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24 pages, 7022 KiB  
Article
Evaluation of the Sensitivity of the Weather Research and Forecasting Model to Changes in Physical Parameterizations During a Torrential Precipitation Event of the El Niño Costero 2017 in Peru
by Alejandro Sánchez Oliva, Matilde García-Valdecasas Ojeda and Raúl Arasa Agudo
Water 2025, 17(2), 209; https://doi.org/10.3390/w17020209 (registering DOI) - 14 Jan 2025
Abstract
This study evaluates the sensitivity of the Weather Research and Forecasting (WRF-ARW) model in its version 4.3.3 during different experiments on a torrential precipitation event associated with the 2017 El Niño Costero in Peru. The results are compared with two reference datasets: precipitation [...] Read more.
This study evaluates the sensitivity of the Weather Research and Forecasting (WRF-ARW) model in its version 4.3.3 during different experiments on a torrential precipitation event associated with the 2017 El Niño Costero in Peru. The results are compared with two reference datasets: precipitation estimations from CHIRPS satellite data and SENAMHI meteorological station values. The event, which had significant economic and social impacts, is simulated using two nested domains with resolutions of 9 km (d01) and 3 km (d02). A total of 22 experiments are conducted, resulting from the combination of two planetary boundary layer (PBL) schemes: Yonsei University (YSU) and Mellor–Yamada–Janjic (MYJ), with five cumulus parameterization schemes: Betts–Miller–Janjic (BMJ), Grell–Devenyi (GD), Grell–Freitas (GF), Kain–Fritsch (KF), and New Tiedtke (NT). Additionally, the effect of turning off cumulus parameterization in the inner domain (d02) or in both (d01 and d02) is explored. The results show that the YSU scheme generally provides better results than the MYJ scheme in detecting the precipitation patterns observed during the event. Furthermore, it is concluded that turning off cumulus parameterization in both domains produces satisfactory results for certain regions when it is combined with the YSU PBL scheme. However, the KF cumulus parameterization is considered the most effective for intense precipitation events in this region, although it tends to overestimate precipitation in high mountain areas. In contrast, for lighter rains, combinations of the YSU PBL scheme with the GD or NT parameterization show a superior performance. It is worth nothing that for all experiments here used, there is a clear underestimation in terms of precipitation, except in high mountain regions, where the model tends to overestimate rainfall. Full article
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39 pages, 1833 KiB  
Article
Question–Answer Methodology for Vulnerable Source Code Review via Prototype-Based Model-Agnostic Meta-Learning
by Pablo Corona-Fraga, Aldo Hernandez-Suarez, Gabriel Sanchez-Perez, Linda Karina Toscano-Medina, Hector Perez-Meana, Jose Portillo-Portillo, Jesus Olivares-Mercado and Luis Javier García Villalba
Future Internet 2025, 17(1), 33; https://doi.org/10.3390/fi17010033 (registering DOI) - 14 Jan 2025
Abstract
In cybersecurity, identifying and addressing vulnerabilities in source code is essential for maintaining secure IT environments. Traditional static and dynamic analysis techniques, although widely used, often exhibit high false-positive rates, elevated costs, and limited interpretability. Machine Learning (ML)-based approaches aim to overcome these [...] Read more.
