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A Meta-Study of Software-Change Intentions ACM Comput. Surv. (IF 16.6) Pub Date : 2024-04-25 Jacob Krüger, Yi Li, Kirill Lossev, Chenguang Zhu, Marsha Chechik, Thorsten Berger, Julia Rubin
Every software system undergoes changes, for example, to add new features, fix bugs, or refactor code. The importance of understanding software changes has been widely recognized, resulting in various techniques and studies, for instance, on change-impact analysis or classifying developers’ activities. Since changes are triggered by developers’ intentions—something they plan or want to change in the
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Deep Learning for Time Series Classification and Extrinsic Regression: A Current Survey ACM Comput. Surv. (IF 16.6) Pub Date : 2024-04-25 Navid Mohammadi Foumani, Lynn Miller, Chang Wei Tan, Geoffrey I. Webb, Germain Forestier, Mahsa Salehi
Time Series Classification and Extrinsic Regression are important and challenging machine learning tasks. Deep learning has revolutionized natural language processing and computer vision and holds great promise in other fields such as time series analysis where the relevant features must often be abstracted from the raw data but are not known a priori. This article surveys the current state of the
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SoK: Security in Real-Time Systems ACM Comput. Surv. (IF 16.6) Pub Date : 2024-04-25 Monowar Hasan, Ashish Kashinath, Chien-Ying Chen, Sibin Mohan
Security is an increasing concern for real-time systems (RTS). Over the last decade or so, researchers have demonstrated attacks and defenses aimed at such systems. In this article, we identify, classify and measure the effectiveness of the security research in this domain. We provide a high-level summary [identification] and a taxonomy [classification] of this existing body of work. Furthermore, we
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Fuzzers for Stateful Systems: Survey and Research Directions ACM Comput. Surv. (IF 16.6) Pub Date : 2024-04-25 Cristian Daniele, Seyed Behnam Andarzian, Erik Poll
Fuzzing is a very effective testing methodology to find bugs. In a nutshell, a fuzzer sends many slightly malformed messages to the software under test, hoping for crashes or incorrect system behaviour. The methodology is relatively simple, although applications that keep internal states are challenging to fuzz. The research community has responded to this challenge by developing fuzzers tailored to
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A Survey of Cutting-edge Multimodal Sentiment Analysis ACM Comput. Surv. (IF 16.6) Pub Date : 2024-04-25 Upendra Singh, Kumar Abhishek, Hiteshwar Kumar Azad
The rapid growth of the internet has reached the fourth generation, i.e., web 4.0, which supports Sentiment Analysis (SA) in many applications such as social media, marketing, risk management, healthcare, businesses, websites, data mining, e-learning, psychology, and many more. Sentiment analysis is a powerful tool for governments, businesses, and researchers to analyse users’ emotions and mental states
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Controllable Data Generation by Deep Learning: A Review ACM Comput. Surv. (IF 16.6) Pub Date : 2024-04-25 Shiyu Wang, Yuanqi Du, Xiaojie Guo, Bo Pan, Zhaohui Qin, Liang Zhao
Designing and generating new data under targeted properties has been attracting various critical applications such as molecule design, image editing and speech synthesis. Traditional hand-crafted approaches heavily rely on expertise experience and intensive human efforts, yet still suffer from the insufficiency of scientific knowledge and low throughput to support effective and efficient data generation
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Warm-Starting and Quantum Computing: A Systematic Mapping Study ACM Comput. Surv. (IF 16.6) Pub Date : 2024-04-25 Felix Truger, Johanna Barzen, Marvin Bechtold, Martin Beisel, Frank Leymann, Alexander Mandl, Vladimir Yussupov
Due to low numbers of qubits and their error-proneness, Noisy Intermediate-Scale Quantum (NISQ) computers impose constraints on the size of quantum algorithms they can successfully execute. State-of-the-art research introduces various techniques addressing these limitations by utilizing known or inexpensively generated approximations, solutions, or models as a starting point to approach a task instead
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Pre-Trained Language Models for Text Generation: A Survey ACM Comput. Surv. (IF 16.6) Pub Date : 2024-04-25 Junyi Li, Tianyi Tang, Wayne Xin Zhao, Jian-Yun Nie, Ji-Rong Wen
