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Digital Twin (DT) Smart City for Air Quality Management

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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Aggregating Structural Features for Computational Analysis of Mutations in BRCT Domains of BRCA1 Protein

Aggregating Structural Features for Computational Analysis o...

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International Conference on Informatics, Multimedia, Cyber and Information System (ICIMCIS)

作者： Alam Ahmad Hidayat Rudi Nirwantono Mahmud Isnan Joko Pebrianto Trinugroho Bens Pardamean Mathematics Department School of Computer Science Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia Biotechnology Department Faculty of Engineering Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia Computer Science Department Bioinformatics and Data Science Research Center BINUS Graduate Program Jakarta Indonesia

Understanding the mechanistic interpretability of mutation effects in a protein can help predict the clinical implications of the genetic variants. Hence, computational variant effect predictions that involve protein structural features of the protein mutations might be suitable in this case. In this work, we focus on BRCT domains of BRCA1 gene that is widely studied in breast cancer studies. We retrieved 88 selected missense variants found in BRCT domains annotated in both ClinVar and gnomAD databases. To computationally characterize the pathogenic property of the mutations we used two types of features extracted from protein structures: a change in free Gibbs energy and a set of features derived from molecular dynamics simulations of each mutant. Using a dimensional reduction and Gaussian mixture model (GMM)-based clustering we demonstrate that the variants are segregated into two regions that may correspond to their pathogenic status. This method can be a potential computational pipeline for providing the preliminary mechanistic interpretation of mutation effects in terms of their thermodynamic and structural features.

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Implementation of expert systems in potassium deficiency in cocoa plants using forward chaining method

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Procedia Computer Science 2023年 216卷 136-143页

作者： Muhammad Titan Hafizal Dian Pratama Putra Herry Wirianata Nanda Satya Nugraha Teddy Suparyanto Alam Ahmad Hidayat Bens Pardamean Faculty of Forestry STIPER Institute of Agriculture Yogyakarta 55282 Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta 11480 Indonesia Computer Science Department BINUS Graduate Program Bina Nusantara University Jakarta 11480 Indonesia

As one of the largest exporters in the world, cocoa (Theobroma cacao L.) production in Indonesia provides an important contribution to the plantation sector that can, directly and indirectly, attribute to the national economic development. However, recent data shows a decline in cocoa productivity in Indonesia. This is arguably caused by various factors, including poor agricultural management and practices in cocoa plantations, that may lead to lower fertility in the soil and an increased risk of diseases and pests. Potassium deficiency is a major contributing factor to the low soil fertility that affects cocoa yields. Therefore, in this work, we implement an application with an expert system utilizing the forward chaining method to detect potassium deficiency in cocoa plants and then give a fertilization-based recommendation based on the plants’ condition. The system employs a set of rules to identify symptoms related to the deficiency on the sample photo of a cocoa leaf according to the channels of red, green, and blue of the image. The sample images of cocoa leaves are submitted to the application with an easy-to-use interface that can show the scanning result and proceed to display the suggested quantity of fertilizers to prevent potassium deficiency. Implementing the system can contribute constructive impacts to improve current practices in the overall cropping system of cocoa plants.

关键词： agriculture cocoa expert system forward chaining recommendation system

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Confidentiality. Integrity, and Availability (CIA) Approach for Private Dataset Management System Design 9

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

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9th International Conference on Information Technology and Digital Applications, ICITDA 2024

作者： Isnan, Mahmud Elwirehardja, Gregorius Natanael Ariansyah, Dedy Rahutomo, Reza Pardamean, Bens School of Computer Science Bina Nusantara University Computer Science Department Jakarta11480 Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia School of Information Systems Bina Nusantara University Information Systems Department Jakarta11480 Indonesia Binus Graduate Program Bina Nusantara University Computer Science Department Jakarta11480 Indonesia

ISBN: (纸本)9798331510732

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. © 2024 IEEE.

