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The OsWRKY72-OsAAT30/OsGSTU26 module mediates reactive oxygen species scavenging to drive heterosis for salt tolerance in hybrid rice

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Journal of Integrative Plant Biology 2024年第4期66卷 709-730页

作者： Citao Liu Bigang Mao Yanxia Zhang Lei tian Biao Ma Zhuo Chen Zhongwei Wei Aifu Li Ye Shao Gongye Cheng Lingling Li Wenyu Li Di Zhang Xiaoping Ding Jiangxiang Peng Yulin Peng Jiwai He Nenghui Ye Dingyang Yuan Chengcai Chu Meijuan Duan Hunan Provincial Key Laboratory of Stress Biology College of AgricultureHunan Agricultural UniversityChangsha 410128China State Key Laboratory of Hybrid Rice Hunan Hybrid Rice Research CenterChangsha 410125China College of Agriculture South China Agricultural UniversityGuangzhou 510642China State Key Laboratory of Wheat and Maize Crop Science Center for Crop Genome EngineeringCollege of AgronomyHenan Agricultural UniversityZhengzhou 450002China College of Horticulture Fujian Agriculture and Forestry UniversityFuzhou 350002China Department of Computational Medicine and Bioinformatics University of MichiganAnn ArborMI 48109 USA Biobin Data Science Co. Ltd.Changsha 410221China

Hybrid rice(Oryza sativa)generally outperforms its inbred parents in yield and stress tolerance,a phenomenon termed heterosis,but the underlying mechanism is not completely ***,we combined transcriptome,proteome,physiological,and heterosis analyses to examine the salt response of super hybrid rice Chaoyou1000(CY1000).In addition to surpassing the mean values for its two parents(mid-parent heterosis),CY1000 exhibited a higher reactive oxygen species scavenging ability than both its parents(over-parent heterosis or heterobeltiosis).Nonadditive expression and allele-specific gene expression assays showed that the glutathione S-transferase gene OsGSTU26 and the amino acid transporter gene OsAAT30 may have major roles in heterosis for salt tolerance,acting in an overdominant fashion in ***,we identified OsWRKY72 as a common transcription factor that binds and regulates OsGSTU26 and *** salt-sensitive phenotypes were associated with the OsWRKY72^(paternal)genotype or the OsAAT30^(maternal)genotype in core rice germplasm ***72^(paternal)specifically repressed the expression of OsGSTU26 under salt stress,leading to salinity sensitivity,while OsWRKY72^(maternal)specifically repressed OsAAT30,resulting in salinity *** results suggest that the OsWRKY72-OsAAT30/OsGSTU26 module may play an important role in heterosis for salt tolerance in an overdominant fashion in CY1000 hybrid rice,providing valuable clues to elucidate the mechanism of heterosis for salinity tolerance in hybrid rice.

关键词： allele-specific gene expression(ASE) heterosis hybrid rice nonadditive effect(NAE) salt tolerance transcriptome and proteome

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data mining for epidemiology: The correlation of typhoid fever occurrence and environmental factors

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Procedia Computer science 2023年 216卷 284-292页

作者： Faisal Asadi Joko Pebrianto Trinugroho Alam Ahmad Hidayat Reza Rahutomo Bens Pardamean Bioinformatics & Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 Information System Department School of Information System Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department BINUS Graduate Program - Master of Computer Science Program Bina Nusantara University Jakarta Indonesia 11480

Typhoid fever is an endemic disease that burdens Indonesia and has a potentially fatal infection multisystem. Salmonella typhi bacterium is responsible for typhoid fever disease. Poor sanitation, crowding, and slums are the main factors of increasing typhoid fever incidences. Environmental factors directly connected to meteorological factors are the main factor in breeding the Salmonella typhi bacterium. This study aims to identify the correlation between meteorological parameters and typhoid fever disease occurrence. The study was carried out in Jakarta, Indonesia, and the Bureau of Meteorological, Climatology, and Geophysics (BMKG) provided the meteorological parameter data. In addition, the Jakarta health surveillance office provided information on typhoid fever hospitalizations from 2019 to 2021. Pearson's concept was utilized d to investigate the correlation between typhoid fever incidences and the meteorological parameters. Humidity, precipitation, and wind speed are the meteorological parameters that significantly affect in contribute to the occurrence of typhoid fever disease. These findings might be used as a reference for Indonesia's government in making public policy to prevent typhoid fever in Indonesia.

