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Search Results (8,659)

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31 pages, 64773 KiB  
Article
Versatility Evaluation of Landslide Risk with Window Sizes and Sampling Techniques Based on Deep Learning
by Fudong Ren and Koichi Isobe
Appl. Sci. 2024, 14(22), 10571; https://doi.org/10.3390/app142210571 (registering DOI) - 16 Nov 2024
Viewed by 59
Abstract
Across the globe, landslides cause significant loss of life, injuries, and widespread damage to homes and infrastructure. Therefore, assessing and analyzing landslide hazards is crucial to human, environmental, cultural, economic, and social sustainability. This study utilizes ArcGIS 10.8 and Python 3.9 to create [...] Read more.
Across the globe, landslides cause significant loss of life, injuries, and widespread damage to homes and infrastructure. Therefore, assessing and analyzing landslide hazards is crucial to human, environmental, cultural, economic, and social sustainability. This study utilizes ArcGIS 10.8 and Python 3.9 to create landslide databases for Niigata Prefecture (NIG), Iwate and Miyagi Prefectures (IWT-MYG), and Hokkaido (HKD), drawing on data obtained from the National Research Institute for Earth Science and Disaster Resilience, Japan. A distinguishing feature of this study is the application of a Convolutional Neural Network (CNN), which significantly outperforms traditional machine learning models in image-based pattern recognition by extracting contextual information from surrounding areas, a distinct advantage in image and pattern recognition tasks. Unlike conventional methods that often require manual feature selection and engineering, CNNs automate feature extraction, enabling a more nuanced understanding of complex patterns. By experimenting with CNN input window sizes ranging from 3 × 3 to 27 × 27 pixels and employing diverse sampling techniques, we demonstrate that larger windows enhance the model’s predictive accuracy by capturing a wider range of environmental interactions critical for effective landslide modeling. CNN models with 19 × 19 pixel windows typically yield the best overall performance, with CNN-19 achieving an AUC of 0.950, 0.982 and 0.969 for NIG, HKD, and IWT-MYG, respectively. Furthermore, we improve prediction reliability using oversampling and a random window-moving method. For instance, in the NIG region, the AUC of the oversampling CNN-19 is 0.983, while the downsampling AUC is 0.950). These techniques, less commonly applied in traditional machine learning approaches to landslide detection, help address the issue of data imbalance often seen in landslide datasets, where instances of landslides are far outnumbered by non-landslide occurrences. While challenges remain in enhancing the model’s generalization, this research makes significant progress in developing more robust and adaptable tools for landslide prediction, which are vital for ensuring environmental and societal resilience. Full article
(This article belongs to the Special Issue Novel Technology in Landslide Monitoring and Risk Assessment)
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Figure 1
<p>Study areas and distributions of historical landslides: (<b>A</b>) NIG study area, (<b>B</b>) IWT-MYG study area, and (<b>C</b>) HKD study area .</p>
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<p>Distribution of landslide and non-landslide data.</p>
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<p>Maps of landslide features.</p>
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<p>Maps of landslide features.</p>
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<p>Maps of landslide features.</p>
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<p>Flowchart of this study.</p>
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<p>Schematic diagram of shifting method.</p>
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<p>Information gain ratio of the landslide feature.</p>
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<p>Distribution frequency of landslides with different features: (<b>a</b>) Elevation, (<b>b</b>) Rainfall, (<b>c</b>) Distance to river, (<b>d</b>) Land use.</p>
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<p>Variation of landslide areas across landslide scale samples and AUC of CNN-i models across landslide scale.</p>
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<p>Average AUC and Pearson correlation coefficients of CNN models for landslide scale.</p>
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<p>ROC curve in downsampling and oversampling in HKD based on CNN-i.</p>
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<p>ROC curve in downsampling and oversampling in NIG based on CNN-i.</p>
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<p>ROC curve in downsampling and oversampling in IWT based on CNN-i.</p>
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<p>LSM, CM, and LIM in CNN-15 (upper: downsampling, lower: oversampling).</p>
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<p>LSM, CM, and LIM of HKD in CNN-19 (upper: downsampling, lower: oversampling).</p>
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<p>LSM, CM, and LIM of HKD in CNN-23 (upper: downsampling, lower: oversampling).</p>
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<p>LSM, CM, and LIM of NIG in CNN-15 (upper: downsampling, lower: oversampling).</p>
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<p>LSM, CM, and LIM of NIG in CNN-19 (upper: downsampling, lower: oversampling).</p>
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<p>LSM, CM, and LIM of NIG in CNN-23 (upper: downsampling, lower: oversampling).</p>
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<p>LSM, CM, and LIM of IWT in CNN-15 (upper: downsampling, lower: oversampling).</p>
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<p>LSM, CM, and LIM of IWT in CNN-19 (upper: downsampling, lower: oversampling).</p>
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<p>LSM, CM, and LIM of IWT in CNN-23 (upper: downsampling, lower: oversampling).</p>
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<p>CM based on the CNN-19 with the oversampling method in HKD. Left to right: IWT, HKD, and NIG.</p>
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<p>CM based on the CNN-19 with the oversampling method in NIG. Left to right: IWT, HKD, and NIG.</p>
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<p>CM based on the CNN-19 with the oversampling method in IWT. Left to right: IWT, HKD, and NIG.</p>
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<p>Maps showing parts of landslide features in NIG area: (<b>a</b>) Land use, (<b>b</b>) Soil, (<b>c</b>) Lithology, and (<b>d</b>) Vegetation.</p>
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<p>Maps showing parts of landslide features in HKD area: (<b>a</b>) Land use, (<b>b</b>) Soil, (<b>c</b>) Lithology, and (<b>d</b>) Vegetation.</p>
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<p>Maps showing parts of landslide features in IWT-MYG area: (<b>a</b>) Land use, (<b>b</b>) Soil, (<b>c</b>) Lithology, and (<b>d</b>) Vegetation.</p>
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<p>Maps showing parts of landslide features in IWT-MYG area: (<b>a</b>) Land use, (<b>b</b>) Soil, (<b>c</b>) Lithology, and (<b>d</b>) Vegetation.</p>
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18 pages, 2587 KiB  
Article
Research on User Demands and Functional Design of an AR-Based Interior Design and Display Platform for Recreational Vehicles
by Xun Zhang, Xiyu Wang and Wei Xu
Appl. Sci. 2024, 14(22), 10568; https://doi.org/10.3390/app142210568 (registering DOI) - 16 Nov 2024
Viewed by 98
Abstract
Background: Augmented Reality (AR) technology provides a new way for product design and display due to its unique interaction, enabling customers to experience products more comprehensively and immersively. Objective: To study the interactive form and application of AR technology in the interior design [...] Read more.
Background: Augmented Reality (AR) technology provides a new way for product design and display due to its unique interaction, enabling customers to experience products more comprehensively and immersively. Objective: To study the interactive form and application of AR technology in the interior design and display of RV, to provide new ideas and solutions for the interior design of RV, to optimize the user experience of customers and improve the work efficiency in the process of customized interior design of RV. Methods: Qualitative and quantitative research methods were adopted, the target customer groups were investigated based on the KANO model, the data were analysed, and the design suggestions for the function and interactive interface of the RV interior design display platform were summarized. Results: Based on the investigation and research, the specific functions of the RV indoor experience design platform and the needs of the target user groups were identified, including 12 essential needs, 5 charm needs, 1 expectation needs and 2 undifferentiated needs, which correspond to different functions, respectively. Finally, the main features of the platform are outlined, and the functional framework of the RV interior design and display platform is drawn. Conclusions: The interactive form of AR RV interior design includes user interface design and interactive mode design, which can greatly enhance user experience, optimize space utilization and enhance customized services. The application of AR technology in RV design has a high potential, providing theoretical and practical support for the design and development of the RV AR RV design display platform. Full article
(This article belongs to the Special Issue Advanced Technologies for User-Centered Design and User Experience)
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<p>RV show.</p>
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<p>Second-hand car market.</p>
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<p>RV factory.</p>
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<p>Occupation bar chart.</p>
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<p>Travel patterns pie chart.</p>
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<p>Better–Worse coefficient demand classification four-quadrant scatter plot example.</p>
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<p>Better–Worse coefficient demand classification four-quadrant scatter plot.</p>
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<p>Three-dimensional scanning effect.</p>
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<p>Frame diagram of function.</p>
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20 pages, 3171 KiB  
Article
Multimodal Trajectory Prediction for Diverse Vehicle Types in Autonomous Driving with Heterogeneous Data and Physical Constraints
by Maoning Ge, Kento Ohtani, Ming Ding, Yingjie Niu, Yuxiao Zhang and Kazuya Takeda
Sensors 2024, 24(22), 7323; https://doi.org/10.3390/s24227323 (registering DOI) - 16 Nov 2024
Viewed by 104
Abstract
The accurate prediction of vehicle behavior is crucial for autonomous driving systems, impacting their safety and efficiency in complex urban environments. To address the challenge of multi-agent trajectory prediction, we propose a novel model integrating multiple input modalities, including historical trajectories, map data, [...] Read more.
