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Search Results (354)

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19 pages, 8890 KiB  
Article
Estimation of Signal Distortion Bias Using Geometry-Free Linear Combinations
by Mohammed Abou Galala and Wu Chen
Remote Sens. 2024, 16(23), 4463; https://doi.org/10.3390/rs16234463 - 28 Nov 2024
Viewed by 65
Abstract
Signal distortion bias (SDB) in Global Navigation Satellite System (GNSS) data processing, defined as the time difference between the distorted chip and the ideal rectangular chip, leads to systematic biases in pseudoranges, affecting satellite and receiver differential code biases (DCBs). The stability of [...] Read more.
Signal distortion bias (SDB) in Global Navigation Satellite System (GNSS) data processing, defined as the time difference between the distorted chip and the ideal rectangular chip, leads to systematic biases in pseudoranges, affecting satellite and receiver differential code biases (DCBs). The stability of SDBs, allowing them to be treated as constant values, highlights the importance of investigating both their stability and estimation accuracy. Two different methods are used to estimate SDBs: (1) the hybrid method and (2) the geometry-free method. Data from approximately 430 stations, spanning the entire year of 2021, were analyzed to evaluate the estimation accuracy and the short-term and long-term stability of GPS SDBs. The analysis focused on two code signals: C1C (L1 Coarse/Acquisition) and C2W (L2 P(Y)). The results show that the short-term and long-term stability of GPS C1C and C2W SDBs is comparable for both methods, with only minor variations between them. Additionally, one month of data were used to validate the accuracy of estimated SDBs across different receiver groups. The results demonstrate that geometry-free SDBs provide stable satellite DCB estimates with an average bias below 0.15 ns and minimal residual biases, while hybrid SDBs provide satellite DCB estimates with an average bias below 0.20 ns. Overall, the comparison underscores the superior performance of geometry-free SDBs in achieving consistent satellite DCB estimates. Full article
(This article belongs to the Special Issue Multi-GNSS Precise Point Positioning (MGPPP))
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<p>Distribution of the IGS stations on 31 January 2021.</p>
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<p>Number of receivers for different receiver groups in 2021.</p>
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<p>Distribution of firmware versions across stations in 2021.</p>
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<p>Flowchart of the source code for SDB estimation using the two methods: (<b>a</b>) the hybrid method and (<b>b</b>) the geometry-free method.</p>
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<p>SDB weekly means of GPS signal C1C for satellite G01 in 2021.</p>
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<p>SDB weekly means of GPS signal C2W for satellite G01 in 2021.</p>
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<p>Annual difference between estimated SDBs for the two methods: SDB C1C (cyan); SDB C2W (blue).</p>
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<p>Annual STDs of C1C SDBs for all receiver groups in 2021.</p>
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<p>Annual STDs of C2W SDBs for all receiver groups in 2021.</p>
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<p>Weekly STDs of C1C SDBs for all receiver groups in 2021.</p>
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<p>Weekly STDs of C2W SDB for all receiver groups in 2021.</p>
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<p>DCB estimates for GPS satellite G06 from 13 receiver groups, under three different scenarios: geometry-free SDBs, geometry-fixed/geometry-free SDBs, and no-correction SDBs.</p>
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<p>Mean bias in satellite DCBs for various receiver groups under the three different scenarios: geometry-free SDBs, geometry-fixed/geometry-free SDBs, and no correction.</p>
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<p>Distribution of biases in satellite DCB for two different scenarios: geometry-free SDBs and geometry-fixed/geometry-free SDBs.</p>
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22 pages, 3053 KiB  
Article
Detecting Self-Admitted Technical Debts via Prompt-Based Method in Issue-Tracking Systems
by Jiaojiao Yu, Hao Tian, Ruiheng Li, Qiankun Zuo and Yi Di
Electronics 2024, 13(23), 4700; https://doi.org/10.3390/electronics13234700 - 28 Nov 2024
Viewed by 164
Abstract
Self-admitted technical debts (SATDs) refer to a solution in software development that selects suboptimal solutions to meet the current requirements and are intentionally introduced and documented by developers. SATDs in issue-tracking systems are a complement to those within source code comments. The effective [...] Read more.
