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Protein-nucleic acid hybrid nanostructures for molecular diagnostic applications

Nano Research 2024年第10期17卷 9003-9014页

作者： Noah R.Sundah Yuxuan Seah Auginia Natalia Xiaoyan Chen Panida Cen Yu Liu Huilin Shao Institute for Health Innovation and Technology National University of SingaporeSingapore 117599Singapore Department of Biomedical Engineering College of Design and EngineeringNational University of SingaporeSingapore 117583Singapore Integrative Sciences and Engineering Programme NUS Graduate SchoolNational University of SingaporeSingapore 119077Singapore Institute of Molecular and Cell Biology Agency for ScienceTechnology and ResearchSingapore 138673Singapore Department of Surgery Yong Loo Lin School of MedicineNational University of SingaporeSingapore 117597Singapore

Molecular diagnostic technologies empower new clinical opportunities in precision ***,existing approaches face limitations with respect to performance,operation and *** molecules including proteins and nucleic acids are being increasingly adopted as tools in the development of new molecular diagnostic *** particular,leveraging their complementary properties—the functional diversity of proteins and the precision programmability of nucleic acids—a wide range of protein–nucleic acid hybrid nanostructures have been *** hybrid structures take diverse forms,ranging from one-dimensional to three-dimensional hybrids,as static assemblies to dynamic machines,and possess myriad functions to recognize target biomarkers,encode vast information and execute catalytic *** by recent advances in this area of molecular nanotechnology,we review the state-of-art design and application of various types of protein–nucleic acid hybrid nanostructures for molecular diagnostics,and present an outlook on the challenges and opportunities for emerging pre-clinical and clinical applications,highlighting the promise for earlier detection,more refined diagnosis and highly tailored treatment decision that ultimately lead to improved patient outcomes.

关键词： molecular nanotechnology DNA-protein hybrid molecular diagnostics precision medicine

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UAV-Assisted Dynamic Avatar Task Migration for Vehicular Metaverse Services: A Multi-Agent Deep Reinforcement Learning Approach

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IEEE/CAA Journal of Automatica Sinica 2024年第2期11卷 430-445页

作者： Jiawen Kang Junlong Chen Minrui Xu Zehui Xiong Yutao Jiao Luchao Han Dusit Niyato Yongju Tong Shengli Xie IEEE School of Automation Guangdong University of TechnologyGuangzhou 510006China 111 Center for Intelligent Batch Manufacturing based on IoT Technology Guangzhou 510006China Key Laboratory of Intelligent Information Processing and System Integration of IoT Ministry of EducationGuangzhou 510006China School of Computer Science and Engineering Nanyang Technological UniversitySingaporeSingapore Pillar of Information Systems Technology and Design Singapore University of Technology and DesignSingaporeSingapore College of Communication Engineering Army Engineering University of PLANanjing 210007China national Natural Science Foundation of China Beijing 100085China Key Laboratory of Intelligent Detection and IoT in Manufacturing Ministry of EducationGuangzhou 510006China Guangdong Key Laboratory of IoT Information Technology Guangzhou 510006China

Avatars, as promising digital representations and service assistants of users in Metaverses, can enable drivers and passengers to immerse themselves in 3D virtual services and spaces of UAV-assisted vehicular Metaverses. However, avatar tasks include a multitude of human-to-avatar and avatar-to-avatar interactive applications, e.g., augmented reality navigation,which consumes intensive computing resources. It is inefficient and impractical for vehicles to process avatar tasks locally. Fortunately, migrating avatar tasks to the nearest roadside units(RSU)or unmanned aerial vehicles(UAV) for execution is a promising solution to decrease computation overhead and reduce task processing latency, while the high mobility of vehicles brings challenges for vehicles to independently perform avatar migration decisions depending on current and future vehicle status. To address these challenges, in this paper, we propose a novel avatar task migration system based on multi-agent deep reinforcement learning(MADRL) to execute immersive vehicular avatar tasks dynamically. Specifically, we first formulate the problem of avatar task migration from vehicles to RSUs/UAVs as a partially observable Markov decision process that can be solved by MADRL algorithms. We then design the multi-agent proximal policy optimization(MAPPO) approach as the MADRL algorithm for the avatar task migration problem. To overcome slow convergence resulting from the curse of dimensionality and non-stationary issues caused by shared parameters in MAPPO, we further propose a transformer-based MAPPO approach via sequential decision-making models for the efficient representation of relationships among agents. Finally, to motivate terrestrial or non-terrestrial edge servers(e.g., RSUs or UAVs) to share computation resources and ensure traceability of the sharing records, we apply smart contracts and blockchain technologies to achieve secure sharing management. Numerical results demonstrate that the proposed approach