关键词： typhoid fever salmonella typhi endemic disease meteorological factors

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A Novel Feature Selection Strategy Based on Salp Swarm Algorithm for Plant Disease Detection

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Plant Phenomics 2023年第2期5卷 209-225页

作者： Xiaojun Xie Fei Xia Yufeng Wu Shouyang Liu Ke Yan Huanliang Xu Zhiwei Ji College of Artificial Intelligence Nanjing Agricultural UniversityNanjingJiangsu 210095China Center for Data Science and Intelligent Computing Nanjing Agricultural UniversityNanjingJiangsu 210095China State Key Laboratory for Crop Genetics and Germplasm Enhancement Bioinformatics CenterAcademy for Advanced Interdisciplinary StudiesNanjing Agricultural UniversityNanjingJiangsu 210095China Academy for Advanced Interdisciplinary Studies Nanjing Agricultural UniversityNanjingJiangsu 210095China Department of the Built Environment College of Design and EngineeringNational University of Singapore4 Architecture DriveSingapore 117566Singapore

Deep learning has been widely used for plant disease recognition in smart agriculture and has proven to be a powerful tool for image classification and pattern ***,it has limited interpretability for deep *** the transfer of expert knowledge,handcrafted features provide a new way for personalized diagnosis of plant ***,irrelevant and redundant features lead to high *** this study,we proposed a swarm intelligence algorithm for feature selection[salp swarm algorithm for feature selection(SSAFS)]in image-based plant disease *** is employed to determine the ideal combination of handcrafted features to maximize classification success while minimizing the number of *** verify the effectiveness of the developed SSAFS algorithm,we conducted experimental studies using SSAFS and 5 metaheuristic *** evaluation metrics were used to evaluate and analyze the performance of these methods on 4 datasets from the UCI machine learning repository and 6 plant phenomics datasets from *** results and statistical analyses validated the outstanding performance of SSAFS compared to existing state-of-the-art algorithms,confirming the superiority of SSAFS in exploring the feature space and identifying the most valuable features for diseased plant image *** computational tool will allow us to explore an optimal combination of handcrafted features to improve plant disease recognition accuracy and processing time.

关键词： Plant image redundant

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Digital Twin (DT) Smart City for Air Quality Management

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Procedia Computer science 2023年 227卷 524-533页

作者： Dedy Ariansyah Mahmud Isnan Reza Rahutomo Bens Pardamean Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta 11480 Indonesia Information Systems Department School of Information Systems Bina Nusantara University Jakarta 11480 Indonesia Computer Science Department BINUS Graduate Program-Master of Computer Science Program Bina Nusantara University Jakarta 11480 Indonesia

Air pollution is a pressing issue in cities, and managing air quality poses a challenge for urban designers and decision-makers. This study proposes a Digital Twin (DT) Smart City integrated with Mixed Reality technology to enhance visualization and collaboration for addressing urban air pollution. The research adopts an applied research approach, with a focus on developing a DT framework. A use case of DT development for Jakarta, the capital of Indonesia, is presented. By integrating air quality data, meteorological information, traffic patterns, and urban infrastructure data, the DT provides a comprehensive understanding of air pollution dynamics. The visualization capabilities of the DT, utilizing Mixed Reality technology, facilitate effective decision-making and the identification of strategies for managing air quality. However, further research is needed to address data management challenges to build a DT for Smart City at scale.

关键词： Digital Twin Smart City Mixed Reality Augmented Reality

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Are dogs not susceptible to retroviral infections?