Self-admitted technical debts (SATDs) refer to a solution in software development that selects suboptimal solutions to meet the current requirements and are intentionally introduced and documented by developers. SATDs in issue-tracking systems are a complement to those within source code comments. The effective identification of SATDs is crucial for software quality assurance and maintenance. Current studies focus on whether issue sections contain debt, but overlook specific SATD types. Meanwhile, they lack solutions for the challenge that SATD features are hard to learn due to the scarcity of instances containing SATDs. To address these problems, we propose a novel method, which is a weighted prompt tuning to identify SATDs, called WPTD. Specifically, WPTD employs a weighted prompt tuning to adapt the model with few-shot samples for insufficient training data. Moreover, to improve the performance of the model, WPTD constructs an SATD verbalizer by extracting keywords through mutual information and refining it with prior contextual information. Furthermore, it also improves SATD representation by extracting weights using the chi-square method and integrating them into the text. Finally, to reduce bias, WPTD computes the average score of results as final predicted distributions. We conduct comprehensive experiments on seven projects and the results show that our method significantly outperforms baseline approaches. In addition, we summarize the project-specific keywords, which can help developers better understand SATDs. Full article
(This article belongs to the Special Issue Software Engineering: Status and Perspectives)
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<p>An example of issue sections with different SATD types.</p>
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<p>Overview of our method.</p>
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<p>The mutual information of features and categories.</p>
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<p>An example of a source code comment containing a Requirement debt.</p>
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<p>An example of an issue containing the Requirement debts.</p>
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<p>Bar diagram of the performance obtained on our method for different number of features.</p>
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22 pages, 15337 KiB  
Article
BDS-3/GNSS Undifferenced Pseudorange and Phase Time-Variant Mixed OSB Considering the Receiver Time-Variant Biases and Its Benefit on Multi-Frequency PPP
by Guoqiang Jiao, Ke Su, Min Fan, Yuze Yang and Huaquan Hu
Remote Sens. 2024, 16(23), 4433; https://doi.org/10.3390/rs16234433 - 27 Nov 2024
Viewed by 183
Abstract
The legacy Global Navigation Satellite System (GNSS) satellite clock offsets obtained by the dual-frequency undifferenced (UD) ionospheric-free (IF) model absorb the code and phase time-variant hardware delays, which leads to the inconsistency of the precise satellite clock estimated by different frequencies. The dissimilarity [...] Read more.
The legacy Global Navigation Satellite System (GNSS) satellite clock offsets obtained by the dual-frequency undifferenced (UD) ionospheric-free (IF) model absorb the code and phase time-variant hardware delays, which leads to the inconsistency of the precise satellite clock estimated by different frequencies. The dissimilarity of the satellite clock offsets generated by different frequencies is called the inter-frequency clock bias (IFCB). Estimates of the IFCB typically employ epoch-differenced (ED) geometry-free ionosphere-free (GFIF) observations from global networks. However, this method has certain theoretical flaws by ignoring the receiver time-variant biases. We proposed a new undifferenced model coupled with satellite clock offsets, and further converted the IFCB into the code and phase time-variant mixed observable-specific signal bias (OSB) to overcome the defects of the traditional model and simplify the bias correction process of multi-frequency precise point positioning (PPP). The new model not only improves the mixed OSB performance, but also avoids the negative impact of the receiver time-variant biases on the satellite mixed OSB estimation. The STD and RMS of the original OSB can be improved by 7.5–60.9% and 9.4–66.1%, and that of ED OSB (it can reflect noise levels) can be improved by 50.0–87.5% and 60.0–88.9%, respectively. Similarly, the corresponding PPP performance for using new mixed OSB is better than that of using the traditional IFCB products. Thus, the proposed pseudorange and phase time-variant mixed OSB concept and the new undifferenced model coupled with satellite clock offsets are reliable, applicable, and effective in multi-frequency PPP. Full article