关键词： Avatar blockchain metaverses multi-agent deep reinforcement learning transformer UAVs

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Design of Protograph LDPC-Coded MIMO-VLC Systems with Generalized Spatial Modulation

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China Communications 2024年第3期21卷 118-136页

作者： Dai Lin Fang Yi Guan Yongliang Mohsen Guizani School of Information Engineering Guangdong University of TechnologyGuangzhou 51006China The State Key Laboratory of Integrated Services Networks Xidian UniversityXi’an 710126China School of Electrical and Electronic Engineering Nanyang Technological UniversitySingapore Department of Machine Learning Mohamed Bin Zayed University of Artificial Intelligence(MBZUAI)Abu DhabiUnited Arab Emirates

This paper investigates the bit-interleaved coded generalized spatial modulation(BICGSM) with iterative decoding(BICGSM-ID) for multiple-input multiple-output(MIMO) visible light communications(VLC). In the BICGSM-ID scheme, the information bits conveyed by the signal-domain(SiD) symbols and the spatial-domain(SpD) light emitting diode(LED)-index patterns are coded by a protograph low-density parity-check(P-LDPC) code. Specifically, we propose a signal-domain symbol expanding and re-allocating(SSER) method for constructing a type of novel generalized spatial modulation(GSM) constellations, referred to as SSERGSM constellations, so as to boost the performance of the BICGSM-ID MIMO-VLC ***, by applying a modified PEXIT(MPEXIT) algorithm, we further design a family of rate-compatible P-LDPC codes, referred to as enhanced accumulate-repeat-accumulate(EARA) codes,which possess both excellent decoding thresholds and linear-minimum-distance-growth property. Both analysis and simulation results illustrate that the proposed SSERGSM constellations and P-LDPC codes can remarkably improve the convergence and decoding performance of MIMO-VLC systems. Therefore, the proposed P-LDPC-coded SSERGSM-mapped BICGSMID configuration is envisioned as a promising transmission solution to satisfy the high-throughput requirement of MIMO-VLC applications.

关键词： bit-interleaved coded modulation generalized spatial modulation multiple-input multipleoutput protograph LDPC codes visible light communication

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Publication characteristics and visualized analysis of research about liver sinusoidal endothelial cells

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iLIVER 2024年第1期3卷 3-14页

作者： Shanshan Zhao Lan Zhang Junzhe Zhao Farah Tasnim Hanry Yu Department of Pharmacy Xuanwu Hospital of Capital Medical UniversityNational Clinical Research Center for Geriatric DiseasesBeijing Engineering Research Center for Nerve System DrugsBeijing Municipal Geriatric Medical Research CenterBeijing 100053China Department of Physiology The Institute for Digital Medicine(WisDM)Yong Loo Lin School of MedicineMD9-04-112 Medical DriveSingapore 117593Singapore Duke-NUS Medical School 8 College RoadSingapore 169857Singapore Biomedical Sciences Industry partnership Office(BMSIPO) A*STAR31 Biopolis WaySingapore 138669Singapore CAMP Singapore-MIT Alliance for Research and Technology1 CREATE WayLevel 4 Enterprise WingSingapore 138602Singapore Mechanobiology Institute National University of SingaporeT-Lab#05-015A Engineering Drive 1Singapore 117411Singapore

