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U1 snRNP regulates alternative promoter activity by inhibiting premature polyadenylation

Molecular Cell 2025年第10期85卷 1968-1981.e7页

作者： Kim, GyeungYun Carroll, Christine L. Wakefield, Zachary Peters Tuncay, Mustafa Fiszbein, Ana Biology Department Boston University Boston 02215 United States Graduate Program in Molecular Biology Cell Biology & Biochemistry Boston University Boston 02215 United States Graduate Program in Cell and Molecular Biology Boston University Boston 02215 United States Bioinformatics Program Faculty of Computing and Data Science Boston University Boston 02215 United States Center for Computing & Data Sciences Boston University Boston 02215 United States

Emerging evidence indicates that splicing factors mediate the close link between transcription and splicing. However, the mechanisms underlying this coupling remain unclear. U1 small nuclear ribonucleoprotein particle (U1 snRNP) not only initiates splicing but also plays a crucial role in preventing premature cleavage and polyadenylation, facilitating long-distance transcriptional elongation. Here, we show that U1 snRNP regulates alternative promoter activity in human cells by inhibiting premature polyadenylation. In genes carrying premature polyadenylation sites between two promoters, U1 snRNP inhibition with antisense oligonucleotides leads to a significant decrease in downstream promoter activity. Conversely, restoring U1 snRNP activity or inhibiting premature polyadenylation rescues downstream promoter activity. Mechanistically, U1 snRNP inhibition correlates with reduced chromatin accessibility, decreased RNA polymerase II serine 5 phosphorylation, and increased promoter-proximal pause at downstream promoters. Our findings support a model in which U1 snRNP favors productive elongation from upstream promoters, triggering downstream promoter activation by destabilizing nucleosomes and promoting promoter escape. © 2025 The Author(s)

关键词： alternative promoters dowsntream promoters promoter-proximal pause splicing factors splicing transcription transcription cooperativity transcription initiation transcription interfierence transcription start sites U1 snRNP

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HAAQI-Net: A Non-intrusive Neural Music Audio Quality Assessment Model for Hearing Aids

arXiv

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arXiv 2024年

作者： Wisnu, Dyah A.M.G. Rini, Stefano Zezario, Ryandhimas E. Wang, Hsin-Min Tsao, Yu Taiwan International Graduate Program—Social Network and Human Centered Computing Institute of Information Science Academia Sinica Taipei Taiwan College of Informatics National Chengchi University Taipei Taiwan Institute of Communications Engineering National Yang Ming Chiao Tung University Hsinchu Taiwan Research Center for Information Technology Innovation Academia Sinica Taipei Taiwan Institute of Information Science Academia Sinica Taipei Taiwan

This paper introduces HAAQI-Net, a non-intrusive deep learning-based music audio quality assessment model for hearing aid users. Unlike traditional methods like the Hearing Aid Audio Quality Index (HAAQI) that require intrusive reference signal comparisons, HAAQI-Net offers a more accessible and computationally efficient alternative. By utilizing a Bidirectional Long Short-Term Memory (BLSTM) architecture with attention mechanisms and features extracted from the pre-trained BEATs model, it can predict HAAQI scores directly from music audio clips and hearing loss patterns. Experimental results demonstrate HAAQI-Net’s effectiveness, achieving a Linear Correlation Coefficient (LCC) of 0.9368, a Spearman’s Rank Correlation Coefficient (SRCC) of 0.9486, and a Mean Squared Error (MSE) of 0.0064 and inference time significantly reduces from 62.52 to 2.54 seconds. To address computational overhead, a knowledge distillation strategy was applied, reducing parameters by 75.85% and inference time by 96.46%, while maintaining strong performance (LCC: 0.9071, SRCC: 0.9307, MSE: 0.0091). To expand its capabilities, HAAQI-Net was adapted to predict subjective human scores like the Mean Opinion Score (MOS) through fine-tuning. This adaptation significantly improved prediction accuracy, validated through statistical analysis. Furthermore, the robustness of HAAQI-Net was evaluated under varying Sound Pressure Level (SPL) conditions, revealing optimal performance at a reference SPL of 65 dB, with accuracy gradually decreasing as SPL deviated from this point. The advancements in subjective score prediction, SPL robustness, and computational efficiency position HAAQI-Net as a scalable solution for music audio quality assessment in hearing aid applications, contributing to efficient and accurate models in audio signal processing and hearing aid technology. Copyright © 2024, The Authors. All rights reserved.