In cybersecurity, identifying and addressing vulnerabilities in source code is essential for maintaining secure IT environments. Traditional static and dynamic analysis techniques, although widely used, often exhibit high false-positive rates, elevated costs, and limited interpretability. Machine Learning (ML)-based approaches aim to overcome these limitations but encounter challenges related to scalability and adaptability due to their reliance on large labeled datasets and their limited alignment with the requirements of secure development teams. These factors hinder their ability to adapt to rapidly evolving software environments. This study proposes an approach that integrates Prototype-Based Model-Agnostic Meta-Learning(Proto-MAML) with a Question-Answer (QA) framework that leverages the Bidirectional Encoder Representations from Transformers (BERT) model. By employing Few-Shot Learning (FSL), Proto-MAML identifies and mitigates vulnerabilities with minimal data requirements, aligning with the principles of the Secure Development Lifecycle (SDLC) and Development, Security, and Operations (DevSecOps). The QA framework allows developers to query vulnerabilities and receive precise, actionable insights, enhancing its applicability in dynamic environments that require frequent updates and real-time analysis. The model outputs are interpretable, promoting greater transparency in code review processes and enabling efficient resolution of emerging vulnerabilities. Proto-MAML demonstrates strong performance across multiple programming languages, achieving an average precision of 98.49%, recall of 98.54%, F1-score of 98.78%, and exact match rate of 98.78% in PHP, Java, C, and C++. Full article
(This article belongs to the Collection Information Systems Security)
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19 pages, 38354 KiB  
Article
Automated Volumetric Milling Area Planning for Acoustic Neuroma Surgery via Evolutionary Multi-Objective Optimization
by Sheng Yang, Haowei Li, Peihai Zhang, Wenqing Yan, Zhe Zhao, Hui Ding and Guangzhi Wang
Sensors 2025, 25(2), 448; https://doi.org/10.3390/s25020448 (registering DOI) - 14 Jan 2025
Abstract
Mastoidectomy is critical in acoustic neuroma surgery, where precise planning of the bone milling area is essential for surgical navigation. The complexity of representing the irregular volumetric area and the presence of high-risk structures (e.g., blood vessels and nerves) complicate this task. In [...] Read more.
Mastoidectomy is critical in acoustic neuroma surgery, where precise planning of the bone milling area is essential for surgical navigation. The complexity of representing the irregular volumetric area and the presence of high-risk structures (e.g., blood vessels and nerves) complicate this task. In order to determine the bone area to mill using preoperative CT images automatically, we propose an automated planning method using evolutionary multi-objective optimization for safer and more efficient milling plans. High-resolution segmentation of the adjacent risk structures is performed on preoperative CT images with a template-based approach. The maximum milling area is defined based on constraints from the risk structures and tool dimensions. Deformation fields are used to simplify the volumetric area into limited continuous parameters suitable for optimization. Finally, a multi-objective optimization algorithm is used to achieve a Pareto-optimal design. Compared with manual planning on six volumes, our method reduced the potential damage to the scala vestibuli by 29.8%, improved the milling boundary smoothness by 78.3%, and increased target accessibility by 26.4%. Assessment by surgeons confirmed the clinical feasibility of the generated plans. In summary, this study presents a parameterization approach to irregular volumetric regions, enabling automated milling area planning through optimization techniques that ensure safety and feasibility. This method is also adaptable to various volumetric planning scenarios. Full article
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12 pages, 4954 KiB  
Article
Enhancing Physical Spatial Resolution of Synthetic Aperture Sonar Images Based on Convolutional Neural Network
by Pan Xu, Dongbao Gao, Shui Yu, Guangming Li, Yun Zhao and Guojun Xu
J. Mar. Sci. Eng. 2025, 13(1), 134; https://doi.org/10.3390/jmse13010134 (registering DOI) - 14 Jan 2025
Abstract
The sonar image has limitations on the physical spatial resolution due to system configuration and underwater environment, which often leads to challenges for underwater targets detection. Here, the deep learning method is applied to enhance the physical spatial resolution of underwater sonar images. [...] Read more.