Text Generation aims to produce plausible and readable text in human language from input data. The resurgence of deep learning has greatly advanced this field, in particular, with the help of neural generation models based on pre-trained language models (PLMs). Text generation based on PLMs is viewed as a promising approach in both academia and industry. In this article, we provide a survey on the
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DevOps Metrics and KPIs: A Multivocal Literature Review ACM Comput. Surv. (IF 16.6) Pub Date : 2024-04-25 Ricardo Amaro, Rúben Pereira, Miguel Mira da Silva
Context: Information Technology organizations are aiming to implement DevOps capabilities to fulfill market, customer, and internal needs. While many are successful with DevOps implementation, others still have difficulty measuring DevOps success in their organization. As a result, the effectiveness of assessing DevOps remains erratic. This emphasizes the need to withstand management in measuring the
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Local Interpretations for Explainable Natural Language Processing: A Survey ACM Comput. Surv. (IF 16.6) Pub Date : 2024-04-25 Siwen Luo, Hamish Ivison, Soyeon Caren Han, Josiah Poon
As the use of deep learning techniques has grown across various fields over the past decade, complaints about the opaqueness of the black-box models have increased, resulting in an increased focus on transparency in deep learning models. This work investigates various methods to improve the interpretability of deep neural networks for Natural Language Processing (NLP) tasks, including machine translation
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A Deep Dive into Robot Vision - An Integrative Systematic Literature Review Methodologies and Research Endeavor Practices ACM Comput. Surv. (IF 16.6) Pub Date : 2024-04-25 Saima Sultana, Muhammad Mansoor Alam, Mazliham Mohd Su’ud, Jawahir Che Mustapha, Mukesh Prasad
Novel technological swarm and industry 4.0 mold the recent Robot vision research into innovative discovery. To enhance technological paradigm Deep Learning offers remarkable pace to move towards diversified advancement. This research considers the most topical, recent, related and state-of-the-art research reviews that revolve around Robot vision, and shapes the research into Systematic Literature
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Intelligent Edge-powered Data Reduction: A Systematic Literature Review ACM Comput. Surv. (IF 16.6) Pub Date : 2024-04-25 Laércio Pioli, Douglas D. J. de Macedo, Daniel G. Costa, Mario A. R. Dantas
The development of the Internet of Things (IoT) paradigm and its significant spread as an affordable data source has brought many challenges when pursuing efficient data collection, distribution, and storage. Since such hierarchical logical architecture can be inefficient and costly in many cases, Data Reduction (DR) solutions have arisen to allow data preprocessing before actual transmission. To increase
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Extended Reality (XR) Toward Building Immersive Solutions: The Key to Unlocking Industry 4.0 ACM Comput. Surv. (IF 16.6) Pub Date : 2024-04-25 A’aeshah Alhakamy
When developing XR applications for Industry 4.0, it is important to consider the integration of visual displays, hardware components, and multimodal interaction techniques that are compatible with the entire system. The potential use of multimodal interactions in industrial applications has been recognized as a significant factor in enhancing humans’ ability to perform tasks and make informed decisions
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Intel TDX Demystified: A Top-Down Approach ACM Comput. Surv. (IF 16.6) Pub Date : 2024-04-25 Pau-Chen Cheng, Wojciech Ozga, Enriquillo Valdez, Salman Ahmed, Zhongshu Gu, Hani Jamjoom, Hubertus Franke, James Bottomley
Intel Trust Domain Extensions (TDX) is an architectural extension in the 4th Generation Intel Xeon Scalable Processor that supports confidential computing. TDX allows the deployment of virtual machines in the Secure-Arbitration Mode (SEAM) with encrypted CPU state and memory, integrity protection, and remote attestation. TDX aims at enforcing hardware-assisted isolation for virtual machines and minimize
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Neural Architecture Search With Progressive Evaluation and Sub-Population Preservation IEEE T. Evolut. Comput. (IF 14.3) Pub Date : 2024-04-25 Yu Xue, Jiajie Zha, Danilo Pelusi, Peng Chen, Tao Luo, Liangli Zhen, Yan Wang, Mohamed Wahib
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An Evolutionary Multitasking Memetic Algorithm for Multi-Objective Distributed Heterogeneous Welding Flow Shop Scheduling IEEE T. Evolut. Comput. (IF 14.3) Pub Date : 2024-04-25 Rui Li, Ling Wang, Wenyin Gong, Fei Ming
