检索结果-内蒙古大学图书馆

arXiv 2022年

作者： Jeong, Minbyul Kang, Jaewoo Department of Computer Science and Engineering Korea University Seoul02841 Korea Republic of Interdisciplinary Graduate Program in Bioinformatics Korea University Seoul Korea Republic of AIGEN Sciences Seoul04778 Korea Republic of

Summary: Named entity recognition (NER) is a fundamental part of extracting information from documents in biomedical applications. A notable advantage of NER is its consistency in extracting biomedical entities in a document context. Although existing document NER models show consistent predictions, they still do not meet our expectations. We investigated whether the adjectives and prepositions within an entity cause a low label consistency, which results in inconsistent predictions. In this paper, we present our method, ConNER, which enhances the label dependency of modifiers (e.g., adjectives and prepositions) to achieve higher label agreement. ConNER refines the draft labels of the modifiers to improve the output representations of biomedical entities. The effectiveness of our method is demonstrated on four popular biomedical NER datasets;in particular, its efficacy is proved on two datasets with 7.5–8.6% absolute improvements in the F1 score. We interpret that our ConNER method is effective on datasets that have intrinsically low label consistency. In the qualitative analysis, we demonstrate how our approach makes the NER model generate consistent predictions. © 2022, CC BY-SA.

关键词： Forecasting

来源：评论

学校读者我要写书评

暂无评论

Towards High Generalization Performance on Electrocardiogram Classification

Towards High Generalization Performance on Electrocardiogram...

引用

2021 Computing in Cardiology, CinC 2021

作者： Han, Hyeongrok Park, Seongjae Min, Seonwoo Choi, Hyun-Soo Kim, Eunji Kim, Hyunki Park, Sangha Kim, Jinkook Park, Junsang An, Junho Lee, Kwanglo Jeong, Wonsun Chon, Sangil Ha, Kwonwoo Han, Myungkyu Yoon, Sungroh Department of Electrical and Computer Engineering Seoul National University Seoul Korea Republic of HUINNO Co. Ltd Seoul Korea Republic of LG AI Research Seoul Korea Republic of Department of Computer Science and Engineering Kangwon National University Chuncheon Korea Republic of Department of Biological Sciences Interdisciplinary Program in Bioinformatics Interdisciplinary Program in Artificial Intelligence ASRI INMC Institute of Engineering Research Seoul National University Seoul Korea Republic of

ISBN: (纸本)9781665479165

Recently, many electrocardiogram (ECG) classification algorithms using deep learning have been proposed. The characteristics of ECG vary from dataset to dataset for various reasons (i.e., hospital, race, etc.). Therefore, it is important for a model to have high generalization performance consistently over all datasets. In this paper, as part of the PhysioNet / Computing in Cardiology Challenge 2021, we present a model developed to classify cardiac abnormalities from 12 lead and reduced-lead ECGs. In particular, to upgrade our previous model for improving generalization performance, we newly adopt constant-weighted cross-entropy loss, additional features, Mixup augmentation, and squeeze/excitation block, OneCycle learning rate scheduler, which are selected via evaluation of generalization performance using leave-one-dataset-out cross-validation setting. With the present model, our DSAILSNU team has received challenge scores of 0.55, 0.58, 0.58, 0.57 and 0.57 (ranked 2nd, 1st, 1st, 2nd, 2nd out of 39 teams) for the 12-lead, 6-lead, 4-lead, 3-lead, and 2-lead versions of the hidden test set, respectively. The present model achieves higher generalization performance over all versions of the hidden test set than the model submitted last year. © 2021 Creative Commons.

关键词： Deep learning

来源：评论

学校读者我要写书评

暂无评论

Statistical testing for uncertainty of P-NET by DeepLIFT

引用

Discover Applied Sciences 2025年第6期7卷

作者： Goo, Taewan Lee, Chanhee Shin, Sangyeon Kim, Haeyoung Park, Taesung Interdisciplinary Program in Bioinformatics Seoul National University Seoul Korea Republic of Department of Statistics Seoul National University Seoul Korea Republic of

In precision medicine, deep learning models have become essential for identifying biomarkers and predicting diagnosis and prognosis of diseases. Although these models have demonstrated considerable success in producing accurate prognostic and diagnostic predictions, their opaque decision-making processes pose challenges for meaningful biological interpretation. In response, biologically informed neural networks (BINNs), such as P-NET, have been introduced to integrate biological domain knowledge. These models commonly employ measures like SHAP and DeepLIFT to determine the importance of their nodes. However, existing models are limited because they rely on importance estimates that does not consider statistical significance of these estimates. This study proposes a novel statistical testing approach designed to address these limitations. Specifically, it introduces two permutation tests–label and gene permutation test–aimed at identifying significant genes and pathways. Our findings show that this framework can measure the statistical significance of genes and pathways. Additionally, significant pathways are biologically associated with the metastasis mechanism of cancer, thereby enhancing both the interpretability and reliability of BINN-derived insights. This approach confidence in model outputs, thereby advancing the clinical applicability of BINNs in precision medicine. © The Author(s) 2025.