The accurate prediction of vehicle behavior is crucial for autonomous driving systems, impacting their safety and efficiency in complex urban environments. To address the challenge of multi-agent trajectory prediction, we propose a novel model integrating multiple input modalities, including historical trajectories, map data, vehicle features, and interaction information. Our approach employs a Conditional Variational Autoencoder (CVAE) framework with a decoder that predicts control actions using the Gaussian Mixture Model (GMM) and then converts these actions into dynamically feasible trajectories through a bicycle model. Evaluated on the nuScenes dataset, the model achieves great performance across key metrics, including minADE5 of 1.26 and minFDE5 of 2.85, demonstrating robust performance across various vehicle types and prediction horizons. These results indicate that integrating multiple data sources, physical models, and probabilistic methods significantly improves trajectory prediction accuracy and reliability for autonomous driving. Our approach generates diverse yet realistic predictions, capturing the multimodal nature of future outcomes while adhering to Physical Constraints and vehicle dynamics. Full article
(This article belongs to the Special Issue AI-Driving for Autonomous Vehicles)
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<p>Trajectory prediction for lane merging maneuvers when merging in front of a sedan (<b>left</b>) and a truck (<b>right</b>), illustrating the predicted paths, acceleration areas, and decision-making process of the autonomous vehicle.</p>
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<p>Architecture of the proposed MTP-HPC model, integrating historical trajectories, vehicle features, environmental data, and Physical Constraints to generate accurate and diverse future vehicle trajectories.</p>
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<p>The semantic map includes three separate channels: (<b>a</b>) drivable areas, (<b>b</b>) road dividers, (<b>c</b>) lane dividers, and (<b>d</b>) a composite RGB image combining the three channels.</p>
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<p>Comparison of mask maps before and after rotation based on the vehicle’s heading direction. (<b>a</b>) Before rotation. (<b>b</b>) After rotation.</p>
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<p>Trajectory prediction metrics over different prediction horizons for all vehicles.</p>
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<p>Performance metrics across vehicle types for varying numbers of predicted trajectories: (<b>a</b>) minFDE, (<b>b</b>) KDE NLL, and (<b>c</b>) minADE for 5, 10, and 15 predictions.</p>
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<p>Trajectories of different vehicle types. (<b>a</b>) Bus trajectory. (<b>b</b>) Car trajectory. (<b>c</b>) Trailer trajectory. (<b>d</b>) Truck trajectory.</p>
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<p>Three-dimensional scatter plot illustrating the relationship between inference time, the number of nodes, and the number of edges in online inference.</p>
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26 pages, 5734 KiB  
Article
Big Data Analysis of ‘VTuber’ Perceptions in South Korea: Insights for the Virtual YouTuber Industry
by Hyemin Kim and Jungho Suh
Journal. Media 2024, 5(4), 1723-1748; https://doi.org/10.3390/journalmedia5040105 (registering DOI) - 15 Nov 2024
Viewed by 214
Abstract
The global VTuber market is experiencing rapid growth, with VTubers extending beyond mere content creators to be utilized in various fields such as social interaction, public relations, and health. VTubers have the potential to expand the existing content market and contribute to increasing [...] Read more.
The global VTuber market is experiencing rapid growth, with VTubers extending beyond mere content creators to be utilized in various fields such as social interaction, public relations, and health. VTubers have the potential to expand the existing content market and contribute to increasing economic and public value. This study aims to investigate the perception of VTubers in South Korea and to provide insights that can contribute to the global activation of the VTuber entertainment industry. For this purpose, unstructured data on VTubers from the past three years, during which interest in VTubers has significantly grown in South Korea, was collected. A total of 57,891 samples were gathered from Naver, Daum, and Google, of which 50 highly relevant data points between VTubers and users were selected for analysis. First, key terms such as ‘Broadcast’, ‘YouTube’, ‘Live’, ‘Game’, ‘Youtuber’, ‘Japan’, ‘Character’, ‘Video’, ‘Sing’, ‘Virtual’, ‘Woowakgood’, ‘Fan’, ‘Idol’, ‘Korea’, ‘Twitch’, ‘IsegyeIdol’, ‘Communication’, ‘Worldview’, ‘VTuberIndustry’, ‘Contents’, ‘AfricaTV’, ‘Nijisanji’, and ‘Streamer’ were extracted. Second, CONCOR analysis revealed four clusters: ‘Famous VTubers’, ‘Features of VTubers’, ‘VTuber Industry’, and ‘VTuber Platforms’. Based on these findings, the study offers various academic and practical implications regarding VTubers in South Korea and explores the potential for global growth in the VTuber industry. Full article
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<p>Trend graph of ‘VTuber’ mentions on Google Trends.</p>
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<p>Time series analysis of data collection for ‘VTubers’.</p>
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<p>Centrality analysis and ego network density analysis for ‘VTuber’.</p>
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<p>CONCOR analysis network of 50 nodes for ‘VTuber’.</p>
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<p>The four groups and clusters among the groups.</p>
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16 pages, 19868 KiB  
Article
Kinetic Features of Degradation of R-Loops by RNase H1 from Escherichia coli
by Aleksandra A. Kuznetsova, Iurii A. Kosarev, Nadezhda A. Timofeyeva, Darya S. Novopashina and Nikita A. Kuznetsov
Int. J. Mol. Sci. 2024, 25(22), 12263; https://doi.org/10.3390/ijms252212263 - 15 Nov 2024
Viewed by 168
Abstract
R-loops can act as replication fork barriers, creating transcription–replication collisions and inducing replication stress by arresting DNA synthesis, thereby possibly causing aberrant processing and the formation of DNA strand breaks. RNase H1 (RH1) is one of the enzymes that participates in R-loop degradation [...] Read more.
R-loops can act as replication fork barriers, creating transcription–replication collisions and inducing replication stress by arresting DNA synthesis, thereby possibly causing aberrant processing and the formation of DNA strand breaks. RNase H1 (RH1) is one of the enzymes that participates in R-loop degradation by cleaving the RNA strand within a hybrid RNA–DNA duplex. In this study, the kinetic features of the interaction of RH1 from Escherichia coli with R-loops of various structures were investigated. It was found that the values of the dissociation constants Kd were minimal for complexes of RH1 with model R-loops containing a 10–11-nt RNA–DNA hybrid part, indicating effective binding. Analysis of the kinetics of RNA degradation in the R-loops by RH1 revealed that the rate-limiting step of the process was catalytic-complex formation. In the presence of RNA polymerase, the R-loops containing a ≤16-nt RNA–DNA hybrid part were efficiently protected from cleavage by RH1. In contrast, R-loops containing longer RNA–DNA hybrid parts, as a model of an abnormal transcription process, were not protected by RNA polymerase and were effectively digested by RH1. Full article
(This article belongs to the Special Issue Role of RNA Decay in Bacterial Gene Regulation)
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<p>The EMSA of the R-loops. The concentration of the RNA primer and of the DNA template and nontemplate strands was 1 µM. The presence/absence of components in the mixture is indicated by +/– signs.</p>
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<p>MST curves characterizing the interaction of RH1 D10N with R-loops.</p>
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<p>The RH1-driven cleavage of an RNA primer contained in the R-loops. The R-loops’ concentrations were 0.5 µM, and the RH1 concentration was 25 nM. Lanes show product accumulation for 0, 10, 20, 30, and 40 s and 1, 2, 5, 10, 20, and 30 min. The presence/absence of components in the mixture is indicated by +/– signs.</p>
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<p>The dependence of the observed rate constant <span class="html-italic">k</span><sub>obs</sub> of the RNA primer cleavage on the RH1 concentration.</p>
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<p>The RH1-driven cleavage of an RNA primer contained in the R-loops in the presence of the RNAP. The R-loops’ concentrations were 0.5 µM, the RNAP concentration was 1.0 µM, and the RH1 concentration was 25 nM. The lanes show product accumulation for 0, 10, 20, 30, and 40 s and 1, 2, 5, 10, 20, and 30 min. The presence/absence of components in the mixture is indicated by +/– signs.</p>
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<p>(<b>A</b>) The extent of the cleavage of an RNA primer by RH1 in the absence (gray) or presence (blue) of the RNAP. (<b>B</b>) Observed rate constant <span class="html-italic">k</span><sub>obs</sub> for RNA primer cleavage induced by RH1 in the absence (gray) or presence (blue) of the RNAP. The extent of the cleavage of an RNA primer was calculated at time point 30 min.</p>
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<p>(<b>A</b>) The crystal structure of a complex of the catalytic domain of <span class="html-italic">Bacillus halodurans</span> RNase HI with RNA–DNA hybrids (PDB ID 5SWM) [<a href="#B68-ijms-25-12263" class="html-bibr">68</a>]. (<b>B</b>) The structural features of the transcription elongation complex.</p>
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<p>The kinetic scheme of the RH1-driven cleavage of an RNA primer contained in R-loops. E: RH1; S: an R-loop; E•S: The catalytic complex of the R-loop with the enzyme; P: a reaction product.</p>
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16 pages, 966 KiB  
Article
A Diachronic Agent-Based Framework to Model MaaS Programs
by Maria Nadia Postorino and Giuseppe M. L. Sarnè
Urban Sci. 2024, 8(4), 211; https://doi.org/10.3390/urbansci8040211 - 15 Nov 2024
Viewed by 206
Abstract
In recent years, mobility as a service (MaaS) has been thought as one of the opportunities for shifting towards shared travel solutions with respect to private transport modes, particularly owned cars. Although many MaaS aspects have been explored in the literature, there are [...] Read more.
