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Enhancing antimicrobial resistance detection with MetaGeneMiner: Targeted gene extraction from metagenomes

中华医学杂志(英文版) 2024年第17期137卷 2024 Jun 27页

作者： Liu Chang Tang Zizhen Li Linzhu Kang Yan Teng Yue Yu Yan Department of Critical Care Medicine West China Hospital Sichuan University Chengdu Sichuan China Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education College of Life Sciences Sichuan University Chengdu Sichuan China State Key Laboratory of Pathogen and Biosecurity Beijing Institute of Microbiology and Epidemiology Beijing China

Background: Accurately and efficiently extracting microbial genomic sequences from complex metagenomic data is crucial for advancing our understanding in fields such as clinical diagnostics, environmental microbiology, and biodiversity. As sequencing technologies evolve, this task becomes increasingly challenging due to the intricate nature of microbial communities and the vast amount of data generated. Especially in intensive care units (ICUs), infections caused by antibiotic-resistant bacteria are increasingly prevalent among critically ill patients, significantly impacting the effectiveness of treatments and patient prognoses. Therefore, obtaining timely and accurate information about infectious pathogens is of paramount importance for the treatment of patients with severe infections, which enables precisely targeted anti-infection therapies, and a tool that can extract microbial genomic sequences from metagenomic dataset would be of ***: We developed MetaGeneMiner to help with retrieving specific microbial genomic sequences from metagenomes using a k-mer-based approach. It facilitates the rapid and accurate identification and analysis of pathogens. The tool is designed to be user-friendly and efficient on standard personal computers, allowing its use across a wide variety of settings. We validated MetaGeneMiner using eight metagenomic samples from ICU patients, which demonstrated its efficiency and ***: The software extensively retrieved coding sequences of pathogensAcinetobacter baumannii and herpes simplex virus type 1 and detected a variety of resistance genes. All documentation and source codes for MetaGeneMiner are freely available at https://***/sculab/***: It is foreseeable that MetaGeneMiner possesses the potential for applications across multiple domains, including clinical diagnostics, environmental microbiology, gut microbiome research, as well as biodiversity and conservation biology. Particularly in

关键词： Metagenomics Genomic sequencing Clinical diagnostics Reference-based assembly Intensive care unit infections Antibiotic resistance

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The impact of carbon emissions trading policy on carbon emission efficiency in Chinese cities:Evidence from a quasi-natural experiment

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中国人口·资源与环境:英文版 2023年第3期21卷 121-136页

作者： Keliang Wang Yuanjie Qiao Liwei Ling Ziheng Zhao Kun Liu School of Economics Ocean University of ChinaQingdao266011China Economic Management Center Chengdu Aircraft Design&Research InstituteChengdu610041China School of Economics Southwestern University of Finance and EconomicsChengdu611130China School of Accounting Southwestern University of Finance and EconomicsChengdu611130China

Based on a panel dataset spanning from 2003 to 2019 and encompassing 284 prefecture-level cities in China,this study treats the implementation of the carbon emissions trading policy(CETP)as a quasi-natural *** addition,it employs a spatial difference-in-differences(DID)framework to quantify both the direct and spatially mediated impacts of CETP on urban carbon emission efficiency(CEE).The investigation further delves into the underlying channels of influence and variations within this *** findings demonstrate that CETP effectively enhances CEE within the cities chosen for piloting;however,it concurrently dampens CEE in nonpiloting neighboring *** conclusions remain robust across diverse sensitivity *** analysis of mechanisms reveals that CETP’s influence on urban CEE primarily operates through the avenues of technological innovation and optimization of energy ***,the study of variances discloses that CETP’s direct effect significantly advances CEE in eastern,old industrial base,and central *** terms of indirect effects,a pronounced adverse spatial spillover effect is observed in eastern and old industrial base cities,while noteworthy positive spatial spillover effects emerge in central ***,the spatial extent of CETP’s influence on urban CEE declines after reaching a distance of 900 *** insights furnish valuable guidance for China in refining its nationwide carbon market and expediting the shift toward a low-carbon economy.

