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DeepSecE:A Deep-Learning-Based Framework for Multiclass Prediction of Secreted Proteins in gram-Negative Bacteria

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Research 2024年第3期2023卷 243-257页

作者： Yumeng Zhang Jiahao guan Chen Li Zhikang Wang Zixin Deng robin Bgasser Jiangning Song Hong-Yu Ou state Key Laboratory of Microbial Metabolism Joint International Laboratory on Metabolic&Developmental SciencesSchool of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai 200240China Shanghai Key Laboratory of Veterinary Biotechnology Shanghai Jiao Tong UniversityShanghai 200240China Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology Monash UniversityMelbourneViC 3800Australia Monash Data Futures Institute Monash UniversityMelbourneViC 3800Australia Melbourne Veterinary School Faculty of ScienceThe University of MelbourneParkvilleVIC 3010Australia.

Proteins secreted by gram-negative bacteria are tightly linked to the virulence and adaptability of these microbes to environmental *** identification of such secreted proteins can facilitate the investigations of infections and diseases caused by these bacterial ***,current bioinformatic methods for predicting bacterial secreted substrate proteins have limited computational efficiency and application scope on a genome-wide ***,we propose a novel deep-learning-based framework—DeepSecE—for the simultaneous inference of multiple distinct groups of secreted proteins produced by gram-negative *** remarkably improves their classification from nonsecreted proteins using a pretrained protein language model and transformer,achieving a macro-average accuracy of 0.883 on 5-fold *** benchmarking suggests that DeepSecE achieves competitive performance with the state-of-the-art binary predictors specialized for individual types of secreted *** attention mechanism corroborates salient patterns and motifs at the N or C termini of the protein *** this pipeline,we further investigate the genome-wide prediction of novel secreted proteins and their taxonomic distribution across~1,000 gram-negative bacterial *** present analysis demonstrates that DeepSecE has major potential for the discovery of disease-associated secreted proteins in a diverse range of gram-negative *** online web server of DeepSecE is also publicly available to predict and explore various secreted substrate proteins via the input of bacterial genome sequences.

关键词： Deep server competitive

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中国手斧技术演化:新进展和未来展望

Science Bulletin 2024年第14期69卷 2161-2165页

作者：李浩王社江 Matt g.Lotter robin Dennell Kathleen Kuman 陈发虎 State Key Laboratory of Tibetan Plateau Earth System Resources and Environment(TPESER)Institute of Tibetan Plateau ResearchChinese Academy of SciencesBeijing 100101China Key Laboratory of Vertebrate Evolution and Human Origins Institute of Vertebrate Paleontology and PaleoanthropologyChinese Academy of SciencesBeijing 100044China Palaeo-Research Institute University of JohannesburgAuckland Park 2006South Africa Department of Archaeology University of ExeterExeter EX44QEUK School of geography Archaeology and Environmental StudiesUniversity of the WitwatersrandJohannesburg WITS 2050South Africa

Handaxes are often regarded as the"tool-type-specimenoof the Acheulean techno-complex,not only because they are a very common artefact but because they contain rich technological,behavioral,and cognitive data that have been used to highlight trends in human evolution and lithic production *** this end,the handaxe is the earliest tool possessing consistent morphological features,in particular,the appearance of a symmetrical concept in handaxe shape when compared with other Acheulean large shaping tools(e.g.,cleavers),and their manufacture is widely regarded as a significant milestone in the evolution of lithic technology,indicating improvements in tool-making hominins’abilities for complex thought and cognition.

关键词：技术演化未来展望 earliest

A study on wildfire impacts on greenhouse gas emissions and regional air quality in South of Orléans,France

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Journal of Environmental Sciences 2024年第1期135卷 521-533页

作者： Chaoyang Xue gisèle Krysztofiak Yangang Ren Min Cai Patrick Mercier Frédéric Le Fur Corinne robin Benoit grosselin Véronique Daele Max RMcgillen Yujing Mu Valéry Catoire Abdelwahid Mellouki Laboratoire de Physique et Chimie de l’Environnement et de l’Espace(LPC2E) CNRS–UniversitéOrléans–CNES(UMR 7328)Orléans Cedex 245071France Institut de Combustion AérothermiqueRéactivitéEnvironnement(ICARE)CNRSOrléans Cedex 245071France Research Centre for Eco-Environmental Sciences Chinese Academy of SciencesBeijing 100085China Lig’Air-Association de surveillance de la qualitéde l’air en région Centre-Val de Loire Saint-Cyr-en-Val 45590France Mohammed V University RabatMorocco