In recent years, mobility as a service (MaaS) has been thought as one of the opportunities for shifting towards shared travel solutions with respect to private transport modes, particularly owned cars. Although many MaaS aspects have been explored in the literature, there are still issues, such as platform implementations, travel solution generation, and the user’s role for making an effective system, that require more research. This paper extends and improves a previous study carried out by the authors by providing more details and experiments. The paper proposes a diachronic network model for representing travel services available in a given MaaS platform by using an agent-based approach to simulate the interactions between travel operators and travelers. Particularly, the diachronic network model allows the consideration of both the spatial and temporal features of the available transport services, while the agent-based framework allows the representation of how shared services might be used and which effects, in terms of modal split, could be expected. The final aim is to provide insights for setting the architecture of an agent-based MaaS platform where transport operators would share their data for providing seamless travel opportunities to travelers. The results obtained for a simulated test case are promising. Particularly, there are interesting findings concerning the traffic congestion boundary values that would move users towards shared travel solutions. Full article
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<p>Overview of the methodological approach.</p>
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<p>Diachronic network: representation of transport supply for scheduled services.</p>
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<p>The agent-based structure including user’s choice by discrete choice models.</p>
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<p>Multi-layers structure in the proposed framework.</p>
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<p>Percentage variations of users’ choices in the simulated MaaS context.</p>
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19 pages, 1645 KiB  
Article
Multi-Level Cross-Modal Interactive-Network-Based Semi-Supervised Multi-Modal Ship Classification
by Xin Song, Zhikui Chen, Fangming Zhong, Jing Gao, Jianning Zhang and Peng Li
Sensors 2024, 24(22), 7298; https://doi.org/10.3390/s24227298 - 15 Nov 2024
Viewed by 237
Abstract
Ship image classification identifies the type of ships in an input image, which plays a significant role in the marine field. To enhance the ship classification performance, various research focuses on studying multi-modal ship classification, which aims at combining the advantages of visible [...] Read more.
Ship image classification identifies the type of ships in an input image, which plays a significant role in the marine field. To enhance the ship classification performance, various research focuses on studying multi-modal ship classification, which aims at combining the advantages of visible images and infrared images to capture complementary information. However, the current methods simply concatenate features of different modalities to learn complementary information, which neglects the multi-level correlation between different modalities. Moreover, the existing methods require a large amount of labeled ship images to train the model. How to capture the multi-level cross-modal correlation between unlabeled and labeled data is still a challenge. In this paper, a novel semi-supervised multi-modal ship classification approach is proposed to solve these issues, which consists of two components, i.e., multi-level cross-modal interactive network and semi-supervised contrastive learning strategy. To learn comprehensive complementary information for classification, the multi-level cross-modal interactive network is designed to build local-level and global-level cross-modal feature correlation. Then, the semi-supervised contrastive learning strategy is employed to drive the optimization of the network with the intra-class consistency constraint based on supervision signals of unlabeled samples and prior label information. Extensive experiments on the public datasets demonstrate that our approach achieves state-of-the-art semi-supervised classification effectiveness. Full article
(This article belongs to the Section Sensor Networks)
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<p>Framework of the proposed approach. Given a batch of multi-modal images, the approach utilizes the multi-level cross-modal interactive network to encode deep correlated features <math display="inline"><semantics> <msup> <mi>ω</mi> <mi>i</mi> </msup> </semantics></math> of multi-modal data through mining the correlation among global-level features <math display="inline"><semantics> <msup> <mi>ς</mi> <mi>i</mi> </msup> </semantics></math> for each modal data and local-level fused features <math display="inline"><semantics> <msup> <mi>ϕ</mi> <mi>f</mi> </msup> </semantics></math>. <math display="inline"><semantics> <msup> <mi>ϕ</mi> <mi>f</mi> </msup> </semantics></math> are based on the fusion between texture features <math display="inline"><semantics> <msup> <mi>ϕ</mi> <mi>i</mi> </msup> </semantics></math> of each modal datum through the spatial and channel attention mechanism. For the optimization of the network, the self-supervised contrastive learning strategy achieves the intra-class consistency constraint based on class distribution <math display="inline"><semantics> <msup> <mi>ϖ</mi> <mi>f</mi> </msup> </semantics></math> of unlabeled data generated through the memory mechanism and prior label information, which contains unsupervised contrastive loss <math display="inline"><semantics> <msub> <mi mathvariant="script">L</mi> <mrow> <mi>c</mi> <mi>o</mi> <mi>n</mi> <mi>t</mi> <mi>r</mi> </mrow> </msub> </semantics></math> and semi-supervised divergence loss <math display="inline"><semantics> <mrow> <mo>(</mo> <msub> <mi mathvariant="script">L</mi> <mrow> <mi>d</mi> <mi>i</mi> <mi>v</mi> </mrow> </msub> <mo>,</mo> <msub> <mi mathvariant="script">L</mi> <mrow> <mi>m</mi> <mi>e</mi> <mi>m</mi> </mrow> </msub> <mo>)</mo> </mrow> </semantics></math>. In addition, A reconstructive loss <math display="inline"><semantics> <msub> <mi mathvariant="script">L</mi> <mrow> <mi>r</mi> <mi>e</mi> <mi>c</mi> </mrow> </msub> </semantics></math> is used to guide the model pre-training. A supervised loss <math display="inline"><semantics> <msub> <mi mathvariant="script">L</mi> <mrow> <mi>s</mi> <mi>p</mi> </mrow> </msub> </semantics></math> is used to learn label information. Contrastive representations <math display="inline"><semantics> <msup> <mi>ϖ</mi> <mi>i</mi> </msup> </semantics></math> are outputs of the unsupervised contrastive head module, which are the input of the memory mechanism.</p>
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<p>Framework of the proposed global-level interactive module.</p>
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<p>precision–recall curves of our approach and other competitors on two label fraction settings: (<b>a</b>–<b>d</b>) are the precision–recall curves of the classes ‘tug boat’, ‘medium passenger ship’, ‘medium other ship’, and ‘small boat’ on the first label fraction setting, respectively; (<b>e</b>–<b>h</b>) are the precision–recall curves of the classes ‘tug boat’, ‘medium passenger ship’, ‘medium other ship’, and ‘small boat’ on the second label fraction setting.</p>
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<p>The confusion matrices of the proposed approach on two label fraction settings, (<b>a</b>,<b>c</b>) denote the confusion matrices of correct sample numbers of each class; (<b>b</b>,<b>d</b>) denote the confusion matrices of the class specific accuracy.</p>
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<p>The analysis of default hyper-parameters on two different label fraction settings, unsupervised contrastive loss weight <math display="inline"><semantics> <mi>α</mi> </semantics></math> and self-supervised divergence loss weight <math display="inline"><semantics> <mi>β</mi> </semantics></math>. (<b>a</b>,<b>c</b>) Varying weight <math display="inline"><semantics> <mi>α</mi> </semantics></math>, which controls the unsupervised contrastive learning. (<b>b</b>,<b>d</b>) Varying weight <math display="inline"><semantics> <mi>β</mi> </semantics></math> for the self-supervised learning.</p>
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17 pages, 320 KiB  
Article
How Built Environment Characteristics Influence Social Interactions During Neighbourhood Walks Among Urban Inhabitants
by Sina Kuzuoglu, Troy D. Glover, Luke Moyer and Joe Todd
Int. J. Environ. Res. Public Health 2024, 21(11), 1519; https://doi.org/10.3390/ijerph21111519 - 15 Nov 2024
Viewed by 235
Abstract
As an accessible and low-risk mode of transportation and recreational activity, walking both produces and is produced by socio-spatial urban features. The health benefits of walking transcend physical fitness, remaining integral to mental health and to fostering social connectedness in urban communities. Understanding [...] Read more.
As an accessible and low-risk mode of transportation and recreational activity, walking both produces and is produced by socio-spatial urban features. The health benefits of walking transcend physical fitness, remaining integral to mental health and to fostering social connectedness in urban communities. Understanding what drives walking behaviour, therefore, warrants attention from a public health perspective. This qualitative case study focuses on the social interactions of inhabitants during neighbourhood walks and how built environment features influence walking patterns and experience. Using diaries, maps, and semi-structured interviews with 45 inhabitants of a mid-sized Canadian city, this research investigates the influence of permanent and temporary physical features on the perceived quality of inhabitants’ walks. The findings show the public visibility of urban modifications influences walking behaviour and improves social interactions, leading to a heightened sense of belonging and community. Inhabitant-led modifications in the urban space were mostly neighbourhood-bound and voyeuristic, whereas administrative interventions were more successful for collectivization. Both types of interventions are argued to foster social connectedness through different mechanisms, with positive impacts on inhabitants’ health and wellbeing. The findings underscore the relevance of community-led and administratively planned interventions in built environments in positioning public health policies associated with social cohesion and connectedness. Full article
23 pages, 5517 KiB  
Article
Research on an Eye Control Method Based on the Fusion of Facial Expression and Gaze Intention Recognition
by Xiangyang Sun and Zihan Cai
Appl. Sci. 2024, 14(22), 10520; https://doi.org/10.3390/app142210520 - 15 Nov 2024
Viewed by 231
Abstract
With the deep integration of psychology and artificial intelligence technology and other related technologies, eye control technology has achieved certain results at the practical application level. However, it is found that the accuracy of the current single-modal eye control technology is still not [...] Read more.
