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CellBiAge: Improved single-cell age classification using data binarization

Cell Reports 2023年第12期42卷 113500页

作者： Yu, Doudou Li, Manlin Linghu, Guanjie Hu, Yihuan Hajdarovic, Kaitlyn H. Wang, An Singh, Ritambhara Webb, Ashley E. Molecular Biology Cell Biology and Biochemistry Graduate Program Brown University Providence 02912 RI United States Data Science Institute Brown University Providence 02912 RI United States Neuroscience Graduate Program Brown University Providence 02912 RI United States Department of Applied Mathematics & Statistics Johns Hopkins University Baltimore 21218 MD United States Department of Computer Science Brown University Providence 02912 RI United States Center for Computational Molecular Biology Brown University Providence 02912 RI United States Department of Molecular Biology Cell Biology and Biochemistry Brown University Providence 02912 RI United States Center on the Biology of Aging Brown University Providence 02912 RI United States Carney Institute for Brain Science Brown University Providence 02912 RI United States Center for Translational Neuroscience Brown University Providence 02912 RI United States

Aging is a major risk factor for many diseases. Accurate methods for predicting age in specific cell types are essential to understand the heterogeneity of aging and to assess rejuvenation strategies. However, classifying organismal age at single-cell resolution using transcriptomics is challenging due to sparsity and noise. Here, we developed CellBiAge, a robust and easy-to-implement machine learning pipeline, to classify the age of single cells in the mouse brain using single-cell transcriptomics. We show that binarization of gene expression values for the top highly variable genes significantly improved test performance across different models, techniques, sexes, and brain regions, with potential age-related genes identified for model prediction. Additionally, we demonstrate CellBiAge's ability to capture exercise-induced rejuvenation in neural stem cells. This study provides a broadly applicable approach for robust classification of organismal age of single cells in the mouse brain, which may aid in understanding the aging process and evaluating rejuvenation methods. © 2023 The Authors

关键词： aging brain CP: Cell biology hypothalamus machine learning single-cell RNA-seq

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Effects of sodium alginate-poly(acrylic acid) cross-linked hydrogel beads on soil conditioner in the absence and presence of phosphate and carbonate ions

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Case Studies in Chemical and Environmental Engineering 2024年 9卷

作者： Hidayat, Endar Sarbani, Nur Maisarah Mohamad Lahiri, Sudip Kumar Samitsu, Sadaki Yonemura, Seiichiro Mitoma, Yoshiharu Harada, Hiroyuki Graduate School of Comprehensive Scientific Research Program in Biological System Sciences Prefectural University of Hiroshima Shobara 727-0023 Japan Department of Life System Science Faculty of Bioresources Science Prefectural University of Hiroshima Shobara 727-0023 Japan Data-driven Polymer Design Group Research Center for Macromolecules and Biomaterials National Institute for Materials Science 1−2−1 Sengen Tsukuba 305-0047 Japan Department of Mechanical & Industrial Engineering University of Toronto Toronto M5S 3G8 ON Canada Faculty of Allied Health Sciences Chettinad Hospital and Research Institute Chettinad Academy of Research and Education Tamil Nadu Kelambakkam 603103 India

Hydrogel beads, composed of polymers, possess the ability to absorb substantial quantities of water simultaneously and gradually release it in dry conditions. In this work, hydrogel beads were synthesized using sodium alginate (S-Alg) and poly (acrylic acid) (P-Acc), either in the absence or presence of phosphate (PO₄ ³⁻) (S-Alg/P-Acc@PO₄ ³⁻) and carbonate (CO₃ ²⁻) anionic ions (S-Alg/P-Acc@CO₃ ²⁻). Subsequently, these beads were crosslinked with Ca²⁺ ions. The scanning electron microscopy (SEM) images demonstrated that the presence of anionic ions has an impact on the structure of the hydrogel beads and enhances porosity expansion while concurrently reducing the concentration of carboxyl (COOH) groups. The hydrogel beads exhibited a great swelling behavior, with S-Alg/P-Acc@CO₃ ²⁻ capable of absorbing up to 73.5 % of water in acidic conditions, but decreased under neutral and basic conditions. Soil water loss (SWL) experiments confirmed the ability of hydrogel beads to retain water in the soil. Additionally, observations of soil characteristics after a 14-day treatment revealed no significant difference in pH and C/N ratio (P-value <0.05). However, soil's available Fe and N–NO₃ ^- significantly reduced (P-value <0.05) while substantially promoting soil N–NH₄ ⁺, available phosphorus (P), cation exchange capacity (CEC), soil organic carbon (SOC), and exchangeable cation (Ca²⁺, K⁺ and Mg²⁺). The presence of hydroxyl (-OH) and –COOH groups was found to be crucial for enhancing soil properties. © 2024 The Authors