The sonar image has limitations on the physical spatial resolution due to system configuration and underwater environment, which often leads to challenges for underwater targets detection. Here, the deep learning method is applied to enhance the physical spatial resolution of underwater sonar images. Specifically, the U-shaped end-to-end neural network which contains down-sampling and up-sampling parts is proposed to improve the physical spatial resolution limited by the array aperture. The single target and multiple cases are considered separately. In both cases, the normalized loss on the testing sets declines rapidly, and the predicted high-resolution images own great agreement with the ground truth eventually. Further improvements in resolution are focused on, that is, compressing the predicted high-resolution image to its physical spatial resolution limitation. The results show that the trained end-to-end neural network could map high resolution targets to the impulse responses at the same location and amplitude with an uncertain target number. The proposed convolutional neural network approach could give a practical alternative to improve the physical spatial resolution of underwater sonar images. Full article
(This article belongs to the Special Issue Artificial Intelligence Applications in Underwater Sonar Images)
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11 pages, 2316 KiB  
Article
In Situ TEM Study of Electrical Property and Mechanical Deformation in MoS2/Graphene Heterostructures
by Suresh Giri, Subash Sharma, Rakesh D. Mahyavanshi, Golap Kalita, Yong Yang and Masaki Tanemura
Nanomaterials 2025, 15(2), 114; https://doi.org/10.3390/nano15020114 (registering DOI) - 14 Jan 2025
Abstract
We present a versatile method for synthesizing high-quality molybdenum disulfide (MoS2) crystals on graphite foil edges via chemical vapor deposition (CVD). This results in MoS2/graphene heterostructures with precise epitaxial layers and no rotational misalignment, eliminating the need for transfer [...] Read more.
We present a versatile method for synthesizing high-quality molybdenum disulfide (MoS2) crystals on graphite foil edges via chemical vapor deposition (CVD). This results in MoS2/graphene heterostructures with precise epitaxial layers and no rotational misalignment, eliminating the need for transfer processes and reducing contamination. Utilizing in situ transmission electron microscopy (TEM) equipped with a nano-manipulator and tungsten probe, we mechanically induce the folding, wrinkling, and tearing of freestanding MoS2 crystals, enabling the real-time observation of structural changes at high temporal and spatial resolutions. By applying a bias voltage through the probe, we measure the electrical properties under mechanical stress, revealing near-ohmic behavior due to compatible work functions. This approach facilitates the real-time study of mechanical and electrical properties of MoS2 crystals and can be extended to other two-dimensional materials, thereby advancing applications in flexible and bendable electronics. Full article
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17 pages, 3556 KiB  
Article
Quantification of Soil–Water Erosion Using the RUSLE Method in the Mékrou Watershed (Middle Niger River)
by Rachid Abdourahamane Attoubounou, Hamidou Diawara, Ralf Ludwig and Julien Adounkpe
ISPRS Int. J. Geo-Inf. 2025, 14(1), 28; https://doi.org/10.3390/ijgi14010028 (registering DOI) - 14 Jan 2025
Abstract
Despite nearly a century of research on water-related issues, water erosion remains one of the greatest threats to soil health and soil ecosystem services around the world. Yet, to date, data on water erosion needed to develop mitigation strategies are scarce, especially in [...] Read more.