关键词： CETP CEE Spatial DID model Spatial spillover effect

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Upper crustal velocity and seismogenic environment of the M7.0 Jiuzhaigou earthquake region in Sichuan, China

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Earth and Planetary Physics 2021年第4期5卷 348-361页

作者： DaHu Li ZhiFeng Ding Yan Zhan PingPing Wu LiJun Chang XiangYu Sun chengdu institute of the Tibetan Plateau Earthquake Research China Earthquake AdministrationChengdu 610041China institute of Geophysics China Earthquake AdministrationBeijing 100081China institute of Geology China Earthquake AdministrationBeijing 100029China

On August 8,2017,a magnitude 7.0 earthquake occurred in Jiuzhaigou County,Sichuan Province,*** deep seismogenic environment and potential seismic risk in the eastern margin of Tibetan Plateau have once again attracted the close attention of seismologists and scholars at home and *** post-earthquake scientific investigation could not identify noticeable surface rupture zones in the affected area;the complex tectonic background and the reason(s)for the frequent seismicity in the Jiuzhaigou earthquake region are *** order to reveal the characteristics of the deep medium and the seismogenic environment of the M7.0 Jiuzhaigou earthquake region,and to interpret the tectonic background and genesis of the seismicity comprehensively,in this paper,we have reviewed all available observation data recorded by the regional digital seismic networks and large-scale,dense mobile seismic array(China Array)for the northern section of the North-South Seismic Belt around Jiuzhaigou earthquake *** double-difference seismic tomography method to invert the three-dimensional P-wave velocity structure characteristics of the upper crust around the Jiuzhaigou earthquake region,we have analyzed and discussed such scientific questions as the relationship between the velocity structure characteristics and seismicity in the Jiuzhaigou earthquake region,its deep tectonic environment,and the ongoing seismic risk in this *** report that:the P-wave velocity structure of the upper crust around the Jiuzhaigoug earthquake region exhibits obvious lateral inhomogeneity;the distribution characteristics of the shallow P-wave velocity structure are closely related to surface geological structure and formation lithology;the M7.0 Jiuzhaigou earthquake sequence is closely related to the velocity structure of the upper crust;the mainshock of the M7.0 earthquake occurred in the upper crust;the inhomogeneous variation of the velocity structure of the Jiuzhaigou earthquake area and

关键词： the M7.0 Jiuzhaigou earthquake 3D P-wave velocity structure deep tectonic seismogenic environment

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An Overview of Formation Mechanism and Disaster Characteristics of Post-seismic Debris Flows Triggered by Subsequent Rainstorms in Wenchuan Earthquake Extremely Stricken Areas

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Acta Geologica Sinica(English Edition) 2014年第4期88卷 1310-1328页

作者： NI Huayong TANG Chuan ZHENG Wanmo XU Ruge TIAN Kai XU Wei State Key Laboratory of Geohazard Prevention and Geoenvironment Protection Chengdu University of Technology chengdu institute of Geology and Mineral Resources China Geological Survey

The Wenchuan earthquake induced large amounts of debris flows and catastrophic incidents triggered by subsequent rainstorms occurred frequently in the past 6 rainy seasons, and thus resulted in serious casualties, huge economic loss and long-term impact. In this paper, post-seismic debris flows distributed in 10 Wenchuan earthquake extremely stricken counties were verified and debris flow database consisting of 609 debris flows was established based on detailed investigation organized by Land and Resources Department of Sichuan Province. Combined with database and related studies, the impact of Wenchuan earthquake on debris flows was analyzed. And then variation of formation conditions including rainfall threshold and landform condition was analyzed by contrasting pre-seismic and post-seismic debris flows. Followed are some typical viewpoints on initiation mechanism of post-seismic debris flows. In the end of this paper, characteristics of postseismic debris flows triggered by subsequent rainstorms were comprehensively summarized, such as regional group occurrence, high frequency, high viscosity, chain effect, huge dynamics, large scale and long duration. We hope this paper will be helpful in understanding the formation mechanism, disaster characteristics and prevention countermeasures of post-seismic debris flows in Wenchuan earthquake extremely stricken areas.

