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Search Results (372)

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24 pages, 51328 KiB  
Article
A Shortest Distance Priority UAV Path Planning Algorithm for Precision Agriculture
by Guoqing Zhang, Jiandong Liu, Wei Luo, Yongxiang Zhao, Ruiyin Tang, Keyu Mei and Penggang Wang
Sensors 2024, 24(23), 7514; https://doi.org/10.3390/s24237514 - 25 Nov 2024
Viewed by 288
Abstract
Unmanned aerial vehicles (UAVs) have made significant advances in autonomous sensing, particularly in the field of precision agriculture. Effective path planning is critical for autonomous navigation in large orchards to ensure that UAVs are able to recognize the optimal route between the start [...] Read more.
Unmanned aerial vehicles (UAVs) have made significant advances in autonomous sensing, particularly in the field of precision agriculture. Effective path planning is critical for autonomous navigation in large orchards to ensure that UAVs are able to recognize the optimal route between the start and end points. When UAVs perform tasks such as crop protection, monitoring, and data collection in orchard environments, they must be able to adapt to dynamic conditions. To address these challenges, this study proposes an enhanced Q-learning algorithm designed to optimize UAV path planning by combining static and dynamic obstacle avoidance features. A shortest distance priority (SDP) strategy is integrated into the learning process to minimize the distance the UAV must travel to reach the target. In addition, the root mean square propagation (RMSP) method is used to dynamically adjust the learning rate according to gradient changes, which accelerates the learning process and improves path planning efficiency. In this study, firstly, the proposed method was compared with state-of-the-art path planning techniques (including A-star, Dijkstra, and traditional Q-learning) in terms of learning time and path length through a grid-based 2D simulation environment. The results showed that the proposed method significantly improved performance compared to existing methods. In addition, 3D simulation experiments were conducted in the AirSim virtual environment. Due to the complexity of the 3D state, a deep neural network was used to calculate the Q-value based on the proposed algorithm. The results indicate that the proposed method can achieve the shortest path planning and obstacle avoidance operations in an orchard 3D simulation environment. Therefore, drones equipped with this algorithm are expected to make outstanding contributions to the development of precision agriculture through intelligent navigation and obstacle avoidance. Full article
(This article belongs to the Special Issue Application of UAV and Sensing in Precision Agriculture)
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<p>Orangery UAV collecting data.</p>
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<p>30 × 30 simulated grid obstacle environment.</p>
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<p>Discrete action set.</p>
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<p>UAV trajectory planning and collision avoidance training framework.</p>
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<p>Structure of Q-learning algorithm.</p>
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<p>Deep Q-Learning algorithm structure.</p>
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<p>Screen shot of the AirSim environment.</p>
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<p>Neural network architecture.</p>
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<p>The 5 × 5 action space.</p>
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<p>Performance of various unmanned aerial vehicle path planning algorithms in the presence of obstacles. (<b>a</b>) A-star. (<b>b</b>) Dijkstra. (<b>c</b>) Original Q-learning. (<b>d</b>) Proposed Q-learning. (<b>e</b>) Proposed Q-learning in the presence of two dynamic obstacles. (<b>f</b>) Proposed Q-learning in the presence of four dynamic obstacles.</p>
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<p>Changes in step count during training in a static environment. (<b>a</b>) steps of Q-learning algorithm; (<b>b</b>) steps of proposed Q-learning algorithm.</p>
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<p>Changes in step count during training in two dynamic environments. (<b>a</b>) steps of Q-learning algorithm; (<b>b</b>) steps of proposed Q-learning algorithm.</p>
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<p>Changes in step count during training in four dynamic environments. (<b>a</b>) steps of Q-learning algorithm; (<b>b</b>) steps of proposed Q-learning algorithm.</p>
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<p>Changes in cumulative rewards during training in a static environment. (<b>a</b>) steps of Q-learning algorithm; (<b>b</b>) steps of proposed Q-learning algorithm.</p>
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<p>Changes in cumulative rewards during training in two dynamic obstacle environments. (<b>a</b>) steps of Q-learning algorithm; (<b>b</b>) steps of proposed Q-learning algorithm.</p>
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<p>Changes in cumulative rewards during training in four dynamic obstacle environments. (<b>a</b>) steps of Q-learning algorithm; (<b>b</b>) steps of proposed Q-learning algorithm.</p>
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<p>Changes in learning rates.</p>
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<p>Training process diagram. (<b>a</b>) represents the loss function plot and (<b>b</b>) represents the maximum reward value.</p>
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<p>The obstacle avoidance process of UAV. (<b>a</b>–<b>d</b>) represents the UAV avoiding obstacles; (<b>e</b>–<b>h</b>) represents the UAV crossing an obstacle.</p>
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17 pages, 3028 KiB  
Article
Numerical Solutions to the Variational Problems by Dijkstra’s Path-Finding Algorithm
by Thanaporn Arunthong, Laddawan Rianthakool, Khanchai Prasanai, Chakrit Na Takuathung, Sakchai Chomkokard, Wiwat Wongkokua and Noparit Jinuntuya
Appl. Sci. 2024, 14(22), 10674; https://doi.org/10.3390/app142210674 - 19 Nov 2024
Viewed by 352
Abstract
In this work, we propose the general idea of using a path-finding algorithm to solve a variational problem. By interpreting a variational problem of finding the function that minimizes a functional integral as a shortest path finding, we can apply the shortest path-finding [...] Read more.
