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Multiomics Reveals Induction of Neuroblastoma SK-N-BE(2)C Cell Death by Mitochondrial Division Inhibitor 1 through Multiple Effects

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Journal of Proteome Research 2024年第1期23卷 301-315页

作者： Wang, Wei-Hsuan Kao, Yi-Chun Hsieh, Chiao-Hui Tsai, Shin-Yu Cheung, Chantal Hoi Yin Huang, Hsuan-Cheng Juan, Hsueh-Fen Genome and Systems Biology Degree Program Academia Sinica and National Taiwan University Taipei 106 Taiwan Department of Life Science National Taiwan University Taipei 106 Taiwan Center for Computational and Systems Biology National Taiwan University Taipei 106 Taiwan Institute of Biomedical Informatics National Yang Ming Chiao Tung University Taipei 112 Taiwan Graduate Institute of Biomedical Electronics and Bioinformatics National Taiwan University Taipei 106 Taiwan Center for Advanced Computing and Imaging in Biomedicine National Taiwan University Taipei 106 Taiwan

Mitochondrial division inhibitor 1 (Mdivi-1) is a well-known synthetic compound aimed at inhibiting dynamin-related protein 1 (Drp1) to suppress mitochondrial fission, making it a valuable tool for studying mitochondrial dynamics. However, its specific effects beyond Drp1 inhibition remain to be confirmed. In this study, we employed integrative proteomics and phosphoproteomics to delve into the molecular responses induced by Mdivi-1 in SK-N-BE(2)C cells. A total of 3070 proteins and 1945 phosphorylation sites were identified, with 880 of them represented as phosphoproteins. Among these, 266 proteins and 97 phosphorylation sites were found to be sensitive to the Mdivi-1 treatment. Functional enrichment analysis unveiled their involvement in serine biosynthesis and extrinsic apoptotic signaling pathways. Through targeted metabolomics, we observed that Mdivi-1 enhanced intracellular serine biosynthesis while reducing the production of C24:1-ceramide. Within these regulated phosphoproteins, dynamic dephosphorylation of proteasome subunit alpha type 3 serine 250 (PSMA3-S250) occurred after Mdivi-1 treatment. Further site-directed mutagenesis experiments revealed that the dephosphorylation-deficient mutant PSMA3-S250A exhibited a decreased cell survival. This research confirms that Mdivi-1’s inhibition of mitochondrial division leads to various side effects, ultimately influencing cell survival, rather than solely targeting Drp1 inhibition. © 2023 American Chemical Society.

关键词： Mdivi-1 multiomics neuroblastoma phosphoproteome proteome targeted metabolome

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Private Continuous Survival Analysis with Distributed Multi-Site Data

Private Continuous Survival Analysis with Distributed Multi-...

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IEEE International Conference on Big Data

作者： Luca Bonomi Marilyn Lionts Liyue Fan Dept. Biomedical Informatics Vanderbilt University Medical Center Nashville TN Dept. Computer Science Vanderbilt University Nashville TN College of Computing and Informatics University of North Carolina Charlotte NC

Effective disease surveillance systems require large-scale epidemiological data to improve health outcomes and quality of care for the general population. As data may be limited within a single site, multi-site data (e.g., from a number of local/regional health systems) need to be considered. Leveraging distributed data across multiple sites for epidemiological analysis poses significant challenges. Due to the sensitive nature of epidemiological data, it is imperative to design distributed solutions that provide strong privacy protections. Current privacy solutions often assume a central site, which is responsible for aggregating the distributed data and applying privacy protection before sharing the results (e.g., aggregation via secure primitives and differential privacy for sharing aggregate results). However, identifying such a central site may be difficult in practice and relying on a central site may introduce potential vulnerabilities (e.g., single point of failure). Furthermore, to support clinical interventions and inform policy decisions in a timely manner, epidemiological analysis need to reflect dynamic changes in the data. Yet, existing distributed privacy-protecting approaches were largely designed for static data (e.g., one-time data sharing) and cannot fulfill dynamic data requirements. In this work, we propose a privacy-protecting approach that supports the sharing of dynamic epidemiological analysis and provides strong privacy protection in a decentralized manner. We apply our solution in continuous survival analysis using the Kaplan-Meier estimation model while providing differential privacy protection. Our evaluations on a real dataset containing COVID-19 cases show that our method provides highly usable results.

