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Cellular and Molecular Requirements for Polar PIN Targeting and Transcytosis in Plants

Molecular Plant 2008年第6期1卷 1056-1066页

作者： Jurgen Kleine-Vehn tukasz tangowski Justyna Wisniewska Pankaj Dhonukshe Philip B Brewer Jiri Friml department of Plant Systems Biology VIB and Department of Molecular Genetics Ghent University 9052 Gent Belgium Zentrum fur Molekularbiologie der Pflanzen (ZMBP) Universitat Tubingen 72076 Tubingen Germany present address: Institute of General and Molecular Biology Nicolas Copernicus University 87-100 Torun Poland present address: department of Biology Utrecht University 3508 TB Utrecht The Netherlands present address: Centre for Integrative Legume Research University of Queensland Brisbane Australia

The polar, sub-cellular localization of PIN auxin efflux carriers determines the direction of intercellular auxin flow, thus defining the spatial aspect of auxin signalling. Dynamic, transcytosis-like relocalizations of PIN proteins occur in response to external and internal signals, integrating these signals into changes in auxin distribution. Here, we examine the cellular and molecular mechanisms of polar PIN delivery and transcytosis. The mechanisms of the ARF-GEF-dependent polar targeting and transcytosis are well conserved and show little variations among diverse Arabidopsis ecotypes consistent with their fundamental importance in regulating plant development. At the cellular level, we refine previous findings on the role of the actin cytoskeleton in apical and basal PIN targeting, and identify a previously unknown role for microtubules, specifically in basal targeting. PIN protein delivery to different sides of the cell is mediated by ARFdependent trafficking with a previously unknown complex level of distinct ARF-GEF vesicle trafficking regulators. Our data suggest that alternative recruitment of PIN proteins by these distinct pathways can account for cell type- and cargo-specific aspects of polar targeting, as well as for polarity changes in response to different signals. The resulting dynamic PIN positioning to different sides of cells defines a three-dimensional pattern of auxin fluxes within plant tissues.

关键词： cytoskeleton polarity protein targeting.

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The boys are back in town: Rethinking the function of ribosomal DNA repeats in the genomic era

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Molecular Plant 2023年第3期16卷 514-516页

作者： Francesca B.Lopez Peter C.McKeown Antoine Fort Galina Brychkova Charles Spillane genetics and Biotechnology Laboratory Plant&AgriBiosciences Research Centre(PABC)Ryan InstituteUniversity of GalwayH91 REW4 GalwayIreland present address:department of Plant Biology and Genome Center University of CaliforniaDavisUC Davis Genome CenterDavisCA 95616USA

Next-generation sequencing technological advances,affording high-throughput,scalable,and fast assemblies,have enabled genome editing techniques that allow us to remove,insert,and modify genes for rapid and precise fun... 详细信息

关键词： remove precise function

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A Framework for Enhancing Privacy and Anonymity in Blockchain-Enabled IoT Devices

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Computers, Materials & Continua 2024年第3期78卷 4263-4282页

作者： Muhammad Saad Muhammad Raheel Bhutta Jongik Kim Tae-Sun Chung department of Artificial Intelligence Ajou UniversitySuwon443-749Korea department of Electrical and Computer Engineering University of Utah Asia CampusIncheon21985Korea department of Artificial Intelligence Chungnam National UniversityDaejeon34134Korea

With the increase in IoT(Internet of Things)devices comes an inherent challenge of *** the world today,privacy is the prime concern of every *** one’s privacy and keeping anonymity throughout the system is a desired functionality that does not come without inevitable trade-offs like scalability and increased complexity and is always exceedingly difficult to *** challenge is keeping confidentiality and continuing to make the person innominate throughout the *** address this,we present our proposed architecture where we manage IoT devices using blockchain *** proposed architecture works on and off blockchain integrated with the closed-circuit television(CCTV)security camera fixed at the rental *** this framework,the CCTV security camera feed is redirected towards the owner and renter based on the smart contract *** entity(owner or renter)can see the CCTV security camera feed at one *** is no third-party dependence except for the CCTV security camera deployment *** contributions include the proposition of framework architecture,a novel smart contract algorithm,and the modification to the ring signatures leveraging an existing cryptographic *** are made based on different systems’security and key management *** an empirical study,our proposed algorithm performed better in key generation,proof generation,and verification *** comparing similar existing schemes,we have shown the proposed architectures’*** now,we have developed this system for a specific area in the real ***,this system is scalable and applicable to other areas like healthcare monitoring systems,which is part of our future work.