Despite nearly a century of research on water-related issues, water erosion remains one of the greatest threats to soil health and soil ecosystem services around the world. Yet, to date, data on water erosion needed to develop mitigation strategies are scarce, especially in the Sahelian regions. The current study therefore sets out to estimate annual soil losses caused by water erosion and to analyze trends over the period of 1981–2020 in the Mékrou watershed, located in the Middle Niger river sub-basin in West Africa. The Revised Universal Soil Loss Equation, remote sensing, and the Geographic Information System (GIS) were deployed in this study. Several types of data were used, including rainfall data, sourced from meteorological stations and reanalysis datasets, which capture the temporal variability of erosive forces. Soil properties, including texture and organic matter content, were derived from FAO global soil databases to assess soil erodibility. High-resolution digital elevation models (30 m) provided detailed topographic information, crucial for calculating slope length and steepness factors. Land use and land cover data were extracted from satellite imagery, enabling the analysis of vegetation cover and anthropogenic impacts over four decades. By integrating and treating these data, this study reveals that the estimated average annual amount of water erosion in the Mékrou watershed is 6.49 t/ha/yr over 1981–2020. The dynamics of the ten-year average are highly variable, with a minimum of 3.45 t/ha/yr between 1981 and 1990, and a maximum of 8.50 t/ha/yr between 1991 and 2000. Even though these average soil losses in the Mékrou basin are below the tolerable threshold of 10 t/ha/yr, mitigation actions are needed for prevention. In addition, the spatial dynamics of water erosion are noticeably heterogeneous. The study reveals that 72.7% of the surface area of the Mékrou watershed is subject to slight water erosion below the threshold, compared with 27.3%, particularly in the mountainous south-western part, which is subject to intense erosion above the threshold. This research is the first study of soil erosion quantification with the RUSLE method and GIS in the Mékrou watershed, and fills a critical knowledge gap of the water erosion in this watershed, providing insights into erosion dynamics and supporting future sustainable land management strategies in vulnerable Sahelian landscapes. Full article
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20 pages, 17838 KiB  
Article
Estimation of Tree Vitality Reduced by Pine Needle Disease Using Multispectral Drone Images
by Langning Huo, Iryna Matsiakh, Jonas Bohlin and Michelle Cleary
Remote Sens. 2025, 17(2), 271; https://doi.org/10.3390/rs17020271 (registering DOI) - 14 Jan 2025
Viewed by 127
Abstract
Multispectral imagery from unmanned aerial vehicles (UAVs) can provide high-resolution data to map tree mortality caused by pests or diseases. Although many studies have investigated UAV-imagery-based methods to detect trees under acute stress followed by tree mortality, few have tested the feasibility and [...] Read more.
Multispectral imagery from unmanned aerial vehicles (UAVs) can provide high-resolution data to map tree mortality caused by pests or diseases. Although many studies have investigated UAV-imagery-based methods to detect trees under acute stress followed by tree mortality, few have tested the feasibility and accuracy of detecting trees under chronic stress. This study aims to develop methods and test how well UAV-based multispectral imagery can detect pine needle disease long before tree mortality. Multispectral images were acquired four times through the growing season in an area with pine trees infected by needle pathogens. Vegetation indices (VIs) were used to quantify the decline in vitality, which was verified by tree needle retention (%) estimated from the ground. Results showed that several VIs had strong correlations with the needle retention level and were used to identify severely defoliated trees (<75% needle retention) with 0.71 overall classification accuracy, while the accuracy of detecting slightly defoliated trees (>75% needle retention) was very low. The results from one study area also implied more defoliation observed from the UAV (top view) than from the ground (bottom view). We conclude that using UAV-based multispectral imagery can efficiently identify severely defoliated trees caused by needle-cast pathogens, thus assisting forest health monitoring. Full article
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43 pages, 19436 KiB  
Article
Quantification of Forest Regeneration on Forest Inventory Sample Plots Using Point Clouds from Personal Laser Scanning
by Sarah Witzmann, Christoph Gollob, Ralf Kraßnitzer, Tim Ritter, Andreas Tockner, Lukas Moik, Valentin Sarkleti, Tobias Ofner-Graff, Helmut Schume and Arne Nothdurft
Remote Sens. 2025, 17(2), 269; https://doi.org/10.3390/rs17020269 - 14 Jan 2025
Viewed by 172
Abstract
The presence of sufficient natural regeneration in mature forests is regarded as a pivotal criterion for their future stability, ensuring seamless reforestation following final harvesting operations or forest calamities. Consequently, forest regeneration is typically quantified as part of forest inventories to monitor its [...] Read more.
