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The CRISPR/Cas9-mediated base editing design of HBV specific gRNA: A computational approach

AIP Conference Proceedings 2024年第1期3080卷

作者： Hartiyowidi Yuliawuri Jeanne Elvia Christian Edvan Arifsaputra Suherman Biology Study Program Faculty of Science and Engineering Calvin Institute of Technology Jl. Industri Blok B14 Kav. 1 Kemayoran Central Jakarta DKI Jakarta 10610 Indonesia

Therapy to cure a persistent infection of the Hepatitis B Virus (HBV) is needed to suppress viral replication. Current therapy with nucleoside analogues does not destroy HBV covalently closed circular DNA (cccDNA). A new strategy using Base Editing is required to tackle this viral latent infection. We designed guide RNAs (gRNAs) to target the pre-S and S genes of HBV for the development of antiviral, based on the dominant HBV genotype in Indonesia. The conserved regions of HBV, pre-S and S genes were used to determine a selected target of the Cas9-mediated base editing system. Base Editing (BE)-Designer web-based software to designed gRNA and SnapGene to visualized the expression vector. We identified 5 candidate sequences, including 3 sequences in the pre-S and 2 sequences in the S gene. These target sequences show no mismatches and GC contains between 45-60%. In addition, the gRNA sequences were checked in Nucleotide BLAST tools (NCBI) to prevent the off-target effect and ensure the differences with the human genome. This study provides the candidate target sequences to be developed in antiviral therapy. The utility and efficiency of the candidate sequences need to be evaluated in viral gene expression by in vitro HBV infection systems.

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Emergent dimer-model topological order and quasi-particle excitations in liquid crystals: combinatorial vortex lattices

arXiv

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arXiv 2025年

作者： Meng, Cuiling Wu, Jin-Sheng Kos, Žiga Dunkel, Jörn Nisoli, Cristiano Smalyukh, Ivan I. Department of Physics and Chemical Physics Program University of Colorado BoulderCO80309 United States Hiroshima University Hiroshima Higashihiroshima Japan Department of Mathematics Massachusetts Institute of Technology CambridgeMA02139 United States Faculty of Mathematics and Physics University of Ljubljana Ljubljana Slovenia Department of Condensed Matter Physics Jožef Stefan Institute Ljubljana Slovenia Theoretical Division Physics of Condensed Matter and Complex Systems Center For Nonlinear Studies Los Alamos National Laboratory Los AlamosNM87545 United States Department of Electrical Computer and Energy Engineering Materials Science and Engineering Program University of Colorado BoulderCO80309 United States Renewable and Sustainable Energy Institute National Renewable Energy Laboratory University of Colorado BoulderCO80309 United States

Liquid crystals have proven to provide a versatile experimental and theoretical platform for studying topological objects such as vortices, skyrmions, and hopfions. In parallel, in hard condensed matter physics, the concept of topological phases and topological order has been introduced in the context of spin liquids to investigate emergent phenomena like quantum Hall effects and high-temperature superconductivity. Here, we bridge these two seemingly disparate perspectives on topology in physics. Combining experiments and simulations, we show how topological defects in liquid crystals can be used as versatile building blocks to create complex, highly degenerate topological phases, which we refer to as ‘Combinatorial Vortex Lattices’ (CVLs). CVLs exhibit extensive residual entropy and support locally stable quasi-particle excitations in the form of charge-conserving topological monopoles, which can act as mobile information carriers and be linked via Dirac strings. CLVs can be rewritten and reconfigured on demand, endowed with various symmetries, and modified through laser-induced topological surgery — an essential capability for information storage and retrieval. We demonstrate experimentally the realization, stability, and precise optical manipulation of CVLs, thus opening new avenues for understanding and technologically exploiting higher-hierarchy topology in liquid crystals and other ordered media. Copyright © 2025, The Authors. All rights reserved.