Wildfire events are increasing globally which may be partly associated with climate change,resulting in significant adverse impacts on local,regional air quality and global *** September 2020,a small wildfire(burned area:36.3 ha)event occurred in Souesmes(Loiret-Cher,Sologne,France),and its plume spread out over 200 km on the following day as observed by the MODIS *** on measurements at a suburban site(~50 km northwest of the fire location)in Orléans and backward trajectory analysis,young wildfire plumes were *** increases in gaseous pollutants(CO,CH_(4),N_(2)O,VOCs,etc.)and particles(including black carbon)were found within the wildfire plumes,leading to a reduced air *** factors,defined as EF(X)=ΔX/ΔCO(where,X represents the target species),of various trace gases and black carbon within the young wildfire plumes were determined accordingly and compared with previous *** in the ambient ions(such as ammonium,sulfate,nitrate,chloride,and nitrite in the particle-and gasphase)and aerosol properties(e.g.,aerosol water content,aerosol p H)were also quantified and ***,we estimated the total carbon and climate-related species(e.g.,CO_(2),CH_(4),N_(2)O,and BC)emissions and compared them with fire emission *** biomass burning emission inventories have uncertainties in estimating small fire burned areas and *** instance,we found that the global Fire Assimilation System(gFAS)may underestimate emissions(e.g.,CO)of this small wildfire while other inventories(gFED and FINN)showed significant *** that it is the first time to record wildfire plumes in this region,related atmospheric implications are presented and discussed.

关键词： Wildfire Air quality Emission factor Emission inventory VOLTAIRE supersite

2023: Weather and Climate Extremes Hitting the globe with Emerging Features

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Advances in Atmospheric Sciences 2024年第6期41卷 1001-1016页

作者： Wenxia ZHANg robin CLARK Tianjun ZHOU Laurent LI Chao LI Juan RIVERA Lixia ZHANg Kexin gUI Tingyu ZHANg Lan LI Rongyun PAN Yongjun CHEN Shijie TANg Xin HUANg Shuai HU State Key Laboratory of Numerical Modeling for Atmospheric Sciences and geophysical Fluid Dynamics Institute of Atmospheric PhysicsChinese Academy of SciencesBeijing 100029China Met Office Hadley Centre Exeter EX13PBUK University of Chinese Academy of Sciences Beijing 100049China Laboratoire de Météorologie Dynamique CNRSSorbonne UniversitéEcole Normale SupérieureEcole PolytechniqueParis 75230France Max Planck Institute for Meteorology Hamburg 20146Germany Instituto Argentino de Nivología Glaciología Y Ciencias Ambientales(IANIGLA)CCT CONICETMendoza CP 5500Argentina Shanghai Typhoon Institute China Meteorological AdministrationShanghai 200030China Asia-Pacific Typhoon Collaborative Research Center Shanghai 201306China

globally,2023 was the warmest observed year on record since at least 1850 and,according to proxy evidence,possibly of the past 100000 *** in recent years,the record warmth has again been accompanied with yet more extreme weather and climate events throughout the ***,we provide an overview of those of 2023,with details and key background causes to help build upon our understanding of the roles of internal climate variability and anthropogenic climate *** also highlight emerging features associated with some of these extreme *** extremes are occurring earlier in the year,and increasingly simultaneously in differing parts of the world(e.g.,the concurrent hot extremes in the Northern Hemisphere in July 2023).Intense cyclones are exacerbating precipitation extremes(e.g.,the North China flooding in July and the Libya flooding in September).Droughts in some regions(e.g.,California and the Horn of Africa)have transitioned into flood *** extremes also show increasing interactions with ecosystems via wildfires(e.g.,those in Hawaii in August and in Canada from spring to autumn 2023)and sandstorms(e.g.,those in Mongolia in April 2023).Finally,we also consider the challenges to research that these emerging characteristics present for the strategy and practice of adaptation.

关键词： weather and climate extremes temperature extremes extreme precipitation drought wildfires

Properties and Characterization of Two Clays Raw Material from Mountain District (West of Côte d’Ivoire) for Use in Low-Carbon Cements

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Advances in Materials Physics and Chemistry 2024年第8期14卷 137-145页

作者： Wedjers Max robin Manouan Bi Irié Hervé gouré Doubi Lébé Prisca Marie-Sandrine Kouakou Atta Kouamé Brice Koffi Alfred Niamien Kouamé Namory Méité UFR Sciences et Technologies Universit de Man Man Cte dIvoire UFR Sciences Biologiques Universit Peleforo GON COULIBALY Korhogo Cte dIvoire Laboratoire de constitution et de raction de la matire Universit Felix Houphout-Boigny Abidan Cte dIvoire

This work was devoted to the study of the physico-chemical properties of two clay minerals from the Mountain District (West Côte d'Ivoire) referenced ME1 and ME2. These samples were characterized by the experimental techniques, such as X-ray diffraction (XRD), Infrared spectroscopy (IR), Inductively Coupled Plasma Atomic Emission Spectrometry (ICP-AES), Differential Thermal Analysis and Thermogravimetry (DTA-Tg), Brunauer, Emett and Teller method (BET), laser particle size analysis and Scanning Electron Microscope (SEM). The main results of these analyses reveal that the two clay samples mainly contain quartz (52.91% for ME1 and 51.72% for ME2), kaolinite (36.60% for ME1 and 41.6% for ME2) and associated phases, namely goethite and hematite (13.47% for ME1 and 11.00% for ME2). The specific surface values obtained for samples ME1 and ME2 are 34.78 m2/g and 29.18 m2/g respectively. The results obtained show that the samples studied belong to the kaolinite family. After calcination, they could have good pozzolanic activity and therefore be used in the manufacture of low-carbon cements.

