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2023 ASEE Annual Conference and Exposition - The Harbor of Engineering: Education for 130 Years, ASEE 2023

作者： Brown, David C. Al-Hossami, Erfan Cheng, Zhuo Alameda, Alyssa Lasmarias Johnson, Tia Nicole Uddin, Mesbah Janies, Daniel Andrew Shaikh, Samira Department of Bioinformatics and Genomics UNC Charlotte United States Department of Computer Science UNC Charlotte United States Department of Geography and Earth Sciences UNC Charlotte United States Department of Mechanical Engineering UNC Charlotte United States

This paper illustrates the final research product resulting from a team of diverse students of many educational stages and backgrounds in cyber intelligence-based research. We chose a real-world dataset of discussion of scientific preprints on SARS-CoV-2 virus and COVID disease on Twitter ™. The selection of the real-world dataset was driven by: (a) misinformation regarding COVID-19 disease and SARS-CoV-2 virus is rampant and undermines our ability to recover from the pandemic, (b) unfounded and false health-related claims are spreading on social media, and (c) the rapid dissemination of health misinformation provides challenging competition with information broadcast by public health or government authorities such as the World Health Organization and the U.S. Centers for Disease Control and Prevention. Thus, we focused on the close symbiosis between preprints, preprint servers (like bioRxiv and medRxiv), Twitter, scientific researchers, journalists, and the public that developed in the early months of the pandemic (e.g. first six months of 2020). This symbiosis, the "Twitter-Rxiv ecosystem", led to the rapid dissemination of results before traditional processes of scientific peer-review before publication. While much of the work in preprints is well-intentioned, concerns have been raised that this symbiosis may be exploited to disseminate spurious results or intentionally incorrect information. In response we constructed networks to represent public discourse surrounding scientific preprint literature on Twitter and develop metrics to score users within these networks. One such metric, peer-review percentage score, is useful for calculating the network prominence (i.e. influence) of a user while weighting that user for the quality of information propagated by the user. Peer-review percentage score can be used to identify subject-matter experts who transmit evidence-based information online. We found that these subject-matter experts outcompeted public health author

关键词： Ecosystems

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Dynamics of synthetic yeast chromosome evolution shaped by hierarchical chromatin organization

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National science Review 2023年第5期10卷 240-250页

作者： Sijie Zhou Yi Wu Yu Zhao Zhen Zhang Limin Jiang Lin Liu Yan Zhang Jijun Tang Ying-Jin Yuan Frontiers Science Center for Synthetic Biology (Ministry of Education) Tianjin University Key Laboratory of Systems Bioengineering(Ministry of Education) School of Chemical Engineering and TechnologyTianjin University Institute for Systems Genetics NYU Langone Health School of Computer Science and Technology College of Intelligence and ComputingTianjin University Epigenetic Group Frasergen Bioinformatics Co.Ltd. Department of Computer Science University of South Carolina

Synthetic genome evolution provides a dynamic approach for systematically and straightforwardly exploring evolutionary *** Chromosome Rearrangement and Modification by LoxP-mediated Evolution(SCRaMbLE) is an evolutionary system intrinsic to the synthetic yeast genome that can rapidly drive structural ***,we detect over 260 000 rearrangement events after the SCRaMbLEing of a yeast strain harboring 5.5 synthetic yeast chromosomes(synⅡ,synⅢ,synⅤ,circular synⅥ,synⅨR and synⅩ).Remarkably,we find that the rearrangement events exhibit a specific landscape of *** further reveal that the landscape is shaped by the combined effects of chromatin accessibili and spatial contact *** rearrangements tend to occur in 3D spatially proximal and chromatin-accessible *** enormous numbers of rearrangements mediated by SCRaMbLE provide a driving force to potentiate directed genome evolution,and the investigation of the rearrangement landscape offers mechanistic insights into the dynamics of genome evolution.

关键词： synthetic biology genome rearrangement hierarchical chromatin organization synthetic yeast genome SCRaMbLE Saccharomyces cerevisiae

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Dynamic k-Anonymity for Electronic Health Records: A Topological Framework 19th

Dynamic k-Anonymity for Electronic Health Records: A Topolo...