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TRAF3 loss-of-function reveals the noncanonical NF-κB pathway as a therapeutic target in diffuse large B cell lymphoma Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-04-25 Michael Y. Li, Lauren C. Chong, Gerben Duns, Andrew Lytle, Bruce Woolcock, Aixiang Jiang, Adèle Telenius, Susana Ben-Neriah, Waqas Nawaz, Graham W. Slack, Ingrid Elisia, Elena Viganò, Tomohiro Aoki, Shannon Healy, Gerald Krystal, Leandro Venturutti, David W. Scott, Christian Steidl
Here, we report recurrent focal deletions of the chr14q32.31-32 locus, including TRAF3 , a negative regulator of NF-κB signaling, in de novo diffuse large B cell lymphoma (DLBCL) (24/324 cases). Integrative analysis revealed an association between TRAF3 copy number loss with accumulation of NIK, the central noncanonical (NC) NF-κB kinase, and increased NC NF-κB pathway activity. Accordingly, TRAF3
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Selective social interactions and speed-induced leadership in schooling fish Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-04-25 Andreu Puy, Elisabet Gimeno, Jordi Torrents, Palina Bartashevich, M. Carmen Miguel, Romualdo Pastor-Satorras, Pawel Romanczuk
Animals moving together in groups are believed to interact among each other with effective social forces, such as attraction, repulsion, and alignment. Such forces can be inferred using “force maps,” i.e., by analyzing the dependency of the acceleration of a focal individual on relevant variables. Here, we introduce a force map technique suitable for the analysis of the alignment forces experienced
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Enriching surface-ordered defects on WO 3 for photocatalytic CO 2 -to-CH 4 conversion by water Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-04-25 Sikang Xue, Changgeng Wei, Min Shen, Xiaocong Liang, Jiali Wang, Can Yang, Wandong Xing, Sibo Wang, Wei Lin, Zhiyang Yu, Yidong Hou, Jimmy C. Yu, Xinchen Wang
Defect engineering has been widely applied in semiconductors to improve photocatalytic properties by altering the surface structures. This study is about the transformation of inactive WO 3 nanosheets to a highly effective CO 2 -to-CH 4 conversion photocatalyst by introducing surface-ordered defects in abundance. The nonstoichiometric WO 3- x samples were examined by using aberration-corrected electron
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Negotiating discord in sustainability transformations Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-04-25 James J. Patterson, Giuseppe Feola, Rakhyun E. Kim
Policy action for sustainability transformation faces inherent and ever-present sources of conflict, pushback, and resistance (i.e., discord). However, conceptual frameworks and policy prescriptions for sustainability transformations often reflect an undue image of accord. This involves simplified assumptions about consensus, steering, friction, discreteness, and additiveness of policy action, conferring
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Intrinsic tensile ductility in strain hardening multiprincipal element metallic glass Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-04-25 Zhibo Zhang, Shan Zhang, Qing Wang, Anliang Lu, Zhaoqi Chen, Ziyin Yang, Junhua Luan, Rui Su, Pengfei Guan, Yong Yang
Traditional metallic glasses (MGs), based on one or two principal elements, are notoriously known for their lack of tensile ductility at room temperature. Here, we developed a multiprincipal element MG (MPEMG), which exhibits a gigapascal yield strength, significant strain hardening that almost doubles its yield strength, and 2% uniform tensile ductility at room temperature. These remarkable properties
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The potential importance of the built-environment microbiome and its impact on human health Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-04-25 Thomas C. G. Bosch, Mark Wigley, Beatriz Colomina, Brendan Bohannan, Forrest Meggers, Katherine R. Amato, Meghan B. Azad, Martin J. Blaser, Kate Brown, Maria Gloria Dominguez-Bello, Stanislav Dusko Ehrlich, Eran Elinav, B. Brett Finlay, Kate Geddie, Naama Geva-Zatorsky, Tamara Giles-Vernick, Philippe Gros, Karen Guillemin, Louis-Patrick Haraoui, Elizabeth Johnson, Frédéric Keck, Jamie Lorimer, Margaret
There is increasing evidence that interactions between microbes and their hosts not only play a role in determining health and disease but also in emotions, thought, and behavior. Built environments greatly influence microbiome exposures because of their built-in highly specific microbiomes coproduced with myriad metaorganisms including humans, pets, plants, rodents, and insects. Seemingly static built