The presence of sufficient natural regeneration in mature forests is regarded as a pivotal criterion for their future stability, ensuring seamless reforestation following final harvesting operations or forest calamities. Consequently, forest regeneration is typically quantified as part of forest inventories to monitor its occurrence and development over time. Light detection and ranging (LiDAR) technology, particularly ground-based LiDAR, has emerged as a powerful tool for assessing typical forest inventory parameters, providing high-resolution, three-dimensional data on the forest structure. Therefore, it is logical to attempt a LiDAR-based quantification of forest regeneration, which could greatly enhance area-wide monitoring, further supporting sustainable forest management through data-driven decision making. However, examples in the literature are relatively sparse, with most relevant studies focusing on an indirect quantification of understory density from airborne LiDAR data (ALS). The objective of this study is to develop an accurate and reliable method for estimating regeneration coverage from data obtained through personal laser scanning (PLS). To this end, 19 forest inventory plots were scanned with both a personal and a high-resolution terrestrial laser scanner (TLS) for reference purposes. The voxelated point clouds obtained from the personal laser scanner were converted into raster images, providing either the canopy height, the total number of filled voxels (containing at least one LiDAR point), or the ratio of filled voxels to the total number of voxels. Local maxima in these raster images, assumed to be likely to contain tree saplings, were then used as seed points for a raster-based tree segmentation, which was employed to derive the final regeneration coverage estimate. The results showed that the estimates differed from the reference in a range of approximately −10 to +10 percentage points, with an average deviation of around 0 percentage points. In contrast, visually estimated regeneration coverages on the same forest plots deviated from the reference by between −20 and +30 percentage points, approximately −2 percentage points on average. These findings highlight the potential of PLS data for automated forest regeneration quantification, which could be further expanded to include a broader range of data collected during LiDAR-based forest inventory campaigns. Full article
(This article belongs to the Section Forest Remote Sensing)
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21 pages, 3125 KiB  
Review
Advances in Cardiovascular Multimodality Imaging in Patients with Marfan Syndrome
by Marco Alfonso Perrone, Sara Moscatelli, Giulia Guglielmi, Francesco Bianco, Deborah Cappelletti, Amedeo Pellizzon, Andrea Baggiano, Enrico Emilio Diviggiano, Maria Ricci, Pier Paolo Bassareo, Akshyaya Pradhan, Giulia Elena Mandoli, Andrea Cimini and Giuseppe Caminiti
Diagnostics 2025, 15(2), 172; https://doi.org/10.3390/diagnostics15020172 - 14 Jan 2025
Viewed by 167
Abstract
Marfan syndrome (MFS) is a genetic disorder affecting connective tissue, often leading to cardiovascular complications such as aortic aneurysms and mitral valve prolapse. Cardiovascular multimodality imaging plays a crucial role in the diagnosis, monitoring, and management of MFS patients. This review explores the [...] Read more.
Marfan syndrome (MFS) is a genetic disorder affecting connective tissue, often leading to cardiovascular complications such as aortic aneurysms and mitral valve prolapse. Cardiovascular multimodality imaging plays a crucial role in the diagnosis, monitoring, and management of MFS patients. This review explores the advancements in echocardiography, cardiovascular magnetic resonance (CMR), cardiac computed tomography (CCT), and nuclear medicine techniques in MFS. Echocardiography remains the first-line tool, essential for assessing aortic root, mitral valve abnormalities, and cardiac function. CMR provides detailed anatomical and functional assessments without radiation exposure, making it ideal for long-term follow-up. CT offers high-resolution imaging of the aorta, crucial for surgical planning, despite its ionizing radiation. Emerging nuclear medicine techniques, though less common, show promise in evaluating myocardial involvement and inflammatory conditions. This review underscores the importance of a comprehensive imaging approach to improve outcomes and guide interventions in MFS patients. It also introduces novel aspects of multimodality approaches, emphasizing their impact on early detection and management of cardiovascular complications in MFS. Full article
(This article belongs to the Section Medical Imaging and Theranostics)
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25 pages, 5747 KiB  
Article
Deformation Detection Method for Substation Noise Barrier Column Based on Deep Learning and Digital Image Technology
by Fayuan Wu, Mengting Mao, Sheng Hu, Xiaomin Dai, Qiang He, Jinhui Tang and Xian Hong
Processes 2025, 13(1), 215; https://doi.org/10.3390/pr13010215 - 14 Jan 2025
Viewed by 214
Abstract
The dynamic identification of the deformation of a noise barrier column is of great significance to the monitoring of its health. At the same time, the maximum stress of the column is an important indicator for the evaluation of its health status. Traditional [...] Read more.