关键词： Diseases

来源：评论

学校读者我要写书评

暂无评论

Integrated analysis of circRNA regulation with ADARB2 enrichment in inhibitory neurons

引用

Computers in Biology and Medicine 2024年 182卷 109212-109212页

作者： Yu, Suwan Ha, Hongseok Kim, Kwangsoo Interdisciplinary Program in Bioinformatics College of Natural Sciences Seoul National University Seoul Korea Republic of Institute of Endemic Disease Seoul National University Medical Research Center Seoul National University Seoul Korea Republic of Department of Medicine College of Medicine Seoul National University Seoul Korea Republic of Department of Transdisciplinary Medicine Institute of Convergence Medicine with Innovative Technology Seoul National University Hospital Seoul Korea Republic of

This study investigates the regulation of circular RNAs (circRNAs) with Adenosine Deaminase RNA Specific B2 (ADARB2) enrichment specifically in inhibitory neurons. Using an integrated analysis combining high-throughput sequencing and bioinformatics approaches, we identified a group of circRNAs that are potentially enhanced by ADARB2. Our findings highlight the pivotal role of ADARB2 in circRNA synthesis within inhibitory neurons, likely through its specific binding to precursor RNAs, which facilitates circRNA biogenesis. © 2024

关键词： Neurons

来源：评论

学校读者我要写书评

暂无评论

In vitro and in vivo toxicity assessment of the senotherapeutic Peptide 14

引用

Toxicology Reports 2022年 9卷 1632-1638页

作者： Zonari, Alessandra Brace, Lear E. Alencar-Silva, Thuany Porto, William F. Foyt, Daniel Guiang, Mylieneth Cruz, Edgar Andres Ochoa Franco, Octavio L. Oliveira, Carolina R. Boroni, Mariana Carvalho, Juliana L. OneSkin Inc San Francisco 94107 CA United States Genomic Sciences and Biotechnology Program Catholic University of Brasilia DF Brasília 70790-160 Brazil DF Brasília 72236–011 Brazil Center of Proteomic Analyses and Biochemistry Genomic Sciences and Biotechnology Program Catholic University of Brasilia DF Brasilia 70790-160 Brazil S-Inova Biotech Biotechnology Program Catholic University Dom Bosco MS Campo Grande 79117-010 Brazil Molecular Pathology Program University of Brasilia DF Brasilia 70.910-900 Brazil Bioinformatics and Computational Biology Lab Brazilian National Cancer Institute (INCA) RJ Rio de Janeiro 20231-050 Brazil Interdisciplinary Biosciences Laboratory Faculty of Medicine University of Brasília DF Brasília 70.910–900 Brazil

Senotherapeutic molecules decrease cellular senescence burden, constituting promising approaches to combat the accumulation of senescent cells observed in chronological aging and age-related diseases. Numerous molecules have displayed senotherapeutic potential, but toxicity has been frequently observed. Recently, a new senotherapeutic compound, Peptide 14, was developed to modulate cellular senescence in the skin. In order to assess the potential toxic and genotoxic effects of the peptide, we observed the viability of human primary dermal fibroblasts and epidermal keratinocytes with Peptide 14 treatment, and show that it is mostly non-toxic in concentrations up to 100 μM. Cancer lines were also used to investigate its potential of modulating proliferation. Different concentrations of the peptide promoted a discrete reduction in the proliferation of cancerous cells of the MeWo and HeLa lineages. In full-thickness human skin equivalents, topically formulated Peptide 14 also failed to exert any significant irritation, nor cellular toxicity when added to the culture media. Genotoxic assays including the Ames, micronucleus, and karyotyping tests also indicate the safety of the peptide. Finally, the irritative potential of the peptide was assessed in human subjects in a repeated insult patch test executed using 1 mM peptide. No visible skin reactions were observed in any of the 54 participants. Taken together, the present data support that Peptide 14 is a senotherapeutic molecule with a positive safety profile as tested with cruelty-free models, justifying further studies involving the peptide. © 2022 The Authors

关键词： 3D skin equivalents Aging Cellular senescence In-vitro toxicology Peptide 14 RIPT

来源：评论

学校读者我要写书评

暂无评论

Ciwars: A Web Server for Antibiotic Resistance Surveillance Using Longitudinal Metagenomic Data