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Impedance of nanocapacitors from molecular simulations to understand the dynamics of confined electrolytes Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-04-25 Giovanni Pireddu, Connie J. Fairchild, Samuel P. Niblett, Stephen J. Cox, Benjamin Rotenberg
Nanoelectrochemical devices have become a promising candidate technology across various applications, including sensing and energy storage, and provide new platforms for studying fundamental properties of electrode/electrolyte interfaces. In this work, we employ constant-potential molecular dynamics simulations to investigate the impedance of gold-aqueous electrolyte nanocapacitors, exploiting a recently
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Deep Multimodal Data Fusion ACM Comput. Surv. (IF 16.6) Pub Date : 2024-04-24 Fei Zhao, Chengcui Zhang, Baocheng Geng
Multimodal Artificial Intelligence (Multimodal AI), in general, involves various types of data (e.g., images, texts, or data collected from different sensors), feature engineering (e.g., extraction, combination/fusion), and decision-making (e.g., majority vote). As architectures become more and more sophisticated, multimodal neural networks can integrate feature extraction, feature fusion, and decision-making
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Redefining Counterfactual Explanations for Reinforcement Learning: Overview, Challenges and Opportunities ACM Comput. Surv. (IF 16.6) Pub Date : 2024-04-24 Jasmina Gajcin, Ivana Dusparic
While AI algorithms have shown remarkable success in various fields, their lack of transparency hinders their application to real-life tasks. Although explanations targeted at non-experts are necessary for user trust and human-AI collaboration, the majority of explanation methods for AI are focused on developers and expert users. Counterfactual explanations are local explanations that offer users advice
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Financial Sentiment Analysis: Techniques and Applications ACM Comput. Surv. (IF 16.6) Pub Date : 2024-04-24 Kelvin Du, Frank Xing, Rui Mao, Erik Cambria
Financial Sentiment Analysis (FSA) is an important domain application of sentiment analysis that has gained increasing attention in the past decade. FSA research falls into two main streams. The first stream focuses on defining tasks and developing techniques for FSA, and its main objective is to improve the performances of various FSA tasks by advancing methods and using/curating human-annotated datasets
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Non-invasive Techniques for Muscle Fatigue Monitoring: A Comprehensive Survey ACM Comput. Surv. (IF 16.6) Pub Date : 2024-04-24 Na Li, Rui Zhou, Bharath Krishna, Ashirbad Pradhan, Hyowon Lee, Jiayuan He, Ning Jiang
Muscle fatigue represents a complex physiological and psychological phenomenon that impairs physical performance and increases the risks of injury. It is important to continuously monitor fatigue levels for early detection and management of fatigue. The detection and classification of muscle fatigue also provide important information in human-computer interactions (HMI), sports injuries and performance
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In This Issue Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-04-23
Proceedings of the National Academy of Sciences, Volume 121, Issue 17, April 2024.
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Deep Learning for Iris Recognition: A Survey ACM Comput. Surv. (IF 16.6) Pub Date : 2024-04-24 Kien Nguyen, Hugo Proença, Fernando Alonso-Fernandez
In this survey, we provide a comprehensive review of more than 200 articles, technical reports, and GitHub repositories published over the last 10 years on the recent developments of deep learning techniques for iris recognition, covering broad topics on algorithm designs, open-source tools, open challenges, and emerging research. First, we conduct a comprehensive analysis of deep learning techniques
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Resilient Machine Learning: Advancement, Barriers, and Opportunities in the Nuclear Industry ACM Comput. Surv. (IF 16.6) Pub Date : 2024-04-24 Anita Khadka, Saurav Sthapit, Gregory Epiphaniou, Carsten Maple
The widespread adoption and success of Machine Learning (ML) technologies depend on thorough testing of the resilience and robustness to adversarial attacks. The testing should focus on both the model and the data. It is necessary to build robust and resilient systems to withstand disruptions and remain functional despite the action of adversaries, specifically in the security-sensitive Nuclear Industry
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Towards Hybrid-Optimization Video Coding ACM Comput. Surv. (IF 16.6) Pub Date : 2024-04-24 Shuai Huo, Dong Liu, Haotian Zhang, Li Li, Siwei Ma, Feng Wu, Wen Gao
