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Commentary on whole-grain intake and pancreatic cancer risk-the danish,diet,cancer and health cohort by Schacht et al.

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Hepatobiliary Surgery and Nutrition 2021年第5期10卷 702-704页

作者： Rick J.Jansen Department of Public Health GenomicsPhenomicsand Bioinformatics ProgramCenter for Immunization Research and Education(CIRE)Center for Diagnostic and Therapeutic Strategies in Pancreatic CancerNorth Dakota State UniversityFargoNDUSA

In their manuscript,“Whole-Grain Intake and Pancreatic Cancer Risk-The Danish,Diet,Cancer and Health Cohort”,Schacht et al.(1)report that total whole-grain product(per 50 g/d serving)intake was significantly associated with lower incidence of pancreatic cancer(HR:0.93;95%CI:0.86,1.00).A sex-specific analysis revealed that this association only held among ***,neither total whole-grain(per 16-g serving)or specific individual whole-grain products and cereals were significantly associated with lower pancreatic cancer *** this commentary,I will describe some of the assumptions and biases associated with assessing dietary intake and attempting to find associations with disease.

关键词： intake cancer

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Mapping the Scientific Landscape of Integrated Scheduling Towards Industry 5.0 with A Bibliometric Analysis 6

Mapping the Scientific Landscape of Integrated Scheduling To...

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6th International Conference on Industry 4.0 and Smart Manufacturing, ISM 2024

作者： Putri Ardyanti, Anak Agung Ayu Xie, Zhiqiang Karnyoto, Andrea Stevens Pardamean, Bens Estiyanti, Ni Made School of Computer Science and Technology Harbin University of Science and Technology Harbin150000 China Faculty of Information Technology and Design Primakara University Bali 80226 Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia Computer Science Department BINUS Graduate Program Master of Computer Science Bina Nusantara University Jakarta 11480 Indonesia School of Management and Business University of Debrecen Debrecen Hungary

The industry is rapidly transitioning from the 4.0 era to the 5.0 era, prompting renewed interest among scholars in scheduling problems. They allow operations to process and assemble various components simultaneously. This bibliometric analysis provides a comprehensive understanding of the diverse research perspectives on the potential challenges of integrated scheduling within the framework. We identified 357 Scopus articles and analysed co-occurrence keyword (CNK) by VOSViewer tools and Global Citation Score (GCS) by Scopus tools. The research data obtained from 1993 to 2023 mainly in the subject areas of Engineering, Computer Science, Maths, and others. CNK identified six cluster keywords, and nine most cited articles based on normalised GCS. These results contribute to our understanding of the development of scheduling algorithms, shifting from an emphasis on manufacturing transfers to contemporary demand-centric research directions. Furthermore, this research provides a valuable perspective for policymakers, plant personnel, and manufacturing managers to make informed decisions. © 2025 The Authors. Published by Elsevier B.V.

关键词： Job shop scheduling

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Predicting dynamic cellular protein-RNA interactions by deep learning using in vivo RNA structures

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细胞研究（英文版） 2021年第5期31卷 495-516页

作者： Lei Sun Kui Xu Wenze Huang Yucheng T.Yang Pan Li Lei Tang Tuanlin Xiong Qiangfeng Cliff Zhang MOE Key Laboratory of Bioinformatics Beijing Advanced Innovation Center for Structural Biology and Frontier Research Center for Biological StructureCenter for Synthetic and Systems BiologySchool of Life SciencesTsinghua UniversityBeijing 100084China Tsinghua-Peking Center for Life Sciences Beijing 100084China Program in Computational Biology and Bioinformatics Yale UniversityNew HavenCT 06520USA Department of Molecular Biophysics and Biochemistry Yale UniversityNew HavenCT 06520USA

Interactions with RNA-binding proteins (RBPs) are integral to RNA function and cellular regulation,and dynamically reflect specific cellular ***,presently available tools for predicting RBP-RNA interactions employ RNA sequence and/or predicted RNA structures,and therefore do not capture their condition-dependent ***,after profiling transcriptome-wide in vivo RNA secondary structures in seven cell types,we developed PrismNet,a deep learning tool that integrates experimental in vivo RNA structure data and RBP binding data for matched cells to accurately predict dynamic RBP binding in various cellular *** results for 168 RBPs support its utility for both understanding CUP-seq results and largely extending such interaction data to accurately analyze additional cell ***,PrismNet employs an 'attention' strategy to computationally identify exact RBP-binding nucleotides,and we discovered enrichment among dynamic RBP-binding sites for structure-changing variants(riboSNitches),which can link genetic diseases with dysregulated RBP *** rich profiling data and deep learning-based prediction tool provide access to a previously inaccessible layer of cell-type-specific RBP-RNA interactions,with clear utility for understanding and treating human diseases.

关键词： bioinformatics Mechanisms of disease Molecular biology

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Undergraduate Education in Computational Pathology Through Global Health Inspired Projects

Undergraduate Education in Computational Pathology Through G...