The dynamic identification of the deformation of a noise barrier column is of great significance to the monitoring of its health. At the same time, the maximum stress of the column is an important indicator for the evaluation of its health status. Traditional contact displacement monitoring installs sensors on the structure, requires a lot of wiring and data acquisition equipment, and establishes a relatively independent and stable displacement reference system. Affected by the environment, wear, and material aging, the efficiency and reliability of data acquisition are reduced. A monitoring method based on digital image has the advantages of non-contact monitoring, high precision, and strong reliability. The existing DIC detection methods are limited by processor performance and image resolution, which are difficult to apply to engineering detection. In this paper, a structural displacement identification method based on convolutional neural networks (CNNs) and DIC technology is proposed. In this method, the data set is formed according to the column displacement cloud image obtained by DIC analysis, and the data set is enhanced by data normalization and region division. Through the analysis of the number of network layers and learning rate, the model design of the deep learning network is carried out. The high-speed camera image results of the test are introduced and identified by the static loading test of the equal-scale sound barrier. The results show that the structural displacement identification method based on CNN and DIC technology can accurately identify the displacement change in the structure, which greatly improves the efficiency of image displacement calculation using DIC technology. Full article
(This article belongs to the Section Energy Systems)
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11 pages, 5416 KiB  
Article
Design, Analysis, and Implementation of the Subdivision Interpolation Technique for the Grating Interferometric Micro-Displacement Sensor
by Jiuhui Tang, Haifeng Peng, Peng Yang, Shangzhou Guo, Wenqiang Sun, Li Jin, Kunyang Xie and Mengwei Li
Photonics 2025, 12(1), 64; https://doi.org/10.3390/photonics12010064 - 13 Jan 2025
Viewed by 215
Abstract
A high-resolution grating interferometric micro-displacement sensor utilizing the subdivision interpolation technique is proposed and experimentally demonstrated. As the interference laser intensity varies sinusoidally with displacement, subdivision interpolation is a promising technique to achieve micro-displacement detection with a high resolution and linearity. However, interpolation [...] Read more.
A high-resolution grating interferometric micro-displacement sensor utilizing the subdivision interpolation technique is proposed and experimentally demonstrated. As the interference laser intensity varies sinusoidally with displacement, subdivision interpolation is a promising technique to achieve micro-displacement detection with a high resolution and linearity. However, interpolation errors occur due to the phase imbalance, offset error, and amplitude mismatch between the orthogonal signals. To address these issues, a subdivision interpolation circuit, along with 90-degree phase-shifter and high-precision DC bias-voltage techniques, converts an analog sinusoidal signal into standard incremental digital signals. This novel methodology ensures that its performance is least affected by the nonidealities induced by fabrication and assembly errors. Detailed design, analysis, and experimentation studies have been conducted to validate the proposed methodology. The experimental results demonstrate that the micro-displacement sensor based on grating interferometry achieved a displacement resolution of less than 1.9 nm, an accuracy of 99.8%, and a subdivision interpolation factor of 208. This research provides a significant guide for achieving high-precision grating interferometric displacement measurements. Full article
(This article belongs to the Section Lasers, Light Sources and Sensors)
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17 pages, 4953 KiB  
Article
Deep-TEMNet: A Hybrid U-Net–2D LSTM Network for Efficient and Accurate 2.5D Transient Electromagnetic Forward Modeling
by Zhijie Qu, Yuan Gao, Kang Xing and Xiaojuan Zhang
Remote Sens. 2025, 17(2), 264; https://doi.org/10.3390/rs17020264 - 13 Jan 2025
Viewed by 196
Abstract
The transient electromagnetic (TEM) method is a crucial tool for subsurface exploration, providing essential insights into the electrical resistivity structures beneath the Earth’s surface. Traditional forward modeling approaches, such as the finite-difference time-domain (FDTD) method and the finite-element method (FEM), are computationally intensive, [...] Read more.