Video coding that pursues the highest compression efficiency is the art of computing for rate-distortion optimization. The optimization has been approached in different ways, exemplified by two typical frameworks: block-based hybrid video coding and end-to-end learned video coding. The block-based hybrid framework encompasses more and more coding modes that are available at the decoder side; an encoder
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Contactless Diseases Diagnoses Using Wireless Communication Sensing: Methods and Challenges Survey ACM Comput. Surv. (IF 16.6) Pub Date : 2024-04-24 Najah Abed Abu Ali, Mubashir Rehman, Shahid Mumtaz, Muhammad Bilal Khan, Mohammad Hayajneh, Farman Ullah, Raza Ali Shah
Respiratory illness diagnosis and continuous monitoring are becoming popular as sensitive markers of chronic diseases. This interest has motivated the increased development of respiratory illness diagnosis by exploiting wireless communication as a sensing system. Several methods for diagnosing a respiratory illness are based on multiple sensors and techniques. Depending on whether the device embeds
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Optimizing with Attractor: A Tutorial ACM Comput. Surv. (IF 16.6) Pub Date : 2024-04-24 Weiqi Li
This tutorial presents a novel search system—the Attractor-Based Search System (ABSS)—that can solve the Traveling Salesman Problem very efficiently with optimality guarantee. From the perspective of dynamical systems, a heuristic local search algorithm for an NP-complete combinatorial problem is a discrete dynamical system. In a local search system, an attractor drives the search trajectories into
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Tutorial on Matching-based Causal Analysis of Human Behaviors Using Smartphone Sensor Data ACM Comput. Surv. (IF 16.6) Pub Date : 2024-04-24 Gyuwon Jung, Sangjun Park, Eun-Yeol Ma, Heeyoung Kim, Uichin Lee
Smartphones can unobtrusively capture human behavior and contextual data such as user interaction and mobility. Thus far, smartphone sensor data have primarily been used to gain behavioral insights through correlation analysis. This article provides a tutorial on the causal analysis of human behavior using smartphone sensor data by reviewing well-known matching methods. The key steps of the causal
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Dual-Tree Genetic Programming With Adaptive Mutation for Dynamic Workflow Scheduling in Cloud Computing IEEE T. Evolut. Comput. (IF 14.3) Pub Date : 2024-04-24 Yifan Yang, Gang Chen, Hui Ma, Sven Hartmann, Mengjie Zhang
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Learning-Based Directional Improvement Prediction for Dynamic Multiobjective Optimization IEEE T. Evolut. Comput. (IF 14.3) Pub Date : 2024-04-24 Yulong Ye, Songbai Liu, Junwei Zhou, Qiuzhen Lin, Min Jiang, Kay Chen Tan
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The nonexistence of a paddlewheel effect in superionic conductors Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-04-24 KyuJung Jun, Byungju Lee, Ronald L. Kam, Gerbrand Ceder
Since the 1980s, the paddlewheel effect has been suggested as a mechanism to boost lithium-ion diffusion in inorganic materials via the rotation of rotor-like anion groups. However, it remains unclear whether the paddlewheel effect, defined as large-angle anion group rotations assisting Li hopping, indeed exists; furthermore, the physical mechanism by which the anion-group dynamics affect lithium-ion
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Brain-inspired computing with fluidic iontronic nanochannels Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-04-24 Tim M. Kamsma, Jaehyun Kim, Kyungjun Kim, Willem Q. Boon, Cristian Spitoni, Jungyul Park, René van Roij
The brain’s remarkable and efficient information processing capability is driving research into brain-inspired (neuromorphic) computing paradigms. Artificial aqueous ion channels are emerging as an exciting platform for neuromorphic computing, representing a departure from conventional solid-state devices by directly mimicking the brain’s fluidic ion transport. Supported by a quantitative theoretical
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Experimental evidence for defect tolerance in Pb-halide perovskites Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-04-24 Naga Prathibha Jasti, Igal Levine, Yishay (Isai) Feldman, Gary Hodes, Sigalit Aharon, David Cahen
The term defect tolerance (DT) is used often to rationalize the exceptional optoelectronic properties of halide perovskites (HaPs) and their devices. Even though DT lacked direct experimental evidence, it became a “fact” in the field. DT in semiconductors implies that structural defects do not translate to electrical and optical effects (e.g., due to charge trapping), associated with such defects.