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Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)

作者： Avery Maddox Robin Fowler Ellen Solomon Arvind Rao Computational Medicine and Bioinformatics University of Michigan Ann Arbor United States Engineering Education Research University of Michigan Ann Arbor United States Multidisciplinary Design Program University of Michigan Ann Arbor United States

ISBN: (数字)9798350371499

ISBN: (纸本)9798350371505

Recent technological advancements are revolutionizing the field of pathology as the practice adopts digital workflows and computational tools to augment the analysis of tissue and enhance its role in patient care. These advancements are poised to make a particularly significant impact in low-income and middle-income countries, which are disproportionately affected by worsening pathology service shortages and rising cancer rates. Courses targeted towards undergraduate students interested in this emergent field of computational pathology (CPATH) are required to prepare the next generation of innovators and leaders in this space. However, such training courses have mostly been lacking and their design presents with several challenges. CPATH exists at the intersection of multiple complex specialties and so, following a traditional bottom-up curriculum, courses are often limited to the graduate level. In addition, standard didactic courses struggle to keep with the rapid pace of advancements driving the field, build the essential multidisciplinary teamwork skills, train the technical skillsets required for success, or emphasize innovation. Structured experiential learning (EL) has a long track record of success in addressing these issues and presents as a natural modality for early CPATH education. We have designed and piloted a project based EL course targeted towards undergraduates to address these limitations in CPATH education. At the core of the course experience, students work together to conceptualize, design, and implement innovative solutions to leverage CPATH towards addressing global health inequity. Here we present our design of the course, review insights from our first two years of piloting this course and share plans for course improvement drawn from these *** relevance— CPATH is making a significant impact on the practice of pathology and is poised to play a major role in addressing global health inequities. This course is designed to prepar

关键词： Training Pathology Technological innovation Target tracking Reviews Medical services Teamwork Standards Next generation networking Biomedical imaging

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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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The phase separation of SGS3 regulates antiviral immunity and fertility in Arabidopsis

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Science China(Life Sciences) 2023年第8期66卷 1938-1941页

作者： Yujie Han Xiaolin Zhang Ran Du Xiaoyi Shan Daoxin Xie MOE Laboratory of Bioinformatics Tsinghua-Peking Center for Life SciencesSchool of Life SciencesTsinghua UniversityBeijing 100084China Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program School of Life SciencesTsinghua UniversityBeijing 100084China Shenzhen Branch of Guangdong Laboratory for Lingnan Modern Agriculture Genome Analysis Laboratory of the Ministry of AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518124China

Dear Editor,As a conserved mechanism among eukaryotic organisms,RNA silencing is vital for suppressing gene expression at the transcriptional or posttranscriptional level to regulate multiple biological *** interfering RNAs(si RNAs)generated by Dicer proteins integrate with Argonaute(AGO)to form an RNA-induced silencing complex(RISC),in which RNA/DNA could be degraded/methylated through a sequence-specific manner(Ding et al.,2004).

关键词： immunity separation

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The Impact of Different Modes of Augmented Reality Information in Assisted Aircraft Cable Assembly 1

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International Conference on Innovative Technologies in Intelligent Systems and Industrial Applications, CITISIA 2022

作者： Ariansyah, Dedy Xi, Khaizuo Erkoyuncu, John Ahmet Pardamean, Bens Bioinformatics and Data Science Research Centre Bina Nusantara University Jakarta11480 Indonesia School of Aerospace Transport and Manufacturing Cranfield University BedfordMK43 0AL United Kingdom Centre of Digital Engineering and Manufacturing School of Aerospace Transport and Manufacturing Cranfield University BedfordMK43 0AL United Kingdom Computer Science Department BINUS Graduate Program Master of Computer Science Program Bina Nusantara University Jakarta11480 Indonesia

ISBN: (数字)9783031290787

ISBN: (纸本)9783031290770

Aircraft avionics systems are complicated systems which involves high number of components and complex cable assembly procedure. To deal with this challenge, Augmented Reality (AR) has been proposed to be an effective method to improve assembly efficiency and to reduce error rates. In this paper, the authors developed AR-based guidance cable assembly and compare the impact of different modes of AR information. The results show that although AR outperformed the paper document assembly guidance, the design of AR information has distinct influence on the successful completion of the cables assembly process. © The Author(s), under exclusive license to Springer Nature Switzerland AG 2023.

关键词： Augmented reality

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Diversity and Evolution of RNA Recognition Motifs: A Case Study on the Utility of RdRp in the phylum Duplornaviricota

Diversity and Evolution of RNA Recognition Motifs: A Case St...