In this work, we propose the general idea of using a path-finding algorithm to solve a variational problem. By interpreting a variational problem of finding the function that minimizes a functional integral as a shortest path finding, we can apply the shortest path-finding algorithm to numerically estimate the optimal function. This can be achieved by discretizing the continuous domain of the variational problem into a spatially weighted graph. The weight of each edge is defined according to the function of the original problem. We adopt the Moser lattice as the discretization scheme since it provides adjustable connections around a vertex. We find that this number of connections is crucial to the estimation of an accurate optimal path. Dijkstra’s shortest path-finding algorithm was chosen due to its simplicity and convenience in implementation. We validate our proposal by applying Dijkstra’s path-finding algorithm to numerically solve three famous variational problems, i.e., the optical ray tracing, the brachistochrone, and the catenary problems. The first two are examples of problems with no constraint. The standard Dijkstra’s algorithm can be directly applied. The third problem is an example of a problem with an isoperimetric constraint. We apply the Lagrangian relaxation technique to relax the optimization in the standard Dijkstra algorithm to incorporate the constraint. In all cases, when the number of sublattices is large enough, the results agree well with the analytic solutions. In all cases, the same path-finding code is used, regardless of the problem details. Our approaches provide more insight and promise to be more flexible than conventional numerical methods. We expect that our method can be useful in practice when an investigation of the optimal path in a complex problem is needed. Full article
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<p>The shortest path from a to b, with the smallest accumulated weight of 20.</p>
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<p>An example of a 3 × 3 Moser lattice (large dots) with 5 sub lattices (small dots).</p>
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<p>Examples of paths join vertices a and b.</p>
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<p>An example of the designation of the weight of an edge connecting the vertices a and b is the ToF t<sub>cd</sub>. The purple arrows are the velocity vector of the wave at vertices c and d, with wave speeds v<sub>c</sub> and v<sub>d</sub>, respectively. The weight is defined as the ToF from vertices c to d along the straight edge, which can be estimated as the ratio of the Euclidian distance s<sub>cd</sub> and the average speed (v<sub>c</sub> + v<sub>d</sub>)/2. The weights of the other edges can be defined similarly.</p>
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<p>Simulation of wave refraction through two homogeneous mediums.</p>
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<p>Simulation of the onset of total internal reflection.</p>
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<p>Comparison of the ray tracing in the axial index of refraction profile. Solid lines are the exact solutions, and the dashed lines are the simulation results from Dijkstra’s algorithm.</p>
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<p>Comparison of the ray tracing in the axial index of refraction profile. Solid lines are the exact solutions, and the dashed lines are the simulation results from Dijkstra’s algorithm.</p>
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<p>Comparison of the catenary curves for various lengths. Solid lines are the exact solutions, and the dashed lines are the simulation results from Dijkstra’s algorithm.</p>
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17 pages, 3991 KiB  
Article
Intelligent Wireless Charging Path Optimization for Critical Nodes in Internet of Things-Integrated Renewable Sensor Networks
by Nelofar Aslam, Hongyu Wang, Muhammad Farhan Aslam, Muhammad Aamir and Muhammad Usman Hadi
Sensors 2024, 24(22), 7294; https://doi.org/10.3390/s24227294 - 15 Nov 2024
Viewed by 627
Abstract
Wireless sensor networks (WSNs) play a crucial role in the Internet of Things (IoT) for ubiquitous data acquisition and tracking. However, the limited battery life of sensor nodes poses significant challenges to the long-term scalability and sustainability of these networks. Wireless power transfer [...] Read more.
Wireless sensor networks (WSNs) play a crucial role in the Internet of Things (IoT) for ubiquitous data acquisition and tracking. However, the limited battery life of sensor nodes poses significant challenges to the long-term scalability and sustainability of these networks. Wireless power transfer technology offers a promising solution by enabling the recharging of energy-depleted nodes through a wireless portable charging device (WPCD). While this approach can extend node lifespan, it also introduces the challenge of bottleneck nodes—nodes whose remaining energy falls below a critical value of the threshold. The paper addresses this issue by formulating an optimization problem that aims to identify the optimal traveling path for the WPCD based on ant colony optimization (WPCD-ACO), with a focus on minimizing energy consumption and enhancing network stability. To achieve it, we propose an objective function by incorporating a time-varying z phase that is managed through linear programming to efficiently address the bottleneck nodes. Additionally, a gateway node continually updates the remaining energy levels of all nodes and relays this information to the IoT cloud. Our findings indicate that the outage-optimal distance achieved by WPCD-ACO is 6092 m, compared to 7225 m for the shortest path and 6142 m for Dijkstra’s algorithm. Furthermore, the WPCD-ACO minimizes energy consumption to 1.543 KJ, significantly outperforming other methods: single-hop at 4.8643 KJ, GR-Protocol at 3.165 KJ, grid clustering at 2.4839 KJ, and C-SARSA at 2.5869 KJ, respectively. Monte Carlo simulations validate that WPCD-ACO is outshining the existing methods in terms of the network lifetime, stability, survival rate of sensor nodes, and energy consumption. Full article
(This article belongs to the Section Intelligent Sensors)
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<p>The layout of the IoT-RWSN with an effect of phase <span class="html-italic">z</span>.</p>
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<p>The remaining energy level is uploaded and accessed from the IoT cloud.</p>
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<p>Data sending rate of bottleneck and other nodes.</p>
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<p>Reward function curve in WPCD-ACO.</p>
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<p>The arrival time of WPCD at each node is from 1 to 50.</p>
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<p>Total traveling time of the WPCD in the field.</p>
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<p>Optimal distance traveled by WPCD.</p>
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<p>Total Energy consumption of RWSN.</p>
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<p>Number of surviving nodes in the RWSN.</p>
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24 pages, 2294 KiB  
Article
Fast Algorithm for Cyber-Attack Estimation and Attack Path Extraction Using Attack Graphs with AND/OR Nodes
by Eugene Levner and Dmitry Tsadikovich
Algorithms 2024, 17(11), 504; https://doi.org/10.3390/a17110504 - 4 Nov 2024
Viewed by 547
Abstract
This paper studies the security issues for cyber–physical systems, aimed at countering potential malicious cyber-attacks. The main focus is on solving the problem of extracting the most vulnerable attack path in a known attack graph, where an attack path is a sequence of [...] Read more.