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Animal Diseases 2024年第3期4卷 217-223页

作者： Jorge Casseb João Henrique Campos Luciano Rodrigo Lopes Laboratory of Investigation in Dermatology and Immunodefciencies Department of DermatologyUniversity of São Paulo Medical SchoolSão PauloSPBrazil Igen-Institute of Immunogenetics São PauloSPBrazil Bioinformatics and Biomedical Data Science Division Health Informatics DepartmentUniversidade Federal de São Paulo–UNIFESP.Rua Botucatu 862Prédio Leal PradotérreoVila ClementinoCEP 04023-062São PauloSPBrazil

Retroviruses have been proven to cause infections and diseases in a series of mammalian hosts but not in ***,this letter discussed the dog susceptibility to retrovirus infection,encompassing arguments to understand why dogs may have not been infected by retroviruses thus *** potential resistance of retrovirus in dogs enables this provocative short communication to discuss this question,looking at some evolutive *** lineage of canids has shown,throughout its evolutionary history,a smaller accumulation of retroviruses in canid genomes,classifed as endogenous *** this context,the genomes of canids seem to ofer obstacles,which have been evolutionarily conserved,in the face of retroviral infection.

关键词： Retrovirus dogs Endogenous retrovirus

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Long Short-Term Memory-based Models for Sleep Quality Prediction from Wearable Device Time Series data

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Procedia Computer science 2023年 227卷 1062-1069页

作者： Alam Ahmad Hidayat Arif Budiarto Bens Pardamean Mathematics Department School of Computer Science Bina Nusantara University Jakarta 11480 Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta 11480 Indonesia Computer Science Department School of Computer Science Bina Nusantara University Jakarta 11480 Indonesia Computer Science Department BINUS Graduate Program – Master of Computer Science Program Bina Nusantara University Jakarta 11480 Indonesia

Several studies suggest that sleep quality is associated with physical activities. Moreover, deep sleep time can be used to determine the sleep quality of an individual. In this work, we aim to find the association between physical activities and deep sleep time by modeling the time series data such as heart rate and a number of steps captured from a commercial wearable device. Our previous study demonstrates that deep learning-based time series modeling is well suited for our problem since the temporal patterns in the two physical parameters need to be captured to obtain more accurate results. We first preprocess our series data to have a time-step size of 10 minutes. To improve our previous effort in this modeling, we compare four different variants of Long Short-Term Memory (LSTM)-based models, ranging from single input to dual input models. Our result shows that the simple stacked LSTM model performs better for our data because the remaining models suffer from overfitting due to a larger number of the trained parameters.

关键词： deep learning forecasting sleep quality time series wearable devices

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Optimizing patient monitoring to prevent clinical deterioration in surgical wards using machine learning

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American Journal of Surgery 2025年 245卷 116138-116138页

作者： Jung, James J. Pou-Prom, Chloé Mamdani, Muhammad Division of Minimally Invasive Surgery Department of Surgery Duke University United States Department of Biostatistics and Bioinformatics Duke University United States Data Science and Advanced Analytics Unity Health Toronto United States

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Confidentiality. Integrity, and Availability (CIA) Approach for Private dataset Management System Design

Confidentiality. Integrity, and Availability (CIA) Approach ...

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Information Technology and Digital Applications (ICITDA), IEEE International Conference on

作者： Mahmud Isnan Gregorius Natanael Elwirehardja Dedy Ariansyah Reza Rahutomo Bens Pardamean Computer Science Department School of Computer Science Bina Nusantara University Jakarta Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia Information Systems Department School of Information Systems Bina Nusantara University Jakarta Indonesia Computer Science Department BINUS Graduate Program - Master of Computer Science Bina Nusantara University Jakarta Indonesia

ISBN: (数字)9798331510732

ISBN: (纸本)9798331510749

dataset management systems are essential for assisting research and development (R&D) organizations in applying data governance protocols, especially in managing the utilization of datasets. In R&D, datasets are vital sources for producing analysis, machine learning prediction, and supporting decision-making. As such, it is important to deploy dataset management systems with considerations regarding the aspects of Confidentiality, Integrity, and Availability (CIA) which is a design principle that emphasized information protection and collaboration facilitation among dataset users. The study proposed an analysis and a design for a dataset management system that takes CIA aspects into account. In the future, the proposed design will be utilized as a benchmark for building a dataset management system. In this study, the Waterfall method was adopted. A use case diagram, an ERD (Entity Relationship Diagram), and an activity diagram were constructed in the design stage. In the project implementation stage, the Laravel framework including Laravel Jetstream was considered to be used.