关键词： Anionic ions Hydrogel beads Poly (acrylic acid) Sodium alginate Soil characteristics Soil water retention Swelling

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Biomedical data and AI

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science China Life sciences 2025年第5期68卷 1536-1540页

作者： Hao Xu Shibo Zhou Zefeng Zhu Vincenzo Vitelli Liangyi Chen Ziwei Dai Ning Yang Luhua Lai Shengyong Yang Sergey Ovchinnikov Zhuoran Qiao Sirui Liu Chen Song Jianfeng Pei Han Wen Jianfeng Feng Yaoyao Zhang Zhengwei Xie Yang-Yu Liu Zhiyuan Li Fulai Jin Hao Li Mohammad Lotfollahi Xuegong Zhang Ge Yang Shihua Zhang Ge Gao Pulin Li Qi Liu Jing-Dong Jackie Han Peking-Tsinghua Center for Life Sciences (CLS) Academy for Advanced Interdisciplinary StudiesPeking University Center for Quantitative Biology (CQB) Academy for Advanced Interdisciplinary StudiesPeking University Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program Academy for Advanced Interdisciplinary StudiesPeking University Department of Physics University of Chicago School of Life Sciences Southern University of Science and Technology Peking University Chengdu Academy for Advanced Interdisciplinary Biotechnologies College of Chemistry and Molecular Engineering Peking University Department of Biotherapy Cancer Center and State Key Laboratory of BiotherapyWest China HospitalSichuan University Department of Biology Massachusetts Institute of Technology Lambic Therapeutics Inc. Changping Laboratory Al for Science Institute Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence Fudan University Department of Obstetrics and Gynecology West China Second University HospitalSichuan University Peking University International Cancer Institute and Peking University-Yunnan Baiyao International Medical Institute and State Key Laboratory of Natural and Biomimetic Drugs Department of Molecular and Cellular PharmacologySchool of Pharmaceutical SciencesPeking University Health Science CenterPeking University Channing Division of Network Medicine Department of MedicineBrigham and Women's Hospital and Harvard Medical School Center for Artificial Intelligence and Modeling the Carl R.Woese Institute for Genomic BiologyUniversity of Illinois Urbana-Champaign Department of Genetics and Genome Sciences School of Medicine and Department of Computer and Data Sciences and Department of Population and Quantitative Health SciencesCase Western Reserve University Department of Biochemistry and Biophysics University of California Sanger Institute Department of Automation Tsinghua University State Key Laboratory of Multimodal Artificial Intelligence Systems I

The development of artificial intelligence(AI) and the mining of biomedical data complement each other. From the direct use of computer vision results to analyze medical images for disease screening, to now integrating biological knowledge into models and even accelerating the development of new AI based on biological discoveries, the boundaries of both are constantly expanding, and their connections are becoming closer.

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Accurately predicting anticancer peptide using an ensemble of heterogeneously trained classifiers

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Informatics in Medicine Unlocked 2023年 42卷

作者： Azim, Sayed Mehedi Sabab, Noor Hossain Nuri Noshadi, Iman Alinejad-Rokny, Hamid Sharma, Alok Shatabda, Swakkhar Dehzangi, Iman Center for Computational and Integrative Biology Rutgers University Camden 08102 NJ United States Department of Computer Science and Engineering United International University Plot 2 United City Madani Avenue BaddaDhaka 1212 Bangladesh Department of Bioengineering University of California Riverside 92507 CA United States BioMedical Machine Learning Lab The Graduate School of Biomedical Engineering The University of New South Wales (UNSW Sydney) Sydney NSW 2052 Australia UNSW Data Science Hub UNSW Sydney Sydney NSW 2052 Australia Health Data Analytics Program AI-enabled Processes Research Centre Macquarie University Sydney 2109 Australia Institute for Integrated and Intelligent Systems Griffith University Brisbane Australia Laboratory for Medical Science Mathematics RIKEN Center for Integrative Medical Sciences Yokohama 230-0045 Japan Department of Computer Science Rutgers University Camden 08102 NJ United States