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Structural and functional reorganization of inhibitory synapses by activity-dependent cleavage of neuroligin-2 Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-04-24 Na Xu, Ran Cao, Si-Yu Chen, Xu-Zhuo Gou, Bin Wang, Hong-Mei Luo, Feng Gao, Ai-Hui Tang
Recent evidence has demonstrated that the transsynaptic nanoscale organization of synaptic proteins plays a crucial role in regulating synaptic strength in excitatory synapses. However, the molecular mechanism underlying this transsynaptic nanostructure in inhibitory synapses still remains unclear and its impact on synapse function in physiological or pathological contexts has not been demonstrated
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PARP1 UFMylation ensures the stability of stalled replication forks Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-04-24 Yamin Gong, Zhifeng Wang, Wen Zong, Ruifeng Shi, Wenli Sun, Sijia Wang, Bin Peng, Shunichi Takeda, Zhao-Qi Wang, Xingzhi Xu
The S-phase checkpoint involving CHK1 is essential for fork stability in response to fork stalling. PARP1 acts as a sensor of replication stress and is required for CHK1 activation. However, it is unclear how the activity of PARP1 is regulated. Here, we found that UFMylation is required for the efficient activation of CHK1 by UFMylating PARP1 at K548 during replication stress. Inactivation of UFL1
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Evolution of homologous recombination rates across bacteria Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-04-24 Ellis L. Torrance, Corey Burton, Awa Diop, Louis-Marie Bobay
Bacteria are nonsexual organisms but are capable of exchanging DNA at diverse degrees through homologous recombination. Intriguingly, the rates of recombination vary immensely across lineages where some species have been described as purely clonal and others as “quasi-sexual.” However, estimating recombination rates has proven a difficult endeavor and estimates often vary substantially across studies
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The fatty liver disease–causing protein PNPLA3-I148M alters lipid droplet–Golgi dynamics Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-04-24 David J. Sherman, Lei Liu, Jennifer L. Mamrosh, Jiansong Xie, John Ferbas, Brett Lomenick, Mark S. Ladinsky, Rati Verma, Ingrid C. Rulifson, Raymond J. Deshaies
Nonalcoholic fatty liver disease, recently renamed metabolic dysfunction-associated steatotic liver disease (MASLD), is a progressive metabolic disorder that begins with aberrant triglyceride accumulation in the liver and can lead to cirrhosis and cancer. A common variant in the gene PNPLA3 , encoding the protein PNPLA3-I148M, is the strongest known genetic risk factor for MASLD. Despite its discovery
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Liver cancer development driven by the AP-1/c-Jun~Fra-2 dimer through c-Myc Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-04-24 Latifa Bakiri, Sebastian C. Hasenfuss, Ana Guío-Carrión, Martin K. Thomsen, Peter Hasselblatt, Erwin F. Wagner
Hepatocellular carcinoma (HCC) is a leading cause of cancer-related death. HCC incidence is on the rise, while treatment options remain limited. Thus, a better understanding of the molecular pathways involved in HCC development has become a priority to guide future therapies. While previous studies implicated the Activator Protein-1 (AP-1) (Fos/Jun) transcription factor family members c-Fos and c-Jun
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SHP2 regulates GluA2 tyrosine phosphorylation required for AMPA receptor endocytosis and mGluR-LTD Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-04-24 Sanghyeon Lee, Jungho Kim, Hyun-Hee Ryu, Hanbyul Jang, DoEun Lee, Seungha Lee, Jae-man Song, Yong-Seok Lee, Young Ho Suh
Posttranslational modifications regulate the properties and abundance of synaptic α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors that mediate fast excitatory synaptic transmission and synaptic plasticity in the central nervous system. During long-term depression (LTD), protein tyrosine phosphatases (PTPs) dephosphorylate tyrosine residues in the C-terminal tail of AMPA receptor
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Class IIa HDAC4 and HDAC7 cooperatively regulate gene transcription in Th17 cell differentiation Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-04-24 Ka Lung Cheung, Li Zhao, Rajal Sharma, Anurupa Abhijit Ghosh, Michael Appiah, Yifei Sun, Anbalagan Jaganathan, Yuan Hu, Alannah LeJeune, Feihong Xu, Xinye Han, Xueting Wang, Fan Zhang, Chunyan Ren, Martin J. Walsh, Huabao Xiong, Alexander Tsankov, Ming-Ming Zhou
Class II histone deacetylases (HDACs) are important in regulation of gene transcription during T cell development. However, our understanding of their cell-specific functions is limited. In this study, we reveal that class IIa Hdac4 and Hdac7 (Hdac4/7) are selectively induced in transcription, guiding the lineage-specific differentiation of mouse T-helper 17 (Th17) cells from naive CD4 + T cells. Importantly