This paper studies the security issues for cyber–physical systems, aimed at countering potential malicious cyber-attacks. The main focus is on solving the problem of extracting the most vulnerable attack path in a known attack graph, where an attack path is a sequence of steps that an attacker can take to compromise the underlying network. Determining an attacker’s possible attack path is critical to cyber defenders as it helps identify threats, harden the network, and thwart attacker’s intentions. We formulate this problem as a path-finding optimization problem with logical constraints represented by AND and OR nodes. We propose a new Dijkstra-type algorithm that combines elements from Dijkstra’s shortest path algorithm and the critical path method. Although the path extraction problem is generally NP-hard, for the studied special case, the proposed algorithm determines the optimal attack path in polynomial time, O(nm), where n is the number of nodes and m is the number of edges in the attack graph. To our knowledge this is the first exact polynomial algorithm that can solve the path extraction problem for different attack graphs, both cycle-containing and cycle-free. Computational experiments with real and synthetic data have shown that the proposed algorithm consistently and quickly finds optimal solutions to the problem. Full article
(This article belongs to the Section Algorithms for Multidisciplinary Applications)
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<p>The flow chart of the proposed algorithm.</p>
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<p>(<b>a</b>) Example 1 adapted from [<a href="#B41-algorithms-17-00504" class="html-bibr">41</a>]. (<b>b</b>) Extracted minimum-length attack path.</p>
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<p>(<b>a</b>) Acyclic attack graph equipped with the node times. (<b>b</b>) Extracted minimum-length attack path for Example 2.</p>
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<p>(<b>a</b>) Attack graph with cycles. (<b>b</b>) Extracted minimum-length attack path.</p>
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<p>(<b>a</b>) The unweighted attack graph with cycles. (<b>b</b>) Extracted minimum-length attack path.</p>
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<p>Attack graph with cycles without an attack path.</p>
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<p>The extended attack graph with the start node (adapted from [<a href="#B20-algorithms-17-00504" class="html-bibr">20</a>]).</p>
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<p>Extracted minimum-length attack path for the attack graph in <a href="#algorithms-17-00504-f007" class="html-fig">Figure 7</a>.</p>
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<p>A scheme of defenders’ response to a malicious attack.</p>
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17 pages, 1260 KiB  
Article
Breast Cancer and Mental Health: Incidence and Influencing Factors—A Claims Data Analysis from Germany
by Alexandra von Au, Dominik Dannehl, Tjeerd Maarten Hein Dijkstra, Raphael Gutsfeld, Anna Sophie Scholz, Kathrin Hassdenteufel, Markus Hahn, Sabine Hawighorst-Knapstein, Alexandra Isaksson, Ariane Chaudhuri, Armin Bauer, Markus Wallwiener, Diethelm Wallwiener, Sara Yvonne Brucker, Andreas Daniel Hartkopf and Stephanie Wallwiener
Cancers 2024, 16(21), 3688; https://doi.org/10.3390/cancers16213688 - 31 Oct 2024
Viewed by 587
Abstract
Background/Objectives: With breast cancer (BC) survival improving due to optimized therapy, enhancing quality of life has become increasingly important. Both diagnosis and treatment, with their potential side effects, pose risks to mental well-being. Our study aimed to analyze the incidence and potential risk [...] Read more.
Background/Objectives: With breast cancer (BC) survival improving due to optimized therapy, enhancing quality of life has become increasingly important. Both diagnosis and treatment, with their potential side effects, pose risks to mental well-being. Our study aimed to analyze the incidence and potential risk factors for mental disorders in BC patients. Methods: This retrospective analysis used claims data from AOK Baden-Wuerttemberg, including 11,553 BC patients diagnosed via ICD code C50 between 2010 and 2020 and 31,944 age-matched controls. Patients with mental disorders in the 12 months prior to diagnosis were excluded. Mental disorders were categorized into eight groups based on ICD codes: anxiety, obsessive compulsive disorder, adjustment disorder, dissociative disorder, hypochondriac disorder, affective disorder, mania, and other neuroses. Results: Mental disorders were significantly more common in BC patients than in controls (64.2% vs. 38.1%, p < 0.01, OR 2.91, 95%CI [2.79, 3.04]). In particular, hypochondriac, anxiety, affective, and adjustment disorders occurred significantly more often in BC patients. No differences were found for mania, bipolar disease, other neuroses, obsessive compulsive-, or dissociative disorders. Furthermore, endocrine therapy was associated with psychological comorbidities (OR 1.69, p < 0.001, 95%CI [1.53, 1.86]), while primarily metastasized patients (stage C) had a lower risk than adjuvant patients in stage A (OR 0.55, p < 0.0001, 95%CI [0.49, 0.61]). Regarding surgical treatment, mastectomy patients showed lower rates of mental illnesses (61.2%) than those with breast-conserving treatment (71.6%), or especially breast reconstruction (78.4%, p < 0.01). Breast reconstruction was also associated with more hypochondriac (p < 0.01) and adjustment disorders (p < 0.01). Conclusions: So, BC patients experience significantly more mental disorders than controls, particularly when treated with endocrine therapy and breast reconstructive surgery. Full article
(This article belongs to the Section Cancer Survivorship and Quality of Life)
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<p>Flow chart regarding exclusion criteria.</p>
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<p>Differences in the occurrence of various mental disorders between BC patients and the control group; (<b>a</b>) mental disorders, (<b>b</b>) affective disorders, (<b>c</b>) anxiety disorders, (<b>d</b>) adjustment disorders, and (<b>e</b>) hypochondriac disorders. Time-to-event analysis (presentation of cumulative incidences in % (<span class="html-italic">y</span>-axis) for the occurrence of the respective event (mental disorder, adjustment disorder, etc.) over a 10-year observation period (<span class="html-italic">x</span>-axis).</p>
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<p>Differences in the occurrence of various mental disorders between BC patients and the control group; (<b>a</b>) mental disorders, (<b>b</b>) affective disorders, (<b>c</b>) anxiety disorders, (<b>d</b>) adjustment disorders, and (<b>e</b>) hypochondriac disorders. Time-to-event analysis (presentation of cumulative incidences in % (<span class="html-italic">y</span>-axis) for the occurrence of the respective event (mental disorder, adjustment disorder, etc.) over a 10-year observation period (<span class="html-italic">x</span>-axis).</p>
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<p>Differences in the occurrence of various mental disorders between BC patients and the control group; (<b>a</b>) mental disorders, (<b>b</b>) affective disorders, (<b>c</b>) anxiety disorders, (<b>d</b>) adjustment disorders, and (<b>e</b>) hypochondriac disorders. Time-to-event analysis (presentation of cumulative incidences in % (<span class="html-italic">y</span>-axis) for the occurrence of the respective event (mental disorder, adjustment disorder, etc.) over a 10-year observation period (<span class="html-italic">x</span>-axis).</p>
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34 pages, 549 KiB  
Review
Graph Neural Networks for Routing Optimization: Challenges and Opportunities
by Weiwei Jiang, Haoyu Han, Yang Zhang, Ji’an Wang, Miao He, Weixi Gu, Jianbin Mu and Xirong Cheng
Sustainability 2024, 16(21), 9239; https://doi.org/10.3390/su16219239 - 24 Oct 2024
Viewed by 1480
Abstract
In this paper, we explore the emerging role of graph neural networks (GNNs) in optimizing routing for next-generation communication networks. Traditional routing protocols, such as OSPF or the Dijkstra algorithm, often fall short in handling the complexity, scalability, and dynamic nature of modern [...] Read more.