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<p>Distribution of the selected GNSS tracking stations for satellite mixed OSB estimation.</p>
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<p>Multi-GNSS pseudorange and phase time-variant mixed OSB service system.</p>
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<p>GPS L5 mixed OSB on DOY 011, 2021.</p>
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<p>The BDS-3 B1C and B2a mixed OSB on DOY 011, 2021.</p>
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<p>The Galileo E5b, E5, and E6 mixed OSB on DOY 011, 2021.</p>
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<p>Amplitudes of the mixed OSB of GPS L5, BDS-3 B1C, B2a, and Galileo E5b, E5, and E6 signals on DOY 011, 2021.</p>
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<p>Pseudorange and phase time-variant mixed epoch-differenced (ED) OSB for GPS L5 signal on DOY 011, 2021.</p>
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<p>Pseudorange and phase time-variant mixed ED OSB for BDS-3 B1C and B2a signals on DOY 011, 2021.</p>
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<p>Daily satellite pseudorange and phase time-variant mixed OSB for Galileo E5b, E5, and E6 signals on DOY 011, 2021.</p>
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<p>Daily receiver pseudorange and phase time-variant mixed OSB for GPS L5, BDS-3 B1C and B2a, and Galileo E5b, E5, and E6 signals on DOY 011, 2021.</p>
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<p>Daily JAVAD TRE-3 receiver pseudorange and phase time-variant mixed OSB at BDS-3 B2a and Galileo E6 signals on DOY 011, 2021.</p>
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<p>Positioning error of the GPS L1 + L2 + L5, BDS-3 B1I + B3I + B2a, BDS-3 B1I + B3I + B1C + B2a, and Galileo E1 + E5a + E5b + E5 + E6 multi-frequency PPP models on DOY 011, 2021.</p>
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<p>Positioning error of the GPS L1 + L2 + L5, BDS-3 B1I + B3I + B2a, BDS-3 B1I + B3I + B1C + B2a, and Galileo E1 + E5a + E5b + E5 + E6 multi-frequency PPP models on DOY 011, 2021.</p>
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<p>Phase residuals of the GPS L1 + L2 + L5, BDS-3 B1I + B3I + B2a, BDS-3 B1I + B3I + B1C + B2a, and Galileo E1 + E5a + E5b + E5 + E6 multi-frequency PPP on DOY 011, 2021.</p>
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<p>Phase residuals of the GPS L1 + L2 + L5, BDS-3 B1I + B3I + B2a, BDS-3 B1I + B3I + B1C + B2a, and Galileo E1 + E5a + E5b + E5 + E6 multi-frequency PPP on DOY 011, 2021.</p>
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<p>Boxplot of the convergence time for GPS L1 + L2 + L5, BDS-3 B1I + B3I + B2a, BDS-3 B1I + B3I + B1C + B2a, and Galileo E1 + E5a + E5b + E5 + E6 multi-frequency PPP models.</p>
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<p>Boxplot of the positioning accuracy for GPS L1 + L2 + L5, BDS-3 B1I + B3I + B2a, BDS-3 B1I + B3I + B1C + B2a, and Galileo E1 + E5a + E5b + E5 + E6 multi-frequency PPP models.</p>
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23 pages, 5624 KiB  
Article
Investigation on the Impact of the 2022 Luding M6.8 Earthquake on Regional Low-Frequency Time Code Signals in Northern China
by Fan Zhao, Ping Feng, Zhen Qi, Langlang Cheng, Xin Wang, Luxi Huang, Qiang Liu, Yingming Chen, Xiaoqian Ren and Yu Hua
Atmosphere 2024, 15(12), 1419; https://doi.org/10.3390/atmos15121419 - 26 Nov 2024
Viewed by 246
Abstract
Low-Frequency Time Code time service technology, as an important means of ground-based radio time dissemination, can be divided into ground wave zone and sky wave zone according to different receiving and transmitting distances. Ground waves travel primarily along the Earth’s surface, while sky [...] Read more.