SSRN

引用

SSRN 2024年

作者： Emon, Muhit Islam Cheung, Yat Fei Stoll, James Rumi, Monjura Afrin Brown, Connor Choi, Joung Min Moumi, Nazifa Ahmed Ahmed, Shafayat Song, Haoqiu Sein, Justin Yao, Shunyu Khan, Ahmad Gupta, Suraj Kulkarni, Rutwik Butt, Ali Vikesland, Peter Pruden, Amy Zhang, Liqing Department of Computer Science Virginia Tech BlacksburgVA24060 United States Fralin Life Science Institute Virginia Tech BlacksburgVA24060 United States Department of Civil and Environmental Engineering Virginia Tech BlacksburgVA24060 United States The Interdisciplinary PhD Program in Genetics Bioinformatics and Computational Biology Virginia Tech BlacksburgVA24060 United States

The rise of antibiotic resistance (AR) poses substantial threats to human and animal health, food security, and economic stability. Wastewater-based surveillance (WBS) has emerged as a powerful strategy for population-level AR monitoring, providing valuable data to guide public health and policy decisions. Metagenomic sequencing is especially promising, as it can yield comprehensive profiles of antibiotic resistance genes (ARGs) and other genes relevant to AR in a single run. However, online analytical platforms to facilitate continuous AR monitoring through longitudinal metagenomic data are lacking. To address this, we introduce Cyberinfrastructure for Waterborne Antibiotic Resistance Surveillance (CIWARS), a web server configured for characterizing key AR trends from longitudinal metagenomic WBS data. CIWARS offers comprehensive ARG and taxonomic profiling, along with detection of anomalous AR indicators over time, aiding in identifying potential events of concern, such as the emergence of resistant strains or outbreaks. Through interactive temporal data visualization, CIWARS enables AR monitoring and demonstrates its potential for informing effective and timely interventions to mitigate the spread and transmission of AR. CIWARS is broadly applicable to longitudinal metagenomic data from any environment and thus could be a valuable tool to support global efforts to combat the evolution and spread of AR, while also guiding agricultural and public health efforts aimed at optimizing antibiotic use when it is needed. The web server is freely available at https://***/. © 2024, The Authors. All rights reserved.

关键词： Gene encoding

来源：评论

学校读者我要写书评

暂无评论

Elongation factor-G1A identified as a novel effector protein translocated into cells and a key modulator of Pseudomonas aeruginosa physiology and host cellular responses

引用

Microbial Pathogenesis 2025年 205卷 107720页

作者： Lee, Yeji Jin, Yongxin Wu, Weihui Ha, Un-Hwan Department of Biotechnology and Bioinformatics Korea University Sejong 30019 South Korea Interdisciplinary Graduate Program for Artificial Intelligence Smart Convergence Technology Korea University Sejong 30019 South Korea State Key Laboratory of Medicinal Chemical Biology Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education Department of Microbiology Nankai University Tianjin 300071 China

Pseudomonas aeruginosa has two closely related elongation factors, EF-G1A and EF-G1B, which share 90 % sequence similarity. Despite their high sequence homology, the role of EF-G in P. aeruginosa pathogenesis remains not fully understood. In our study, we found that compared to EF-G1B, EF-G1A expression reduced bacterial growth and twitching motility, while increasing swimming motility. Notably, EF-G1A was translocated into host cells in a T6SS-dependent manner. This translocation was significantly reduced, though not completely abolished, in strains with mutations in both the T6SS spike protein VgrG1a and the tube protein Hcp1, suggesting that while EF-G1A translocation is influenced by T6SS, additional components are also involved. Moreover, EF-G1A expression reduced T3SS-mediated morphological alterations, as evidenced by the downregulation of T3SS effectors such as ExoS and ExoT. EF-G1A was also found to suppress activation of the NF-κB signaling pathway, leading to decreased production of inflammatory cytokines including IL-6, IL-8, and TNFα. These findings highlight EF-G1A as a key modulator, affecting both P. aeruginosa physiology and host cellular responses, thereby providing new insights into the complex role of EF-G1A in bacterial pathogenesis. © 2025 Elsevier Ltd

关键词： Elongation factor-G1A Pseudomonas aeruginosa T3SS T6SS Translocation

来源：评论

学校读者我要写书评

暂无评论

Characterization of Antioxidative Flavonoids in Wild and Cultivated Soybean by Ion-Filtering Strategy-Combined Lc-Hrmsn Analysis

SSRN

引用

SSRN 2024年

作者： No, Kyoung Tai Kim, Kwan Joong Cho, Min Hyung Lee, Sangwon Ha, Jang-Ho Chu, Sung-June Chung, Gyuhwa Kim, Dae-Ok Bioinformatics & Molecular Design Research Center Incheon21983 Korea Republic of Department of Biotechnology Chonnam National University Yeosu59626 Korea Republic of Graduate School of Biotechnology Kyung Hee University Yongin17104 Korea Republic of Interdisciplinary Graduate Program Department of Integrative Biotechnology & Translational Medicine Yonsei University Incheon21983 Korea Republic of Yonsei University Korea Republic of