The transient electromagnetic (TEM) method is a crucial tool for subsurface exploration, providing essential insights into the electrical resistivity structures beneath the Earth’s surface. Traditional forward modeling approaches, such as the finite-difference time-domain (FDTD) method and the finite-element method (FEM), are computationally intensive, limiting their practicality for real-time, high-resolution, or large-scale investigations. To address these challenges, we present Deep-TEMNet, an advanced deep learning framework specifically designed for two-dimensional TEM forward modeling. Deep-TEMNet integrates the U-Net architecture with a tailored two-dimensional long short-term memory (2D LSTM) module, allowing it to effectively capture complex spatial-temporal relationships in TEM data. The U-Net component enables high-resolution spatial feature extraction, while the 2D LSTM module enhances temporal modeling by processing spatial sequences in two dimensions, thereby optimizing the representation of electromagnetic field dynamics over time. Trained on high-fidelity FEM-generated datasets, Deep-TEMNet achieves exceptional accuracy in reproducing electromagnetic field distributions across diverse geological scenarios, with a mean squared error of 0.00000134 and a root mean square percentage error of 0.002373019. The framework offers over 150 times the computational speed of traditional FEMs, with an average inference time of just 3.26 s. Extensive validation across varied geological conditions highlights Deep-TEMNet’s robustness and adaptability, establishing its potential for efficient, large-scale subsurface mapping and real-time data processing. By combining U-Net’s spatial resolution capabilities with the sequential processing strength of the 2D LSTM module, Deep-TEMNet significantly advances computational efficiency and accuracy, positioning it as a valuable tool for geophysical exploration, environmental monitoring, and other applications requiring scalable, real-time TEM analyses that are easily integrated into remote sensing workflows. Full article
23 pages, 6475 KiB  
Article
Genetic Algorithm-Enhanced Direct Method in Protein Crystallography
by Ruijiang Fu, Wu-Pei Su and Hongxing He
Molecules 2025, 30(2), 288; https://doi.org/10.3390/molecules30020288 - 13 Jan 2025
Viewed by 245
Abstract
Direct methods based on iterative projection algorithms can determine protein crystal structures directly from X-ray diffraction data without prior structural information. However, traditional direct methods often converge to local minima during electron density iteration, leading to reconstruction failure. Here, we present an enhanced [...] Read more.
Direct methods based on iterative projection algorithms can determine protein crystal structures directly from X-ray diffraction data without prior structural information. However, traditional direct methods often converge to local minima during electron density iteration, leading to reconstruction failure. Here, we present an enhanced direct method incorporating genetic algorithms for electron density modification in real space. The method features customized selection, crossover, and mutation strategies; premature convergence prevention; and efficient message passing interface (MPI) parallelization. We systematically tested the method on 15 protein structures from different space groups with diffraction resolutions of 1.35∼2.5 Å. The test cases included high-solvent-content structures, high-resolution structures with medium solvent content, and structures with low solvent content and non-crystallographic symmetry (NCS). Results showed that the enhanced method significantly improved success rates from below 30% to nearly 100%, with average phase errors reduced below 40°. The reconstructed electron density maps were of sufficient quality for automated model building. This method provides an effective alternative for solving structures that are difficult to predict accurately by AlphaFold3 or challenging to solve by molecular replacement and experimental phasing methods. The implementation is available on Github. Full article
(This article belongs to the Special Issue Advanced Research in Macromolecular Crystallography)
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10 pages, 2538 KiB  
Article
Rapid Acquisition of High-Pixel Fluorescence Lifetime Images of Living Cells via Image Reconstruction Based on Edge-Preserving Interpolation
by Yinru Zhu, Yong Guo, Xinwei Gao, Qinglin Chen, Yingying Chen, Ruijie Xiang, Baichang Lin, Luwei Wang, Yuan Lu and Wei Yan
Biosensors 2025, 15(1), 43; https://doi.org/10.3390/bios15010043 - 13 Jan 2025
Viewed by 279
Abstract
Fluorescence lifetime imaging (FLIM) has established itself as a pivotal tool for investigating biological processes within living cells. However, the extensive imaging duration necessary to accumulate sufficient photons for accurate fluorescence lifetime calculations poses a significant obstacle to achieving high-resolution monitoring of cellular [...] Read more.