关键词： Mean square error

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CapST: An Enhanced and Lightweight Method for Deepfake Video Classification

arXiv

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arXiv 2023年

作者： Ahmad, Wasim Peng, Yan-Tsung Chang, Yuan-Hao Ganfure, Gaddisa Olani Khan, Sarwar Shahzad, Sahibzada Adil Institute of Information Science Academia Sinica Taipei11529 Taiwan Department of Computer Science National Chengchi University Taipei116 Taiwan Social Networks Human-Centered Computing Taiwan International Graduate Program Academia Sinica Taipei11529 Taiwan Dire Dawa University Ethiopia Research Center for Information Technology Innovation Academia Sinica Taipei11529 Taiwan

The proliferation of deepfake videos, synthetic media produced through advanced Artificial Intelligence techniques, has raised significant concerns across various sectors, encompassing realms such as politics, entertainment, and security. In response, this research introduces an innovative and streamlined model designed to classify deepfake videos generated by five distinct encoders adeptly. Our approach not only achieves state-of-the-art performance but also optimizes computational resources. At its core, our solution employs part of a VGG19_bn as a backbone to efficiently extract features, a strategy proven effective in image-related tasks. We integrate a Capsule Network coupled with a Spatial-Temporal attention mechanism to bolster the model’s classification capabilities while conserving resources. This combination captures intricate hierarchies among features, facilitating robust identification of deepfake attributes. Delving into the intricacies of our innovation, we introduce an existing video-level fusion technique that artfully capitalizes on temporal attention mechanisms. This mechanism serves to handle concatenated feature vectors, capitalizing on the intrinsic temporal dependencies embedded within deepfake videos. By aggregating insights across frames, our model gains a holistic comprehension of video content, resulting in more precise predictions. Experimental results on an extensive benchmark dataset of deepfake videos (DFDM) showcase the efficacy of our proposed method. Notably, our approach achieves up to a 4% improvement in accurately categorizing deepfake videos compared to baseline models, all while demanding fewer computational resources. Copyright © 2023, The Authors. All rights reserved.

关键词： Routing algorithms

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Characteristics Fluctuation of Sub-3-nm Bulk FinFET Devices Induced by Random Interface Traps

Characteristics Fluctuation of Sub-3-nm Bulk FinFET Devices ...

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IEEE Conference on Nanotechnology

作者： Sekhar Reddy Kola Min-Hui Chuang Yiming Li Parallel and Scientific Computing Laboratory Electrical Engineering and Computer Science International Graduate Program National Yang Ming Chiao Tung University Hsinchu Taiwan Department of Electronics and Electrical Engineering Institute of Communications Engineering Institute of Biomedical Engineering Institute of Pioneer Semiconductor Innovation Institute of Artificial Intelligence Innovation National Yang Ming Chiao Tung University Hsinchu Taiwan

Three-dimensional (3D) bulk fin-typed field effect transistors (FinFETs) have emerged as key devices that can scale down the technology node beyond 22-nm. However, the scaled devices have created new sources of fluctuation inherent in 3D geometry. The interface trap is one such fluctuation that is caused by the trapping and de-trapping of charge carriers and has an adverse effect on device characteristics and variability. In this work, we study impacts of random interface traps (RITs) on electrical characteristic of bulk FinFETs by using a 3D quantum-mechanically corrected device simulation. RIT position effects on short channel effects (SCEs) are examined with physical governed influence to show the major fluctuations. More than 50% reductions of the RITs-induced characteristic fluctuation of the germanium (Ge) devices are observed, compared with Si devices. The Ge ones can reduce SCE variations and exhibit high immunity to RITs.