In this paper, we explore the emerging role of graph neural networks (GNNs) in optimizing routing for next-generation communication networks. Traditional routing protocols, such as OSPF or the Dijkstra algorithm, often fall short in handling the complexity, scalability, and dynamic nature of modern network environments, including unmanned aerial vehicle (UAV), satellite, and 5G networks. By leveraging their ability to model network topologies and learn from complex interdependencies between nodes and links, GNNs offer a promising solution for distributed and scalable routing optimization. This paper provides a comprehensive review of the latest research on GNN-based routing methods, categorizing them into supervised learning for network modeling, supervised learning for routing optimization, and reinforcement learning for dynamic routing tasks. We also present a detailed analysis of existing datasets, tools, and benchmarking practices. Key challenges related to scalability, real-world deployment, explainability, and security are discussed, alongside future research directions that involve federated learning, self-supervised learning, and online learning techniques to further enhance GNN applicability. This study serves as the first comprehensive survey of GNNs for routing optimization, aiming to inspire further research and practical applications in future communication networks. Full article
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<p>The timeline of routing optimization methods.</p>
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<p>The comparison between centralized and distributed routing schemes [<a href="#B10-sustainability-16-09239" class="html-bibr">10</a>]. (<b>a</b>) Centralized routing; (<b>b</b>) Distributed routing.</p>
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<p>An example of the suboptimal routing decision made by OSPF [<a href="#B54-sustainability-16-09239" class="html-bibr">54</a>].</p>
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<p>The general framework of applying supervised learning for routing optimization [<a href="#B10-sustainability-16-09239" class="html-bibr">10</a>].</p>
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<p>The general framework of applying reinforcement learning for routing optimization.</p>
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<p>The general framework of applying GNNs in a supervised learning approach for routing optimization.</p>
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16 pages, 6207 KiB  
Article
Time-Efficient RSA over Large-Scale Multi-Domain EON
by Tong Xi, Xuehua Li and Xin Wang
Sensors 2024, 24(21), 6802; https://doi.org/10.3390/s24216802 - 23 Oct 2024
Viewed by 386
Abstract
The poor timeliness of routing has always been an urgent problem in practical operator networks, especially in situations with large-scale networks and multiple network domains. In this article, a pruning idea of routing integrated with Dijkstra’s shortest path searching is utilized to accelerate [...] Read more.
The poor timeliness of routing has always been an urgent problem in practical operator networks, especially in situations with large-scale networks and multiple network domains. In this article, a pruning idea of routing integrated with Dijkstra’s shortest path searching is utilized to accelerate the process of routing in large-scale multi-domain elastic optical networks (EONs). The layered-graph approach is adopted in the spectrum allocation stage. To this end, an efficient heuristic algorithm is proposed, called “Branch-and-Bound based Routing and Layered Graph based Spectrum Allocation algorithm (BBR-LGSA)”, which is an integrated RSA algorithm. Notably, the significant reduction in algorithm time complexity is not only reflected in the pruning method used in the routing stage but also in the construction of auxiliary graphs during the spectrum allocation stage utilizing the Branch-and-Bound method. Simulation results show that the proposed BBR-LGSA significantly reduces the average running time by nearly 78% with higher spectrum utilization in large-scale multi-domain EONs, compared with benchmark algorithms. In addition, the impact of key parameters on performance comparisons of different algorithms is evaluated. Full article
(This article belongs to the Section Sensor Networks)
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<p>The infrastructure of an EON.</p>
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<p>Example diagram of the MDEON.</p>
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<p>The BBR-LGSA algorithm disassembles the network topology.</p>
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<p>An example of a multi-domain service.</p>
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<p>The Layered Graph Method imbued with the Pruning Concept.</p>
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<p>The flowchart of BBR-LGSA algorithm.</p>
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<p>As number of service requests changes, comparison of different algorithms in terms of (<b>a</b>) average running time and (<b>b</b>) occupied FS number in small-scale networks.</p>
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<p>As number of service requests changes, comparison of different algorithms in terms of (<b>a</b>) average running time and (<b>b</b>) occupied FS number in large-scale networks.</p>
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<p>Performance comparison of algorithms based on average running time and total occupied FSs across varying network scales: (<b>a</b>) average running time for small-scale service requests, (<b>b</b>) total occupied FSs for small-scale service requests, (<b>c</b>) average running time for large-scale service requests, and (<b>d</b>) total occupied FSs for large-scale service requests.</p>
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<p>Performance comparison of different algorithms in terms of (<b>a</b>) average running time and (<b>b</b>) total number of FSs occupied as the number of domains changes.</p>
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<p>Performance comparison of different algorithms in terms of running time and total number of FSs occupied as the value of network average degree changes.</p>
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<p>Performance comparison of different algorithms in terms of average running time and total number of FSs occupied as the number of service requests changes (real network).</p>
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12 pages, 2909 KiB  
Review
Exploring Fish Parvalbumins through Allergen Names and Gene Identities
by Johannes M. Dijkstra, Annette Kuehn, Eiji Sugihara and Yasuto Kondo
Genes 2024, 15(10), 1337; https://doi.org/10.3390/genes15101337 - 18 Oct 2024
Viewed by 668
Abstract
Parvalbumins are the main source of food allergies in fish meat, with each fish possessing multiple different parvalbumins. The naming convention of these allergens in terms of allergen codes (numbers) is species-specific. Allergen codes for parvalbumin isoallergens and allergen variants are based on [...] Read more.
