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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...

引用

2023 International Conference on Informatics, Multimedia, Cyber and Information systems, ICIMCIS 2023

作者： Hidayat, Alam Ahmad Nirwantono, Rudi Isnan, Mahmud Trinugroho, Joko Pebrianto Pardamean, Bens Bina Nusantara University School of Computer Science Bioinformatics and Data Science Research Center Mathematics Department Jakarta11480 Indonesia Bina Nusantara University Faculty of Engineering Bioinformatics and Data Science Research Center Biotechnology Department Jakarta11480 Indonesia Bina Nusantara University Bioinformatics and Data Science Research Center Jakarta11480 Indonesia Binus Graduate Program Bioinformatics and Data Science Research Center Computer Science Department Jakarta11480 Indonesia

ISBN: (纸本)9798350307306

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. © 2023 IEEE.

关键词： Proteins

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Influence of Local Lag on Reaction Force in Networked Virtual Environment with Haptic Sense

Influence of Local Lag on Reaction Force in Networked Virtua...

引用

computer Applications (ICCA), IEEE Conference on

作者： Khaing Zar Win Yutaka Ishibashi Khaing Htet Win Faculty of Computer Science University of Computer Studies Yangon Yangon Myanmar Graduate School of Engineering Nagoya Institute of Technology Nagoya Japan Faculty of Computer Systems and Technologies University of Computer Studies Yangon Yangon Myanmar

ISBN: (数字)9798350353624

ISBN: (纸本)9798350353631

This paper investigates the influence of local lag on the reaction forces in a networked virtual maze system incorporating haptic feedback by experiment. In the experiment, participants move a box from the starting position to the target point by using Raising method with haptic device. We measure the average operation time and the average of average reaction force for three different moving velocities and three distinct local lags. Experimental results reveal that as the moving velocity increases and the local lag becomes higher, the two measures become larger. Thus, we illustrate that there exists a strong relationship among the average operation time, the average of average reaction force, moving velocity, and local lag, through multiple regression analysis.

关键词： Force measurement Force Virtual environments computer applications Particle measurements Control systems Time measurement

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GAN.s Approach On Generating Synthetical Skin Image Dataset for Imbalance Dataset

GAN.s Approach On Generating Synthetical Skin Image Dataset ...

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International Conference on Information Technology, Information systems and Electrical engineering (ICITISEE)

作者： Tri Agus Setiawan Yaya Heryadi Lukas Lili Ayu Wulandari Ilvico Sonata Computer Science Department BINUS Graduate Program -Doctor of Computer Science Bina Nusantara University Jakarta Indonesia Cognitive Engineering Research Group (CERG) Universitas Katolik Indonesia - Atma Jaya Jakarta Indonesia

ISBN: (数字)9798350368970

ISBN: (纸本)9798350368987

The use of balanced medical datasets is essential to improve the precision and accuracy of machine learning models in the healthcare field. However, dataset imbalance often becomes an obstacle, especially in the diagnosis of skin diseases. This research aims to develop a Generative Adversarial Networks (GAN) method that is more effective in generating synthetic skin datasets to overcome problems in integrating medical datasets. The methods used include developing and training a GAN model to produce realistic synthetic skin images, with a focus on improving the quality and diversity of the synthetic data produced. Important results from this research show that the developed GAN model is able to produce synthetic skin images that are not only realistic but also able to balance the original dataset. The implications of these findings include improving the accuracy and performance of machine learning models in the diagnosis of skin diseases, as well as the potential use of these methods in other medical fields that face similar problems with imbalanced datasets.

关键词： Training Accuracy Machine learning Generative adversarial networks Reliability engineering Skin Data models Medical diagnostic imaging Diseases Synthetic data

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Real Time Nanoscale Cleaning Phenomenon Observation During Enforcing MHz Wave By Evanescent Field 241

Real Time Nanoscale Cleaning Phenomenon Observation During E...