Low-Frequency Time Code time service technology, as an important means of ground-based radio time dissemination, can be divided into ground wave zone and sky wave zone according to different receiving and transmitting distances. Ground waves travel primarily along the Earth’s surface, while sky waves propagate over long distances by reflecting off the ionosphere. This paper utilizes the raw observation data received by the Low-Frequency Time Code dissemination monitoring stations before and after the 6.8 magnitude earthquake in Luding, Sichuan, China on 5 September 2022. A Low-Frequency Time Code time service monitoring system was built in Xi’an to continuously monitor the 68.5 kHz time signal broadcast by the BPC station. The data was then processed and analyzed through visualization. Simultaneously, we analyzed the signal fluctuation for multiple days before and after the earthquake to see the changes in the Low-Frequency Time Code signal during the earthquake. By combining seismic activity, solar activity, and geomagnetic data, this study aims to explore the causes and patterns of signal parameter variations. The results show that the field strength of the Low-Frequency Time Code signal fluctuated significantly within a short period during the earthquake. The value began to decrease about 60 min before the earthquake, dropping by approximately 8.9 dBμV/m, and gradually recovered 2 h after the earthquake. The phase also mutated by 1.36 μs at the time of the earthquake, and the time deviation fluctuated greatly compared to the 2 days before and after. Earthquake occurrences influence ionospheric variations, leading to changes in the sky wave propagation of Low-Frequency Time Code signals. Analysis of the influence of earthquakes on the propagation of Low-Frequency Time Code signals can provide references for research on Low-Frequency Time Code signal propagation models and earthquake prediction. Full article
(This article belongs to the Section Planetary Atmospheres)
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<p>Earthquake location on 5 September 2022 source: “<a href="https://www.mem.gov.cn/xw/yjglbgzdt/202209/t20220911_422190.shtml" target="_blank">https://www.mem.gov.cn/xw/yjglbgzdt/202209/t20220911_422190.shtml</a> (accessed on 20 September 2022)”.</p>
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<p>Principal diagram of the timing deviation calculation.</p>
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<p>Phase measurement diagram.</p>
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<p>Trend of DST and Kpindex over 5 days “<a href="https://omniweb.gsfc.nasa.gov/form/dx1.html" target="_blank">https://omniweb.gsfc.nasa.gov/form/dx1.html</a> (accessed on 3 May 2023)”.</p>
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<p>Location of BPC time service station, BPC receiving point (Test location), and earthquake location.</p>
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<p>Low-Frequency Time Code monitoring principal model diagram.</p>
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<p>Timing deviation test setup for the Low-Frequency Time Code monitoring receiver.</p>
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<p>The measurement results of field strength before and after the earthquake.</p>
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<p>The distribution map of field strength value.</p>
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<p>(<b>a</b>–<b>e</b>) Five charts for 3–7 September 2022, the measurement results of Low-Frequency Time Code timing deviation.</p>
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<p>Low-Frequency Time Code phase measurement results before and after the earthquake.</p>
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<p>Phase change diagram.</p>
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<p>Comparison between seismic day and non-geomagnetic day of the measurement results of field strength.</p>
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24 pages, 1944 KiB  
Article
Investigating Offensive Language Detection in a Low-Resource Setting with a Robustness Perspective
by Israe Abdellaoui, Anass Ibrahimi, Mohamed Amine El Bouni, Asmaa Mourhir, Saad Driouech and Mohamed Aghzal
Big Data Cogn. Comput. 2024, 8(12), 170; https://doi.org/10.3390/bdcc8120170 - 25 Nov 2024
Viewed by 393
Abstract
Moroccan Darija, a dialect of Arabic, presents unique challenges for natural language processing due to its lack of standardized orthographies, frequent code switching, and status as a low-resource language. In this work, we focus on detecting offensive language in Darija, addressing these complexities. [...] Read more.