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HYPK: A marginally disordered protein sensitive to charge decoration Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-04-24 Arash Firouzbakht, Austin Haider, Kari Gaalswyk, Sepehr Alaeen, Kingshuk Ghosh, Martin Gruebele
Intrinsically disordered proteins (IDPs) that lie close to the empirical boundary separating IDPs and folded proteins in Uversky’s charge–hydropathy plot may behave as “marginal IDPs” and sensitively switch conformation upon changes in environment (temperature, crowding, and charge screening), sequence, or both. In our search for such a marginal IDP, we selected Huntingtin-interacting protein K (HYPK)
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Different states of synaptic vesicle priming explain target cell type–dependent differences in neurotransmitter release Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-04-24 Mohammad Aldahabi, Erwin Neher, Zoltan Nusser
Pronounced differences in neurotransmitter release from a given presynaptic neuron, depending on the synaptic target, are among the most intriguing features of cortical networks. Hippocampal pyramidal cells (PCs) release glutamate with low probability to somatostatin expressing oriens-lacunosum-moleculare (O-LM) interneurons (INs), and the postsynaptic responses show robust short-term facilitation
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Senolytic and senomorphic agent procyanidin C1 alleviates structural and functional decline in the aged retina Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-04-24 Yidan Liu, Xiuxing Liu, Xuhao Chen, Zhenlan Yang, Jianqi Chen, Weining Zhu, Yangyang Li, Yuwen Wen, Caibin Deng, Chenyang Gu, Jianjie Lv, Rong Ju, Yehong Zhuo, Wenru Su
Increased cellular senescence burden contributes in part to age-related organ dysfunction and pathologies. In our study, using mouse models of natural aging, we observed structural and functional decline in the aged retina, which was accompanied by the accumulation of senescent cells and senescence-associated secretory phenotype factors. We further validated the senolytic and senomorphic properties
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Superpixel Segmentation Based Evolutionary Multitasking Algorithm for Feature Selection of Hyperspectral Images IEEE T. Evolut. Comput. (IF 14.3) Pub Date : 2024-04-23 Lingjie Li, Yuze Zhang, Qiuzhen Lin, Zhong Ming, Carlos A. Coello Coello, Victor C. M. Leung
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Identification of the potassium-binding site in serotonin transporter Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-04-23 Eva Hellsberg, Danila Boytsov, Qingyang Chen, Marco Niello, Michael Freissmuth, Gary Rudnick, Yuan-Wei Zhang, Walter Sandtner, Lucy R. Forrest
Clearance of serotonin (5-hydroxytryptamine, 5-HT) from the synaptic cleft after neuronal signaling is mediated by serotonin transporter (SERT), which couples this process to the movement of a Na + ion down its chemical gradient. After release of 5-HT and Na + into the cytoplasm, the transporter faces a rate-limiting challenge of resetting its conformation to be primed again for 5-HT and Na + binding
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The political fallout of air pollution Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-04-23 Luna Bellani, Stefano Ceolotto, Benjamin Elsner, Nico Pestel
This paper studies the effect of air pollution on voting outcomes. We use data from 60 federal and state elections in Germany from 2000 to 2018 and exploit plausibly exogenous fluctuations in ambient air pollution within counties across election dates. Higher air pollution on election day shifts votes away from incumbent parties and toward opposition parties. An increase in the concentration of particulate
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c-di-AMP determines the hierarchical organization of bacterial RCK proteins Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-04-23 Rita Rocha, João M. P. Jorge, Celso M. Teixeira-Duarte, Inês R. Figueiredo-Costa, Tatiana B. Cereija, Paula F. Ferreira-Teixeira, Christina Herzberg, Jörg Stülke, João H. Morais-Cabral
In bacteria, intracellular K + is involved in the regulation of membrane potential, cytosolic pH, and cell turgor as well as in spore germination, environmental adaptation, cell-to-cell communication in biofilms, antibiotic sensitivity, and infectivity. The second messenger cyclic-di-AMP (c-di-AMP) has a central role in modulating the intracellular K + concentration in many bacterial species, controlling