The use of therapeutic peptides for the treatment of cancer has received tremendous attention in recent years. Anticancer peptides (ACPs) are considered new anticancer drugs which have several advantages over chemistry-based drugs including high specificity, strong tumor penetration capacity, and low toxicity level for normal cells. Due to the rise of experimentally verified bioactive peptides, several in silico approaches became imperative for the investigation of the characteristics of ACPs. In this paper, we proposed a new machine learning tool named iACP-RF that uses a combination of several sequence-based features and an ensemble of three heterogeneously trained Random Forest classifiers to accurately predict anticancer peptides. Experimental results show that our proposed model achieves an accuracy of 75.9% which outperforms other state-of-the-art methods by a significant margin. We also achieve 0.52, 75.6%, and 76.2% in terms of Matthews Correlation Coefficient (MCC), Sensitivity, and Specificity, respectively. iACP-RF as a standalone tool and its source code are publicly available at: https://***/MLBC-lab/iACP-RF. © 2023 The Authors

关键词： Anticancer peptides Ensemble learning Feature extraction Heterogeneous classifiers Machine learning Random Forest

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Factors that affect the technological transition of firms toward the industry 4.0 technologies

arXiv

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arXiv 2022年

作者： Kim, Seung Hwan Jeon, Jeong hwan Aridi, Anwar Jun, Bogang Technology Management Economics and Policy Program Seoul National University Seoul Korea Republic of Department of Electrical Engineering Ulsan National Institute of Science and Technology Ulsan Korea Republic of Graduate School of Artificial Intelligence Ulsan National Institute of Science and Technology Ulsan Korea Republic of Finance Competitiveness and Innovation Global Practice Europe and Central Asia Unit The World Bank Group Department of Economics Inha University Korea Republic of Department of Data Science Inha University Korea Republic of Research Center for Small Businesses Ecosystem Inha University Korea Republic of

This research aims to identify factors that affect the technological transition of firms toward industry 4.0 technologies (I4Ts) focusing on firm capabilities and policy impact using relatedness and complexity measures. For the analysis, a unique dataset of Korean manufacturing firms’ patent and their financial and market information was used. Following the Principle of Relatedness, which is a recently shaped empirical principle in the field of economic complexity, economic geography, and regional studies, we build a technology space and then trace each firm’s footprint on the space. Using the technology space of firms, we can identify firms that successfully develop a new industry 4.0 technology and examine whether their accumulated capabilities in their previous technology domains positively affect their technological diversification and which factors play a critical role in their transition towards industry 4.0. In addition, by combining data on whether the firms received government support on R&D activities, we further analyzed the role of government policy in supporting firms’ knowledge activity in new industry 4.0 technologies. We found that firms with higher related technologies and more government support are more likely to enter new I4Ts. We expect our research to inform policymakers who aim to diversify firms’ technological capabilities into I4Ts. © 2022, CC BY.

关键词： Industry 4.0

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Financial transaction database design for jamu small-medium enterprises

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AIP Conference Proceedings 2023年第1期2594卷

作者： R. Rahutomo A. Permatasari Y. Lie B. Pardamean Information Systems Department School of Information Systems Bina Nusantara University Jakarta Indonesia 11480 Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department BINUS Graduate Program Master of Computer Science Bina Nusantara University Jakarta Indonesia 11480

As jamu small-medium enterprises (SMEs) concentrate on establishing online sales and computerized systems, Point of Sales (PoS) becomes a strategic solution to maintain financial ...