关键词： Privacy anonymity blockchain IoT smart contracts

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ASLP-DL—A Novel Approach Employing Lightweight Deep Learning Framework for Optimizing Accident Severity Level Prediction

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Computers, Materials & Continua 2024年第2期78卷 2535-2555页

作者： Saba Awan Zahid Mehmood department of Software Engineering University of Engineering and TechnologyTaxila47050Pakistan department of Computer Engineering University of Engineering and TechnologyTaxila47050Pakistan

Highway safety researchers focus on crash injury severity,utilizing deep learning—specifically,deep neural networks(DNN),deep convolutional neural networks(D-CNN),and deep recurrent neural networks(D-RNN)—as the preferred method for modeling accident *** learning’s strength lies in handling intricate relation-ships within extensive datasets,making it popular for accident severity level(ASL)prediction and *** prior success,there is a need for an efficient system recognizing ASL in diverse road *** address this,we present an innovative Accident Severity Level Prediction Deep Learning(ASLP-DL)framework,incorporating DNN,D-CNN,and D-RNN models fine-tuned through iterative hyperparameter selection with Stochastic Gradient *** framework optimizes hidden layers and integrates data augmentation,Gaussian noise,and dropout regularization for improved *** and factor contribution analyses identify influential *** on three diverse crash record databases—NCDB 2018–2019,UK 2015–2020,and US 2016–2021—the D-RNN model excels with an ACC score of 89.0281%,a Roc Area of 0.751,an F-estimate of 0.941,and a Kappa score of 0.0629 over the NCDB *** proposed framework consistently outperforms traditional methods,existing machine learning,and deep learning techniques.

关键词： Injury severity prediction deep learning feature

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PICOTEES:a privacy-preserving online service of phenotype exploration for genetic-diagnostic variants from Chinese children cohorts

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Journal of genetics and Genomics 2024年第2期51卷 243-251页

作者： Xinran Dong Yulan Lu Lanting Guo Chuan Li Qi Ni Bingbing Wu Huijun Wang Lin Yang Songyang Wu Qi Sun Hao Zheng Wenhao Zhou Shuang Wang Center for Molecular Medicine Children's Hospital of Fudan UniversityShanghai 201102China Key Laboratory of Birth Defects Children's Hospital of Fudan UniversityShanghai 201102China department of Bioinformatics Hangzhou Nuowei Information Technology Co.LtdHangzhouZhejiang 310000China The Third Research Institute of the Ministry of Public Security Shanghai 200031China Xiamen Campus of Children's Hospital of Fudan University XiamenFujian 361006China Institutes for Systems genetics West China HospitalChengduSichuan 610041China Shanghai Putuo People's Hospital Tongji UniversityShanghai 200060China

The growth in biomedical data resources has raised potential privacy concerns and risks of genetic information leakage. For instance, exome sequencing aids clinical decisions by comparing data through web services, but it requires significant trust between users and providers. To alleviate privacy concerns, the most commonly used strategy is to anonymize sensitive data. Unfortunately, studies have shown that anonymization is insufficient to protect against reidentification attacks. Recently, privacy-preserving technologies have been applied to preserve application utility while protecting the privacy of biomedical data. We present the PICOTEES framework, a privacy-preserving online service of phenotype exploration for genetic-diagnostic variants (https://***:3000/). PICOTEES enables privacy-preserving queries of the phenotype spectrum for a single variant by utilizing trusted execution environment technology, which can protect the privacy of the user's query information, backend models, and data, as well as the final results. We demonstrate the utility and performance of PICOTEES by exploring a bioinformatics dataset. The dataset is from a cohort containing 20,909 genetic testing patients with 3,152,508 variants from the Children's Hospital of Fudan University in China, dominated by the Chinese Han population (>99.9%). Our query results yield a large number of unreported diagnostic variants and previously reported pathogenicity.

关键词： Privacy protecti on Rare diseases in children Genetic testing Web system Trusted executi on envir onment

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Decomposition of biomass gasification tar model compounds over waste tire pyrolysis char

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Waste Disposal and Sustainable Energy 2022年第2期4卷 75-89页

作者： Amal S.Al-Rahbi Paul T.Williams present address:Applied Sciences department Higher College of TechnologyUniversity of Technology and Applied SciencesMuscatSultanate of Oman School of Chemical and Process Engineering University of LeedsLeedsLS29JTUK