关键词： Laser surgery

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Innovation and utilization of coffee skin waste (Coffea robusta L) as a superior compost for the growth of pepper cuttings (Piper nigrum L.)

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AIP Conference Proceedings 2025年第1期3186卷

作者： Awalul Fatiqin Dewi Lestari R. A. Hoetary Tirta Amalia Riri Novita Sunarti Ike Apriani Anita Restu Puji Raharjeng Rr Mini Sari Wulan Thathit Suprayogi Yahya Febrianto Sudarman Rahman Shesanthi Citrariana Rokiy Alfanaar Mu’afa Purwa Arsana Yithro Serang Wansadaj Jaroenram Biology Study Program Faculty of Mathematics and Natural Sciences Palangka Raya University Palangka Raya Central Kalimantan Indonesia Biology Study Program Faculty of Science and Technology Universitas Islam Negeri Raden Fatah Palembang Palembang South Sumatra Indonesia Education Biology Study Program Faculty of Teacher Training and Education Universitas Islam Negeri Raden Fatah Palembang Palembang South Sumatra Indonesia Physics Study Program Faculty of Mathematics and Natural Sciences Palangka Raya University Palangka Raya Central Kalimantan Indonesia Pharmacy Study Program Faculty of Mathematics and Natural Sciences Palangka Raya University Palangka Raya Central Kalimantan Indonesia Chemistry Study Program Faculty of Mathematics and Natural Sciences Palangka Raya University Palangka Raya Central Kalimantan Indonesia Mathematics Study Program Faculty of Mathematics and Natural Sciences Palangka Raya University Palangka Raya Central Kalimantan Indonesia Department of applied chemistry Chaoyang University of Technology Taichung City Taiwan National center for genetic engineering and biotechnology (BIOTEC) Pathum Thani Thailand

This study aimed to determine the potential of coffee skin waste (Coffea robusta L) as a superior compost innovation for the growth of pepper-cutting seedlings (Piper nigrum L). This study used an experimental method with a completely randomized design using five treatments and five repeats, variations in the dose of coffee skin waste used P0 (control), P1 (90 g), P2 (135 g), P3 (180 g), and P4 (225 g). The shoot height, number of leaves, number of roots, and length of roots were measured. The results showed that coffee skin waste compost significantly affected shoot height, especially at P1 (90 g), resulting in an average growth height of 7.24 cm. In addition, the highest number of leaves was found at a concentration of P1 (90 g), with an average of two leaves. Although there was no significant effect on the number of roots, the concentration of P1 (90 g) yielded the best results, with an average of 33 root blades, and the best root length was obtained at the concentration of P1 (90 g), with an average of 44.6 cm. Therefore, coffee skin waste significantly influenced shoot height and the number of leaves on pepper-cut seedlings (Piper nigrum L.) in the P1 treatment (90 g).

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The effects of UV light wavelength and distance differences in viral genetic material integrity

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AIP Conference Proceedings 2024年第1期3155卷

作者： Arya Adiningrat Ahmad Ghitha Fadhlurrahman Yuli Rismawanto Tony Khristanto Hariadi Maria Ulfa Rama Okta Wiyagi Muhammad Yusvin Mustar Molecular Medicine and Therapy Laboratory Faculty of Medicine and Health Science Universitas Muhammadiyah Yogyakarta Yogyakarta Indonesia Oral Biology and Biomedical Sciences Faculty of Dentistry Universitas Muhammadiyah Yogyakarta Bantul Indonesia Department of Electrical Engineering Faculty of Electrical Engineering Universitas Muhammadiyah Yogyakarta Bantul Indonesia Master of Hospital Administration Postgraduate Program Universitas Muhammadiyah Yogyakarta Bantul Indonesia