关键词： Wenchuan earthquake Post-seismic debris flow Gully-type debris flow Formationmechanism Disaster characteristic

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Distribution and quantitative zonation of unloading cracks at a proposed large hydropower station dam Site

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Journal of Mountain Science 2017年第10期14卷 2106-2121页

作者： ZHAO Wei-hua FROST J.D. HUANG Run-qiu YAN Ming JIN Long-de State Key Laboratory of Geohazard Prevention and Geoenvironment Protection Chengdu University of TechnologyChengdu School of Civil and Environmental Engineering Georgia Institute of Technology

Rock mass unloading is an important rock engineering problem because unloading may impact the stability of a rock mass slope. Based on hydroelectric engineering principles, this study focuses on the classification of unloading zones to reflect the rock mass structure characteristics. Geological background and slope structure of the study region were considered to investigate the distribution and deformation of the unloading process. Quantitative indices were classified according to the formation mechanisms and the geological exhibition of unloading zones. The P-wave velocity(V_P), the ratio of the wave velocity(V_p) the ratio of the test P-wave velocity along the adit depth to the P-wave velocity of intact rock, the sum of joint openings every 2 meters(S_t), and the density of open joints(D_t) were calculated as quantitative indices for the rock mass unloading zone. The characteristics of the unloading zone of rock mass slopes at the dam site were successfully determined. The method of combining qualitative data with quantitative indices was found to be effective for the classification of slope unloading zones.

关键词： Slope Structure Unloading Phenomena Classify Unloading Zones Quantitative Indexes

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investigation on impurity transport using LBO technique

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Plasma Science and Technology 2001年第3期3卷 797-802页

作者：郑银甲王瑞荣冯震钱尚介 Southwestern institute of Physics Chengdu 610041 China

Impurity transport has been investigated on the HL-IM tokamak under the conditions of the ohmically heated discharge (OHD) and the lower hybrid current drive (LHCD). A small quantity of metallic impurity Al were injected into the plasma using the laser blow-off (LBO) technique. The ionized metallic impurity lines were measured using a vacuum ultra-violet (VUV) spectrometry. Al impurity transports in the plasma under the conditions of the OHD and LHCD were analyzed. The diffusion coefficient (D(r)) and inward convection velocity (V(r)) were oh tamed using numerical simulation with the impurity transport code (ITC). The simulation results showed that the transport coefficient during the LHCD decreased by fifty per cent compared with that during the OHD. Therefore the impurity-confined characteristics of the LHCD plasma was obviously improved.

关键词： LHCD LBO VUV

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investigation of the effect of berberines alkaloids in Coptis chinensis Franch on Bacillus shigae growthby microcalorimetry

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Science China Chemistry 2007年第5期50卷 638-642页

作者： YAN Dan1,2,3, JIN Cheng1, XIAO XiaoHe1 & DONG XiaoPing2 1 institute of Chinese Medicine, 302 Hospital of People’s Liberation Army, Beijing 100039, China 2 chengdu University of Traditional Chinese Medicine, chengdu 610075, China 3 Chongqing institute of Technology, Chongqing 400050, China institute of Chinese Medicine 302 Hospital of People’s Liberation Army Beijing China chengdu University of Traditional Chinese Medicine Chengdu China Chongqing institute of Technology Chongqing China

The inhibitory effects of five berberines alkaloids (BAs) from rhizoma ofCoptis chinensis Franch,a traditional Chinese medicinal (TCM) herb,on Bacillus shigae(***)growth were investigated by *** power-time curves of *** with and without BAswere acquired;meanwhile,the extent and duration of inhibitory effects on the metabolism wereevaluated by growth rate constants (k1,k2),half inhibitory ratio (IC50),maximum heat output(P_(max)),and peak time (t_p).The values of k1 and k2 of a shigae in the presence of the five BAsdecreased with the increasing concentrations of ***,P_(max) was reduced,and the value oft_p increased with increasing concentrations of the five *** inhibitory activity varied withdifferent ***50 of the five BAs was respectively 75 mu g/mL for berberine,90 ng/mL forcoptisine,115 mu g/mL for palmatine,220 mu g/mL for epiberberine,and 400 mu g/mL *** sequence of antimicrobial activity of the five BAs:berberine > coptisine >palmatine > epiberberine > *** functional groups methylenedioxy at C2 and C3 on phenylring improve antimicrobial activity more strongly than methoxyl at C2 and C3 on ***,the effect of bacteriostasis is not significant with methylenedioxy or methoxyl at C9and C10 on phenyl ring.