Gasification of biomass produces a syngas containing trace amounts of viscous hydrocarbon tar,which causes serious problems in downstream pipelines,valves and processing *** study focuses on the use of tire-derived pyrolysis char for tar conversion using biomass tar model compounds representative of *** catalytic decomposition of tar model compounds,including methylnaphthalene,furfural,phenol,and toluene,over tire char was investigated using a fixed bed reactor at a bed temperature of 700℃and 60 min time on *** influence of temperature,reaction time,porous texture,and acidity of the tire char was investigated with the use of methylnaphthalene as the tar model *** tar model compounds were found to have higher conversion than those containing a single or multi-aromatic *** reactivity of tar compounds followed the order of furfural>phenol>toluene>*** conversion of the model compounds in the presence of the tire char was much higher than tar thermal *** production increased dramatically with the introduction of tire *** H_(2)potential for the studied tar model compounds was found to be in the range of 40%–50%.The activity of tire char for naphthalene removal was compared with two commercial activated carbons possessing a very well-developed porous *** results suggest that the influence of Brunauer-Emmett-Teller surface area of the carbon on tar cracking is negligible compared with the mineral content in the carbon samples.

关键词： Biomass Gasification Syngas Tar Tire Char

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Unveiling DNA methylation in Alzheimer’s disease:a review of array-based human brain studies

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Neural Regeneration Research 2024年第11期19卷 2365-2376页

作者： Victoria Cunha Alves Eva Carro Joana Figueiro-Silva Neurodegenerative Diseases Group Hospital Universitario 12 de Octubre Research Institute(imas12)MadridSpain Network Center for Biomedical Research Neurodegenerative Diseases(CIBERNED)MadridSpain PhD Program in Neuroscience Autonoma de Madrid UniversityMadridSpain Neurotraumatology and Subarachnoid Hemorrhage Group Hospital Universitario 12 de Octubre Research Institute(imas12)MadridSpain Neurobiology of Alzheimer’s Disease Unit Functional Unit for Research Into Chronic DiseasesInstituto de Salud Carlos IIIMadridSpain Institute of Medical genetics University of ZurichZurichSwitzerland department of Molecular Life Science University of ZurichZurichSwitzerland

The intricacies of Alzheimer’s disease pathogenesis are being increasingly illuminated by the exploration of epigenetic mechanisms,particularly DNA *** review comprehensively surveys recent human-centered studies that investigate whole genome DNA methylation in Alzheimer’s disease *** examination of various brain regions reveals distinctive DNA methylation patterns that associate with the Braak stage and Alzheimer’s disease *** entorhinal cortex emerges as a focal point due to its early histological alterations and subsequent impact on downstream regions like the ***,ANK1 hypermethylation,a protein implicated in neurofibrillary tangle formation,was recurrently identified in the entorhinal ***,the middle temporal gyrus and prefrontal cortex were shown to exhibit significant hypermethylation of genes like HOXA3,RHBDF2,and MCF2L,potentially influencing neuroinflammatory *** complex role of BIN1 in late-onset Alzheimer’s disease is underscored by its association with altered methylation *** the disparities across studies,these findings highlight the intricate interplay between epigenetic modifications and Alzheimer’s disease *** research efforts should address methodological variations,incorporate diverse cohorts,and consider environmental factors to unravel the nuanced epigenetic landscape underlying Alzheimer’s disease progression.

关键词： Alzheimer’s disease ANK1 BIN1 DNA methylation epigenome-wide association studies HOXA3 MCF2L RHBDF2

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Biomolecular condensates and disease pathogenesis

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Science China Life Sciences 2024年第9期67卷 1792-1832页

作者： Ke Ruan Ge Bai Yanshan Fang Dan Li Tingting Li Xingguo Liu Boxun Lu Qing Lu Zhou Songyang Shuguo Sun Zheng Wang Xin Zhang Wen Zhou Hong Zhang Neurology department at Huashan Hospital State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science Institutes of Brain Science School of Life Sciences Fudan University Key Laboratory for the genetics of Developmental and Neuropsychiatric Disorders Ministry of Education Bio-X Institutes Shanghai Jiao Tong University State Key Laboratory of Biocontrol MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research School of Life Sciences Sun Yat-sen Memorial HospitalSun Yat-sen University department of Human Anatomy Histology and Embryology School of Basic Medicine Tongji Medical College Huazhong University of Science and Technology The Second Affiliated Hospital School of Basic Medical Sciences Institute of Biomedical Innovation Jiangxi Medical College Nanchang University Westlake Laboratory of Life Sciences and Biomedicine department of Immunology and Microbiology School of Life Sciences Southern University of Science and Technology National Laboratory of Biomacromolecules Institute of Biophysics Chinese Academy of Sciences College of Life Sciences University of Chinese Academy of Sciences The First Affiliated Hospital & School of Life Sciences Ministry of Education Key Laboratory for Membrane-less Organelles & Cellular Dynamics Hefei National Research Center for Interdisciplinary Sciences at the Microscale Center for Advanced Interdisciplinary Science and Biomedicine of IHM Division of Life Sciences and Medicine University of Science and Technology of China Nanhu Brain-computer Interface Institute department of Neurology of Second Affiliated Hospital and School of Brain Science and Brain Medicine Zhejiang University School of Medicine Interdisciplinary Research Center on Biology and Chemistry Shanghai Institute of Organic Chemistry Chinese Academy of Sciences University of Chinese Academy of Sciences Bio-X Institutes Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of