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Towards Adversarial Robustness for Multi-Mode Data through Metric Learning

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Sensors 2023年第13期23卷 6173页

作者： Khan, Sarwar Chen, Jun-Cheng Liao, Wen-Hung Chen, Chu-Song Research Center for Information Technology Innovation Academia Sinica Taipei11529 Taiwan Social Networks Human-Centered Computing Taiwan International Graduate Program Academia Sinica Taipei11529 Taiwan Department of Computer Science National Chengchi University Taipei11605 Taiwan Department of Computer Science and Information Engineering National Taiwan University Taipei106319 Taiwan

Adversarial attacks have become one of the most serious security issues in widely used deep neural networks. Even though real-world datasets usually have large intra-variations or multiple modes, most adversarial defense methods, such as adversarial training, which is currently one of the most effective defense methods, mainly focus on the single-mode setting and thus fail to capture the full data representation to defend against adversarial attacks. To confront this challenge, we propose a novel multi-prototype metric learning regularization for adversarial training which can effectively enhance the defense capability of adversarial training by preventing the latent representation of the adversarial example changing a lot from its clean one. With extensive experiments on CIFAR10, CIFAR100, MNIST, and Tiny ImageNet, the evaluation results show the proposed method improves the performance of different state-of-the-art adversarial training methods without additional computational cost. Furthermore, besides Tiny ImageNet, in the multi-prototype CIFAR10 and CIFAR100 where we reorganize the whole datasets of CIFAR10 and CIFAR100 into two and ten classes, respectively, the proposed method outperforms the state-of-the-art approach by 2.22% and 1.65%, respectively. Furthermore, the proposed multi-prototype method also outperforms its single-prototype version and other commonly used deep metric learning approaches as regularization for adversarial training and thus further demonstrates its effectiveness. © 2023 by the authors.

关键词： Deep neural networks

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An improved evolutionary hybrid method for cloud provider selection 8

An improved evolutionary hybrid method for cloud provider se...

引用

8th Brazilian Conference on Intelligent Systems, BRACIS 2019

作者： Borges De Moraes, Lucas Fiorese, Adriano Stubs Parpinelli, Rafael Graduate Program in Applied Computing Santa Catarina State University Joinville Brazil

ISBN: (纸本)9781728142531

Cloud computing (CC) popularization unleashed the creation and competition of a large number of new companies providing CC services, the so called Cloud Providers (CPs). Thus, select the smallest CP set with the lowest price that are the most suitable to a given request (customer's needs, such as demanded resources and desired service quality) becomes a hard problem. Nonetheless, robust search methods like metaheuristics ones are used to solve it, for instance Evolutionary Algorithms (EAs). Performance Indicators (PIs) were used to quantify features of each CP used later to select them using a method. This paper proposes an improved hybrid method which uses in sequence: a deterministic, an EA and a local search method to find the most suitable possible CP set in the solution search space. This hybrid method was tested and has the highest assertiveness among all others methods developed to solve this problem, becoming a promising solution to a real application. © 2019 IEEE.

关键词： Benchmarking

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Preliminary Design for Reference tracking feedback for Medical Cyber-Physical Pharmacokinetic Systems

Preliminary Design for Reference tracking feedback for Medic...

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IEEE International Conference on Automatica (ICA-ACCA)

作者： Pedro M. Oliveira Daniel Bustos Rodolfo Lobo Márcio J. Lacerda Jonathan M. Palma Graduate Program in Electrical Engineering Federal University of Minas Gerais Belo Horizonte Brazil Dept. of Translational Medicine Universidad Católica del Maule Talca Chile Ingenieria en Telecomunicaciones e Informática Universidad Diego Portales Santiago Chile Centre for Communications Technology School of Computing and Digital Media London Metropolitan University London UK Faculty of Engineering Universidad de Talca Curicó Chile

ISBN: (数字)9798350378115

ISBN: (纸本)9798350378122

This paper addresses the reference tracking control problem for Medical Cyber-Physical Systems (MCPS). The control theory is employed to guarantee the suitable concentration of drugs in the body of patients to guarantee a safe treatment. The MCPS is modeled as a switched system, and the modes consider the different scenarios for the problem. A discrete-time model is utilized for the pharmacokinetic process, and the zero input control strategy is employed to design state-feedback controllers with a guaranteed exponential convergence rate. A numerical experiment is presented to illustrate the validity and effectiveness of our method.