关键词： berberines alkaloids, microcalorimetry, Bacillus shigae, inhibitory effect

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Visualization analysis of rainfall-induced landslides hazards based on remote sensing and geographic information system-an overview

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International Journal of Digital Earth 2023年第1期16卷 2374-2402页

作者： Zhengli Yang Heng Lu Zhijie Zhang Chao Liu Ruihua Nie Wanchang Zhang Gang Fan Chen Chen Lei Ma Xiaoai Dai Min Zhang Donghui Zhang State Key Laboratory of Hydraulics and Mountain River Engineering Sichuan UniversityChengduPeople’s Republic of China College of Hydraulic and hydroelectric Engineering Sichuan UniversityChengduPeople’s Republic of China School of Geography Development&EnvironmentUniversity of ArizonaTucsonAZUSA Key Laboratory of Digital Earth Science Aerospace Information Research InstituteChinese Academy of SciencesBeijingPeople’s Republic of China School of Geography and Ocean Science Nanjing UniversityNanjingPeople’s Republic of China College of Earth Science Chengdu University of TechnologyChengduPeople’s Republic of China School of Environmental and Geographical Sciences Shanghai Normal UniversityShanghaiPeople’s Republic of China

In recent years,RS and GIS technologies have played an increasingly important role in various aspects of rainfall induced landslide *** order to systematically understand their application situation,this paper extensively used various visualization analysis technologies for in-depth analysis of 1,161 documents collected by the WOS data platform in the past 27 years by combining quantitative and qualitative ***,this article focuses on sub domain analysis from four aspects:landslide detection and monitoring,prediction models,sensitivity mapping,and risk *** study found that the number of literature in thisfield has steadily increased and is expected to continue to *** literature review has attracted widespread attention from the academic community,but it challenging to meet research *** and effective cooperationis between countries,institutions,and authors is very beneficial for promoting progress in *** future development direction is a new intelligent hybrid model that integrates multiple research *** study can provide researchers in thisfield with the core research force,hot topic evolution,and future development trends of future rainfall-induced landslides and contribute to landslide prevention and control decision-making and achieving the United Nations’sustainable development goals.

关键词： Landslide rainfall-induced detection and monitoring predictive model sensitivity mapping risk assessment visual analysis

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GLOBAL STRUCTURE OF A KIND OF PREDATOR-PREY SYSTEM

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Applied Mathematics and Mechanics(English Edition) 1988年第10期9卷 999-1003页

作者：丁孙荭 institute of Mathematical Sciences Chengdu Branch Academia Sinica Chengdu

In this paper we prove a theorem, theorem 2, on nonexistence of closed trajectory for a general predator-prey system. Then, using this theorem and another theorem on existence and uniqueness of limit cycle for predator-prey system, we complete the investigation of a concrete model of predator-prey system (?)=γx(1-x/K)-yx~n/(a+x~2) (?)=y(μx~n/(a+x~2)-D)(n=1,2)under the conditions of all kinds of parameters.

关键词： In GLOBAL STRUCTURE OF A KIND OF PREDATOR-PREY SYSTEM cycle

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How Government Policy Is Implemented in the Private University:A Case Study from China

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Frontiers of Education in China 2018年第3期13卷 426-447页

作者： LIU Xu institute of Fashion and Art design Sichuan Normal UniversityChengdu 610010China institute of Education University College LondonLondon WC1H 0ALEngland

This article is based on original research into institutional governance in private *** provides an in-depth qualitative study of how the private university in China has responded in practice to government *** analysis focuses on three dimensions:the roles of the university council,the president,and the university *** study adopted two methods of data collection:31 separate semi-structured interviews with 21 informants as well as extensive documentary *** revealed that while external policies provide an impetus for change for each university,how key actors in institutional governance understand these policies has a significant effect on how the policies are *** can result in change that can be viewed as either symbolic alteration or as operational *** study provides insights from an empirical investigation by way of a case study on private university governance in China,and also a referential perspective on the governance of private universities in general for policy makers,senior managers,and academics.

关键词： policy implementation accountability governance China

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