Moroccan Darija, a dialect of Arabic, presents unique challenges for natural language processing due to its lack of standardized orthographies, frequent code switching, and status as a low-resource language. In this work, we focus on detecting offensive language in Darija, addressing these complexities. We present three key contributions that advance the field. First, we introduce a human-labeled dataset of Darija text collected from social media platforms. Second, we explore and fine-tune various language models on the created dataset. This investigation identifies a Darija RoBERTa-based model as the most effective approach, with an accuracy of 90% and F1 score of 85%. Third, we evaluate the best model beyond accuracy by assessing properties such as correctness, robustness and fairness using metamorphic testing and adversarial attacks. The results highlight potential vulnerabilities in the model’s robustness, with the model being susceptible to attacks such as inserting dots (29.4% success rate), inserting spaces (24.5%), and modifying characters in words (18.3%). Fairness assessments show that while the model is generally fair, it still exhibits bias in specific cases, with a 7% success rate for attacks targeting entities typically subject to discrimination. The key finding is that relying solely on offline metrics such as the F1 score and accuracy in evaluating machine learning systems is insufficient. For low-resource languages, the recommendation is to focus on identifying and addressing domain-specific biases and enhancing pre-trained monolingual language models with diverse and noisier data to improve their robustness and generalization capabilities in diverse linguistic scenarios. Full article
(This article belongs to the Special Issue Advances in Natural Language Processing and Text Mining)
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<p>Machine learning workflow with metamorphic testing using adversarial data.</p>
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<p>Distribution of sentence lengths in the dataset.</p>
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<p>Algorithm for finding important words in a sentence.</p>
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18 pages, 3968 KiB  
Article
Comparative and Spatial Transcriptome Analysis of Rhododendron decorum Franch. During the Flowering Period and Revelation of the Plant Defense Mechanism
by Weiwei Liu, Chenghua Yu, Kaiye Yang, Ling Wang, Zhongyu Fan and Xinchun Mo
Genes 2024, 15(11), 1482; https://doi.org/10.3390/genes15111482 - 18 Nov 2024
Viewed by 502
Abstract
Background: Rhododendron is a globally distributed and extensive genus, comprising over 1000 species. In the southwestern mountains of China, there exists a remarkable diversity of Rhododendron, with Yunnan Province alone harboring more than 600 species. R. decorum Franch. has long been utilized [...] Read more.
Background: Rhododendron is a globally distributed and extensive genus, comprising over 1000 species. In the southwestern mountains of China, there exists a remarkable diversity of Rhododendron, with Yunnan Province alone harboring more than 600 species. R. decorum Franch. has long been utilized by local communities for its medicinal and edible properties. However, the transcriptional regulation function, medicinal properties, and edibility characteristics of R. decorum Franch. currently lack a solid theoretical basis. Methods: Total RNA was extracted from leaves, corollas and androecium/gynoecium of R. decorum Franch. in Heqing county, followed by the construction of cDNA libraries and the de novo assembly of transcriptomes. Results: A total of 63,050 unigenes were extracted from the flowers and leaf organs of R. decorum Franch. Among these unigenes, 43,517 were predicted to be coding sequences, with 32,690 being effectively annotated. Differential gene expression enrichment was observed among different organs within their respective transcriptomes; notably floral organs exhibited significant defense against plant diseases along with signal transduction functions. Furthermore, during the flower harvesting period, all floral organs exhibited gene enrichment pathways associated with carbohydrate metabolism. Additionally, the stamen and pistil displayed flavonoid metabolism pathways, suggesting their potential applications as functional food or medicine. Conclusions: Our results shed light on plant–pathogen defense mechanisms and the molecular bias of flavonoids biosynthesis on flower organs during the flowering period, which might help to understand the consumption of R. decorum Franch. corollas by the Bai nationality of Heqing county. Full article
(This article belongs to the Special Issue Molecular Genetics and Multi-omics in Medicinal Plants)
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<p>GO functional classifications of <span class="html-italic">Rhododendron decorum</span> Franch. unigenes.</p>
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<p>KEGG annotation of <span class="html-italic">R. decorum</span> Franch. unigenes. (<b>A</b>) KEGG functional classification of assembled unigenes. (<b>B</b>) Classifications of subcategory “metabolism of terpenoids and polyketides”. (<b>C</b>) Classifications of the subcategory “biosynthesis of other secondary metabolites”.</p>
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<p>Statistics of differential expressed genes and comparisons between different groups. (<b>A</b>) Differentially expressed genes in different compared groups. The horizontal axis represents distinct sets of differentially expressed genes, where blue color represents the differential expressed genes in different groups, red color indicates upregulated, and green signifies downregulated. Meanwhile, the vertical axis corresponds to the number of differential expressed genes. (<b>B</b>) Volcano plot of differentially expressed genes in HQI/HQL. (<b>C</b>) Volcano plot of differentially expressed genes in HQI/HQO. (<b>D</b>) Volcano plot of differentially expressed genes in HQO/HQL. Each point on the graph represents a gene, with the horizontal axis indicating the logarithmic-fold change in gene expression between two samples. The vertical axis represents the negative logarithm of the false discovery rate. Blue points represent downregulated differentially expressed genes, red points represent upregulated differentially expressed genes, and gray points represent non-differentially expressed genes.</p>