关键词： Data integrity

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Transfer Learning from Chest X-Ray Pre-trained Convolutional Neural Network for Learning Mammogram Data

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Procedia Computer Science 2018年 135卷 400-407页

作者： Bens Pardamean Tjeng Wawan Cenggoro Reza Rahutomo Arif Budiarto Ettikan Kandasamy Karuppiah Computer Science Department BINUS Graduate Program - Master of Computer Science Program Bina Nusantara University Jakarta Indonesia 11480 Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department School of Computer Science Bina Nusantara University Jakarta Indonesia 11480 NVIDIA Corporation

Breast cancer is one of the deadliest cancer for female nowadays. Despite of the rapid advancement in medical image analysis with the rise of deep learning, development of breast cancer detection system is limited due to relatively small size of the publicly available mammogram dataset. In this paper, we discover an effective configuration for transfer learning from Chest X-Ray pre-trained Convolutional Neural Network to overcome the small-size mammogram dataset problem. We found that the best configuration achieve 90.38% validation accuracy for modified.

关键词： Transfer learning Convolutional neural network Medical image analysis Chest X-ray Mammogram

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Evolution Of SARS-CoV-2 In The Presence Of Vaccines.

Evolution Of SARS-CoV-2 In The Presence Of Vaccines.

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IEEE International Conference on bioinformatics and Biomedicine (BIBM)

作者： Vishwajeet Marathe Changhui Yan Department of Computer Scienceline North Dakota State University Fargo ND USA Department of Computer Science Genomics Phenomics and Bioinformatics Graduate Program North Dakota State University Fargo ND USA

ISBN: (数字)9781665468190

ISBN: (纸本)9781665468206

The COVID pandemic has caused tremendous loss worldwide. Now vaccines are the primary weapon to combat the pandemic. Understanding how SARS-CoV-2, the virus that causes the COVID, may mutate in the presence of the vaccines is critical for designing drugs and vaccines for future variants of the virus. In this study, we investigated the numbers of mutations that SARS-CoV-2 accumulated on each protein over time. We found that different proteins of the virus accumulated different levels of mutations and their mutation rates changed over time following different patterns. We also presented evidence that the mutation of the Spike protein might have been suppressed by the vaccines. This is the first time that such a relation was reported based on real world data. Although the discovery was not meant to be conclusive, this study sheds light onto how the virus may response to the vaccines. If confirmed by further studies, the discovery will have significant impacts on many fields, including drug and vaccine designs.

关键词： Proteins Drugs COVID-19 Protein engineering Pandemics Weapons Vaccines

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Genetic load makes cancer cells more sensitive to common drugs: Evidence from Cancer Cell Line Encyclopedia

arXiv

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arXiv 2017年

作者： Pavel, Ana B. Korolev, Kirill S. Graduate Program in Bioinformatics Boston University 44 Cummington Mall BostonMA02215 United States Department of Physics Boston University 590 Commonwealth Avenue BostonMA02215 United States

Genetic alterations initiate tumors and enable the evolution of drug resistance. The pro-cancer view of mutations is however incomplete, and several studies show that mutational load can reduce tumor fitness. Given its negative effect, genetic load should make tumors more sensitive to anticancer drugs. Here, we test this hypothesis across all major types of cancer from the Cancer Cell Line Encyclopedia, that provides genetic and expression data of 496 cell lines together with their response to 24 common anticancer drugs. We found that the efficacy of 9 out of 24 drugs showed significant association with genetic load in a pan-cancer analysis. The associations for some tissue-drug combinations were remarkably strong with genetic load explaining up to 83% of the variance in the drug response. Overall, the role of genetic load depended on both the drug and the tissue type with 10 tissues being particularly vulnerable to genetic load. We also identified changes in gene expression associated with increased genetic load, which included cell-cycle checkpoints, DNA damage and apoptosis. Our results show that genetic load is an important component of tumor fitness and can predict drug sensitivity. Beyond being a biomarker, genetic load might be a new, unexplored vulnerability of cancer. Copyright © 2017, The Authors. All rights reserved.