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Liver Tumor Decision Support System on Human Magnetic Resonance Images:A Comparative Study

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Computer Systems Science & Engineering 2023年第8期46卷 1653-1671页

作者： Hiam Alquran Yazan Al-Issa Mohammed Alslatie Isam Abu-Qasmieh Amin Alqudah Wan Azani Mustafa Yasmin Mohd Yacob Department of Biomedical Systems and Informatics Engineering Yarmouk University 556Irbid21163Jordan Department of Biomedical Engineering Jordan University of Science and TechnologyIrbid22110Jordan Department of Computer Engineering Yarmouk University 556Irbid21163Jordan The of Biomedical Technology King Hussein Medical CenterRoyal Jordanian Medical ServiceAmman11855Jordan Faculty of Electrical Engineering&Technology Campus Pauh PutraUniversiti Malaysia PerlisArau02600PerlisMalaysia Faculty of Electronic Engineering&Technology Campus Pauh PutraUniversiti Malaysia PerlisArau02600PerlisMalaysia Advanced Computing Centre of Excellence(CoE)Universiti Malaysia PerlisArau02600PerlisMalaysia

Liver cancer is the second leading cause of cancer death *** tumor detection may help identify suitable treatment and increase the survival *** imaging is a non-invasive tool that can help uncover abnormalities in human *** Resonance Imaging(MRI),in particular,uses magnetic fields and radio waves to differentiate internal human organs ***,the interpretation of medical images requires the subjective expertise of a radiologist and ***,building an automated diagnosis computer-based system can help specialists reduce incorrect *** paper proposes a hybrid automated system to compare the performance of 3D features and 2D features in classifying magnetic resonance liver tumor *** paper proposed two models;the first one employed the 3D features while the second exploited the 2D *** first system uses 3D texture attributes,3D shape features,and 3D graphical deep descriptors beside an ensemble classifier to differentiate between four 3D tumor *** top of that,the proposed method is applied to 2D slices for comparison *** proposed approach attained 100%accuracy in discriminating between all types of tumors,100%Area Under the Curve(AUC),100%sensitivity,and 100%specificity and precision as well in 3D liver *** the other hand,the performance is lower in 2D *** maximum accuracy reached 96.4%for two classes and 92.1%for four *** top-class performance of the proposed system can be attributed to the exploitation of various types of feature selection methods besides utilizing the ReliefF features selection technique to choose the most relevant features associated with different *** novelty of this work appeared in building a highly accurate system under specific circumstances without any processing for the images and human input,besides comparing the performance between 2D and 3D *** the future,the presented work can be extended to be

关键词： Liver tumors ensemble classifier 3D shape features 3D cooccurrence matrix ResNet101

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Elevating Ocular Diagnosis: Harnessing the Power of EfficientNet for Eye Disease Classification

Elevating Ocular Diagnosis: Harnessing the Power of Efficien...