To profiling flavonoids in wild soybean (WB;Glycine soja Sieb & Zucc.) and cultivated soybean (CB;Glycine max (L.) Merr.), liquid chromatography-high resolution mass spectrometry (LC-HRMS), antioxidant assays, and chemometrics method were used. Total 70 flavonoids were tentatively identified with ion filter strategies containing precursor ion list, mass defect filter, nitrogen rule filter, and diagnostic ion filter from 20,999 features in WB and CB. Semi-quantification result revealed that WB has 1.4-, 93.1-, 6.3-, and 1.9-fold higher contents in isoflavone, flavan, procyanidin, and flavone than that of CB. In antioxidant assays, WB showed 1.89- to 5.83-fold higher antioxidant capacities than CB in four antioxidant capacity assays. In orthogonal partial least squares discriminant analysis, WB and CB were clearly classified, and 31 characteristic flavonoids were identified by variable importance in projection. Furthermore, epicatechin and procyanidins of WB showed significantly positive correlation with antioxidant capacities by Pearson's correlation. © 2024, The Authors. All rights reserved.

关键词： Flavonoids

来源：评论

学校读者我要写书评

暂无评论

Pseudomonas aeruginosa-derived DnaJ induces TLR2 expression through TLR10-mediated activation of the PI3K-SGK1 pathway in macrophages

引用

Microbes and Infection 2025年第4期27卷 105481页

作者： Lee, Jaehoo Jin, Yongxin Wu, Weihui Lee, Yeji Ha, Un-Hwan Department of Biotechnology and Bioinformatics Korea University Sejong 30019 South Korea Interdisciplinary Graduate Program for Artificial Intelligence Smart Convergence Technology Korea University Sejong 30019 South Korea State Key Laboratory of Medicinal Chemical Biology Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education Department of Microbiology Nankai University Tianjin 300071 China

TLR2 is a key component of the innate immune system, responsible for recognizing Gram-positive bacterial components and initiating inflammatory signaling cascades that activate defense responses. However, little is known about the regulatory effects of Pseudomonas aeruginosa (P. aeruginosa) on TLR2 expression. In this study, we investigated the potential link between P. aeruginosa-derived DnaJ and TLR2 expression in macrophages, as well as the activation of downstream signaling pathways. Our findings revealed that DnaJ significantly induced TLR2 expression in a dose- and time-dependent manner, predominantly affecting TLR2 with minimal impact on other TLRs, such as TLR4 and TLR5, which detect bacterial PAMPs. The DnaJ-mediated TLR2 induction was driven by activation of the PI3K-SGK1 signaling pathway, with TLR10 playing a crucial role in facilitating these effects. This increase in TLR2 expression led to enhanced production of inflammatory cytokines in response to secondary Staphylococcus aureus infections, indicating a role in boosting host defense mechanisms. In conclusion, these findings suggest that P. aeruginosa-derived DnaJ promotes TLR2 expression via TLR10-mediated activation of the PI3K-SGK1 pathway, thereby enhancing host immune responses against Gram-positive bacterial infections. © 2025 Institut Pasteur

关键词： DnaJ Pseudomonas aeruginosa SGK1 TLR10 TLR2

来源：评论

学校读者我要写书评

暂无评论

Impact of statins on the survival of patients with cancer: a nationwide population-based cohort study in South Korea

引用

Cancer Communications 2022年第2期42卷 184-187页

作者： Juhee Ahn Sungho Won Sanghun Lee Department of Public Health Science Seoul National UniversityGwanak-guSeoul 08826Republic of Korea Interdisciplinary Program of Bioinformatics Seoul National UniversityGwanak-guSeoul 08826Republic of Korea Institute of Health and Environment Seoul National UniversityGwanak-guSeoul 08826Republic of Korea Department of Bioconvergence&Engineering Dankook UniversityYongin-siGyeonggi-do 16890Republic of Korea Channing Division of Network Medicine Brigham and Women’s HospitalBostonMassachusetts 02115the United States of America

Dear Editor For over 30 years,3-hydroxy-3-methylglutaryl-coenzyme A(HMG-CoA)reductase inhibitors,statins,have been recommended worldwide as cost-effective lipid-lowering drugs for cardiovascular disease[1].Cheng et *** that lipid synthesis inhibitors are a promising anti-cancer treatment in preclinical studies and early phases of clinical trials[2].However,the association between statin use and cancer incidence or survival remains controversial[3,4].

关键词： cancer clinical drugs

来源：评论

学校读者我要写书评

暂无评论

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案：

请选择收藏分类：

通借通还

建议与咨询 留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案： 新增检索档案 确定 取消

请选择收藏分类： 新增自定义分类 确定 取消

通借通还

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

请选择保存的检索档案：

请选择收藏分类：