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19th International Workshop on Data Privacy Management, DPM 2024, 8th International Workshop on Cryptocurrencies and Blockchain Technology, CBT 2024 and 10th Workshop on the Security of Industrial Control Systems and of Cyber-Physical Systems, CyberICPS 2024 which were held in conjunction with the 29th European Symposium on Research in computer Security, ESORICS 2024

作者： Swaminathan, Arjhun Akgün, Mete Medical Data Privacy and Privacy Preserving Machine Learning Department of Computer Science University of Tübingen Tübingen Germany Institute for Bioinformatics and Medical Informatics Tübingen Germany

ISBN: (纸本)9783031823480

With the rapid digitization of Electronic Health Records (EHRs), fast and adaptive data anonymization methods have become increasingly important. While tools from topological data analysis (TDA) have been proposed to anonymize static datasets—allowing the creation of multiple generalizations for different anonymization needs from a single computation—the application to dynamic datasets remains unexplored. To address this, our work adapts existing methodologies to the dynamic setting. We develop an improved version of weighted persistence barcodes that track higher-dimensional holes in data, allowing us to edit persistence information on the fly. Additionally, we introduce filtration trimming, a novel technique designed to update persistence data quickly with minimal computing effort when data is added. Our work represents a significant advancement in healthcare data privacy, offering a refined approach to protecting highly sensitive and evolving patient data through dynamic k-anonymity. © The Author(s), under exclusive license to Springer Nature Switzerland AG 2025.

关键词： Electronic health record

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Perspectives on the convergence of human and machine intelligence

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Discover Artificial Intelligence 2025年第1期5卷 1-6页

作者： Sharma, Nilesh Kumar Singh, Rashmi Cancer and Translational Research Lab Department of Biotechnology Dr. D.Y. Patil Biotechnology & Bioinformatics Institute Dr. D.Y. Patil Vidyapeeth Maharashtra Pune411033 India Department of Computer Science Dr. D. Y. Patil Arts Commerce and Science College Akurdi Maharashtra Pune India

In recent times, profound curiosities have been generated to explore potential synergies between human and artificial intelligence, which could either result in a multiplied combined intelligence or an additive accumulation of intelligence. Additionally, propositions are lacking that can link human intelligence and machine intelligence for a better understanding of and complexities of intelligence. A better view of the intelligence of humans and machines can contribute to the evolution of society and the environment. Perspective views and equations on the intelligence of humans and machines are presented. © The Author(s) 2025.

关键词： Ambient intelligence

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Effect of Introducing Leucine Residues into 2-Aminoisobutyric Acid-Based Amphiphilic Helical Peptides on Intermolecular Interactions and Peptide Self-Assembly

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ACS Omega 2025年第21期10卷 22184-22190页

作者： Yamaguchi, Kasumi Kusumoto, Tomoichiro Araki, Takeshi Gomibuchi, Yuki Yasunaga, Takuo Osada, Satoshi Taira, Junichi Department of Chemistry and Applied Chemistry Faculty of Science and Engineering Saga University Saga 840-8502 Japan Department of Bioscience and Bioinformatics Fukuoka 820-8502 Japan Department of Physics and Information Technology Graduate School of Computer Science and Systems Engineering Kyushu Institute of Technology Fukuoka 820-8502 Japan

In recent years, self-assembling de novo-designed peptides have attracted increasing attention as materials for constructing submicrometer-scale structures. We have previously conducted structure-activity relationship studies on the BXBA-20 series of 20-residue amphiphilic peptides containing 2-aminoisobutyric acid (Aib) [Higashimoto, Y. et al. (1999) J. Biochem. 125, 705-712;Hara, T. et al. (2001) J. Biochem. 130, 749-755;Taira, J. et al. (2010) J. Pept. Sci. 16, 607-612]. These peptides share the common sequence Ac-(Aib-Xxx-Aib-Ala)₅-NH₂, where the introduction of a hydrophilic amino acid at the Xxx position results in the formation of a hydrophilic face on one side of the helix. Among them, some peptides exhibited weak intermolecular association and interactions with lipid membranes, though none demonstrated the ability to form submicrometer-scale structures through self-assembly. In this study, we present BKBL-20, a new member of this peptide series incorporating leucine on the hydrophobic face and lysine on the hydrophilic face. Circular dichroism spectroscopy indicated strong association in buffer, while hemolysis assays revealed significant membrane disruption. Transmission electron microscopy further confirmed the formation of ordered fibrous or array-like structures. These findings suggest that BKBL-20 successfully combines self-assembly and membrane-disruptive functions. © 2025 The Authors. Published by American Chemical Society.