关键词： Protocols data security Decision making Organizations Machine learning Encryption Protection Information technology Research and development System analysis and design

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Asymptotics of Bayesian uncertainty estimation in random features regression 23

Asymptotics of Bayesian uncertainty estimation in random fea...

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Proceedings of the 37th International Conference on Neural Information Processing Systems

作者： Youngsoo Baek Samuel I. Berchuck Sayan Mukherjee Department of Statistical Science Duke University Durham NC Department of Biostatistics & Bioinformatics Duke University Durham NC Center for Scalable Data Analysis and Artificial Intelligence Universität Leipzig Leipzig

In this paper, we compare and contrast the behavior of the posterior predictive distribution to the risk of the maximum a posteriori (MAP) estimator for the random features regression model in the overparameterized regime. We will focus on the variance of the posterior predictive distribution (Bayesian model average) and compare its asymptotics to that of the risk of the MAP estimator. In the regime where the model dimensions grow faster than any constant multiple of the number of samples, asymptotic agreement between these two quantities is governed by the phase transition in the signal-to-noise ratio. They also asymptotically agree with each other when the number of samples grows faster than any constant multiple of model dimensions. Numerical simulations illustrate finer distributional properties of the two quantities for finite dimensions. We conjecture they have Gaussian fluctuations and exhibit similar properties as found by previous authors in a Gaussian sequence model, which is of independent theoretical interest.

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Pyramid Scene Parsing Net Model for Automated Paddy Field Map using SPOT 6 Satellite Images 5

Pyramid Scene Parsing Net Model for Automated Paddy Field Ma...

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5th IEEE Asia-Pacific Conference on Geoscience, Electronics and Remote Sensing Technology, AGERS 2022

作者： Heryadi, Yaya Irwansyah, Edy Miranda, Eka Soeparno, Haryono Herlawati Hashimoto, Kiyota Bina Nusantara University Binus Graduate Program-Doctor of Computer Science Computer Science Department Jakarta11480 Indonesia School of Computer Science Bina Nusantara University Computer Science Department Jakarta11480 Indonesia School of Information Systems Bina Nusantara University Information Systems Department Jakarta11480 Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia Prince of Songkla University Faculty of Technology and Environment Phuket83120 Thailand

ISBN: (纸本)9798350398212

Food sustainability is still one of the main priorities for many countries as it contributes to the economy and stability of the nation. For government in many countries whose peoples consumes rice as its staple food, food self-sufficiency initiatives highly depend on accurate prediction of paddy field map. Mapping paddy field task is a challenging problem which cannot be handled manually especially when the paddy fields are spread out in very wide geographical areas such as those in Indonesia. Fortunately, wide availability of satellite imagery and the advent of deep learning technology in the past ten years have made it possible to improve efficiency of most parts of those manual works involving image semantic segmentation tasks. However, satellite image-based semantic segmentation is a challenging task. High object complexity, cloud partial occlusion, larger image size than a computer memory can stored can hinder accuracy of the image segmentation results. This paper presents a method for paddy field map generating using semantic image segmentation approach in which Pyramid Scene Parsing Net model is used for segmenting satellite imagery. The generated paddy map can be used as a basis for decision-making, especially in the agricultural sector. Analysis of local land use/land cover dynamics. The results of his experiments using SPOT 6 satellite imagery from the Pahung region of Central Kalimantan achieved average training accuracy, best training accuracy and test accuracy of 0.85, 0.86 and 0.89 respectively. These results indicated that the semantic segmentation model is suitable for addressing the same task in different crops. © 2022 IEEE.

关键词： Image enhancement

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