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<p>GO enrichment analysis of differential expression genes within different organ comparison groups. (<b>A</b>) GO terms of DEGs in HQI/HQL group. (<b>B</b>) GO terms of DEGs in HQI/HQO group. (<b>C</b>) GO terms of DEGs in HQO/HQL group.</p>
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<p>The heatmaps of DEG expression patterns in different groups of <span class="html-italic">R. decorum</span> Franch. (<b>A</b>) DEG expression patterns in HQO/HQL group. (<b>B</b>) DEG expression patterns in HQI/HQL group. (<b>C</b>) DEG expression patterns in HQI/HQO group. Clustering plot depicting the differential expression analysis of genes belonging to the EF-hand protein family. Blue color represents the downregulated and red color the upregulated.</p>
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19 pages, 3345 KiB  
Article
Integrating Generative Artificial Intelligence and Problem-Based Learning into the Digitization in Construction Curriculum
by Reza Maalek
Buildings 2024, 14(11), 3642; https://doi.org/10.3390/buildings14113642 - 15 Nov 2024
Viewed by 415
Abstract
This study proposes incorporating generative artificial intelligence large language models (LLMs) into the Master of Science (M.Sc.) curriculum on digitization in construction. The aim was to help students generate computer code to solve, automate, and streamline practical challenges in advanced construction engineering and [...] Read more.
This study proposes incorporating generative artificial intelligence large language models (LLMs) into the Master of Science (M.Sc.) curriculum on digitization in construction. The aim was to help students generate computer code to solve, automate, and streamline practical challenges in advanced construction engineering and management (CEM). To this end, a host of problem-based learning (PBL) individual assignments and collaborative team projects were developed, alongside a combination of flipped classroom models and blended learning lessons, in order to teach effective interactions with LLMs and mitigate concerns, such as bias and hallucination. The effective interaction with LLMs not only facilitated code generation, which would otherwise be complex without additional formal training, but also provided a platform for strengthening basic project management skills, such as departmentalization, work breakdown structuring, modularization, activity delegation, and defining key performance indicators. The effectiveness of this approach was quantitatively and qualitatively evaluated within two new modules, Digital Engineering and Construction and Digital Technologies in Field Information Modeling. These modules were offered over three semesters each as part of a new M.Sc. program in Technology and Management in Construction at the Karlsruhe Institute of Technology. It was observed that 86.4% of students fully completed the PBL projects, while the remaining 13.6% achieved over 50% completion across all six semesters. Furthermore, anonymous student surveys indicated a teaching quality index of 100% in five semesters and 96.4% in one semester. These preliminary results suggest that the proposed strategy can be used to effectively integrate LLMs to support students in code generation for open-ended projects in CEM. Further research was, however, found to be necessary to ensure the sustainable revision and redesign of the problems as LLM capabilities evolve. Full article
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<p>Solar panel module arrangement optimization assignment; description of the objectives followed by the typical bungalow single family home and the roof, where the desired panel arrangements will be installed. Note that Table 1 mentioned in the assignment text does not refer to Table 1 of this manuscript.</p>
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<p>Floor detection from point clouds assignment; description of the objectives followed by steps for the detection and segmentation of floors from 3D point clouds: (<b>a</b>) point cloud of the lab; (<b>b</b>) histogram of point height; and (<b>c</b>) colored/segmented flat (planar) surfaces (e.g., floor as green). Note that Figure 1 mentioned in the assignment text refers to the figure just below the text and not the Figure 1 of this manuscript.</p>
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<p>Assignment on app development for point cloud object detection in building information modeling (BIM) projects; description of the objectives followed by examples of designed apps: (<b>a</b>) automatic registration of rectilinear projects; and (<b>b</b>) AI-based model fitting of non-analytic structures. Note that Figure 1 mentioned in the assignment text refers to the figure just below the text and not the Figure 1 of this manuscript.</p>
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<p>PBL project for robotic arm optimization; description of objectives and project, followed by the schematics of the concrete column: (<b>a</b>) point cloud; (<b>b</b>) sample hollow section member for initialization; (<b>c</b>) optimal topology to minimize mass; and (<b>d</b>) robotic-arm design simulation. Note that Figure 1 mentioned in the assignment text refers to the figure just below the text and not the Figure 1 of this manuscript.</p>
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24 pages, 7272 KiB  
Article
Comprehensive Analysis of BDS/GNSS Differential Code Bias and Compatibility Performance
by Yafeng Wang, Dongjie Yue, Hu Wang, Hongyang Ma, Zhiqiang Liu and Caiya Yue
Remote Sens. 2024, 16(22), 4217; https://doi.org/10.3390/rs16224217 - 12 Nov 2024
Viewed by 630
Abstract
High-precision DCBs are essential for effective multi-frequency and multi-constellation GNSS integration, especially in processing compatible signal observations. This study utilizes data from MGEX, iGMAS, and CORS stations to estimate and analyze long time series of BDS/GNSS DCBs, focusing on stability and influencing factors. [...] Read more.