关键词： Tumors

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A novel label-free electrochemical immunosensor for the detection of heat shock protein 70 of lung adenocarcinoma cell line following paclitaxel treatment using l-cysteine-functionalized Au@MnO2/MoO3 nanocomposites

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RSC Advances 2023年第43期13卷 29847-29861页

作者： Chen, Yi-An Shie, Ming-You Ho, Chia-Che Ye, Sheng-Wen Chen, I.-Wen Peter Shih, Yu-Yin Shen, Yu-Fang Chen, Yi-Wen x-Dimension Center for Medical Research and Translation China Medical University Hospital Taichung City404332 Taiwan The Master Program for Biomedical Engineering China Medical University Taichung City406040 Taiwan Department of Biomedical Engineering China Medical University Taichung City40447 Taiwan Department of Bioinformatics and Medical Engineering Asia University Taichung City41354 Taiwan Department of Chemistry National Cheng Kung University Tainan70101 Taiwan Graduate Institute of Biomedical Sciences China Medical University Taichung City40447 Taiwan

The future trend in achieving precision medicine involves the development of non-invasive cancer biomarker sensors that offer high accuracy, low cost, and time-saving benefits for risk clarification, early detection, disease detection, and therapeutic monitoring. A facile approach for the synthesis of MoO3 nanosheets was developed by thermally oxidizing MoS2 nanosheets in air followed by thermal annealing. Subsequently, Au@MnO2 nanocomposites were prepared using a combined hydrothermal process and in situ chemical synthesis. In this study, we present a novel immunosensor design strategy involving the immobilization of antiHSP70 antibodies on Au@MnO2/MoO3 nanocomposites modified on a screen-printed electrode (SPE) using EDC/NHS chemistry. This study establishes HSP70 as a potential biomarker for monitoring therapeutic response during anticancer therapy. Impedance measurements of HSP70 on the Au@MnO2/MoO3/SPE immunosensor using EIS showed an increase in impedance with an increase in HSP70 concentration. The electrochemical immunosensor demonstrated a good linear response in the range of 0.001 to 1000 ng mL−1 with a detection limit of 0.17 pg mL−1 under optimal conditions. Moreover, the immunosensor was effective in detecting HSP70 at low concentrations in a lung adenocarcinoma cell line following Paclitaxel treatment, indicating its potential for early detection of the HSP70 biomarker in organ-on-a-chip and clinical applications. © 2023 The Royal Society of Chemistry.

关键词： Nanosheets

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New sector morphologies emerge from anisotropic colony growth

arXiv

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arXiv 2024年

作者： Swartz, Daniel W. Lee, Hyunseok Kardar, Mehran Korolev, Kirill S. Department of Physics Massachusetts Institute of Technology CambridgeMA02139 United States Department of Physics Graduate Program in Bioinformatics and Biological Design Center Boston University BostonMA02215 United States

Competition during range expansions is of great interest from both practical and theoretical view points. Experimentally, range expansions are often studied in homogeneous Petri dishes, which lack spatial anisotropy that might be present in realistic populations. Here, we analyze a model of anisotropic growth, based on coupled Kardar-Parisi-Zhang and Fisher-Kolmogorov-Petrovsky-Piskunov equations that describe surface growth and lateral competition. Compared to a previous study of isotropic growth, anisotropy relaxes a constraint between parameters of the model. We completely characterize spatial patterns and invasion velocities in this generalized model. In particular, we find that strong anisotropy results in a distinct morphology of spatial invasion with a kink in the displaced strain ahead of the boundary between the strains. This morphology of the out-competed strain is similar to a shock wave and serves as a signature of anisotropic growth. Copyright © 2024, The Authors. All rights reserved.

关键词： Strain

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Competition on the edge of an expanding population

arXiv

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arXiv 2023年

In growing populations, the fate of mutations depends on their competitive ability against the ancestor and their ability to colonize new territory. Here we present a theory that integrates both aspects of mutant fitness by coupling the classic description of one-dimensional competition (Fisher equation) to the minimal model of front shape (KPZ equation). We solved these equations and found three regimes, which are controlled solely by the expansion rates, solely by the competitive abilities, or by both. Collectively, our results provide a simple framework to study spatial competition. Copyright © 2023, The Authors. All rights reserved.

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