The pandemic has shown viral capacity in massive spreading and environmental adaptability for years. It has infected millions of people with several symptoms leading to millions of mortality worldwide. Its fast-spreading capacity, unpredictability prognosis and variants appearance are leading big threats, particularly to the health facilities. Therefore, appropriate health protection equipment, including adequate and safe decontamination procedures, is required to support the facilities in overcoming potential future contaminating pathogens. Unfortunately, only a few studies evaluated the utilization of medical decontamination devices. Rapid and massive manufacturing of decontamination devices without further and adequate post-monitoring may have several side effects. Therefore, careful and continuing consideration and evaluation studies are necessary to maintain the devices’ quality and performance. This study aims to evaluate the ability of UV lights as laboratory devices to impair viral components. Clinical RNA samples were provided by the COVID-19 laboratory examiner as blinded samples without any subject information. SARS-CoV2 RNA (a viral representative RNA material) extract was exposed to 5 different UV lights, with different distances and exposure duration. The exposed RNA was then sequentially used as a cDNA template and DNA amplification. Amplification products were visualized by electrophoresis and densitometry analysis. Visualization and densitometry analysis showed that the UV-LED Nichia NCSU 334 had the most significant disruptive ability among the tested lights. The exposure duration and distance altered the effectiveness of UV light in damaging viral genetic material. UV-LED Nichia NCSU 334 could be suggested as an alternative UV source in a UV light-based disinfection system. This study proposed direct evidence for evaluating decontamination devices to ensure the effectiveness of the decontamination process.

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Model Technology Service E-Participation - Voting (E-PV) for Political Communication between the Council of Regional Representatives (DPRD) and the Citizens Using the Framework Information Technology Infrastructure Library (ITIL V.3) Transition Domain Service 7

Model Technology Service E-Participation - Voting (E-PV) for...

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7th International Conference on ICT for Smart Society, ICISS 2020

作者： Hilabi, Shofa Shofiah Harso Supangat, Suhono Hendric Spits Warnars, Harco Leslie Prabowo, Harjanto Mursitama, Tirta Nugraha Universitas Buana Perjuangan Faculty of Engineering and Computer Science Karawang Indonesia Institute of Technology Bandung School of Electrical Engineering and Informatics Bandung Indonesia Nusantara University Doctor of Computer Science Bina Computer Science Department BINUS Graduate Program Jakarta11530 Indonesia Bina Nusantara University Doctor of Computer Science Jakarta11530 Indonesia Bina Nusantara University Faculty of Humanities International Relations Department Jakarta11480 Indonesia

ISBN: (纸本)9781665404228

E-voting is an electronic voting information technology service, while E-participation is an information technology service for citizens of the public to provide reports, polls, or suggestions on government policies electronically. The Technology Services E-Participation-VOT (EPV) model is a combined E-Participation and E-Voting service model. The concept of this service model is that citizens transform from E-participation and E-voting services into an EPV model. The purpose of this model is to provide information to participants (citizens) about online-based voting services. This method of developing the EP-Voting Anticipation (EPV) technology model uses agile methods that are effective and flexible in various cases of designing Information Technology models for Information Technology (IT) services that apply a Framework Information Technology Infrastructure Library (ITIL). The results obtained from this study are an Information Technology service system model that provides recommendations for participation in conducting electronic elections (E-Voting). © 2020 IEEE.

关键词： Surveys

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Canopy cover estimation based on support vector regression derived from Lidar & Landsat 8 OLI 40

Canopy cover estimation based on support vector regression d...