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Artificial Intelligence For Internet of Things (AIIoT), International Conference on

作者： Vankadari Mohith Kalpana Raja I. R. Oviya Department of Computer Science and Engineering Amrita School of Computing Amrita Vishwa Vidyapeetham Chennai India Section for Biomedical Informatics and Data Science School of Medicine Yale University New Haven USA

ISBN: (数字)9798350372120

ISBN: (纸本)9798350372137

In response to the evolving landscape of healthcare technology this study addresses the need for automated diagnostic tools in the field of ophthalmology. By utilizing deep learning methods specifically leveraging the EfficientNetV2S framework we achieve an overall accuracy rate of 94.6% in classifying images depicting common eye conditions like cataract, diabetic retinopathy, glaucoma, and normal cases. Our model exhibits capabilities across a diverse spectrum of medical conditions due to meticulous preprocessing and fine-tuning procedures. The results highlight the potential for automated technology integration in healthcare settings, which might improve patient care and treatment plans. This paper highlights the use of advanced neural network designs in the diagnosis of ocular illnesses, offering insights at the nexus of learning and medical image processing.

关键词： Glaucoma Deep learning Diabetic retinopathy Accuracy Computational modeling Neural networks Medical treatment

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ETHACA - A Container-Based Cyber Range for Research and Education 29

ETHACA - A Container-Based Cyber Range for Research and Educ...

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29th IEEE International Workshop on Computer Aided Modeling and Design of Communication Links and Networks, CAMAD 2024

作者： Chouliaras, Nestoras Kantzavelou, Ioanna Pantziou, Grammati Maglaras, Leandros Chouliara-Sidera, Panagiota Adamakos, Antonis Chalatsakos, Panagiotis University of West Attica Department of Informatics and Computer Engineering Athens Greece School of Computing Edinburgh Napier University EdinburghEH10 5DT United Kingdom University of Thessaly Department of Computer Science and Biomedical Infromatics Lamia Greece Senior Software Engineer at *** Athens Greece Open University of Cyprus Faculty of Pure and Applied Sciences Nicosia Cyprus

ISBN: (纸本)9798350377644

The advent of Industry 4.0 and the Industrial Internet of Things (IIoT) has revolutionized manufacturing and production systems, enhancing efficiency and communication through the integration of advanced technologies such as IoT devices and AI. However, this increased digitization has also led to heightened cybersecurity risks, with a notable rise in the frequency and complexity of cyber-attacks. Cyber Ranges emerges as a critical solution in addressing these challenges, offering a controlled environment for simulating cyber-attack scenarios, training cybersecurity teams, and developing robust defense strategies. The escalating demand for cybersecurity professionals has highlighted the crucial need for effective training solutions. This article presents an open-source Cyber Range constructed on container-based architecture, meticulously engineered for efficient operation with minimal resource consumption. In response to the scarcity of cybersecurity experts, this platform prioritizes extensive scalability and robust isolation between exercises, ensuring secure learning environments, and also integrates a complex developed exercise series aimed at strengthening cybersecurity learning experiences. These exercises encompass a variety of scenarios and challenges, catering to professionals at different skill levels. Each exercise replicates real-world cyber threats, offering practical, hands-on learning opportunities. Additionally, a comprehensive questionnaire accompanies these exercises, designed to gather feedback on participants' experiences. © 2024 IEEE.

关键词： Cyber attacks

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EMPATHIC: Emulating Human-Like Multimodal Personality Architecture Through Thoughtful Human-AI Conversation

EMPATHIC: Emulating Human-Like Multimodal Personality Archit...

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International Conference on Confluence The Next Generation Information Technology Summit (Confluence)

作者： Varshini Devi I I. R. Oviya Kalpana Raja Department of Computer Science and Engineering Amrita School of Computing Amrita Vishwa Vidyapeetham Chennai India Section for Biomedical Informatics and Data Science School of Medicine Yale University New Haven Connecticut USA