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241st ECST Meeting

作者： Terayama, Yutaka Khajornrungruang, Panart Suzuki, Keisuke Mori, Ryotaro Hamada, Satomi Wada, Yutaka Hiyama, Hirokuni Mechanical Science and Technology Division Graduate School of Computer Science and Systems Engineering Kyushu Institute of Technology Fukuoka iizuka820-8502 Japan Mechanical Science and Technology Division Department of Intelligent and Control Systems Ebara Corporation Ltd. Kanagawa fujisawa144-8510 Japan

ISBN: (纸本)9781607685395

Post-CMP Cleaning phenomenon is considered as the detachment of the nanoparticle from the substrate surface to be cleaned, and the occasional reattachment of the nanoparticle to surface in nanoscale. However, residual contamination on the substrate has been usually inspected only after the cleaning process. Therefore, the cleaning mechanism of nanoparticles has not already clearly known. Hence, we have established dynamically observation of cleaning phenomena near the surface by applying the evanescent light which occurred a few hundred nm from the surface. In this article, detachments of φ30, 50, 70 nm silica particles and the acoustic cavitation effect were observed during enforcing 1.1 MHz waves in 60 frames per second. The main phenomenon was described that some of each silica nanoparticles were randomly intermittently detached from the surface when the cavitation effect repeatedly irregularly occurs and decays near the surface or remained on the surface during enforcing MHz wave. © 2022 ECS - The Electrochemical Society.

关键词： Silica nanoparticles

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Identification of Meteorological Parameters Affecting Dengue Hemorrhagic Fever Incidences 4

Identification of Meteorological Parameters Affecting Dengue...

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4th International Conference on Informatics, Multimedia, Cyber and Information System, ICIMCIS 2022

作者： Asadi, Faisal Trinugroho, Joko Pebrianto Hidayat, Alam Ahmad Rahutomo, Reza Pardamean, Bens Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia School of Information Systems Bina Nusantara University Information System Department Jakarta11480 Indonesia Binus Graduate Program Master of Computer Science Bina Nusantara University Computer Science Department Jakarta11480 Indonesia

ISBN: (纸本)9781665473279

Tropical disease is one of the infectious diseases that affect Indonesia. Many people die because of tropical diseases, such as dengue hemorrhagic fever (DHF), chikungunya, leprosy, lymphatic, and filariasis. The Indonesian government's lack of public policy is the main problem in treating and preventing tropical diseases. The paper aims to describe the analysis results of the incidence of DHF in Jakarta, Indonesia. The analysis used the DHF incidences data from the Jakarta Health service surveillance office representative and combined it with the meteorological parameters data. The meteorological parameters were collected from the Bureau of Meteorological Climatology and Geophysics (BMKG). The statistical analysis of this research used Pearson's correlation. The results show that the meteorological parameters affecting DHF incidences are temperature, humidity, and wind speed. © 2022 IEEE.

关键词： Correlation methods

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Analysis of delay factors on drilling projects on PT China Oilfields Services Limited 2

Analysis of delay factors on drilling projects on PT China O...

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2nd International Conference on Biospheric Harmony Advanced Research, ICOBAR 2020

作者： Sardjono, W. Perdana, W.G. Ansori, R. Utama, D.N. Information Systems Management Department BINUS Graduate Program-Master of Information Systems Management BINA NUSANTARA University Jakarta11480 Indonesia Post Graduate Program School of Environmental Science University of Indonesia Jakarta Indonesia Graduate Program Master of Business Administration Faculty of Economic and Business University of Gadjahmada Yogyakarta Indonesia Computer Science Department BINUS Graduate Program-Master of Computer Science Bina Nusantara University Jakarta11480 Indonesia

In carrying out drilling projects at PT China Oilfields Services Limited ( COSL) Indo, especially Project 1 to Project 4, there were a mismatch between the initial plan of the project and the actualisation in the field because there were inhibiting factors in implementing the project. The purpose of the research was to look the factors that caused for the additional time in well drilling project at PT. COSL Indo, to build a relationship model of these factors, and formulate a strategy for the company to be able to overcome the occurrence of additional time in the future project. Data analysis was conducted by using a factor analysis method and the location of the research was carried out in just one company with 102 valid respondents. The results of the research indicate that there are four factors that influence the time gap, namely Project Management Activities, Risk Analysis and Procurement, Manage Stairs, and Project Planning Development. By knowing the causes of the delay, companies can find the best solutions for future learning and the impact on environmental, social and economic problems can also be anticipated so that sustainable development occurs in the context of petroleum management. © Published under licence by IOP Publishing Ltd.

关键词： Risk analysis

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Object Detection as Gram Positive Cocci in Gram Stained Smear Images 12

Object Detection as Gram Positive Cocci in Gram Stained Smea...