Parvalbumins are the main source of food allergies in fish meat, with each fish possessing multiple different parvalbumins. The naming convention of these allergens in terms of allergen codes (numbers) is species-specific. Allergen codes for parvalbumin isoallergens and allergen variants are based on sequence identities relative to the first parvalbumin allergen discovered in that particular species. This means that parvalbumins with similar allergen codes, such as catfish Pan h 1.0201 and redfish Seb m 1.0201, are not necessarily the most similar proteins, or encoded by the same gene. Here, we aim to elucidate the molecular basis of parvalbumins. We explain the complicated genetics of fish parvalbumins in an accessible manner for fish allergen researchers. Teleost or modern bony fish, which include most commercial fish species, have varying numbers of up to 22 parvalbumin genes. All have derived from ten parvalbumin genes in their common ancestor. We have named these ten genes “parvalbumin 1-to-10” (PVALB1-to-PVALB10), building on earlier nomenclature established for zebrafish. For duplicated genes, we use variant names such as, for example, “PVALB2A and PVALB2B”. As illustrative examples of our gene identification system, we systematically analyze all parvalbumin genes in two common allergy-inducing species in Japan: red seabream (Pagrus major) and chum salmon (Oncorhynchus keta). We also provide gene identifications for known parvalbumin allergens in various fish species. Full article
(This article belongs to the Section Animal Genetics and Genomics)
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<p>Parvalbumins have six α-helices A-to-F and two “EF-hand” domains for binding Ca<sup>2+</sup> ions (indicated as spheres). (<b>A</b>) The structure, in cartoon format, of common carp pvalb4_(Chr.A3) (a β2-parvalbumin; PDB accession 4CPV) [<a href="#B7-genes-15-01337" class="html-bibr">7</a>], which was the first parvalbumin of which the structure was elucidated [<a href="#B8-genes-15-01337" class="html-bibr">8</a>]. Different α-helices are in different colors. (<b>B</b>) Superimposition of various parvalbumin structures, in ribbon format, reveals a common structure. Light pink, human α-parvalbumin (1RK9); pink, pike pvalb7 α-parvalbumin (2PAS); magenta, spotless smooth-hound shark SPV-I α-parvalbumin (5ZGM); green, human oncomodulin (1TTX); splitpea green, chicken CPV3-oncomodulin (2KYF); soft purple, chicken ATH β2-parvalbumin (3FS7); cyan, Atlantic cod pvalb2 β2-parvalbumin (2MBX); green cyan, pike pvalb3 β2-parvalbumin (1PVB); aquamarine, common carp pvalb4_(Chr.A3) β2-parvalbumin (4CPV); light teal, spotless smooth-hound shark SPV-II β2-parvalbumin (5ZH6). (<b>C</b>) The structure, in ribbon format, of common carp pvalb4_(Chr.A3) (PDB accession 4CPV), shows in black those residues that are well conserved throughout EF-hand domain family molecules and in gray other residues that are well conserved throughout parvalbumins; the sidechains of these residues are shown in sticks format. This figure is used, with permission, from our open access article [<a href="#B9-genes-15-01337" class="html-bibr">9</a>], and the figures were created with the help of Pymol 2.5.2 software (<a href="https://pymol.org/2/" target="_blank">https://pymol.org/2/</a> (accessed on 27 October 2022)).</p>
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<p>Parvalbumins in extant teleost fish derive from ten parvalbumin genes in their common ancestor and belong to three different ancient parvalbumin lineages. (<b>A</b>) The immediate ancestor of extant teleost fish possessed at least the genes <span class="html-italic">PVALB1</span>-to-<span class="html-italic">PVALB10</span>, spread over four different chromosomal regions deriving from two whole-genome duplication (WGD) events. The parvalbumin genes are indicated with thick-lined boxes that are pointed in the gene direction and are colored magenta for α-parvalbumins, green for oncomodulins, and different kinds of blue for <span class="html-italic">PVALB1</span>-to-4, e<span class="html-italic">PVALB5</span>, and <span class="html-italic">PVALB10</span>. Neighboring non-parvalbumin genes are indicated by lower boxes with their name abbreviations inside. (<b>B</b>) Parvalbumin gene organization in red seabream and chum salmon, with the direction of the depicted scaffolds adjusted for homogenization. For relevant genomic region information, or Genbank accession numbers providing access to such information, see <a href="#app1-genes-15-01337" class="html-app">Supplementary Files S1 and S2</a>. Most symbols are as in (<b>A</b>), and the boxes with dashed lines and Ψ symbols indicate probable pseudogenes. (<b>C</b>) A condensed part of a phylogenetic tree created by the Maximum Likelihood method using 209 parvalbumin amino acid sequences of fishes and other species. Only the teleost fish sequences are indicated here, with between brackets the number of teleost sequences condensed in the respective part of the tree. For the complete tree and sequence information, see [<a href="#B9-genes-15-01337" class="html-bibr">9</a>]. The percentage of trees in which the associated taxa clustered together is shown next to the branches if &gt;50. Percentages of aa identity, calculated with the help of Clustal Omega (<a href="https://www.ebi.ac.uk/jdispatcher/msa/clustalo" target="_blank">https://www.ebi.ac.uk/jdispatcher/msa/clustalo</a> (accessed on 25 March 2024)), are indicated per cluster.</p>