关键词： Quartz Kaolinite Mountain District Low-Carbon Cements

Code modernization and modularization of APEX and SWAT watershed simulation models

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International Journal of Agricultural and Biological Engineering 2015年第3期8卷 81-94页

作者： robin A.J.Taylor Jaehak Jeong Michael White Jeffrey g.Arnold Blackland Research&Extension Center Texas A&M AgriLife ResearchTempleTexas 76502USA grassland Soil&Water Research Laboratory USDA-ARS TempleTexas 76502USA

SWAT(Soil and Water Assessment Tool)and APEX(Agricultural Policy/Environmental eXtender)are respectively large and small watershed simulation models derived from EPIC(Environmental Policy Integrated Climate),a field-scale agroecology simulation *** three models are coded in Fortran and have evolved over several *** are widely used to analyze anthropogenic influences on soil and water quality and *** of the original Fortran code has been retained even though Fortran has been through several cycles of *** now provides functionality originally restricted to languages like C,designed to communicate directly with the operating system and *** can now use an object-oriented style of programming in Fortran,including inheritance,run-time polymorphism and *** order to enhance their utility in research and policy-making,the models are undergoing a major revision to use some of the new Fortran *** these new programming paradigms the developers of SWAT,APEX,and EPIC are working to make communication between the two models *** paper describes the ongoing revision of these models that will make them easier to use,maintain,modify and *** is intended that they will converge as they continue to evolution,while maintaining their distinctive features,capabilities and identities.

关键词： code modernization modularization object-oriented programming Fortran 2008 landscape-scale models APEX EPIC SWAT

An Uncertainty-aware Workflow for Keyhole Surgery Planning using Hierarchical Image Semantics

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Visual Informatics 2018年第1期2卷 26-36页

作者： Christina gillmann robin g.C.Maack Tobias Post Thomas Wischgoll Hans Hagen University of Kaiserslautern Erwin-Schroedinger-Strasse 167663 Kaiserslautern Wright State University 3640 Colonel Glenn HwyDaytonOH

Keyhole surgeries become mcreasingly important in clinical daily routine as they help minimizing the damage of a patient's healthy *** planning of keyhole surgeries is based on medical imaging and an important factor that influences the surgeries**** to the image reconstruction process,medical image data contains uncertainty that exacerbates the planning of a keyhole *** this paper we present a visual workflow that helps clinicians to examine and compare different surgery paths as well as visualizing the patientsJ affected *** analysis is based on the concept of hierarchical image semantics,that segment the underlying image data with respect to the input images'uncertainty and the users understanding of tissue *** can define arbitrary surgery paths that they need to investigate *** defined paths can be queried by a rating function to identify paths that fulfill user-defined *** workflow allows a visual inspection of the affected tissues and its ***,the workflow includes a linked view system indicating the three-dimensional location of selected surgery paths as well as how these paths affect the patients *** show the effectiveness of the presented approach,we applied it to the planning of a keyhole surgery of a brain tumor removal and a kneecap surgery.

关键词： Wsual Analytics Workflow Uncertainty sualization Keyhole Surgery Planning

Advances in Science and Engineering II

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Conservation of Traditional Agriculture as Living Knowledge Systems,Not Cultural Relics

丛书名： Applied Mechanics and Materials, v. 135-136

2012年

作者： Ju, Yongfeng Qiu, robin g. World Association of Science Engineering

Selected, peer reviewed papers from the 2011 WASE global Conference on Science Engineering (gCSE 2011), December 10-11, 2011, Taiyuan & Xian, China

ISBN: (纸本)9783037852903;9783038137191

Selected, peer reviewed papers from the 2011 WASE global Conference on Science Engineering (gCSE 2011), December 10-11, 2011, Taiyuan & Xian, China

关键词： Materials science--Technological innovations Engineering--Congresses

来源：畅想之星图书光盘版（南... 评论

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Journal of Resources and Ecology 2016年第3期7卷 231-236页

作者： NILES Daniel ROTH robin 综合地球环境学研究所日本京都府603-8047 圭尔夫大学地理学院加拿大圭尔夫N1G2W1

Agricultural heritage has potential significance far beyond its common representation as the ＂traditional＂ system of ＂traditional peoples＂.The *** and Agricultural Organization＇s globally Important Agricultural Heritage Systems（gIAHS） program is an important designation that treats heritage agro-ecosystems as living systems,rather than cultural *** order for the gIAHS designation to achieve its full potential,however,the role of human knowledge within the continuous cultural and ecological evolution of gIAHS requires much closer examination and *** paper explores the limits of contemporary nature and cultural conservation,and draws on a coevolutionary theoretical framework in order to better conceptualize the dynamism of such complex agro-ecological *** such a view,gIAHS can be seen as evolving systems of sustainable agriculture of great potentail relevance to contemporary society-environment challenges,rather than as relics of the past.

关键词： globally Important Agricultural Heritage Systems(gIAHS) conservation cultural preservation UNESCO coevolution dynamic conservation knowledge systems