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40th Asian Conference on Remote Sensing: Progress of Remote Sensing Technology for Smart Future, ACRS 2019

作者： Hudjimartsu, Sahid Tampinongkol, Felliks Rudianto, Yoga Setiawan, Yudi Prasetyo, Lilik Budi Forests2020 Programme Environmental Analysis and Spatial Modelling Laboratory Department of Forest Resource Conservation Faculty of Forestry Bogor Agricultural University Bogor West Java Indonesia Geoinformatic of Informatics Engineering Study Program Faculty of Engineering and Science Ibn Khaldun University Jalan KH Soleh Iskandar KM 2 Tanah Sereal Bogor West Jawa Indonesia

Light detection and ranging (LiDAR) provides geospatial information with massive amounts of data to use in a variety of applications. Canopy cover percentage of tree crown is one application that is estimated through LiDAR data. This study aims to estimate a canopy cover derived from LiDAR used as reference data with multispectral Landsat 8 OLI. Statistical or machine learning approaches can be used to estimate a canopy cover. In statistical inference, the form of distribution chosen by the analyst and parameter is estimated from the data. This will be a problem in the construction function for the National scale, due to many ecosystems and then will have many functions for each ecosystem. Machine learning (ML) methods, in contrast, are various kinds of algorithms that are used to learn the mapping function or classification rules inductively, directly from the training data. ML can solve problems related to big data and global method and it will be used as a methodical approach to estimate canopy cover on the National scale. In this study, we use a support vector regression (SVR) as ML method to estimate the canopy cover. The estimated percentage of canopy cover will be used as one of the parameters to classify a forest. © 2020 40th Asian Conference on Remote Sensing, ACRS 2019: "Progress of Remote Sensing Technology for Smart Future". All rights reserved.

关键词： Ecosystems

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X-ray application of micro-computed tomography for biological sample test

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AIP Conference Proceedings 2023年第1期2614卷

作者： Susilo Yuni Wijayanti Fitria Azmi Rudi Setiawan Ulil Albab Taufiq Ian Yulianti Physics Department Faculty of Mathematics and Natural Sciences Universitas Negeri Semarang Semarang Indonesia Public Health Study Program Universitas Negeri Semarang Semarang Indonesia Radiodiagnostic Engineering and Radiotherapy Study Program STIKES An Nasher Cirebon Indonesia Faculty of Science and Mathematics Universitas Diponegoro Semarang Indonesia

Homemade micro-CT equipment has been successfully developed in the Physics Laboratory of Universitas Negeri Semarang (UNNES). The micro-CT was tested and could be used properly for non-destructive testing (NDT) using a phantom as the object. However, the application of the micro-CT for biological samples has not been investigated. Therefore, in this work, an investigation of the homemade micro-CT for biological samples was done. Tilapia fish was used an object. The fish was exposed to the X-ray using exposure factors of 45 kV, 32 mA, and 0.08 s. The object was rotated with rotation angle range of 0°-360° with increment of 1.40625° and the images at every rotation angle increment was recorded. The three-dimensional (3D) image was then reconstructed from the collection of the two-dimensional (2D) images obtained during rotation. The quality of the images was then analyzed using contrast to noise ratio method (CNR). The results showed that the highest CNR was obtained at the image taken with rotation angle of 315° which was 81.163. Therefore, it can be concluded that the homemade micro-CT equipment could be used for biological sample and can be further applied in other applications such as CT-scan.

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Multi-perspective review on application of self-healing concrete and its prospect in Asia

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AIP Conference Proceedings 2022年第1期2489卷

作者： Christian Hadhinata Amalina Amira Arini Nurjanna Athalafi Ramadhan Indrasara Nu’matul Hasanah M. Mirza Abdillah Pratama 1Civil Engineering Education Study Program Department of Civil Engineering Faculty of Engineering Universitas Negeri Malang Malang Indonesia 2Biology Study Program Department of Biology Faculty of Mathematics and Natural Science Universitas Negeri Malang Malang Indonesia 3Department of Civil Engineering Faculty of Engineering Universitas Negeri Malang Malang Indonesia