As jamu small-medium enterprises (SMEs) concentrate on establishing online sales and computerized systems, Point of Sales (PoS) becomes a strategic solution to maintain financial stability with its capabilities in recording electronic transactions accurately. As the initial step in technology empowerment for jamu SMEs, the research proposes a concept in facilitating jamu SMEs to adapt in online business. A combination of Connolly and Begg's database design principles and McCarthy's Marketing Mix 4P generates a conceptual design of PoS database targeted specifically for jamu SMEs. The database design manages online purchasing transactions for jamu products by involving not only jamu SMEs and consumers but also a system administrator who manages data verification and extraction.

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Questionnaire design for analyzing important risk factors of cervical cancer

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AIP Conference Proceedings 2023年第1期2594卷

作者： K. Purwandari D. Sudigyo A. S. Perbangsa A. Irwan B. Pardamean Bioinformatics & Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 Information Systems Department School of Information Systems Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department BINUS Graduate Program - Master of Computer Science Bina Nusantara University Jakarta Indonesia 11480

Cervical cancer is Indonesia's second leading cause of death, following only breast cancer. According to the World Health Organization (WHO), non-communicable disorders will be blamed for 70% of all deaths and illnesses in 2020, while other disease types will account for 60%. Cervical cancer can be detected earlier, lowering the chance of death. This study aims to validate and check the pap smear test results obtained from the previously conducted pap smear screening program. The pap smear questionnaire developed would help in the compilation of a patient's habit history that has undergone a pap smear test during his life based on the factors associated with the occurrence of cervical cancer. Specific details, social-demographic features, diet, genital hygiene activities, reproductive background and behaviors, and health care and cancer prevention behavior are also included in the questionnaire template. The consequence of this design is the completeness of evidence on the theory of anomalies dependent on the findings of pap smear sampling.

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Effects of Mobile Health Care App "Asmile" on Physical Activity of 80,689 Users in Osaka Prefecture, Japan: Longitudinal Observational Study

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Journal of Medical Internet Research 2025年 27卷 e65943页

作者： Oyama, Asuka Taguchi, Kenshiro Seto, Hiroe Kanaya, Reiko Kotoku, Jun'ichi Yamakawa, Miyae Toki, Hiroshi Yamamoto, Ryohei Health and Counseling Center The University of Osaka Toyonaka Japan Graduate Degree Program of Health Data Science Teikyo University Tokyo Japan Graduate School of Human Sciences The University of Osaka Suita Japan Division of Health Sciences Graduate School of Medicine The University of Osaka Suita Japan Graduate School of Medical Care and Technology Teikyo University Tokyo Japan Department of Nephrology Graduate School of Medicine The University of Osaka Suita Japan Laboratory of Behavioral Health Promotion Department of Health Promotion Graduate School of Medicine The University of Osaka Suita Japan Institute for Sports and Global Health The University of Osaka Suita Japan

Background: Lifestyle-related diseases can be controlled by improving individuals’ lifestyles;however, improving and maintaining a healthy lifestyle is difficult. Mobile health (mHealth) applications have recently attracted attention as tools for maintaining and improving health, and their use may also increase physical activity. Objective: This study aimed to verify the effect of registration in Asmile, an mHealth application provided by the Osaka Prefectural Government, on step counts using a Causal Impact approach based on the step count data recorded in the Asmile application. Methods: This observational study included Osaka residents aged 20-79 years, newly registered to Asmile, between the fiscal years 2020 and 2023. Of these, 80,689 participants with step count records for 4 weeks before and after the day they registered to Asmile were included in the analysis. We used daily step counts that were automatically transferred from a standard smartphone health care app into Asmile. We used a Causal Impact model to estimate the increase in step count after registration to Asmile. Results: Of the 80,689 participants analyzed, 38.5% (31,082/80,689) were men, and the mean age was 51.6 (SD 13.2) years. The mean step count before registration was 5923 (SD 4860) steps per day, with the highest proportion of new users registered in spring (38,389/80,689, 47.6%) and in fiscal year 2020 (34,491/80,689, 42.7%). The analysis revealed that the effect of Asmile registration on step counts was 360 steps (95% CI 331-389) per day and 10,041 steps (95% CI 9632-10,450) over 4 weeks. Stratified analysis showed that the impact of increased step count was more pronounced in younger groups and groups with fewer step counts before registration. Conversely, the effect of registration on step count was relatively minor in the groups registered in summer or winter. Conclusions: This study demonstrates increased physical activity among users registered with the Asmile app. These findings sug

关键词： app apps Causal Impact Causal Inference exercise healthy lifestyle Japan lifestyle-related disease mHealth mobile health mobile phone observational study Osaka physical activity smartphone step counts

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Provoking Tweets by Indonesia Media Twitter in the Initial Month of Coronavirus Disease Hit

Provoking Tweets by Indonesia Media Twitter in the Initial M...