Fluorescence lifetime imaging (FLIM) has established itself as a pivotal tool for investigating biological processes within living cells. However, the extensive imaging duration necessary to accumulate sufficient photons for accurate fluorescence lifetime calculations poses a significant obstacle to achieving high-resolution monitoring of cellular dynamics. In this study, we introduce an image reconstruction method based on the edge-preserving interpolation method (EPIM), which transforms rapidly acquired low-resolution FLIM data into high-pixel images, thereby eliminating the need for extended acquisition times. Specifically, we decouple the grayscale image and the fluorescence lifetime matrix and perform an individual interpolation on each. Following the interpolation of the intensity image, we apply wavelet transformation and adjust the wavelet coefficients according to the image gradients. After the inverse transformation, the original image is obtained and subjected to noise reduction to complete the image reconstruction process. Subsequently, each pixel is pseudo-color-coded based on its intensity and lifetime, preserving both structural and temporal information. We evaluated the performance of the bicubic interpolation method and our image reconstruction approach on fluorescence microspheres and fixed-cell samples, demonstrating their effectiveness in enhancing the quality of lifetime images. By applying these techniques to live-cell imaging, we can successfully obtain high-pixel FLIM images at shortened intervals, facilitating the capture of rapid cellular events. Full article
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10 pages, 2010 KiB  
Proceeding Paper
Learnable Weight Graph Neural Network for River Ice Classification
by Yifan Qu, Armina Soleymani, Denise Sudom and Katharine Andrea Scott
Proceedings 2024, 110(1), 30; https://doi.org/10.3390/proceedings2024110030 - 13 Jan 2025
Viewed by 141
Abstract
Monitoring river ice is crucial for planning safe navigation routes, with ice–water classification being one of the most important tasks in ice mapping. While high-resolutions satellite imagery, such as synthetic aperture radar (SAR), is well-suited to this task, manual interpretation of these data [...] Read more.
Monitoring river ice is crucial for planning safe navigation routes, with ice–water classification being one of the most important tasks in ice mapping. While high-resolutions satellite imagery, such as synthetic aperture radar (SAR), is well-suited to this task, manual interpretation of these data is challenging due to the large data volume. Machine learning approaches are suitable methods to overcome this; however, training the models might not be time-effective when the desired result is a narrow structure, such as a river, within a large image. To address this issue, we proposed a model incorporating a graph neural network (GNN), called learnable weights graph convolution network (LWGCN). Focusing on the winters of 2017–2021 with emphasis on the Beauharnois Canal and Lake St Lawrence regions of the Saint Lawrence River. The model first converts the SAR image into graph-structured data using simple linear iterative clustering (SLIC) to segment the SAR image, then connecting the centers of each superpixel to form graph-structured data. For the training model, the LWGCN learns the weights on each edge to determine the relationship between ice and water. By using the graph-structured data as input, the proposed model training time is eight times faster, compared to a convolution neural network (CNN) model. Our findings also indicate that the LWGCN model can significantly enhance the accuracy of ice and water classification in SAR imagery. Full article
(This article belongs to the Proceedings of The 31st International Conference on Geoinformatics)
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