In the evolving landscape of human-computer interaction, this paper introduces an innovative framework poised to revolutionize chatbot systems. Our framework, meticulously designed for emotionally aware multimodal chatbots, seamlessly integrates real-time face and emotion recognition with natural language processing. Currently in the developmental phase, the framework exhibits a distinctive proficiency in executing a diverse array of human instructions. These instructions span tasks such as generating detailed captions, object counting, and responding to general queries. Leveraging parameter-efficient fine-tuning from OpenFlamingo, augmented by the inclusion of the Low-rank Adapter (LoRA), our framework strategically prioritizes versatility and operational efficiency. The core of our approach lies in the establishment of instruction templates that intricately merge both vision and language data. This strategic integration forms the backbone of our multi-modality instruction tuning methodology, enhancing the adaptability of the chatbot. Recognizing the pivotal role of high-quality training data, we emphasize its significance in shaping the dialogue performance of the chatbot. As the framework progresses through its developmental stages, this research lays a robust foundation for the creation of a versatile conversational agent. The envisioned applications of this agent range from enhancing customer service experiences to providing valuable support in mental health scenarios.

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Predicting Protein-Protein Interactions Using Self-Attention-Based Deep Neural Networks and FastText Embeddings

Predicting Protein-Protein Interactions Using Self-Attention...

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International Conference on computing and Networking Technology (ICCNT)

作者： I. R. Oviya N Shanmukha Sravya Kalpana Raja Department of Computer Science Engineering Amrita School Of Computing Amrita Vishwa Vidyapeetham Chennai India Section for Biomedical Informatics and Data Science School of Medicine Yale University New Haven Connecticut USA

ISBN: (数字)9798350370249

ISBN: (纸本)9798350370270

Predicting Protein-protein interactions are central to understanding the intricate mechanisms governing cellular functions, as proteins seldom act in isolation. While current machine learning and deep learning models focus on encoding protein sequences based on residue composition or physicochemical properties, they often overlook the complex relationships between amino acid segments within lengthy sequences. To address these limitations, we propose a novel hybrid model that combines a self-attention to enhance Deep neural network feature extraction with an with FastText Protein embeddings for predicting PPI. Utilizing transfer learning via the unsupervised FastText embedding technique to derive statistical representations of protein sequences, offers advantages over traditional protein encoding techniques in the context of analysing k-Mer sequences. Our model’s performance is assessed through $\mathbf{5 - f o l d}$ cross-validation on datasets of *** and Human-Bacillus Anthracis protein interactions, resulting in accuracies of $\mathbf{9 2. 2 8 \%}$ and $\mathbf{9 4. 0 8 \%}$, respectively. Compared to existing machine learning models, our model demonstrates superior performance on both datasets.

关键词： Proteins Accuracy Transfer learning Pathogenesis Artificial neural networks Organizations Predictive models Feature extraction Encoding Vectors

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Pan-Cancer Tumor Infiltrating Lymphocyte Detection based on Federated Learning

Pan-Cancer Tumor Infiltrating Lymphocyte Detection based on ...

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2024 IEEE International Conference on Big Data, BigData 2024

作者： Baid, Ujjwal Pati, Sarthak Kurc, Tahsin M. Gupta, Rajarsi Bremer, Erich Abousamra, Shahira Thakur, Siddhesh P. Saltz, Joel H. Bakas, Spyridon Division of Computational Pathology Department of Pathology & Laboratory Medicine Indiana University School of Medicine IndianapolisIN United States Department of Radiology & Imaging Sciences Indiana University School of Medicine IndianapolisIN United States Indiana University Melvin and Bren Simon Comprehensive Cancer Center IndianapolisIN United States Department of Informatics Technical University of Munich Munich Germany Department of Biomedical Informatics Stony Brook University Stony BrookNY United States Department of Computer Science Stony Brook University Stony BrookNY United States Department of Computer Science Luddy School of Informatics Computing and Engeineering Indiana University IndianapolisIN United States