With the deep integration of psychology and artificial intelligence technology and other related technologies, eye control technology has achieved certain results at the practical application level. However, it is found that the accuracy of the current single-modal eye control technology is still not high, which is mainly caused by the inaccurate eye movement detection caused by the high randomness of eye movements in the process of human–computer interaction. Therefore, this study will propose an intent recognition method that fuses facial expressions and eye movement information and expects to complete an eye control method based on the fusion of facial expression and eye movement information based on the multimodal intent recognition dataset, including facial expressions and eye movement information constructed in this study. Based on the self-attention fusion strategy, the fused features are calculated, and the multi-layer perceptron is used to classify the fused features, so as to realize the mutual attention between different features, and improve the accuracy of intention recognition by enhancing the weight of effective features in a targeted manner. In order to solve the problem of inaccurate eye movement detection, an improved YOLOv5 model was proposed, and the accuracy of the model detection was improved by adding two strategies: a small target layer and a CA attention mechanism. At the same time, the corresponding eye movement behavior discrimination algorithm was combined for each eye movement action to realize the output of eye behavior instructions. Finally, the experimental verification of the eye–computer interaction scheme combining the intention recognition model and the eye movement detection model showed that the accuracy of the eye-controlled manipulator to perform various tasks could reach more than 95 percent based on this scheme. Full article
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<p>The technical route of this paper’s research.</p>
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<p>Face image dataset example.</p>
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<p>This eye movement intent detection flow chart describes the conversion of eye movement data to intent classification.</p>
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<p>Integration framework based on attention mechanism.</p>
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<p>Comparison of performance in single-mode and multimodal prediction.</p>
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<p>Line charts of five indicators of different models.</p>
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<p>Loss function curve of Anchor method before and after improvement.</p>
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<p>Structure diagram of the CA attention mechanism [<a href="#B9-applsci-14-10520" class="html-bibr">9</a>].</p>
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<p>Improved YOLOv5 model structure.</p>
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<p>Improved loss variation diagram for the YOLOv5 model.</p>
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<p>Improved loss variation diagram for the YOLOv5 model.</p>
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<p>The average accuracy (AP) curve of the improved model.</p>
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<p>The F1 score curve of the improved model.</p>
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<p>Test results before and after improvement.</p>
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<p>Human–computer interaction experiment platform.</p>
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<p>The overall flow chart of the experiment.</p>
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<p>Comparison of calculation efficiency indicators.</p>
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<p>Complete human–computer interaction process.</p>
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<p>Test results.</p>
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<p>Test results for different tasks.</p>
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22 pages, 3147 KiB  
Review
Biocomposite Scaffolds for Tissue Engineering: Materials, Fabrication Techniques and Future Directions
by Naznin Sultana, Anisa Cole and Francine Strachan
Materials 2024, 17(22), 5577; https://doi.org/10.3390/ma17225577 - 15 Nov 2024
Viewed by 254
Abstract
Tissue engineering is an interdisciplinary field that combines materials, methods, and biological molecules to engineer newly formed tissues to replace or restore functional organs. Biomaterials-based scaffolds play a crucial role in developing new tissue by interacting with human cells. Tissue engineering scaffolds with [...] Read more.
Tissue engineering is an interdisciplinary field that combines materials, methods, and biological molecules to engineer newly formed tissues to replace or restore functional organs. Biomaterials-based scaffolds play a crucial role in developing new tissue by interacting with human cells. Tissue engineering scaffolds with ideal characteristics, namely, nontoxicity, biodegradability, and appropriate mechanical and surface properties, are vital for tissue regeneration applications. However, current biocomposite scaffolds face significant limitations, particularly in achieving structural durability, controlled degradation rates, and effective cellular integration. These qualities are essential for maintaining long-term functionality in vivo. Although commonly utilized biomaterials can provide physical and chemical properties needed for tissue regeneration, inadequate biomimetic properties, as well as insufficient interactions of cells-scaffolds interaction, still need to be improved for the application of tissue engineering in vivo. It is impossible to achieve some essential features using a single material, so combining two or more materials may accomplish the requirements. In order to achieve a proper scaffold design, a suitable fabrication technique and combination of biomaterials with controlled micro or nanostructures are needed to achieve the proper biological responses. This review emphasizes advancements in scaffold durability, biocompatibility, and cellular responsiveness. It focuses on natural and synthetic polymer combinations and innovative fabrication techniques. Developing stimulus-responsive 3D scaffolds is critical, as these scaffolds enhance cell adhesion and promote functional tissue formation while maintaining structural integrity over time. This review also highlights the natural polymers, smart materials, and recent advanced techniques currently used to create emerging scaffolds for tissue regeneration applications. Full article
(This article belongs to the Special Issue Advances in Functional Soft Materials—2nd Volume)
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<p>Schematic diagram of Tissue Engineering Construct (Created with <a href="http://BioRender.com" target="_blank">BioRender.com</a>).</p>
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<p>Scanning electron micrograph of pectin/chitosan and Gelatin scaffold fabricated using the technique.</p>
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<p>Morphology of electrospun composite scaffold and HSF cell growth after three days of culture on Polycaprolactone/Gelatin scaffold (reproduced from [<a href="#B38-materials-17-05577" class="html-bibr">38</a>]).</p>
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34 pages, 4568 KiB  
Review
Nanothermodynamics: There’s Plenty of Room on the Inside
by Ralph V. Chamberlin and Stuart M. Lindsay
Nanomaterials 2024, 14(22), 1828; https://doi.org/10.3390/nano14221828 - 15 Nov 2024
Viewed by 304
Abstract
Nanothermodynamics provides the theoretical foundation for understanding stable distributions of statistically independent subsystems inside larger systems. In this review, it is emphasized that extending ideas from nanothermodynamics to simplistic models improves agreement with the measured properties of many materials. Examples include non-classical critical [...] Read more.
Nanothermodynamics provides the theoretical foundation for understanding stable distributions of statistically independent subsystems inside larger systems. In this review, it is emphasized that extending ideas from nanothermodynamics to simplistic models improves agreement with the measured properties of many materials. Examples include non-classical critical scaling near ferromagnetic transitions, thermal and dynamic behavior near liquid–glass transitions, and the 1/f-like noise in metal films and qubits. A key feature in several models is to allow separate time steps for distinct conservation laws: one type of step conserves energy and the other conserves momentum (e.g., dipole alignment). This “orthogonal dynamics” explains how the relaxation of a single parameter can exhibit multiple responses such as primary, secondary, and microscopic peaks in the dielectric loss of supercooled liquids, and the crossover in thermal fluctuations from Johnson–Nyquist (white) noise at high frequencies to 1/f-like noise at low frequencies. Nanothermodynamics also provides new insight into three basic questions. First, it gives a novel solution to Gibbs’ paradox for the entropy of the semi-classical ideal gas. Second, it yields the stable equilibrium of Ising’s original model for finite-sized chains of interacting binary degrees of freedom (“spins”). Third, it confronts Loschmidt’s paradox for the arrow of time, showing that an intrinsically irreversible step is required for maximum entropy and the second law of thermodynamics, not only in the thermodynamic limit but also in systems as small as N=2 particles. Full article
(This article belongs to the Section Synthesis, Interfaces and Nanostructures)