Background and aims:Through visual analysis of related literature,the main research direction and hot spots of liver sinusoidal endothelial cells(LSECs)in recent 24 years were ***:This study used bibliometric analysis with CiteSpace,VOSviewer,Biblioshiny and online analytic tool *** to provide a quantitative analysis,hot spot mining,and commentary of articles published in the field of LSECs *** relevant literature in the Web of Science Core Collection(WOSCC)was searched from 2000 to *** publications with topics or titles or keywords containing LSECs were included into this *** countries,organizations,journals,authors,and keywords of the publications were summarized and ***:This study included 3,747 publications from 14,132 authors belonging to 389 institutions in 61 countries/regions and published in 150 journals,with 156,309 *** United States contributed most(1,150)to the *** most productive institution was the university of *** accounts for the most output(293,7.8%),European authors had a widespread *** most productive author was Adam DH with 68 *** function of LSECs is research hot ***:This study highlights key trends based on a large dataset of the most influential publications about LSECs research over a 24-year *** provides important clues and ideas for researchers focusing in this area and facilitates future liver disease mechanism,understanding,and treatment.

关键词： Bibliometrics Liver sinusoidal endothelial cells CiteSpace VOSviewer

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A Novel RGL2-DOF6 Complex Contributes to Primary Seed Dormancy in Arabidopsis thaliana by Regulating a GATA Transcription Factor

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Molecular Plant 2017年第10期10卷 1307-1320页

作者： Pratibha Ravindran Vivek Verma Petra Stamm Prakash P. Kumar Department of Biological Sciences Faculty of Science National University of Singapore Singapore 117543 Singapore present address: Department of Biosciences Durham University South Road Durham DH1 3LE UK

The DELLA protein RGA-LIKE2 （RGL2） is a key transcriptional repressor of gibberellic acid （GA） signaling that regulates seed germination. We identified GATA12, a gene encoding a GATA-type zinc finger transcription factor, as one of the downstream targets of RGL2 in Arabidopsis thaliana. Our data show that freshly harvested （unstratified） seeds of GATA 12 antisense suppression lines have reduced dormancy compared with the wild-type, while ectopic expression lines show enhanced seed dormancy. We show that GATA12 expression is negatively regulated by GA, and its transcript levels decline dramatically under dormancy- breaking conditions such as dry storage and cold stratification of seeds. GATA12 promoter has several GAMYB- and DOF-associated motifs that are known to be GA- and RGL2-responsive, respectively. Chromatin immunoprecipitation assay showed that a protein complex containing RGL2 can bind to GATA12 promoter and thereby regulate its expression. RGL2 lacks a DNA binding domain and requires a transcription factor to induce GATA12 expression. Our data show that this RGL2-containing protein complex includes DNA BINDING1 ZINC FINGER6 （DOF6）, which is a known negative regulator of germination in freshly harvested seeds. We further show that this novel RGL2-DOF6 complex is required for activating GATA12 expression, thus revealing a molecular mechanism to enforce primary seed dormancy.

关键词： seed germination primary dormancy DELLA RGL2 DOF6 gibberellin

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Minimax Optimal Rates of Convergence for Multicategory Classifications

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Acta Mathematica Sinica,English Series 2007年第8期23卷 1419-1426页

作者： Di Rong CHEN Xu YOU Department of Mathematics and LMIB Beijing University of Aeronautics and Astronautics Beijing 100083 P. R. China

In the problem of classification （or pattern recognition）, given a set of n samples, we attempt to construct a classifier gn with a small misclassification error. It is important to study the convergence rates of the misclassification error as n tends to infinity. It is known that such a rate can＇t exist for the set of all distributions. In this paper we obtain the optimal convergence rates for a class of distributions L^（λ,ω） in multicategory classification and nonstandard binary classification.

关键词： rate of convergence error probability modulus of continuity multicategory classification

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The Cauchy problem for non-autonomous nonlinear Schr(o)dinger equations

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Science China Mathematics 2005年第4期48卷 522-538页

作者： Peter Y. H. Pang Department of Mathematics

In this paper we study the Cauchy problem for cubic nonlinear Schr(o)dinger equation with space-and time-dependent coefficients on Rm and Tm. By an approximation argument we prove that for suitable initial values, the... 详细信息

关键词： non-autonomous Schr(o)dinger equations, local existence, global existence.