关键词： Drugs Switched systems Design methodology Process control Medical services Cyber-physical systems Numerical models Control theory Pharmacokinetics Convergence

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An Efficient Three-Factor Authenticated Key Agreement Technique Using FCM Under HC-IoT Architectures

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Computers, Materials & Continua 2022年第7期72卷 1373-1389页

作者： Chandrashekhar Meshram Agbotiname Lucky Imoize Sajjad Shaukat Jamal Parkash Tambare Adel R.Alharbi Iqtadar Hussain Department of Post Graduate Studies and Research in Mathematics Jayawanti Haksar Government Post-Graduation CollegeCollege of Chhindwara UniversityBetul460001M.P.India Department of Electrical and Electronics Engineering Faculty of EngineeringUniversity of LagosAkokaLagos100213Nigeria Department of Electrical Engineering and Information Technology Institute of Digital CommunicationRuhr University44801BochumGermany Department of Mathematics College of ScienceKing Khalid UniversityAbhaSaudi Arabia Water Resources&Applied Mathematics Research Lab Nagpur440027India College of Computing and Information Technology University of TabukTabuk71491Saudi Arabia Mathematics Program Department of MathematicsStatistics and PhysicsCollege of Arts and SciencesQatar University2713DohaQatar

The Human-Centered Internet of Things(HC-IoT)is fast becoming a hotbed of security and privacy *** users can establish a common session key through a trusted server over an open communication channel using a three-party authenticated key *** of the early authenticated key agreement systems relied on pairing,hashing,or modular exponentiation processes that are computationally intensive and *** order to address this problem,this paper offers a new three-party authenticated key agreement technique based on fractional chaotic *** new scheme uses fractional chaotic maps and supports the dynamic sensing of HC-IoT devices in the network architecture without a password *** projected security scheme utilized a hash function,which works well for the resource-limited HC-IoT *** results show that our new technique is resistant to password guessing attacks since it does not use a ***,our approach provides users with comprehensive privacy protection,ensuring that a user forgery attack causes no ***,our new technique offers better security features than the techniques currently available in the literature.

关键词： Three-party authenticated key agreement anonymity fractional chaotic maps Chebyshev polynomial password table human-centered internet of things(HC-IoT)

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Learning-Based Complexity Reduction Scheme for VVC Intra-Frame Prediction

Learning-Based Complexity Reduction Scheme for VVC Intra-Fra...

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IEEE Visual Communications and Image Processing (VCIP)

作者： Mário Saldanha Gustavo Sanchez César Marcon Luciano Agostini Graduate Program in Computing (PPGC) Federal University of Pelotas Pelotas Brazil IF Farroupilha Alegrete Brazil Pontificial Catholic University of Rio Grande do Sul Porto Alegre Brazil

ISBN: (纸本)9781728173221

This paper presents a learning-based complexity reduction scheme for Versatile Video Coding (VVC) intra-frame prediction. VVC introduces several novel coding tools to improve the coding efficiency of the intra-frame prediction at the cost of a high computational effort. Thus, we developed an efficient complexity reduction scheme composed of three solutions based on machine learning and statistical analysis to reduce the number of intra prediction modes evaluated in the costly Rate-Distortion Optimization (RDO) process. Experimental results demonstrated that the proposed solution provides 18.32% encoding timesaving with a negligible impact on the coding efficiency.

关键词： Video coding Image coding Visual communication Statistical analysis Current measurement Rate-distortion Machine learning

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Analysis of VVC Intra Prediction Block Partitioning Structure

Analysis of VVC Intra Prediction Block Partitioning Structur...

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IEEE Visual Communications and Image Processing (VCIP)

作者： Mário Saldanha Gustavo Sanchez César Marcon Luciano Agostini Federal University of Pelotas-Graduate Program in Computing (PPGC) Pelotas Brazil IF Farroupilha Alegrete Brazil Pontificial Catholic University of Rio Grande do Sul- Porto Alegre Brazil

ISBN: (纸本)9781728173221

This paper presents an encoding time and encoding efficiency analysis of the Quadtree with nested Multi-type Tree (QTMT) structure in the Versatile Video Coding (VVC) intra-frame prediction. The QTMT structure enables VVC to improve the compression performance compared to its predecessor standard at the cost of a higher encoding complexity. The intra-frame prediction time raised about 26 times compared to the HEVC reference software, and most of this time is related to the new block partitioning structure. Thus, this paper provides a detailed description of the VVC block partitioning structure and an in-depth analysis of the QTMT structure regarding coding time and coding efficiency. Based on the presented analyses, this paper can guide outcoming works focusing on the block partitioning of the VVC intra-frame prediction.

关键词： Video coding Image coding Costs Visual communication Focusing Software Computational complexity

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