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IEEE International Conference on bioinformatics and Biomedicine (BIBM)

作者： Mikyung Je Myeongji Cho Hyeon S. Son Interdisciplinary Graduate Program in Bioinformatics College of Natural Science Seoul National University Seoul Republic of Korea Lab. of Computational Biology & Bioinformatics Graduate School of Public Health Seoul National University Seoul Republic of Korea Institute of Health and Environment Seoul National University Seoul Republic of Korea

Viruses possess specific conserved regions known as RNA recognition motifs, which are shared within taxonomic groups. Applying these to the Baltimore virus classification system, there are genes/proteins that serve as biomarkers for each of the seven groups. Mutations in conserved sequence regions can have a significant impact on the function of a virus, especially if these conserved regions are part of a major protein. In this study, we analyzed the RdRp gene, known to be a representative RRM of RNA viruses, from viruses of five families (Alternaviridae, Chrysoviridae, Totiviridae, Sedoreoviridae, and Spinareoviridae) within the phylum Duplornaviricota. Data were retrieved from the NCBI non-redundant (nr) database (https://***/protein) applying a cut-off of 300 amino acids in length. RdRp protein sequences were aligned using PROMALS3D, and PhyML (v3.0) was used for phylogenetic analysis. In the next step, we utilized the officially provided ICTV taxonomy and bioinformatics tools to assign the phylogenetic position of RdRp. Although this analysis focused solely on RdRp, it can be concluded that using this gene as a marker may be sufficient for taxonomic assignment. Subsequent analyses will target DNA viruses and RT viruses to perform a more comprehensive assessment. This extensive analysis aims to validate the usefulness of marker genes in the overall viral taxonomy.

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A bioinformatics Analysis and Homology 3D Modeling of Dihydroxy-orotate-dehydrogenase of Plasmodium ovale

A Bioinformatics Analysis and Homology 3D Modeling of Dihydr...

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

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

The infection of Plasmodium vivax is relatively less virulent than the deathliest Plasmodium falciparum. However, it still can lead to a fatal case and often induces recurring malaria due to dormant parasites in the liver. Thus, the research to study the drug to treat Plasmodium vivax is essential, where the enzyme dihydroorotate dehydrogenase (DHODH) has recently become a new drug target. However, the drug-enzyme interaction study has only recently been conducted in Plasmodium falciparum (pfDHODH) due to the lack of the 3D structure of enzyme DHODH from Plasmodium vivax that is crucial for the study. Therefore, this study aimed to perform the modelling study of Plasmodium vivax DHODH (PvDHODH) to create a 3D structure as a basis for drug-protein interaction study in upcoming studies. Sequence pvDHODH (Accession: SCO68359.1) was used in homology modelling using Modeller 10.2 with the crystal structure of DHODH from DHODH (Accession: 7KZY) as a template. Overall, the model generated from the homology modelling was considered a good model, and the 3D structure was close to the native state according to several parameters, including DOPE score, GA341 score, QMEAN4 value, 3D-1D score, ERRAT2 score, and ProSA score. Ramachandran plot also revealed that almost all amino acids were distributed in the desirable and allowed area (99.1%), and only 0.9% were in generously allowed regions. Superimposition of the model with the template also indicated that the model has an almost similar structure and amino acids positioning, including in the binding pocket and active site. Therefore, the model can be used for downstream analysis in drug-protein interaction studies. Nevertheless, some improvements can still be performed to upgrade the quality of the model by deleting unaligned residues on the C-terminal and realigning the residues at the doubting site.

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Comprehensive and critical evaluation of individualized pathway activity measurement tools on pan-cancer data (vol 21, bby097, 2018)

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BRIEFINGS IN bioinformatics 2020年第3期21卷 1118-1118页

作者： Lim, Sangsoo Lee, Sangseon Jung, Inuk Rhee, Sungmin Kim, Sun Interdisciplinary Program in Bioinformatics Seoul National University Seoul Korea Department of Computer Science and Engineering Seoul National University Seoul Korea Bioinformatics Institute Seoul National University Seoul Korea Department of Computer Science and Engineering Seoul National University Seoul Korea Interdisciplinary Program in Bioinformatics Seoul National University Seoul Korea Department of Computer Science and Engineering Seoul National University Seoul Korea Bioinformatics Institute Seoul National University Seoul Korea Corresponding author: Sun Kim Interdisciplinary Program in Bioinformatics Department of Computer Science and Engineering and Bioinformatics Institute Seoul National University Seoul 08826 Korea. Tel.: +82-2-880-7280 Fax: +82-2-888-9623 Email: sunkim.bioinfo@snu.ac.kr

Motivation Biological pathways are extensively used for the analysis of transcriptome data to characterize biological mechanisms underlying various phenotypes. There are a number of computational tools that summarize transcriptome data at the pathway level. However, there is no comparative study on how well these tools produce useful information at the cohort level, enabling comparison of many samples or *** In this study, we systematically compared and evaluated 13 different pathway activity inference tools based on 5 comparison criteria using pan-cancer data set. This study has two major contributions. First, our study provides a comprehensive survey on computational techniques used by existing pathway activity inference tools. The tools use different strategies and assume different requirements on data: input transformation, use of labels, necessity of cohort-level input data, use of gene relations and scoring metric. Second, we performed extensive evaluations on the performance of these tools. Because different tools use different methods to map samples to the pathway dimension, the tools are evaluated at the pathway level using five comparison criteria. Starting from measuring how well a tool maintains the characteristics of original gene expression values, robustness was also investigated by adding noise into gene expression data. Classification tasks on three clinical variables (tumor versus normal, survival and cancer subtypes) were performed to evaluate the utility of tools for their clinical applications. In addition, the inferred activity values were compared between the tools to see how similar they are along with the scoring schemes they use.

关键词： pathway analysis individualized pathway activity pathway activity inference pan-cancer analysis

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