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Roles, Functions, and Mechanisms of Long Non-coding RNAs in Cancer

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Genomics, Proteomics & Bioinformatics 2016年第1期14卷 42-54页

作者： Yiwen Fang Melissa J. Fullwood cancer science institute of singapore national university of singapore Singapore 117599 Singapore School of Biological Sciences Nanyang Technological University Singapore 637551 Singapore Institute of Molecular and Cell Biology Agency for Science Technology and Research (A*STAR) Singapore 138673 Singapore Yale-NUS Liberal Arts College Singapore 138527 Singapore

Long non-coding RNAs （ineRNAs） play important roles in cancer. They are involved in chromatin remodeling, as well as transcriptional and post-transcriptional regulation, through a vari- ety of chromatin-based mechanisms and via cross-talk with other RNA species, lncRNAs can func- tion as decoys, scaffolds, and enhancer RNAs. This review summarizes the characteristics of lncRNAs, including their roles, functions, and working mechanisms, describes methods for identi- fying and annotating lncRNAs, and discusses future opportunities for lncRNA-based therapies using antisense oligonucleotides.

关键词： IncRNAS Chromatin Transcription regulation Antisense oligonucleotides Cancer

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Polynomial Approach to Optimal One-wafer Cyclic Scheduling of Treelike Hybrid Multi-Cluster Tools via Petri Nets

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IEEE/CAA Journal of Automatica Sinica 2018年第1期5卷 270-280页

作者： Fajun Yang Naiqi Wu Yan Qiao Rong Su Department of Industrial Engineering School of Electro-Mechanical Engineering Guangdong University of Technology Guangzhou 510006 China School of Electrical and Electronic Engineering at Nanyang Technological university 639798 Singapore Institute of Systems Engineering Macao University of Science and Technology Taipa Macao 999078 China school of Electro-Mechanical Engineering Guangdong University of Technology Guangzhou 510006 China IEEE

A treelike hybrid multi-cluster tool is composed of both single-arm and dual-arm cluster tools with a treelike topology. Scheduling such a tool is challenging. For a hybrid treelike multi-cluster tool whose bottleneck individual tool is process-bound, this work aims at finding its optimal one-wafer cyclic schedule. It is modeled with Petri nets such that a onewafer cyclic schedule is parameterized as its robots' waiting *** on the model, this work proves the existence of its onewafer cyclic schedule that features with the ease of industrial implementation. Then, computationally efficient algorithms are proposed to find the minimal cycle time and optimal onewafer cyclic schedule. Multi-cluster tool examples are given to illustrate the proposed approach. The use of the found schedules enables industrial multi-cluster tools to operate with their highest productivity.

关键词： Multi-cluster tool Petri nets scheduling semiconductor manufacturing

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On the constructions of constant-composition codes from perfect nonlinear functions

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Science in China(Series F) 2009年第6期52卷 964-973页

作者： LI Chao LI Qiang LING San Department of Mathematics and System Sciences Science College national university of Defense Technology Changsha 410073 China national Mobile Communications Research Laboratory Southeast university Nanjing 210096 China Division of Mathematical Sciences School of Physical and Mathematical Sciences Nanyang Technological university singapore 637313 Republic of singapore

A new construction of constant-composition codes based on all known perfect nonlinear functions from Fqm to itself is presented, which provides a kind of unified constructions of constant-composition codes based on all known perfect nonlinear functions from F qm to *** is proved that the new constant-composition codes are optimal with respect to the Luo-Fu-Vinck-Chen bound, when m is an odd positive integer greater than ***, we point out that two constructions of constant-composition codes, proposed by Ding Cunsheng et *** 2005, are equivalent to two special types of the new constant-composition codes.

关键词： constant-composition codes perfect nonlinear functions quadratic forms

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