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<p>Parvalbumin amino acid consensus sequences. Consensus sequences were created using WebLogo 2.8.2 (<a href="https://weblogo.berkeley.edu/logo.cgi" target="_blank">https://weblogo.berkeley.edu/logo.cgi</a> (accessed on 25 March 2024)) software for analysis of the parvalbumin sequences listed in [<a href="#B9-genes-15-01337" class="html-bibr">9</a>], which tried to provide a broad overview of parvalbumin sequences while focusing on teleost parvalbumins. (<b>A</b>) Sequence logo for all analyzed 209 parvalbumin sequences, with helices indicated above the alignment based on the structure of common carp pvalb4_(Chr.A3) protein (PDB database 4CPV). (<b>B</b>) Frequency plots for residues at positions that help to distinguish between the α-parvalbumins (<span class="html-italic">n</span> = 45; 30 from teleosts), oncomodulins (<span class="html-italic">n</span> = 43; 30 from teleosts), and β2-parvalbumins (<span class="html-italic">n</span> = 121; 87 from teleosts). (<b>C</b>) Frequency plots for residues at positions that help to distinguish between the combined pvalb1-to-4 sequences (<span class="html-italic">n</span> = 64), pvalb5 (<span class="html-italic">n</span> = 13), and pvalb10 (<span class="html-italic">n</span> = 10) of teleosts. (<b>D</b>) Frequency plots for residues at positions that help to distinguish between teleost pvalb1 (<span class="html-italic">n</span> = 15), pvalb2 (<span class="html-italic">n</span> = 10), pvalb3 (<span class="html-italic">n</span> = 17), and pvalb4 (<span class="html-italic">n</span> = 22). The letters represent amino acids and their sizes correspond with their level of conservation. For a discussion of the structural importance of these characteristic residues, see [<a href="#B9-genes-15-01337" class="html-bibr">9</a>]. *, many parvalbumins are a bit shorter and do not have a residue at position 109.</p>
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<p>Percentages of amino acid identity between parvalbumins of red seabream, Atlantic cod, chum salmon, chicken, and human. Colors highlight comparisons between parvalbumins belonging to the same family: β2-parvalbumins (teleost pvalb1-to-4), blue (cyan); α-parvalbumins, pink; oncomodulins, green.</p>
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19 pages, 985 KiB  
Article
On the Energy Behaviors of the Bellman–Ford and Dijkstra Algorithms: A Detailed Empirical Study
by Othman Alamoudi and Muhammad Al-Hashimi
J. Sens. Actuator Netw. 2024, 13(5), 67; https://doi.org/10.3390/jsan13050067 - 12 Oct 2024
Viewed by 910
Abstract
The Single-Source Shortest Paths (SSSP) graph problem is a fundamental computation. This study attempted to characterize concretely the energy behaviors of the two primary methods to solve it, the Bellman–Ford and Dijkstra algorithms. The very different interactions of the algorithms with the hardware [...] Read more.
The Single-Source Shortest Paths (SSSP) graph problem is a fundamental computation. This study attempted to characterize concretely the energy behaviors of the two primary methods to solve it, the Bellman–Ford and Dijkstra algorithms. The very different interactions of the algorithms with the hardware may have significant implications for energy. The study was motivated by the multidisciplinary nature of the problem. Gaining better insights should help vital applications in many domains. The work used reliable embedded sensors in an HPC-class CPU to collect empirical data for a wide range of sizes for two graph cases: complete as an upper-bound case and moderately dense. The findings confirmed that Dijkstra’s algorithm is drastically more energy efficient, as expected from its decisive time complexity advantage. In terms of power draw, however, Bellman–Ford had an advantage for sizes that fit in the upper parts of the memory hierarchy (up to 2.36 W on average), with a region of near parity in both power draw and total energy budgets. This result correlated with the interaction of lighter logic and graph footprint in memory with the Level 2 cache. It should be significant for applications that rely on solving a lot of small instances since Bellman–Ford is more general and is easier to implement. It also suggests implications for the design and parallelization of the algorithms when efficiency in power draw is in mind. Full article
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<p>Average energy consumption (in logarithmic scale), with a view on small cases (linear scale). A region where the trend reverses is highlighted. (<b>a</b>) Fully dense (complete) graphs; (<b>b</b>) Moderately dense graphs.</p>
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<p>Average execution time (logarithmic), with a linear scale view on small cases. Regions identified from the energy figures are highlighted. (<b>a</b>) Fully dense (complete) graphs; (<b>b</b>) Moderately dense graphs.</p>
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<p>Average power consumption in watts. (<b>a</b>) Fully dense (complete graph) cases; (<b>b</b>) Moderately dense cases.</p>
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<p>Graph data structure size (KiB) in memory of a sample of random graphs (base-2 logarithmic). Shaded areas mark the cases that fit in the 256 KiB L2 cache. The inner view (in linear scale) focuses on cases that fit in 512 KiB for perspective.</p>
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<p>Average cache misses by the fully dense (complete) graphs. In (<b>b</b>), the first apparent jump is insignificant and was exaggerated by the logarithmic scale. (<b>a</b>) Level 2 cache miss counts; (<b>b</b>) Level 3 cache miss counts.</p>
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<p>Moderately dense graphs (in lighter color) compared against fully dense ones. (<b>a</b>) L2 cache miss behavior; (<b>b</b>) power consumption patterns.</p>
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16 pages, 2396 KiB  
Article
Congestion-Based Earthquake Emergency Evacuation Simulation Model for Underground Structure
by Mintaek Yoo, Sunnie Haam and Woo Seung Song
Buildings 2024, 14(10), 3217; https://doi.org/10.3390/buildings14103217 - 10 Oct 2024
Viewed by 559
Abstract
Herein, the Dijkstra algorithm was used to develop a model that considers evacuee congestion and derives an optimal evacuation route in underground structures in the event of an earthquake. The ground conditions and seismic intensities were varied, and the evacuation route was analyzed [...] Read more.