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International Conference on Information Management and Technology (ICIMTech)

作者： Ika Nurlaila Reza Rahutomo Kartika Purwandari Bens Pardamean BINUS Online Learning Bina Nusantara University Jakarta Indonesia Bioinformatics & Data Science Research Center Bina Nusantara University Jakarta Indonesia BINUS Graduate Program - Master of Computer Science Program Bina Nusantara University Jakarta Indonesia

ISBN: (数字)9781728170718

ISBN: (纸本)9781728170725

After months in denial, on 2 nd March 2020 the first case of COVID-19 in Indonesia was announced and soon was declared as a national pandemic. COVID-19 was since being the headlines of the news offline and online. This trigger either positive or negative responses from the readers, which in turn affect at least the depth of understanding and furthermore the effectiveness of any enforced intervention taken with the purpose to control the transmission of the COVID-19. In order to assess how likely the COVID-19-containing news being forwarded to reach more readers and how the pertinent news bridge further virtual interaction, we crawled data from Twitter as the major online microblogging platform to analyze how likely COVID-19-containing tweets were echoed and what typical tweet about COVID-19 that gained attentions. This is critical to evaluate how people virtually responded against the tweets. Our analyzed data is visualized using Matplotlib by Python and Graph Prism8 accordingly. We figured out that timing and number of followers are not determinative for the tweets being retweeted. Instead, provoking headline add likelihood for the tweets to be moving forward. Also appeared in our analysis that the top two media (Detik and Kompas) shared the same proportion on their tweet type fractions on where information dominated the fraction of their tweets.

关键词： Twitter Media Corona Tagging Diseases data visualization

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Hybrid Intelligent-Annotation Organ Segmentation on Medical datasets

Hybrid Intelligent-Annotation Organ Segmentation on Medical ...

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IEEE International Conference on Systems, Man and Cybernetics

作者： Tao Peng Jing Zhao Yidong Gu Gongye Di Lei Zhang Jing Cai School of Future Science and Engineering Soochow University Suzhou China Department of Radiation Oncology UT Southwestern Medical Center Dallas TX USA Department of Ultrasound Tsinghua University Affiliated Beijing Tsinghua Changgung Hospital Beijing China Department of Medical Ultrasound Suzhou Municipal Hospital The Affiliated Suzhou Hospital of Nanjing Medical University Suzhou Jiangsu China Department of Ultrasonic The Affiliated Taizhou People's Hospital of Nanjing Medical University Taizhou China Graduate Program of Medical Physics and Data Science Research Center Duke Kunshan University Kunshan Jiangsu China Department of Health Technology and Informatics The Hong Kong Polytechnic University Hong Kong China

Ultrasound image segmentation is crucial for early disease detection and treatment planning but remains a challenging task due to the low contrast of organ boundaries and varying image quality. Current methods often require manual intervention or have limited accuracy. In this paper, we propose a novel hybrid framework that combines an automatic option polygon segment (AOPS) algorithm and a distributed- and memory-based evolution (DME) algorithm for precise ultrasound organ segmentation. Our pipeline consists of two cascaded stages: (1) a coarse segmentation step using the AOPS algorithm, which determines the number of vertices/clusters without human intervention, and (2) a refinement step using the DME algorithm to hunt for the optimal neural network, which is then used to represent a smooth, explainable mathematical expression of the organ boundary. We employ the fractional backpropagation learning network with L2 regularization (FBLN) for training and use the scaled exponential linear unit (SELU) activation function to address the vanishing gradient problem. This is a new attempt such a hybrid framework is applied to ultrasound organ segmentation tasks, and it demonstrates significant contributions in terms of accuracy, smoothness, and computational efficiency.

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