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<p>Finite-size thermal effects. Inset gives Hill’s fundamental equation of small-system thermodynamics, with a simple (three-energy-level) diagram for each term (adapted from [<a href="#B25-nanomaterials-14-01828" class="html-bibr">25</a>]). The first three terms on the right side (black) give the standard ways to increase the total internal energy of a system: add heat (<math display="inline"><semantics> <mrow> <mi>T</mi> <mi>d</mi> <msub> <mrow> <mi>S</mi> </mrow> <mrow> <mi>t</mi> </mrow> </msub> <mo>&gt;</mo> <mn>0</mn> </mrow> </semantics></math>), do work on the system (<math display="inline"><semantics> <mrow> <mo>−</mo> <mi>P</mi> <msub> <mrow> <mi>V</mi> </mrow> <mrow> <mi>t</mi> </mrow> </msub> <mo>&gt;</mo> <mn>0</mn> </mrow> </semantics></math>), or add particles (<math display="inline"><semantics> <mrow> <mi>μ</mi> <mi>d</mi> <msub> <mrow> <mi>N</mi> </mrow> <mrow> <mi>t</mi> </mrow> </msub> <mo>&gt;</mo> <mn>0</mn> </mrow> </semantics></math>). The fourth term (red) contains finite-size effects (surface states, length-scale terms, fluctuations, etc.) that change the width of the levels when the number of subdivisions changes if the subdivision potential is nonzero (<math display="inline"><semantics> <mrow> <mo>ℇ</mo> <mo>≠</mo> <mn>0</mn> </mrow> </semantics></math>). The main figure shows how free energy might change with the number of subdivisions, from <math display="inline"><semantics> <mrow> <mo>∆</mo> <msub> <mrow> <mi>F</mi> </mrow> <mrow> <mi>t</mi> </mrow> </msub> <mo>=</mo> <mn>0</mn> </mrow> </semantics></math> in the thermodynamic limit of no subdivisions (<math display="inline"><semantics> <mrow> <mi>η</mi> <mo>=</mo> <mn>0</mn> </mrow> </semantics></math>) to <math display="inline"><semantics> <mrow> <mo>∆</mo> <msub> <mrow> <mi>F</mi> </mrow> <mrow> <mi>t</mi> </mrow> </msub> <mo>=</mo> <mi mathvariant="normal">m</mi> <mi mathvariant="normal">i</mi> <mi mathvariant="normal">n</mi> </mrow> </semantics></math> in the nanothermodynamic limit for stable equilibrium of subsystems inside bulk samples (<math display="inline"><semantics> <mrow> <mi mathvariant="normal">ℇ</mi> <mo>=</mo> <mn>0</mn> </mrow> </semantics></math>).</p>
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<p>Schematic representation of various multiplicities. A canonical system (<b>top</b>) has two indistinguishable particles that may be on the left side (L), right side (R), or opposite sides. There is only one way to subdivide this system into canonical subsystems (<b>middle</b>), but there are many ways to subdivide it into nanocanonical subsystems (<b>bottom</b>). Adapted from [<a href="#B25-nanomaterials-14-01828" class="html-bibr">25</a>].</p>
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<p>Sketch showing two solutions to Gibbs’ paradox for combining two types of particles: X’s (blue) and O’s (red). (<b>A</b>–<b>C</b>) Canonical ensemble, where all particles of the same type are indistinguishable over all distances. (<b>D</b>–<b>F</b>) Nanocanonical ensemble, comprised of nanoscale subsystems, where similar particles can be distinguished by their location when in different subsystems. Adapted from [<a href="#B25-nanomaterials-14-01828" class="html-bibr">25</a>].</p>
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<p>Sketch showing a stable solution of the 1D Ising model at a given <math display="inline"><semantics> <mrow> <mi>T</mi> </mrow> </semantics></math>. Ten spins are in the chain. Each spin may be up or down. Each interaction between neighboring spins may be low energy (<math display="inline"><semantics> <mrow> <mo>●</mo> </mrow> </semantics></math>), high energy (<b>X</b>), or a no-energy “break” (<b>O</b>) in the interaction.</p>
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<p>(<b>D</b>) Temperature dependence of the effective scaling exponent from data (symbols) and models (lines) sketched in (<b>A</b>–<b>C</b>). Each red box encloses a separate set of spins that can be treated using mean-field theory. (<b>A</b>) Standard mean-field theory yields <math display="inline"><semantics> <mrow> <mi>γ</mi> <mo>=</mo> <mn>1</mn> </mrow> </semantics></math> (dotted line in (<b>D</b>)). (<b>B</b>) Simulations of the standard Ising model yield a monotonic increase in <math display="inline"><semantics> <mrow> <mi>γ</mi> </mrow> </semantics></math> with decreasing <math display="inline"><semantics> <mrow> <mi>T</mi> </mrow> </semantics></math> (dashed line in (<b>D</b>)). (<b>C</b>) The mean-field cluster model yields non-monotonic behavior in <math display="inline"><semantics> <mrow> <mi>γ</mi> </mrow> </semantics></math> (solid lines in (<b>D</b>)), similar to measurements on EuO (circles) and Gd (squares). Difficulty in determining <math display="inline"><semantics> <mrow> <msub> <mrow> <mi>T</mi> </mrow> <mrow> <mi>C</mi> </mrow> </msub> </mrow> </semantics></math> yields uncertainty as <math display="inline"><semantics> <mrow> <mi>T</mi> <mo>→</mo> <msub> <mrow> <mi>T</mi> </mrow> <mrow> <mi>C</mi> </mrow> </msub> </mrow> </semantics></math>, but not for <math display="inline"><semantics> <mrow> <mrow> <mrow> <mi mathvariant="normal">log</mi> <mo>[</mo> </mrow> <mo>⁡</mo> <mrow> <mo>(</mo> <mi>T</mi> <mo>−</mo> <msub> <mrow> <mi>T</mi> </mrow> <mrow> <mi>C</mi> </mrow> </msub> <mo>)</mo> <mo>/</mo> <msub> <mrow> <mi>T</mi> </mrow> <mrow> <mi>C</mi> </mrow> </msub> <mo>]</mo> </mrow> </mrow> <mo>&gt;</mo> <mo>−</mo> <mn>2</mn> </mrow> </semantics></math> where <math display="inline"><semantics> <mrow> <mi>γ</mi> </mrow> </semantics></math> of the standard Ising model shows only gradual and monotonic behavior, unlike the measurements. Adapted from [<a href="#B26-nanomaterials-14-01828" class="html-bibr">26</a>].</p>
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<p>Log-log plot of frequency-dependent loss from the orthogonal Ising model. The loss is deduced from the power spectral density (PSD) using the fluctuation-dissipation theorem. The frequency is normalized by <math display="inline"><semantics> <mrow> <msub> <mrow> <mi>f</mi> </mrow> <mrow> <mn>0</mn> </mrow> </msub> </mrow> </semantics></math> to put the microscopic peak at <math display="inline"><semantics> <mrow> <mrow> <mrow> <mi mathvariant="normal">log</mi> </mrow> <mo>⁡</mo> <mrow> <mo>(</mo> <mi>f</mi> <mo>/</mo> <msub> <mrow> <mi>f</mi> </mrow> <mrow> <mn>0</mn> </mrow> </msub> <mo>)</mo> </mrow> </mrow> <mo>~</mo> <mn>12</mn> </mrow> </semantics></math>. Simulations are made on subsystems of two sizes, each at two temperatures, as given in the legends. Adapted from [<a href="#B57-nanomaterials-14-01828" class="html-bibr">57</a>].</p>
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<p>Primary response time of glycerol. Abscissa is inverse temperature, <math display="inline"><semantics> <mrow> <msub> <mrow> <mi>T</mi> </mrow> <mrow> <mi>c</mi> </mrow> </msub> <mo>/</mo> <mi>T</mi> </mrow> </semantics></math>, where <math display="inline"><semantics> <mrow> <msub> <mrow> <mi>T</mi> </mrow> <mrow> <mi>c</mi> </mrow> </msub> </mrow> </semantics></math> is the mean-field critical temperature. The ordinate in (<b>A</b>) is <math display="inline"><semantics> <mrow> <mrow> <mrow> <mi mathvariant="normal">log</mi> </mrow> <mo>⁡</mo> <mrow> <mo>(</mo> <msub> <mrow> <mi>τ</mi> </mrow> <mrow> <mi>α</mi> </mrow> </msub> <mo>)</mo> </mrow> </mrow> </mrow> </semantics></math>, and in (<b>B</b>) it comes from a type of Stickel plot [<a href="#B84-nanomaterials-14-01828" class="html-bibr">84</a>] utilizing finite differences of <math display="inline"><semantics> <mrow> <mrow> <mrow> <mi mathvariant="normal">ln</mi> </mrow> <mo>⁡</mo> <mrow> <mo>(</mo> <msub> <mrow> <mi>τ</mi> </mrow> <mrow> <mi>α</mi> </mrow> </msub> <mo>)</mo> </mrow> </mrow> </mrow> </semantics></math>, which removes the prefactor and linearize the VFT2 function. Symbols are from measurements (Stickel [<a href="#B85-nanomaterials-14-01828" class="html-bibr">85</a>]). Various lines are from the VFT2 function Equation (6) (black), VFT function (red), and MYEGA function (blue) [<a href="#B86-nanomaterials-14-01828" class="html-bibr">86</a>]. The inset is a sketch of a simple free-energy diagram, containing two minima separated by a barrier. Primary response in the orthogonal Ising model involves fluctuations in energy that open pathways between the minima. Adapted from [<a href="#B57-nanomaterials-14-01828" class="html-bibr">57</a>].</p>
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<p>1/<span class="html-italic">f</span>-like noise from maintaining maximum entropy during equilibrium fluctuations. (<b>A</b>–<b>E</b>) Sketch of all distinct configurations of <math display="inline"><semantics> <mrow> <mi>n</mi> <mo>=</mo> <mn>4</mn> </mrow> </semantics></math> spins, arranged in order of decreasing alignment from <math display="inline"><semantics> <mrow> <mi>m</mi> <mo>=</mo> <mo>+</mo> <mn>1</mn> </mrow> </semantics></math> (<b>top</b>) to <math display="inline"><semantics> <mrow> <mo>−</mo> <mn>1</mn> </mrow> </semantics></math> (<b>bottom</b>). The multiplicity for the alignment entropy of the subsystem comes from the number of configurations in each box. (<b>F</b>) Temperature-dependent exponent for noise that varies as a function of frequency, <math display="inline"><semantics> <mrow> <mi>P</mi> <mi>S</mi> <mi>D</mi> <mo>(</mo> <mi>f</mi> <mo>)</mo> <mo>∝</mo> <mn>1</mn> <mo>/</mo> <msup> <mrow> <mi>f</mi> </mrow> <mrow> <mi>α</mi> </mrow> </msup> </mrow> </semantics></math>, with the abscissa normalized by <math display="inline"><semantics> <mrow> <mi>α</mi> <mo>=</mo> <mn>1</mn> </mrow> </semantics></math> at <math display="inline"><semantics> <mrow> <msub> <mrow> <mi>T</mi> </mrow> <mrow> <mn>1</mn> </mrow> </msub> </mrow> </semantics></math>. Solid symbols (color) are from measurements [<a href="#B88-nanomaterials-14-01828" class="html-bibr">88</a>] of noise in thin films for the metals given in the legend. Open symbols (black) are from simulations of a 3D Ising subsystems having <math display="inline"><semantics> <mrow> <mi>n</mi> <mo>=</mo> <mn>27</mn> </mrow> </semantics></math> spins with dynamics utilizing a local bath to maintain maximum entropy during fluctuations in alignment. Solid line is the best linear fit to the simulations, weighted by the inverse variance of each point. Dashed line is from a random fluctuation model [<a href="#B89-nanomaterials-14-01828" class="html-bibr">89</a>]. Adapted from [<a href="#B60-nanomaterials-14-01828" class="html-bibr">60</a>].</p>