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Developing a pipeline for identification,characterization and molecular editing of cis-regulatory elements:a case study in potato

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aBIOTECH 2025年第1期6卷 91-96页

作者： Min Wan Handan Xie Hongwei Guo Shenglin Jing Deying Zeng Bing Li Bo Zhu Zixian Zeng Department of Biological Science College of Life SciencesSichuan Normal UniversityChengdu 610101China Plant Functional Genomics and Bioinformatics Research Center Sichuan Normal UniversityChengdu 610101China Crop Research Institute Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan ProvinceSichuan Academy of Agricultural SciencesChengdu 610066China

Crop breeding requires a balance of tradeoffs among key agronomic traits caused by gene *** molecular manipulation of genes can effectively improve target traits,but this may not reduce gene pleiotropy,potentially leading to undesirable traits or even lethal ***,molecular editing of cis-regulatory elements(CREs)of target genes may facilitate the dissection of gene pleiotropy to fine-tune gene *** this study,we developed a pipeline,in potato,which employs open chromatin to predict candidate CREs,along with both transient and genetic assays to validate the function of CREs and CRISPR/Cas9 to edit candidate *** used StCDF1 as an example,a key gene for potato tuberization and identified a 288 bp-core promoter region,which showed photoperiodic inducibility.A homozygous CRISPR/Cas9-editing line was established,with two deletions in the core promoter,which displayed a reduced expression level,resulting in late tuberization under both longday and short-day *** pipeline provides an alternative pathway to improve a specific trait with limited downside on other phenotypes.

关键词： Cis-regulatory element Potato CRISPR Genome-editing

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Development of homozygous tetraploid potato and whole genome doubling-induced the enrichment of H3K27ac and potentially enhanced resistance to cold-induced sweetening in tubers

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Horticulture Research 2023年第3期10卷 271-283页

作者： Hongwei Guo Min Zhou Guoyan Zhang Li He Caihong Yan Min Wan Jianjun Hu Wei He Deying Zeng Bo Zhu Zixian Zeng Department of Biological Science College of Life SciencesSichuan Normal UniversityChengdu 610101SichuanChina Plant Functional Genomics and Bioinformatics Research Center Sichuan Normal UniversityChengdu 610101SichuanChina Crop Research Institute Sichuan Academy of Agricultural SciencesChengdu 610066China Horticulture Institute Sichuan Academy of Agricultural SciencesChengdu 610066China

Polyploid plants typically display advantages on some agronomically important traits over their diploid *** studies have shown genetic,transcriptomic,and epigenetic dynamics upon polyploidization in multiple plant ***,few studies have unveiled those alternations imposed only by ploidy level,without any interference from *** potato is highly ***,in this study,we developed two homozygous autotetraploid lines and one homozygous diploid line in parallel from a homozygous diploid *** confirmed their ploidy levels using chloroplast counting and ***-FISH and genome re-sequencing validated that these potato lines are nearly *** investigated variations in phenotypes,transcription,and histone modifications between two *** autotetraploid lines produced larger but fewer tubers than the diploid ***,each autotetraploid line displayed ploidy-related differential expression for various *** also discovered a genomewide enrichment of H3K27ac in genic regions upon whole-genome doubling(WGD).However,such enrichment was not associated with the differential gene expression between two *** tetraploid lines may exhibit better resistance to cold-induced sweetening(CIS)than the diploid line in tubers,potentially regulated through the expression of CIS-related key genes,which seems to be associated with the levels of H3K4me3 in cold-stored *** findings will help to understand the impacts of autotetraploidization on dynamics of phenotypes,transcription,and histone modifications,as well as on CIS-related genes in response to cold storage.

关键词： homozygous doubling resistance

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Comparing Sequence-Based and Literature-Based Pathogenicity Scoring Methods for Human Variants

Comparing Sequence-Based and Literature-Based Pathogenicity ...

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34th Medical Informatics Europe Conference, MIE 2024

作者： Mottin, Luc Naderi, Nona Mottaz, Anaïs Michel, Pierre-André Been, Gerieke Johansson, Lennart Swertz, Morris Stubbs, Andrew Pasche, Emilie Gobeill, Julien Ruch, Patrick HES-SO\HEG Genève Geneva Switzerland SIB Text Mining Swiss Institute of Bioinformatics Geneva Switzerland Department of Computer Science Université Paris-Saclay CNRS Laboratoire Interdisciplinaire des Sciences du Numérique Orsay France University of Groningen University Medical Centre Groningen Department of Genetics Genomics Coordination Centre Groningen Netherlands Department of Pathology and Clinical Bioinformatics Erasmus University Medical Centre Rotterdam Netherlands

ISBN: (纸本)9781643685335

Assessing the pathogenicity of genetic variants is a critical aspect of genomic medicine and precision healthcare. Over the last decades, the identification of genetic variants and their characterization has become simpler (advent of high-throughput sequencing technologies, analysis, and visualization support tools, etc.). However, the quality of assessments to distinguish benign from pathogenic variants is critical to inform clinical decision-making and improve patient outcomes. In this article, we investigate the relationships using correlation tests between the characterization of genetic variants in the literature and their pathogenicity scores computed by two state-of-the-art assessment tools (SIFT and PolyPhen-2). © 2024 The Authors.