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12th International Congress on Advanced Applied Informatics, IIAI-AAI 2022

作者： Sugimoto, Hitoshi Hirata, Kouichi Kyushu Institute of Technology Graduate School of Computer Science and Systems Engineering Iizuka820-8502 Japan Kyushu Institute of Technology Department of Artificial Intelligence Iizuka820-8502 Japan

In this paper, we detect Gram positive cossi in Gram stained smear images as object detection. As detectors, we adopt Faster R-CNN, RetinaNet and YOLOv5. Then, we give experimental results for detecting Gram positive ... 详细信息

ISBN: (数字)9781665497558

ISBN: (纸本)9781665497558

关键词： Object detection

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Classifying Gram Positive Cocci and Gram Negative Bacilli in Gram Stained Smear Images 12

Classifying Gram Positive Cocci and Gram Negative Bacilli in...

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12th International Congress on Advanced Applied Informatics, IIAI-AAI 2022

作者： Kawano, Ibuki Kurumida, Eri Terada, Syoma Hirata, Kouichi Kyushu Institute of Technology Department of Artificial Intelligence Iizuka820-8502 Japan Kyushu Institute of Technology Graduate School of Computer Science and Systems Engineering Iizuka820-8502 Japan

ISBN: (数字)9781665497558

ISBN: (纸本)9781665497558

In this paper, we classify Gram positive cocci and Gram negative bacilli in Gram stained smear images. We adopt pre-trained models of VGG16, VGG19, MobileNet and DenseNet by using ImageNet as learning models. Then, we give experimental results for classifying them, and the classification by MobileNet and DenseNet are more successful than that by VGG16 and VGG19. © 2022 IEEE.

关键词： Bacilli

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A Note on Even-Sized Spectral Clustering

A Note on Even-Sized Spectral Clustering

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International Symposium on Soft Computing and Intelligent systems (SCIS)

作者： Hiroki MIYAKAWA Yasunori ENDO Graduate School of Science and Technology Degree Programs in Systems and Information Engineering Master's Program in Risk and Resilience Engineering University of Tsukuba Tsukuba Ibaraki Japan Institute of Systems and Information Engineering University of Tsukuba Tsukuba Ibaraki Japan

ISBN: (数字)9798350373332

ISBN: (纸本)9798350373349

Clustering is a typical unsupervised learning method for classifying unsupervised data. One of the clustering meth-ods, even-sized clustering based on optimization (ECBO), is a clustering algorithm that imposes a constraint to equalize the size of each cluster. ECBO has been suggested to be effective in delivery and other problems. However, it is limited to Euclidean space. On the other hand, spectral clustering with a wide range of applicability for partitioning graph data has been proposed. In this paper, we propose even-sized spectral clustering, which imposes a size-equal constraint on spectral clustering, and show that it is an extension of the graph partitioning problem. We also verify the validity of the results through numerical examples.

关键词： Clustering algorithms Partitioning algorithms Classification algorithms Optimization Unsupervised learning

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E-Government Interoperability: Provincial-Level Architecture Model to Enable Fast Healthcare Interoperability Resources (FHIR)

E-Government Interoperability: Provincial-Level Architecture...

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International Conference on Information Management and Technology (ICIMTech)

作者： Diana Wijayanti Satriawansyah Urbaya Taufiq Sitompul Verry Adrian Department of Information Systems BINUS Graduate Program Bina Nusantara University Jakarta Indonesia Country Health Information Systems and Data Use (CHISU) Program USAID Indonesia Jakarta Indonesia Department of Informatics University of Oslo Oslo Norway Computer Science Department Binus Graduate Program – Doctor Computer Science Bina Nusantara University Jakarta Indonesia Center of Data and Information Technology Jakarta Provincial Health Office Jakarta Indonesia

ISBN: (数字)9798350390025

ISBN: (纸本)9798350390032

The process of using ICT to provide services to the public is known as the Indonesian e-Government system, or Sistem Pemerintahan Berbasis Elektronik (SPBE). The e-Government initiative in Jakarta Provincial Health Office involves enhancing collaboration among public health entities for efficient data exchange and streamlined processes, especially between the Provincial and District Health Offices, public hospitals, government clinics, and primary health care centers (Puskesmas). Achieving interoperability requires standardized protocols and a well-defined architectural model to integrate data seamlessly. This study presents a provincial-level architectural model focused on improving electronic health records interoperability, aiming to promote the adoption of the national Fast Healthcare Interoperability Resources (FHIR) health information exchange platform and enhance the integrity of health data in Jakarta. The study methodology involves conducting literature reviews, observations, and discussions with representatives from healthcare facilities to develop the e-Government architecture model and prototype of the infrastructure layer aiming to facilitate the interoperability of Electronic Health Records (EHRs) across 93 healthcare facilities, all of which are part of the SPBE users.

关键词： Prototypes Medical services Data models Security Public healthcare Electronic medical records Interoperability Information exchange Standards Electronic government

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