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<p>Influence of energy on the amplitude of alignment fluctuations via orthogonal dynamics. (<b>A</b>–<b>E</b>) Configurations of <math display="inline"><semantics> <mrow> <mi>b</mi> <mo>=</mo> <mn>4</mn> </mrow> </semantics></math> interactions, arranged in order of decreasing energy. (<b>F</b>) Simulation of energy (<math display="inline"><semantics> <mrow> <mi>u</mi> <mo>/</mo> <mi>J</mi> </mrow> </semantics></math>, red) and magnetization (<math display="inline"><semantics> <mrow> <mi>m</mi> </mrow> </semantics></math>, black) as a function of time for the 1D Ising model containing <math display="inline"><semantics> <mrow> <mi>b</mi> <mo>=</mo> <mn>1000</mn> </mrow> </semantics></math> interactions, with a local bath to maintain maximum entropy. Note how the amplitude of fluctuations in <math display="inline"><semantics> <mrow> <mi>m</mi> </mrow> </semantics></math> tends to be slightly larger when <math display="inline"><semantics> <mrow> <mi>u</mi> <mo>/</mo> <mi>J</mi> <mo>&lt;</mo> <mo>−</mo> <mn>0.3</mn> </mrow> </semantics></math>. Adapted from [<a href="#B25-nanomaterials-14-01828" class="html-bibr">25</a>].</p>
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<p>Noise power spectral densities from simulations (lines) and measurements (symbols). Solid lines are from fluctuations in alignment of 1D chains of <math display="inline"><semantics> <mrow> <mi>b</mi> <mo>+</mo> <mn>1</mn> </mrow> </semantics></math> Ising spins using orthogonal dynamics while maintaining maximum entropy. Note that <math display="inline"><semantics> <mrow> <mi>b</mi> <mo>=</mo> <mn>50</mn> </mrow> </semantics></math> (blue) is a small enough subsystem to show separate Lorentzians in a 1/<span class="html-italic">f</span>-like spectrum, while <math display="inline"><semantics> <mrow> <mi>b</mi> <mo>=</mo> <mn>1000</mn> </mrow> </semantics></math> (red) is large enough to show a crossover from white noise at high frequencies (dotted) to 1/<span class="html-italic">f</span>-like noise at low frequencies with an exponent of <math display="inline"><semantics> <mrow> <mi>α</mi> <mo>=</mo> <mn>0.92</mn> </mrow> </semantics></math> (dashed). Symbols are from measurements of flux noise (solid) and tunnel-coupling noise (open) in a qubit [<a href="#B92-nanomaterials-14-01828" class="html-bibr">92</a>]. Each set of measurements has been shifted in amplitude and frequency to match the simulations. Adapted from [<a href="#B25-nanomaterials-14-01828" class="html-bibr">25</a>].</p>
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<p>Time dependence of entropies per particle (<b>A</b>–<b>E</b>) and inverse effective temperatures (<b>F</b>). Simulations utilize a Creutz-like model of 1D Ising-like spins coupled to a <span class="html-italic">ke</span> bath of Einstein oscillators. Top three left-side graphs show the time-dependence of <math display="inline"><semantics> <mrow> <mi>S</mi> <mo>/</mo> <mo>(</mo> <mi>N</mi> <mi>k</mi> <mo>)</mo> </mrow> </semantics></math> for the spins (<b>C</b>), <span class="html-italic">ke</span> bath (<b>B</b>), and their sum (<b>A</b>) in a large system, <math display="inline"><semantics> <mrow> <mi>N</mi> <mo>=</mo> <mn>2</mn> <mo>×</mo> <msup> <mrow> <mn>10</mn> </mrow> <mrow> <mn>6</mn> </mrow> </msup> </mrow> </semantics></math>. Symbols come from first averaging 10,000 sweeps, then averaging three separate simulations of each type, with error bars visible if larger than the symbol size. A simulation with irreversible dynamics (red circles) precedes every simulation with reversible dynamics (black squares). Thus, the total entropy always decreases when the dynamics becomes reversible, as indicated by the orange arrow in (<b>A</b>). Furthermore, when the rate of break-change attempts is reduced to 1/10 the rate of spin-change attempts (middle third of every simulation), reversible simulations have an entropy that depends on the dynamics. Right-side graphs show the total entropies, as in (<b>A</b>) but without time-averaging, over a greatly expanded time scale. Here the differences between reversible (black) and irreversible (red) behavior are clearly visible at the start (<b>D</b>) and end (<b>E</b>) of the simulations. The inset shows corresponding differences in the power-spectral densities of the simulations. Symbols in (<b>F</b>) give the logarithm of the ratio of probabilities of neighboring energy levels in the <span class="html-italic">ke</span> bath, <math display="inline"><semantics> <mrow> <mrow> <mrow> <mi mathvariant="normal">ln</mi> </mrow> <mo>⁡</mo> <mrow> <mo>(</mo> <msub> <mrow> <mi>p</mi> </mrow> <mrow> <mi>i</mi> </mrow> </msub> <mo>/</mo> <msub> <mrow> <mi>p</mi> </mrow> <mrow> <mi>i</mi> <mo>+</mo> <mn>1</mn> </mrow> </msub> <mo>)</mo> </mrow> </mrow> </mrow> </semantics></math>, with <math display="inline"><semantics> <mrow> <mi>i</mi> <mo>=</mo> <mn>0</mn> </mrow> </semantics></math> (squares), <math display="inline"><semantics> <mrow> <mi>i</mi> <mo>=</mo> <mn>1</mn> </mrow> </semantics></math> (circles), <math display="inline"><semantics> <mrow> <mi>i</mi> <mo>=</mo> <mn>2</mn> </mrow> </semantics></math> (up triangles), and <math display="inline"><semantics> <mrow> <mi>i</mi> <mo>=</mo> <mn>3</mn> </mrow> </semantics></math> (down triangles). These values are proportional to the difference in inverse effective temperature of the adjacent levels. A single temperature applies only to irreversible dynamics in the thermodynamic limit (red), not for reversible dynamics in this limit (black) nor for irreversible dynamics of small subsystems, <math display="inline"><semantics> <mrow> <mi>N</mi> <mo>=</mo> <mn>128</mn> </mrow> </semantics></math> (green). Adapted from [<a href="#B16-nanomaterials-14-01828" class="html-bibr">16</a>].</p>
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<p>Fluctuations in potential energy from MD simulations of Lennard–Jones crystals. Main figure shows normalized <span class="html-italic">pe</span> fluctuations for blocks of <math display="inline"><semantics> <mrow> <mi>n</mi> <mo>=</mo> <mn>32</mn> </mrow> </semantics></math> atoms in a system of <math display="inline"><semantics> <mrow> <mi>N</mi> <mo>=</mo> <mn>442,368</mn> </mrow> </semantics></math> atoms as a function interaction cutoff radius, <math display="inline"><semantics> <mrow> <msub> <mrow> <mi>r</mi> </mrow> <mrow> <mi>c</mi> </mrow> </msub> </mrow> </semantics></math>, at three temperatures given in the legend. Note that the data (open symbols) tend to be relatively constant (independent of <math display="inline"><semantics> <mrow> <mi>T</mi> </mrow> </semantics></math> and <math display="inline"><semantics> <mrow> <msub> <mrow> <mi>r</mi> </mrow> <mrow> <mi>c</mi> </mrow> </msub> </mrow> </semantics></math>) when interactions are robustly harmonic, having interaction between nearest-neighbor atoms only, <math display="inline"><semantics> <mrow> <mn>1.12</mn> <mo>≈</mo> <msup> <mrow> <mn>2</mn> </mrow> <mrow> <mn>1</mn> <mo>/</mo> <mn>6</mn> </mrow> </msup> <mo>≤</mo> <msub> <mrow> <mi>r</mi> </mrow> <mrow> <mi>c</mi> </mrow> </msub> <mo>≤</mo> <msup> <mrow> <mn>2</mn> </mrow> <mrow> <mn>4</mn> <mo>/</mo> <mn>6</mn> </mrow> </msup> <mo>≈</mo> <mn>1.59</mn> </mrow> </semantics></math>. Insets show the time dependence of energy autocorrelations in blocks (black squares) and energy correlations between nearest-neighbor blocks (red circles). Simulations are made at <math display="inline"><semantics> <mrow> <mi>k</mi> <mi>T</mi> <mo>/</mo> <msub> <mrow> <mi>ε</mi> </mrow> <mrow> <mn>0</mn> </mrow> </msub> <mo>=</mo> <mn>0.0005</mn> </mrow> </semantics></math> for blocks containing a single unit cell of the crystal, <math display="inline"><semantics> <mrow> <mi>n</mi> <mo>=</mo> <mn>4</mn> </mrow> </semantics></math>. The lower inset shows that neighboring blocks are positively correlated when all atoms have robustly harmonic interactions (<math display="inline"><semantics> <mrow> <msub> <mrow> <mi>r</mi> </mrow> <mrow> <mi>c</mi> </mrow> </msub> <mo>=</mo> <mn>1.5</mn> </mrow> </semantics></math>), while the upper inset (<math display="inline"><semantics> <mrow> <msub> <mrow> <mi>r</mi> </mrow> <mrow> <mi>c</mi> </mrow> </msub> <mo>=</mo> <mn>2.0</mn> </mrow> </semantics></math>) shows that neighboring blocks are anticorrelated when interactions include second-neighbor atoms that are anharmonic. Adapted from [<a href="#B15-nanomaterials-14-01828" class="html-bibr">15</a>] with permission from Elsevier.</p>
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27 pages, 3743 KiB  
Article
Performance Analysis and Improvement of Machine Learning with Various Feature Selection Methods for EEG-Based Emotion Classification
by Sherzod Abdumalikov, Jingeun Kim and Yourim Yoon
Appl. Sci. 2024, 14(22), 10511; https://doi.org/10.3390/app142210511 - 14 Nov 2024
Viewed by 538
Abstract
Emotion classification is a challenge in affective computing, with applications ranging from human–computer interaction to mental health monitoring. In this study, the classification of emotional states using electroencephalography (EEG) data were investigated. Specifically, the efficacy of the combination of various feature selection methods [...] Read more.
