can be readily extended to future versions of GWPD by adding more functional modules and connecting to other data sources, such as epidemic databases, to support risk assessment and control in the context of “One Health.”

关键词： Pathogen     Antibiotic resistance genes     Biological risk factors     Metagenome     Engineered water system     Wastewater treatment    

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利用基因组特异性引物和Cas12a介导技术快速检测稻瘟菌小麦致病型 Article

康厚祥, 彭烨, Kangyu Hua, 邓雨飞, Maria Bellizzi, Dipali Rani Gupta, Nur Uddin Mahmud, Alfredo S. Urashima, Sanjoy Kumar Paul, Gary Peterson, 周益林, 周雪平, Md Tofazzal Islam, 王国梁

《工程（英文）》 2021年 第7卷 第9期   页码 1326-1335 doi: 10.1016/j.eng.2020.07.016

摘要：

麦瘟病由稻瘟菌小麦致病型（MoT）引起，是一种存在于南美洲和孟加拉国的毁灭性病害。由于MoT通常不会在抽穗期之前使小麦显现染病症状，但在抽穗期其侵染会一直加剧，因此仅根据肉眼观察来使用杀菌剂是无效的。为了开发一种在苗期和营养期准确、灵敏检测MoT以控制病害蔓延的方法，我们对来自巴西的两个MoT分离株的基因组进行了测序，并确定了两个DNA片段：MoT-6098 和MoT-6099，它们存在于麦瘟病菌（MoT）基因组中，但不存在于感染稻瘟病菌（MoO）的水稻基因组中。利用聚合酶链反应（PCR），我们在来自南美洲和孟加拉国的53 株MoT和MoO分离株中证实了这两对标记引物的特异性。为了测试这两对标记引物的有效性，我们首先建立了一种环介导等温扩增（LAMP）方法。在等温条件下，这种方法在不使用常规PCR仪器的情况下也能检测MoT。随后，我们使用Cas12a 蛋白及导向RNA（gRNA）靶向MoT-6098 和MoT-6099 序列，两个靶标被识别后，均能激活Cas12a 非特异切割单链脱氧核糖核酸酶（ssDNAase）的活性，我们将依赖靶向Cas12a 激活ssDNase 活性，同时将重组酶聚合酶扩增（RPA）和核酸侧流免疫分析法（NALFIA）相结合，开发出一种准确、灵敏且经济高效地检测受感染小麦植株中MoT特异性DNA序列的方法。这种新技术可应用于田间麦瘟病和其他重要植物病害的快速检测。

关键词： 麦瘟病     稻瘟菌小麦致病型     Cas12a     核酸侧流免疫分析     田间检测    

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标题 作者 时间 类型 操作

spp., foodborne pathogens threatening neonates and infants

Qiming CHEN, Yang ZHU, Zhen QIN, Yongjun QIU, Liming ZHAO

期刊论文

Systems understanding of plant–pathogen interactions through genome-wide protein–protein interaction

Hong LI,Ziding ZHANG

期刊论文

Extracellular Vesicles in Pathogenic Infection, Transmission, and Immunity

Junyao Xiong,Usama Ashraf,Jing Ye,Shengbo Cao,

期刊论文

Locally enhanced electric field treatment (LEEFT) for water disinfection

Jianfeng Zhou, Ting Wang, Cecilia Yu, Xing Xie

期刊论文

PathogenTrack and Yeskit: tools for identifying intracellular pathogens from single-cell RNA-sequencing datasets as illustrated by application to COVID-19

期刊论文

Clinical manifestations and pathogen characteristics in children admitted for suspected COVID-19

Xiaofang Cai, Hanlan Jiang, Simin Zhang, Shengying Xia, Wenhui Du, Yaoling Ma, Tao Yu, Wenbin Li

期刊论文

Composition, dispersion, and health risks of bioaerosols in wastewater treatment plants: A review

Yunping Han, Lin Li, Ying Wang, Jiawei Ma, Pengyu Li, Chao Han, Junxin Liu

期刊论文

Pathogen evolution, prevention/control strategy and clinical features of COVID-19: experiences from China

期刊论文

Effect of the ultraviolet/chlorine process on microbial community structure, typical pathogens, and antibiotic resistance genes in reclaimed water

期刊论文

海水养殖细菌性病害检测方法研究进展

肖婧凡,王玥,张元兴,雷霁霖

期刊论文

鲆鲽类主要病原菌抗血清的制备及应用

甘玲玲,王蔚芳,高淳仁,雷霁霖

期刊论文

New insights in the battle between wheat and

Chunlei TANG,Xiaojie WANG,Yulin CHENG,Minjie LIU,Mengxin ZHAO,Jinping WEI,Zhensheng KANG

期刊论文

GWPD: a multifunctional platform to unravel biological risk factors in global engineered water systems

Aijie Wang,Fang Huang,Wenxiu Wang,Yanmei Zhao,Yiyi Su,Zelin Lei,Rui Gao,Yu Tao,Jun Wei,Haoyi Cheng,Jinsong Liang,Bin Liang,Jianhua Guo,Jiping Jiang,Lu Fan,Shu-Hong Gao,

期刊论文

利用基因组特异性引物和Cas12a介导技术快速检测稻瘟菌小麦致病型

康厚祥, 彭烨, Kangyu Hua, 邓雨飞, Maria Bellizzi, Dipali Rani Gupta, Nur Uddin Mahmud, Alfredo S. Urashima, Sanjoy Kumar Paul, Gary Peterson, 周益林, 周雪平, Md Tofazzal Islam, 王国梁

期刊论文