关键词： Text mining

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The Phytophthora nucleolar effector Pi23226 targets host ribosome biogenesis to induce necrotrophic cell death

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Plant Communications 2023年第5期4卷 263-276页

作者： Soeui Lee Jaehwan Kim Myung-Shin Kim Cheol Woo Min Sun Tae Kim Sang-Bong Choi Joo Hyun Lee Doil Choi Plant Immunity Research Center Seoul National UniversitySeoul 08826Republic of Korea Plant Genomics and Breeding Institute Department of AgricultureForestry and BioresourcesCollege of Agriculture and Life ScienceSeoul National UniversitySeoul 08826Republic of Korea Interdisciplinary Programs in Agricultural Genomics College of Agriculture and Life ScienceSeoul National UniversitySeoul 08826Republic of Korea Department of Plant Bioscience Life and Industry Convergence Research InstitutePusan National UniversityMiryang 50463Republic of Korea Division of Bioscience and Bioinformatics Myongji UniversityYongin 449-728Republic of Korea

Pathogen effectors target diverse subcellular organelles to manipulate the plant immune *** the nucleolus has emerged as a stress marker and several effectors are localized in the nucleolus,the roles of nucleolar-targeted effectors remain *** this study,we showed that Phytophthora infestans infection of Nicotiana benthamiana results in nucleolar inflation during the transition from the biotrophic to the necrotrophic *** *** effectors were localized in the nucleolus:Pi23226 induced cell death in *** and nucleolar inflation similar to that observed in the necrotrophic stage of infection,whereas its homolog Pi23015 and a deletion mutant(Pi23226DC)did not induce cell death or affect nucleolar *** immunoprecipitation and individual-nucleotide-resolution UV crosslinking and immunoprecipitation sequencing analysis indicated that Pi23226 bound to the 30 end of 25S rRNA precursors,resulting in accumulation of unprocessed 27S *** nucleolar stress marker NAC082 was strongly upregulated under Pi23226-expressing ***23226 subsequently inhibited global protein translation in host cells by interacting with ***23226 enhanced *** pathogenicity,indicating that Pi23226-induced ribosome malfunction and cell death were beneficial for pathogenesis in the *** results provide evidence for the molecular mechanism underlying RNA-binding effector activity in host ribosome biogenesis and lead to new insights into the nucleolar action of effectors in pathogenesis.

关键词： Phytophthora infestans hemibiotroph nucleolar effector cell death ribosome biogenesis translation inhibition

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Enhanced Image Concealment: Leveraging LSB and Brotli Compression 3

Enhanced Image Concealment: Leveraging LSB and Brotli Compre...

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3rd International Conference for Advancement in Technology, ICONAT 2024

作者： Yacoob, Shaik Sabnis, Vikrant Jain, Jay Kumar Mansarovar Global University MP Bhopal India Mansarovar Global University Faculty of Engineering and Technology Department of Computer Science MP Bhopal India Maulana Azad National Institute of Technology Department of Mathematics Bioinformatics and Computer Applications MP Bhopal India

ISBN: (纸本)9798350354171

Steganography a cryptographic technique enables the concealment of confidential data within multimedia files like images and videos. This method facilitates the exchange of encrypted information through unconventional means, ensuring that only intended recipients can decipher the hidden message. The LSB technique has attracted significant attention in the literature due to its capability to conceal secret message bits within the least significant parts of image pixels. Although LSB has performed well in image steganography, there is some way to go in terms of its development, especially in the ways in which messages are dealt with. This paper presents a new technique of image steganography basing on the LSB method and the BROTLI algorithm. It uses the compression algorithm to compress message text. After that, to scramble the text, one LSB embedding technique is then used to hide the compressed text in the cover image. Applying the methods of data analysis on the benchmark images, the new approach developed outperforms the standard methods that exist at the present stage. This supports the idea of performing BROTLI on data with a view of compressing the data to be embedded in LSBs. © 2024 IEEE.

关键词： Steganography

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