Emotion classification is a challenge in affective computing, with applications ranging from human–computer interaction to mental health monitoring. In this study, the classification of emotional states using electroencephalography (EEG) data were investigated. Specifically, the efficacy of the combination of various feature selection methods and hyperparameter tuning of machine learning algorithms for accurate and robust emotion recognition was studied. The following feature selection methods were explored: filter (SelectKBest with analysis of variance (ANOVA) F-test), embedded (least absolute shrinkage and selection operator (LASSO) tuned using Bayesian optimization (BO)), and wrapper (genetic algorithm (GA)) methods. We also executed hyperparameter tuning of machine learning algorithms using BO. The performance of each method was assessed. Two different EEG datasets, EEG Emotion and DEAP Dataset, containing 2548 and 160 features, respectively, were evaluated using random forest (RF), logistic regression, XGBoost, and support vector machine (SVM). For both datasets, the experimented three feature selection methods consistently improved the accuracy of the models. For EEG Emotion dataset, RF with LASSO achieved the best result among all the experimented methods increasing the accuracy from 98.78% to 99.39%. In the DEAP dataset experiment, XGBoost with GA showed the best result, increasing the accuracy by 1.59% and 2.84% for valence and arousal. We also show that these results are superior to those by the previous other methods in the literature. Full article
(This article belongs to the Special Issue Advances in Biosignal Processing)
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<p>EEG brainwave dataset training.</p>
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<p>Flowchart of GA.</p>
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<p>Violin plots of statistical features in the EEG Emotion dataset: (<b>a</b>) mean, (<b>b</b>) mean difference (computed between windows), (<b>c</b>) min, (<b>d</b>) min difference (computed between windows), (<b>e</b>) min difference (computed for each quarter window), (<b>f</b>) max, (<b>g</b>) max difference (computed between windows), (<b>h</b>) max difference (computed for each quarter window), (<b>i</b>) standard deviation, (<b>j</b>) standard deviation difference (computed between windows), (<b>k</b>) log, (<b>l</b>) correlation, (<b>m</b>) entropy, (<b>n</b>) FFT.</p>
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<p>Violin plot of ten randomly selected features included in the DEAP dataset.</p>
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<p>FFT-based frequency analysis of the EEG dataset: randomly selected FFT of a sample with (<b>a</b>) positive and (<b>b</b>) negative emotion levels; emotion level analysis of the DEAP dataset: (<b>c</b>) neutral labels from the EEG Emotion dataset, (<b>d</b>) valence level, and (<b>e</b>) arousal level from the DEAP dataset.</p>
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<p>Graph comparing the four performance indicators of feature selection methods on the EEG Emotion dataset: (<b>a</b>) filter-based feature selection method; (<b>b</b>) embedded-based feature selection method; (<b>c</b>) wrapper-based feature selection method.</p>
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<p>Graph comparing the four performance indicators of feature selection methods on the EEG Emotion dataset: (<b>a</b>) filter-based feature selection method; (<b>b</b>) embedded-based feature selection method; (<b>c</b>) wrapper-based feature selection method.</p>
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<p>Graph comparing the four performance indicators of feature selection methods on the DEAP dataset: (<b>a</b>) filter-based feature selection method; (<b>b</b>) embedded-based feature selection method; (<b>c</b>) wrapper-based feature selection method.</p>
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<p>Correlation heatmaps: (<b>a</b>) before feature selection, (<b>b</b>) after feature selection for the EEG Emotion dataset, (<b>c</b>) before feature selection for the DEAP dataset, (<b>d</b>) after feature selection for the valence label in the DEAP dataset, and (<b>e</b>) after feature selection for the arousal label in the DEAP dataset.</p>
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19 pages, 3072 KiB  
Article
Coordinate-Corrected and Graph-Convolution-Based Hand Pose Estimation Method
by Dang Rong and Feng Gang
Sensors 2024, 24(22), 7289; https://doi.org/10.3390/s24227289 - 14 Nov 2024
Viewed by 204
Abstract
To address the problem of low accuracy in joint point estimation in hand pose estimation methods due to the self-similarity of fingers and easy self-obscuration of hand joints, a hand pose estimation method based on coordinate correction and graph convolution is proposed. First, [...] Read more.
To address the problem of low accuracy in joint point estimation in hand pose estimation methods due to the self-similarity of fingers and easy self-obscuration of hand joints, a hand pose estimation method based on coordinate correction and graph convolution is proposed. First, the standard coordinate encoding is improved by generating an unbiased heat map, and the distribution-aware method is used for decoding coordinates to reduce the error in decoding the coordinate encoding of joints. Then, the complex dependency relationship between the joints and the relationship between pixels and joints of the hand are modeled by using graph convolution, and the feature information of the hand joints is enhanced by determining the relationship between the hand joints. Finally, the skeletal constraint loss function is used to impose constraints on the joints, and a natural and undistorted hand skeleton structure is generated. Training tests are conducted on the public gesture interaction dataset STB, and the experimental results show that the method in this paper can reduce errors in hand joint point detection and improve the estimation accuracy. Full article
(This article belongs to the Section Sensing and Imaging)
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<p>A global network model for hand pose estimation.</p>
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<p>Hourglass network model.</p>
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<p>Residual block module.</p>
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<p>Joint graph reasoning module.</p>
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<p>Skeletal topology of the hand.</p>
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<p>Hand pose estimation visualization results.</p>
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<p>Comparison of the experimental results of different methods.</p>
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15 pages, 6200 KiB  
Article
Identification of Host Factors Interacting with Movement Proteins of the 30K Family in Nicotiana tabacum
by David Villar-Álvarez, Mikhail Oliveira Leastro, Vicente Pallas and Jesús Ángel Sánchez-Navarro
Int. J. Mol. Sci. 2024, 25(22), 12251; https://doi.org/10.3390/ijms252212251 - 14 Nov 2024
Viewed by 286
Abstract
The interaction of viral proteins with host factors represents a crucial aspect of the infection process in plants. In this work, we developed a strategy to identify host factors in Nicotiana tabacum that interact with movement proteins (MPs) of the 30K family, a [...] Read more.
The interaction of viral proteins with host factors represents a crucial aspect of the infection process in plants. In this work, we developed a strategy to identify host factors in Nicotiana tabacum that interact with movement proteins (MPs) of the 30K family, a group of viral proteins around 30 kDa related to the MP of tobacco mosaic virus, which enables virus movement between plant cells. Using the alfalfa mosaic virus (AMV) MP as a model, we incorporated tags into its coding sequence, without affecting its functionality, enabling the identification of 121 potential interactors through in vivo immunoprecipitation of the tagged MP. Further analysis of five selected candidates (histone 2B (H2B), actin, 14-3-3A protein, eukaryotic initiation factor 4A (elF4A), and a peroxidase-POX-) were conducted using bimolecular fluorescence complementation (BiFC). The interactions between these factors were also studied, revealing that some form part of protein complexes associated with AMV MP. Moreover, H2B, actin, 14-3-3, and eIF4A interacted with other MPs of the 30K family. This observation suggests that, beyond functional and structural features, 30K family MPs may share common interactors. Our results demonstrate that tagging 30K family MPs is an effective strategy to identify host factors associated with these proteins during viral infection. Full article
(This article belongs to the Special Issue Plant Pathogen Interactions: 2nd Edition)
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<p>(<b>A</b>) Schematic representation of the AMV RNA 3 carrying the green fluorescence protein (GFP). Boxes correspond to the open reading frames of the GFP, the movement protein (MP), and the coat protein (CP), while arrows indicate the subgenomic promoter. The insertion site for the tags 1HA, 2HA, 3HA, or 3myc, between amino acids P256 and S257, is marked just before the C-terminal 44 amino acids of the MP (A44). (<b>B</b>) A quantitative analysis of the number (expressed as Nº foci/µm<sup>2</sup>) and size (expressed in mm<sup>2</sup>) of foci generated upon inoculation of transcripts corresponding to AMV cDNA3 wild type (control) or the constructs whose MPs carried 1HA, 2HA, 3HA, or 3myc epitopes is presented. The images on the right illustrate the infection foci generated by each of the aforementioned constructs. (<b>C</b>) Schematic representation of the procedure used to identify AMV MP interactors. <span class="html-italic">Nicotiana tabacum</span> p12 plants (plants constitutively overexpressing AMV replicase subunits 1 and 2) were inoculated with AMV cDNA3 transcripts carrying GFP at the 5′ end. Two versions of this cDNA3 were utilized: one with the MP bearing two HA tags and an untagged version, which served as a control. At six days post-inoculation, infected tissue was collected by visualizing the foci of infection. Subsequently, the total protein extraction and successive immunoprecipitation of AMV MP via the HA epitope were performed. The resulting immunoprecipitate was then subjected to mass spectrometry analysis. Experiments were performed in triplicate. Statistical analysis (Student’s <span class="html-italic">t</span>-test, <span class="html-italic">p</span> &lt; 0.05) of the data enabled the identification of differences between groups, which are represented in the graph by the letters a, b, and c.</p>
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<p>Ontological analysis of the proteins immunoprecipitated with the AMV MP. The graphs corresponding to the three ontological categories, (<b>A</b>) biological process, (<b>B</b>) molecular function, and (<b>C</b>) cellular component, are shown. Each graph illustrates the various subcategories into which the set of proteins under analysis was classified. The proportion of proteins in the sample assigned to each subcategory is indicated in brackets. Each protein can be assigned to more than one subcategory.</p>
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<p>The bimolecular fluorescence complementation (BiFC) between MPs of AMV, TMV, CMV, CPMV, and CaMV and the selected interactors (histone 2B (H2B), actin (Act), 14-3-3A, eukaryotic initiation factor 4A (eIF4A), and peroxidase (POX)) is presented. (<b>A</b>) Confocal microscopy images of representative combinations of the analysis of each interaction with the AMV MP are shown. The scale bar represents 20 µm. (<b>B</b>) Table summarizing the results of the BiFC experiments on the interaction of the MPs of the five viruses with each of the proteins analyzed. The table shows all BiFC combinations in which the Nt or Ct fragments of the GFP are placed at the N-terminus (5′Nt [GFP], 5′Ct [GFP]), or the C-terminus (3′Nt [GFP], 3′Ct [GFP]) of the corresponding protein. The results are indicated as positive (+, green) or negative (−, red), and the intensity of the signal obtained under the same conditions (+, low intensity; ++, medium intensity; +++, high intensity) is noted. The most likely cellular location suggested by the images (C, cytoplasm; M, membrane; N, nucleus; P, plasmodesmata) is also indicated. The free Nt end of GFP was employed in the BiFC negative controls for all proteins analyzed.</p>
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<p>The bimolecular fluorescence complementation (BiFC) experiments conducted among all candidate interactors with each other (histone 2B [H2B], actin [Act], 14-3-3A, eukaryotic initiation factor 4A [eIF4A], and peroxidase [POX]). (<b>A</b>) Confocal microscopy images of representative combinations of the analysis of each interaction are shown. The scale bar represents 20 µm. (<b>B</b>) Table summarizing the results of the BiFC experiments conducted among all candidate interactors (H2B, Act, 14-3-3A, eIF4A, and POX). The table shows all BiFC combinations in which the Nt or Ct fragments of the GFP are placed at the N-terminus (5′Nt [GFP], 5′Ct [GFP]) or the C-terminus (3′Nt [GFP], 3′Ct [GFP]) of the corresponding protein. The results are indicated as positive (+, green) or negative (−, red), and the intensity of the signal obtained under the same conditions (+, low intensity; ++, medium intensity +++, high intensity) is noted. The most likely cellular location suggested by the images (C, cytoplasm; M, membrane; N, nucleus; P, plasmodesmata) is also indicated.</p>
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<p>The proposed interactome is presented graphically, comprising the host factors studied with the five MP of the 30K family. The interactors are histone 2B (H2B), actin (Act), 14-3-3A, eukaryotic initiation factor 4A (eIF4A), and peroxidase (POX). MPs are identified by the name of the virus to which they belong: cauliflower mosaic virus (CaMV), cowpea mosaic virus (CPMV), cucumber mosaic virus (CMV), tobacco mosaic virus (TMV), and alfalfa mosaic virus (AMV). Solid and dashed lines between each component indicate positive and negative BiFC interaction, respectively.</p>
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34 pages, 12661 KiB  
Article
Discovery of Alanomyces manoharacharyi: A Novel Fungus Identified Using Genome Sequencing and Metabolomic Analysis
by Shiwali Rana and Sanjay K. Singh
J. Fungi 2024, 10(11), 791; https://doi.org/10.3390/jof10110791 - 14 Nov 2024
Viewed by 267
Abstract
In this study, a new species of Alanomyces was isolated as an endophyte from the bark of Azadirachta indica from Mulshi, Maharashtra. The identity of this isolate was confirmed based on the asexual morphological characteristics as well as multi-gene phylogeny based on the [...] Read more.