Biomolecular condensates or membraneless organelles(MLOs) formed by liquid-liquid phase separation(LLPS) divide intracellular spaces into discrete compartments for specific functions. Dysregulation of LLPS or aberrant phase transition that disturbs the formation or material states of MLOs is closely correlated with neurodegeneration, tumorigenesis, and many other pathological processes. Herein, we summarize the recent progress in development of methods to monitor phase separation and we discuss the biogenesis and function of MLOs formed through phase separation. We then present emerging proof-of-concept examples regarding the disruption of phase separation homeostasis in a diverse array of clinical conditions including neurodegenerative disorders, hearing loss, cancers, and immunological diseases. Finally, we describe the emerging discovery of chemical modulators of phase separation.

关键词： liquid-liquid phase separation biomolecular condensate membraneless organelle

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OsWRKY62 is a Negative Regulator of Basal and Xa21-Mediated Defense against Xanthomonas orvzae pv. orvzae in Rice

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Molecular Plant 2008年第3期1卷 446-458页

作者： Ying Peng Laura E. Bartley Xuewei Chen Christopher Dardick Mawsheng Chern Randy Ruan Patrick E. Canlas Pamela C. Ronald department of Plant Pathology University of California Davis CA 95616 USA present address: Monsanto Corporation Davis CA 95616 USA present address: USDA-ARS Appalachian Fruit Research Station Kearneysville WV 25430 USA

The rice Xa21 gene, which confers resistance to the bacterial pathogen Xanthomonas oryzae pv. oryzae （Xoo）, encodes a receptor-like kinase, Few components involved in transducing the Xa21-mediated defense response have yet been identified. Here, we report that XA21 binds to a WRKY transcription factor, called OsWRKY62. The OsWRKY62 gene encodes two splice variants （OsWRKY62.1 and OsWRKY62.2）. OsWRKY62.1：smGFP2 and OsWRKY62.2：smGFP2 fusion pro- teins partially localize to the nucleus. Transgenic plants overexpressing OsWRKY62.1 are compromised in basal defense and Xa21-mediated resistance to Xoo. Furthermore, overexpression of OsWRKY62.1 suppresses the activation of defenserelated genes. These results imply that OsWRKY62 functions as a negative regulator of innate immunity in rice, and serves as a critical mediator of both basal and race-specific defense responses.

关键词： rice OsWRKY62 Xa21 defense response.

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Circumventing the phonon bottleneck by multiphonon-mediated hot exciton cooling at the nanoscale

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npj Computational Materials 2023年第1期9卷 845-852页

作者： Dipti Jasrasaria Eran Rabani department of Chemistry University of CaliforniaBerkeleyCA 94720USA Materials Sciences Division Lawrence Berkeley National LaboratoryBerkeleyCA 94720USA The Sackler Center for Computational Molecular and Materials Science Tel Aviv UniversityTel Aviv 69978Israel present address:department of Chemistry Columbia UniversityNew YorkNY 10027USA

Nonradiative processes govern efficiencies of semiconductor nanocrystal(NC)-based devices.A central process is hot exciton cooling,or the nonradiative relaxation of a highly excited electron/hole pair to form a band-edge *** to quantum confinement effects,the timescale and mechanism of cooling are not well understood.A mismatch between electronic energy gaps and phonon frequencies has led to the hypothesis of a phonon bottleneck and extremely slow cooling,while enhanced electron-hole interactions have suggested ultrafast *** measurements of the cooling timescale range six orders of ***,we develop an atomistic approach to describe phonon-mediated exciton dynamics and simulate cooling in NCs of experimentally relevant *** find that cooling occurs on~30 fs timescales in CdSe NCs,in agreement with the most recent measurements,and that the phonon bottleneck is circumvented through a cascade of multiphonon-mediated relaxation ***,we identify NC handles for tuning the cooling timescale.

关键词： phonon relaxation excited

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