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Low-latency gravitational wave alert products and their performance at the time of the fourth LIGO-Virgo-KAGRA observing run Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-04-23 Sushant Sharma Chaudhary, Andrew Toivonen, Gaurav Waratkar, Geoffrey Mo, Deep Chatterjee, Sarah Antier, Patrick Brockill, Michael W. Coughlin, Reed Essick, Shaon Ghosh, Soichiro Morisaki, Pratyusava Baral, Amanda Baylor, Naresh Adhikari, Patrick Brady, Gareth Cabourn Davies, Tito Dal Canton, Marco Cavaglia, Jolien Creighton, Sunil Choudhary, Yu-Kuang Chu, Patrick Clearwater, Luke Davis, Thomas Dent
Multimessenger searches for binary neutron star (BNS) and neutron star-black hole (NSBH) mergers are currently one of the most exciting areas of astronomy. The search for joint electromagnetic and neutrino counterparts to gravitational wave (GW)s has resumed with ALIGO’s, AdVirgo’s and KAGRA’s fourth observing run (O4). To support this effort, public semiautomated data products are sent in near real-time
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Maximum entropy determination of mammalian proteome dynamics Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-04-23 Alexander J. Dear, Gonzalo A. Garcia, Georg Meisl, Galen A. Collins, Tuomas P. J. Knowles, Alfred L. Goldberg
Full understanding of proteostasis and energy utilization in cells will require knowledge of the fraction of cell proteins being degraded with different half-lives and their rates of synthesis. We therefore developed a method to determine such information that combines mathematical analysis of protein degradation kinetics obtained in pulse–chase experiments with Bayesian data fitting using the maximum
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Plasmid partitioning driven by collective migration of ParA between nucleoid lobes Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-04-23 Robin Köhler, Seán M. Murray
The ParABS system is crucial for the faithful segregation and inheritance of many bacterial chromosomes and low-copy-number plasmids. However, despite extensive research, the spatiotemporal dynamics of the ATPase ParA and its connection to the dynamics and positioning of the ParB-coated cargo have remained unclear. In this study, we utilize high-throughput imaging, quantitative data analysis, and computational
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Decorin suppresses tumor lymphangiogenesis: A mechanism to curtail cancer progression Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-04-23 Dipon K. Mondal, Christopher Xie, Gabriel J. Pascal, Simone Buraschi, Renato V. Iozzo
The complex interplay between malignant cells and the cellular and molecular components of the tumor stroma is a key aspect of cancer growth and development. These tumor–host interactions are often affected by soluble bioactive molecules such as proteoglycans. Decorin, an archetypical small leucine-rich proteoglycan primarily expressed by stromal cells, affects cancer growth in its soluble form by
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Organ-delimited gene regulatory networks provide high accuracy in candidate transcription factor selection across diverse processes Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-04-23 Rajeev Ranjan, Sonali Srijan, Somaiah Balekuttira, Tina Agarwal, Melissa Ramey, Madison Dobbins, Rachel Kuhn, Xiaojin Wang, Karen Hudson, Ying Li, Kranthi Varala
Organ-specific gene expression datasets that include hundreds to thousands of experiments allow the reconstruction of organ-level gene regulatory networks (GRNs). However, creating such datasets is greatly hampered by the requirements of extensive and tedious manual curation. Here, we trained a supervised classification model that can accurately classify the organ-of-origin for a plant transcriptome
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Out-of-equilibrium interactions and collective locomotion of colloidal spheres with squirming of nematoelastic multipoles Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-04-23 Bohdan Senyuk, Jin-Sheng Wu, Ivan I. Smalyukh
Many living and artificial systems show similar emergent behavior and collective motions on different scales, starting from swarms of bacteria to synthetic active particles, herds of mammals, and crowds of people. What all these systems often have in common is that new collective properties like flocking emerge from interactions between individual self-propelled or driven units. Such systems are naturally
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A mammalian tripartite enhancer cluster controls hypothalamic Pomc expression, food intake, and body weight Proc. Natl. Acad. Sci. U.S.A. (IF 11.1) Pub Date : 2024-04-23 Daniela Rojo, Clara E. Hael, Agustina Soria, Flávio S. J. de Souza, Malcolm J. Low, Lucía F. Franchini, Marcelo Rubinstein
Food intake and energy balance are tightly regulated by a group of hypothalamic arcuate neurons expressing the proopiomelanocortin ( POMC) gene. In mammals, arcuate-specific POMC expression is driven by two cis -acting transcriptional enhancers known as nPE1 and nPE2. Because mutant mice lacking these two enhancers still showed hypothalamic Pomc mRNA, we searched for additional elements contributing