In this study, a new species of Alanomyces was isolated as an endophyte from the bark of Azadirachta indica from Mulshi, Maharashtra. The identity of this isolate was confirmed based on the asexual morphological characteristics as well as multi-gene phylogeny based on the internal transcribed spacer (ITS) and large subunit (LSU) nuclear ribosomal RNA (rRNA) regions. As this was the second species to be reported in this genus, we sequenced the genome of this species to increase our knowledge about the possible applicability of this genus to various industries. Its genome length was found to be 35.01 Mb, harboring 7870 protein-coding genes as per Augustus and 8101 genes using GeMoMa. Many genes were annotated using the Clusters of Orthologous Groups (COGs) database, the Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Ontology (GO), Swiss-Prot, NCBI non-redundant nucleotide sequences (NTs), and NCBI non-redundant protein sequences (NRs). The number of repeating sequences was predicted using Proteinmask and RepeatMasker; tRNA were detected using tRNAscan and snRNA were predicted using rfam_scan. The genome was also annotated using the Pathogen–Host Interactions Database (PHI-base) and AntiSMASH. To confirm the evolutionary history, average nucleotide identity (ANIb), phylogeny based on orthologous proteins, and single nucleotide polymorphisms (SNPs) were carried out. Metabolic profiling of the methanolic extract of dried biomass and ethyl acetate extract of the filtrate revealed a variety of compounds of great importance in the pharmaceutical and cosmetic industry. The characterization and genomic analysis of the newly discovered species Alanomyces manoharacharyi highlights its potential applicability across multiple industries, particularly in pharmaceuticals and cosmetics due to its diverse secondary metabolites and unique genetic features it possesses. Full article
(This article belongs to the Special Issue Taxonomy, Systematics and Evolution of Forestry Fungi, 2nd Edition)
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<p>Molecular phylogenetic analysis of the new species <span class="html-italic">Alanomyces manoharacharyi</span> based on the ML method using combined ITS and LSU sequence data. The new species is shown in blue. Statistical support values of 70% or more are displayed next to each node and UFBS values and SH−aLRT are obtained from 1000 replicates using IQ−TREE and the TIM2e + I + G4 model.</p>
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<p>Colonies on various media after 10 days. (<b>A</b>,<b>B</b>) MEA; (<b>C</b>,<b>D</b>) V8 juice agar; (<b>E</b>,<b>F</b>) CMA; (<b>G</b>,<b>H</b>) RBA; (<b>I</b>,<b>J</b>) CDA; (<b>K</b>,<b>L</b>) PCA; (<b>M</b>,<b>N</b>) SDA; (<b>O</b>,<b>P</b>) PDA; (<b>A</b>,<b>C</b>,<b>E</b>,<b>G</b>,<b>I</b>,<b>K</b>,<b>M</b>,<b>O</b>) front view; (<b>B</b>,<b>D</b>,<b>F</b>,<b>H</b>,<b>J</b>,<b>L</b>,<b>N</b>,<b>P</b>) reverse view.</p>
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<p><span class="html-italic">Alanomyces manoharacharyi</span> NFCCI 5738; (<b>A</b>–<b>D</b>) Hyphae; (<b>E</b>) Hyphae showing anastomosis; (<b>F</b>,<b>G</b>) Conidiomata; (<b>H</b>) Ruptured conidiomata; (<b>I</b>) Ruptured conidiomata showing numerous dense conidiophores; the black arrow shows ampulliform conidiogenous cells; the white arrow shows short, stumpy conidiophores; (<b>J</b>) Ruptured conidiomata with numerous conidia; (<b>K</b>–<b>M</b>) Conidia. Bar = 20 µm (<b>A</b>–<b>K</b>), 10 µm (<b>L</b>,<b>M</b>).</p>
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<p>MALDI-TOF MS spectra of <span class="html-italic">Alanomyces manoharacharyi</span> NFCCI 5738 indicating the protein profile (2–20 KD).</p>
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<p>Genome diagram of <span class="html-italic">Alanomyces manoharacharyi</span> NFCCI 5738; A: Contig; B: Negative Gene; C: Positive Gene; D: Reference Map with <span class="html-italic">Aplosporella punicola</span> CBS 121167; E: Signal Peptide with cleavage sites (Signal LIP); F: Repeat regions; G: rRNA Genes; H: GC variation and I: GC skew.</p>
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<p>Functional annotation of <span class="html-italic">Alanomyces manoharacharyi</span> NFCCI 5738 genes encoding for proteins using the Clusters of Orthologous Genes (COGs) database.</p>
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<p>Functional annotation of <span class="html-italic">Alanomyces manoharacharyi</span> NFCCI 5738 genes encoding for proteins using Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis.</p>
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<p>Functional annotation of <span class="html-italic">Alanomyces manoharacharyi</span> NFCCI 5738 predicted genes encoding for proteins using Gene Ontology (GO) analysis; Red bars represent biological processes, blue bars represent cellular component and green represent molecular function.</p>
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<p>Carbohydrate-active enzyme (CAZyme) functional classification and corresponding genes present in the <span class="html-italic">Alanomyces manoharacharyi</span> NFCCI 5738 genome. (<b>A</b>): Carbohydrate-active enzyme functional classes; (<b>B</b>): Carbohydrate-active enzyme functional subclasses.</p>
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<p>Distribution map of mutation types in the pathogen PHI phenotype of <span class="html-italic">Alanomyces manoharacharyi</span> NFCCI 5738.</p>
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<p>Comparison of biosynthetic gene cluster components in <span class="html-italic">Alanomyces manoharacharyi</span> NFCCI 5738 with known biosynthetic gene clusters for the biosynthesis of (<b>A</b>) Patulin; (<b>B</b>) Tetrahydroxynaphthalene; (<b>C</b>) Biotin; (<b>D</b>) Aspterric acid; (<b>E</b>) Mellein; (<b>F</b>) Chaetocin; (<b>G</b>) Viridicatumtoxin; (<b>H</b>) Cryptosporioptide; (<b>I</b>) Phomasetin; and (<b>J</b>) Dimerum acid.</p>
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<p>Heatmap of ANIb percentage identity between the allied genera strains compared with the <span class="html-italic">Alanomyces manoharacharyi</span> NFCCI 5738. ANIb analysis was carried out for all 55 genomes calculated based on genome sequences.</p>
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<p>Phylogenetic analysis of 55 taxa of <span class="html-italic">Alanomyces manoharacharyi</span> NFCCI 5738 and allied taxa based on the orthologous proteins identified using OrthoFinder. The new species is shown in blue. Only the bootstrap values higher than 70 are shown.</p>
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<p>The maximum phylogenetic tree is based on the 130874 core genome SNPs identified using Panseq. The number of bootstraps is indicated as well. Only the bootstrap values higher than 70 are shown. The new species is shown in blue.</p>
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<p>Results of TargetP analysis. Cumulative count of predicted proteins containing a signal peptide (SP), mitochondrial translocation signal (mTP), and no-targeting peptides (other).</p>
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<p>LC–MS analysis of extracts from <span class="html-italic">Alanomyces manoharacharyi</span> NFCCI 5738 for the identification of constituents. (<b>A</b>) Methanolic extract, Positive ion mode; (<b>B</b>) Ethyl acetate extract, Positive ion mode; (<b>C</b>) Methanolic extract, Negative ion mode; (<b>D</b>) Ethyl acetate extract, Negative ion mode.</p>
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<p>Metabolites identified from the methanolic extract of biomass and the ethyl acetate extract of the filtrate <span class="html-italic">Alanomyces manoharacharyi</span> NFCCI 5738 using LC–MS in positive and negative ion mode.</p>
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