Concrete is the most popular material construction which can be applied in broad construction projects. In addition, concrete is also featured with robust strength, durability, reflectivity, and versatility. However, concrete is prone to rupture that results in decreasing life span and its quality, so it requires additional cost for repair toward its damage. Self-healing concrete is one of the innovations developed by researchers to solve the cracks in concrete allowing the concrete to recover the cracks through the healing process. A self-healing concrete has more superior mechanical properties compared with normal concrete. Self-healing mechanisms can be divided into two types: autogenic and autonomic self-healing. Autogenic self-healing takes advantage of the formation of calcium carbonate crystals from unhydrated cement or mineral particles. Meanwhile, autonomic self-healing uses a healing agent capsulized into microvascular, microencapsulation, and pallets. Researchers applied self-healing concrete on a macro-scale, such as in panel walls, roof slabs, and river floodgates. This paper uses the literature review method to collect the data about self-healing concrete. This study aims to discuss self-healing concrete, its mechanical properties, durability, and analysis of the use of self-healing concrete from multi-perspective disciplines including economy, health and environment, construction, and public policy in Asia’s countries.

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Development of Educational Game for Indonesian History Lesson Focusing on Indonesia Pre-Literacy Relics 'Prehistoria' for Grade X High School Student

Development of Educational Game for Indonesian History Lesso...

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2020 International Conference on Computer engineering, Network, and Intelligent Multimedia, CENIM 2020

作者： Nugroho, Supeno Mardi Susiki Rahman, Muhammad Daffa Abiyyu Hariadi, Mochamad Arief, Muhammad Faculty of Intelligent Electrical and Informatics Technology Sepuluh Nopember Institute of Technology Computer Engineering Department Surabaya Indonesia Tokyo University of Technology Media Science Program Graduate School of Bionics Computer and Media Sciences Tokyo Japan

ISBN: (纸本)9781728182834

The development of game technology has opened up new possibilities in learning methods through educational games. However, in Indonesia, the application of this concept is lacking. One lesson that can benefit from educational games is Indonesian History in class X, with a focus on history in the pre-literacy period. This study aims to create a puzzle-Adventure type of digital game that can help educate students about the pre-literacy period, developed with Unity, and uses WebGL as a target device while referring to Indonesia's revised 2013 national curriculum. The result of this research is the creation of a digital game that can be played on average of 254.36 seconds, with potential for educational use. A survey result shows that many of the ancient objects and some of the ages are well-recognized. However, the survey also shows many of the gameplay aspects, such as UI, gameplay features, and adventure elements, need improvements. © 2020 IEEE.

关键词： Surveys

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Scientometric Analysis of Artificial Intelligence Research in Agriculture

Scientometric Analysis of Artificial Intelligence Research i...

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

作者： Fairuz Iqbal Maulana Andi Pramono Miftahul Hamim Sukeipah Yuli Prihatin Rahman Arifuddin Computer Science Department School of Computer Science Bina Nusantara University Jakarta Indonesia Interior Design Department School of Design Bina Nusantara University Jakarta Indonesia Entrepreneurship Business Creation BINUS Business School Bina Nusantara University Jakarta Indonesia Informatics Study Program Politeknik Kota Malang Malang Indonesia Department of Electrical Engineering University of Merdeka Malang Malang Indonesia

ISBN: (纸本)9781665473286

Artificial Intelligence Research in Agriculture has grown so common, and the potential they provide is so revolutionary that it is considered essential for competitive growth. Until we conducted this research, only 1064 academic documents on Trends of Artificial Intelligence Research in Agriculture that we found from 2012 to 2021 were obtained by searching the Scopus database. This study uses bibliometric analysis methods to map scientific publications worldwide. We use an article selection process, the year limitation, then the database is exported to RIS and CSV format files. Researchers in the United States had the most published articles and were indexed by Scopus among the most prolific authors ( $\mathrm{N}=287$ ), followed by the United Kingdom at second ( $\mathrm{N}=139$ ) and Italy with 66 academic publications. Data analysis reveals an increasing trend in the number of Trends of Artificial Intelligence Research in Agriculture publications worldwide, as measured by the Scopus index.

关键词： Data analysis Databases Multimedia systems Bibliometrics Market research Agriculture Indexes

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