Herein, the Dijkstra algorithm was used to develop a model that considers evacuee congestion and derives an optimal evacuation route in underground structures in the event of an earthquake. The ground conditions and seismic intensities were varied, and the evacuation route was analyzed for four cases. The damage index for each underground structure due to an earthquake was determined considering the ground conditions and structure depth, and the evacuation speed reduction was evaluated as a function of the damage index. A congestion coefficient was applied when the evacuation capacity exceeded the threshold to reflect the evacuation speed reduction due to increased congestion in the same evacuation route. The evacuation route in some sections changed when congestion was considered, and the final evacuation time increased significantly when the congestion coefficient was applied. When the evacuation capacity at each node exceeded the threshold, the 1/3 value was applied as the congestion coefficient to evacuation velocity. When the original evacuation route was used after applying the congestion coefficient, the evacuation time increased by up to 220%. However, the evacuation time can be reduced by applying an alternative route that considers congestion. When an alternative route derived from considering congestion was used, the evacuation time decreased by up to 45% compared to that when the original route was used, and the time required decreased by up to 840 s. Hence, the reduction in evacuation speed due to evacuee congestion must be considered to derive alternative, optimal evacuation routes in the event of a disaster. In addition, evacuation routes should account for the location of evacuees using technologies such as real-time indoor positioning to consider the congestion level of evacuees. Full article
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<p>Schematic of Dijkstra‘s algorithm.</p>
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<p>The flowchart of Dijkstra‘s algorithm.</p>
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<p>Schematic of the underground station.</p>
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<p>Node and cross-section diagram of the underground station.</p>
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<p>Results of seismic risk analysis. (Green color: None damage section).</p>
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<p>Evacuation speed as a function of the seismic damage index.</p>
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<p>Evacuation time for underground structure. (Green color: None damage section).</p>
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<p>Evacuation time for underground structure. (Green color: None damage section).</p>
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<p>Evacuation route with applying alternative route and original route with congestion coefficient. (Green color: alternative route, Orange color: original route).</p>
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22 pages, 15288 KiB  
Article
Global Pipe Optimization for Ship Engine Room
by Allessandro Utomo, Toranosuke Hotta, Naokazu Taniguchi, Tadashi Yoshimoto, Yoshitaka Tanabe, Takanobu Shimizu, Gunawan and Kunihiro Hamada
J. Mar. Sci. Eng. 2024, 12(10), 1803; https://doi.org/10.3390/jmse12101803 - 10 Oct 2024
Viewed by 593
Abstract
Pipe routing in ship design presents significant challenges because of its time-consuming nature and the need for considerable attention to detail. In recent years, the decreasing number of pipe designers has impacted the quality of pipe-routing designs. However, optimizing pipe routing is crucial [...] Read more.
Pipe routing in ship design presents significant challenges because of its time-consuming nature and the need for considerable attention to detail. In recent years, the decreasing number of pipe designers has impacted the quality of pipe-routing designs. However, optimizing pipe routing is crucial for reducing construction costs and ship production time. This study focused on optimizing the procedure and routes, considering over 500 pipes throughout the engine room of an 82,000-ton Panamax bulk carrier with three decks. Procedure optimization was based on a genetic algorithm and a system that considered individual pipe characteristics, such as type, diameter, and length. For pipe-route optimization, we used the Dijkstra algorithm, which aims to provide the shortest pipe routing by minimizing branching, bending, crossing, and obstacle avoidance. Pipe-routing optimization was divided into “basic” and “detailed” designs to derive rough and detailed routes, respectively. The basic design allowed intersections and horizontal bending, while the detailed design provided a route without intersections and minimized all bending. The optimized design was compared with pipe routing designed by diameter and shorter-path orders. In ship construction, pipe-routing optimization reduced the overall cost of pipe routing by 7% compared to other systems that typically use diameter and shortest-route orders. The study’s findings highlight the practical cost benefits and potential applications of the pipe-routing process in ship construction. Full article
(This article belongs to the Section Ocean Engineering)
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<p>Research target area consists of three decks of ship’s engine room.</p>
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<p>Statement of research problem: (<b>a</b>) route optimization; (<b>b</b>) procedure optimization. Note: ① and ② refers to the sequence of design method from small to large diameter pipe or vice versa.</p>
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<p>Overview of research problem: (<b>a</b>) basic design; (<b>b</b>) detailed design (third deck).</p>
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<p>Global optimization system configuration flow.</p>
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<p>Problem definition for basic design.</p>
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<p>High-level problem for basic design. Note: ① and ② refers to the sequence of design method from small to large diameter pipe or vice versa.</p>
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<p>Low-level problem for basic design.</p>
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<p>Basic-design grid system; (<b>a</b>) front and (<b>b</b>) back side of third deck floor plan.</p>
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<p>Basic-design grid system; (<b>a</b>) front and (<b>b</b>) back side of third deck floor plan.</p>
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<p>Basic-design pipe cost from weighted edges. Note: the colored lines (besides black lines), represent each edge for the corresponding connections of nodes.</p>
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<p>Basic-design result of pipe-routing schematics example: (<b>a</b>) third deck front side, and (<b>b</b>) third deck back side. Note: besides the pipe line schematics, please refer to <a href="#jmse-12-01803-f008" class="html-fig">Figure 8</a> for the penalty information of each floor plan area.</p>
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<p>Low-level problem procedure for detailed design.</p>
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<p>Detailed-design pipe-routing schematic results.</p>
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<p>Early pipe design set for optimization and diameter-order system procedure.</p>
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<p>Piping positions of optimizations and diameter order early design sequence of third deck.</p>
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<p>Heatmap of pipe-design space utilization of third deck. Note: the red square indicated areas predominantly used to place with high number of pipes.</p>
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16 pages, 2345 KiB  
Article
Performance Evaluation of Routing Algorithm in Satellite Self-Organizing Network on OMNeT++ Platform
by Guoquan Wang, Jiaxin Zhang, Yilong Zhang, Chang Liu and Zhaoyang Chang
Electronics 2024, 13(19), 3963; https://doi.org/10.3390/electronics13193963 - 9 Oct 2024
Viewed by 672
Abstract
Self-organizing networks of small satellites have gradually gained attention in recent years. However, self-organizing networks of small satellites have high topological change frequency, large transmission delay, and complex communication environments, which require appropriate networking and routing methods. Therefore, this paper, considering the characteristics [...] Read more.