ISBN: (纸本)9798350362480

Advances in deep learning (DL) have shown great promise in revolutionizing healthcare, notwithstanding their success hinging on the availability of centralized large and diverse data. Such centralization is challenging because of numerous concerns relating to privacy, data-ownership, intellectual property, and compliance with varying regulatory policies. Federated learning (FL), offers a new decentralized paradigm to train DL models in healthcare. In this study, we evaluate the effect of FL in developing DL models for the analysis of digitized tissue sections, specifically whole slide images (WSIs). A classification application was considered as the example use case, to quantify the distribution of Tumor Infiltrating Lymphocytes (TILs), which are a critical biomarker in cancer research, providing valuable insights into patient outcomes. We trained a VGG classification model using 50 × 50 micron patches extracted from the WSIs with their associated TIL/nonTIL label. We simulated a FL environment, where different cancer types are included across each collaborating node. Our results show that the model trained with the federated training approach achieves similar performance, both quantitatively and qualitatively, to that of a model trained with all the training data pooled at a centralized location. Our study shows that FL has tremendous potential for enabling the development of more robust and accurate models for histopathology image analysis without having to collect large and diverse training data at a single location. Particularly for TILs, our FL approach yields a single DL model trained across numerous anatomical sites and able to robustly generalize to unseen cancer types. © 2024 IEEE.

关键词： Federated learning

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R2V-PPI: Enhancing Prediction of Protein-Protein Interactions Using Word2Vec Embeddings and Deep Neural Networks

R2V-PPI: Enhancing Prediction of Protein-Protein Interaction...

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Advances in Electrical, computing, Communication and Sustainable Technologies (ICAECT), International Conference on

作者： I. R. Oviya Shanmukha Sravya N Kalpana Raja Department of Computer Science Engineering Amrita School Of Computing Amrita Vishwa Vidyapeetham Chennai India Section for Biomedical Informatics and Data Science School of Medicine Yale University New Haven Connecticut USA

Proteins play a crucial role in living organisms, and understanding protein-protein interactions is vital for comprehending their functions and aiding drug discovery. In recent years, advanced deep learning models have been developed to predict protein-protein interactions from sequences. However, these large-scale approaches often suffer from deficiencies, resulting in both false positive and false negative predictions. Traditional encoding methods struggle to effectively represent the semantic meaning of individual residues in protein sequences and their impact on neighbouring residues. To overcome these deficiencies, we propose a novel method named R2V-PPI (Residue-to-Vector embeddings based Protein-Protein Interaction Framework) that effectively represents protein sequences and predicts protein-protein interactions. Inspired by Word2Vec, R2V-PPI learns informative representations of individual amino acid residues, capturing the context and relationships between them in raw protein sequences. These representations provide valuable input features for a downstream deep learning model. Our methodology offers a robust and versatile approach for predicting protein-protein interactions, especially when structural information is limited or unavailable. Evaluation on the S. cerevisiae dataset demonstrates that R2V-PPI outperforms existing state-of-the-art machine learning models.

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The Goofus & Gallant Story Corpus for Practical Value Alignment

The Goofus & Gallant Story Corpus for Practical Value Alignm...

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International Conference on Machine Learning and Applications (ICMLA)

作者： Md Sultan Al Nahian Tasmia Tasrin Spencer Frazier Mark Riedl Brent Harrison Institute for Biomedical Informatics University of Kentucky Lexington KY USA School of Interactive Computing Georgia Institute of Technology Atlanta GA USA Department of Computer Science University of Kentucky Lexington KY USA

ISBN: (数字)9798350374889

ISBN: (纸本)9798350374896

Values or principles are key elements of human society that influence people to behave and function according to an accepted standard set of social rules to maintain social order. As AI systems are becoming ubiquitous in human society, it is a major concern that they could violate these norms or values and potentially cause harm. Thus, to prevent intentional or unintentional harm, AI systems are expected to take actions that align with these principles. Training systems to exhibit this type of behavior is difficult and often requires a specialized dataset. This work presents a multi-modal dataset illustrating normative and non-normative behavior in real-life situations described through natural language and artistic images. This training set contains curated sets of images that are designed to teach young children about social principles. We argue that this is an ideal dataset to use for training socially normative agents given this fact.

关键词： Training Ethics Natural languages Machine learning Standards

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