Self-organizing networks of small satellites have gradually gained attention in recent years. However, self-organizing networks of small satellites have high topological change frequency, large transmission delay, and complex communication environments, which require appropriate networking and routing methods. Therefore, this paper, considering the characteristics of satellite networks, proposes the shortest queue length-cluster-based routing protocol (SQL-CBRP) and has built a satellite self-organizing network simulation platform based on OMNeT++. In this platform, functions such as the initial establishment of satellite self-organizing networks and cluster maintenance have been implemented. The platform was used to verify the latency and packet loss rate of SQL-CBRP and to compare it with Dijkstra and Greedy Perimeter Stateless Routing (GPSR). The results show that under high load conditions, the delay of SQL-CBRP is reduced by up to 4.1%, and the packet loss rate is reduced by up to 7.1% compared to GPSR. When the communication load is imbalanced among clusters, the delay of SQL-CBRP is reduced by up to 12.7%, and the packet loss rate is reduced by up to 16.7% compared to GPSR. Therefore, SQL-CBRP performs better in networks with high loads and imbalance loads. Full article
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<p>Satellite self-organizing network scenario.</p>
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<p>Node distribution in simulation.</p>
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<p>Structure of satellite and ground node.</p>
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<p>Functions of network layer and Mac layer of satellite and ground node.</p>
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<p>Cluster maintenance process of different nodes. (<b>a</b>) Cluster maintenance process of cluster head. (<b>b</b>) Cluster maintenance process of member. (<b>c</b>) Cluster maintenance process of isolate node.</p>
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<p>Packet loss rate and delay of voice, message, and video service in Dijkstra, GPSR, and SQL-CBRP. (<b>a</b>) Packet loss rate of different types of packets; (<b>b</b>) Delay of different types of packets.</p>
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<p>Packet loss rate and delay of Dijkstra, GPSR, and SQL-CBRP when the probability of sending packet is 60%, 80%, and 100%. (<b>a</b>) Packet loss rate of different packet-sending probability; (<b>b</b>) Delay of different packet-sending probability.</p>
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<p>Packet loss rate and delay of Dijkstra, GPSR, and SQL-CBRP when the number of heavy load clusters is 4, 8, and 12. (<b>a</b>) Packet loss rate of different numbers of heavy load clusters; (<b>b</b>) Delay of different numbers of heavy load clusters.</p>
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14 pages, 1386 KiB  
Article
Solving the Robust Shortest Path Problem with Multimodal Transportation
by Jinzuo Guo, Tianyu Liu, Guopeng Song and Bo Guo
Mathematics 2024, 12(19), 2978; https://doi.org/10.3390/math12192978 - 25 Sep 2024
Viewed by 824
Abstract
This paper explores the challenges of finding robust shortest paths in multimodal transportation networks. With the increasing complexity and uncertainties in modern transportation systems, developing efficient and reliable routing strategies that can adapt to various disruptions and modal changes is essential. By incorporating [...] Read more.
This paper explores the challenges of finding robust shortest paths in multimodal transportation networks. With the increasing complexity and uncertainties in modern transportation systems, developing efficient and reliable routing strategies that can adapt to various disruptions and modal changes is essential. By incorporating practical constraints in parameter uncertainty, this paper establishes a robust shortest path mixed-integer programming model based on a multimodal transportation network under transportation time uncertainty. To solve robust shortest path problems with multimodal transportation, we propose a modified Dijkstra algorithm that integrates parameter uncertainty with multimodal transportation. The effectiveness of the proposed multimodal transportation shortest path algorithm is verified using empirical experiments on test sets of different scales and a comparison of the runtime using a commercial solver. The experimental results on the multimodal transportation networks demonstrate the effectiveness of our approach in providing robust and efficient routing solutions. The results demonstrate that the proposed method can generate optimal solutions to the robust shortest path problem in multimodal transportation under time uncertainty and has practical significance. Full article
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<p>A sample of a transportation network.</p>
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<p>Simulation results under the normal distribution.</p>
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<p>Simulation results under the uniform distribution.</p>
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2 pages, 177 KiB  
Reply
Reply to Bouva et al. Comment on “Dijkstra et al. A False-Negative Newborn Screen for Tyrosinemia Type 1—Need for Re-Evaluation of Newborn Screening with Succinylacetone. Int. J. Neonatal Screen. 2023, 9, 66”
by Allysa M. Dijkstra, Kimber Evers-van Vliet, M. Rebecca Heiner-Fokkema, Frank A. J. A. Bodewes, Dennis K. Bos, József Zsiros, Koen J. van Aerde, Klaas Koop, Francjan J. van Spronsen and Charlotte M. A. Lubout
Int. J. Neonatal Screen. 2024, 10(4), 66; https://doi.org/10.3390/ijns10040066 - 24 Sep 2024
Viewed by 481
Abstract
We thank the authors for their comments [...] Full article
2 pages, 147 KiB  
Comment
Comment on Dijkstra et al. A False-Negative Newborn Screen for Tyrosinemia Type 1—Need for Re-Evaluation of Newborn Screening with Succinylacetone. Int. J. Neonatal Screen. 2023, 9, 66
by Marelle J. Bouva, Rose E. Maase and Ruurd M. van Elburg
Int. J. Neonatal Screen. 2024, 10(4), 65; https://doi.org/10.3390/ijns10040065 - 24 Sep 2024
Cited by 1 | Viewed by 420
Abstract
The assessment of newborn screening (NBS) algorithms’ performance to ensure quality improvements is a continuous process: false-positive referrals can enable optimisations in the shorter term, but false-negative referrals are often only discovered many years after the screening has taken place [...] Full article
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