High-precision DCBs are essential for effective multi-frequency and multi-constellation GNSS integration, especially in processing compatible signal observations. This study utilizes data from MGEX, iGMAS, and CORS stations to estimate and analyze long time series of BDS/GNSS DCBs, focusing on stability and influencing factors. Results indicate that DCBs for the same signal, but different channels exhibit similar ranges and trends. Among BDS DCBs, those from satellites with rubidium atomic clocks are more stable than those with hydrogen atomic clocks. An upgrade and maintenance of BDS in late 2022, reported by NABU, likely contributed to DCB jumps. BDS-compatible signal DCBs show weaker stability compared to GPS and Galileo. Variations in GNSS signal processing and receiver algorithms also impact DCB stability. Converting DCBs to OSBs and performing RMS statistics revealed that smaller differences between signals increase the susceptibility of observation equations to observation quality. Full article
(This article belongs to the Topic GNSS Measurement Technique in Aerial Navigation)
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<p>Distribution of multi-frequency and multi-system measurement stations (GPS: red, GLONASS: green, Galileo: purple, BDS: yellow).</p>
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<p>BDS DCB time series between B1I signal and B2I, B3I, B1C, B2a, B2b, and B2 (a + b) signals from January 2021 to August 2023 for BDS.</p>
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<p>BDS DCB time series between B1I signal and B2I, B3I, B1C, B2a, B2b, and B2 (a + b) signals from January 2021 to August 2023 for BDS.</p>
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<p>The overall stability of BDS B1I signal and B2I, B3I, B1C, B2a, B2b, and B2 (a + b) signals.</p>
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<p>Time series of GPS/Galileo/BDS in January 2021 to August 2023, where (<b>a</b>) GPS DCB; (<b>b</b>) Galileo DCB; (<b>c</b>) BDS DCB.</p>
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<p>GPS/Galileo/BDS DCB mean STD in January 2021 to August 2023.</p>
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<p>BDS C1P–C5P receiver DCB time series.</p>
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<p>BDS C1X–C5X receiver DCB time series.</p>
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<p>GAL C1C–C5Q receiver DCB time series.</p>
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<p>GAL C1X–C5X receiver DCB time series.</p>
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<p>GPS C1C–C5Q receiver DCB time series.</p>
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<p>GPS C1W–C5X receiver DCB time series.</p>
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<p>Comparison results of BDS DCB mean bias and STD.</p>
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<p>Comparison results of GPS and Galileo DCB mean bias and STD.</p>
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<p>Mean RMS of BDS OSB.</p>
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15 pages, 11620 KiB  
Article
Insights into Mitochondrial Rearrangements and Selection in Accipitrid Mitogenomes, with New Data on Haliastur indus and Accipiter badius poliopsis
by Jumaporn Sonongbua, Thanyapat Thong, Thitipong Panthum, Trifan Budi, Worapong Singchat, Ekaphan Kraichak, Aingorn Chaiyes, Narongrit Muangmai, Prateep Duengkae, Ratiwan Sitdhibutr, Chaiyan Kasorndorkbua and Kornsorn Srikulnath
Genes 2024, 15(11), 1439; https://doi.org/10.3390/genes15111439 - 7 Nov 2024
Viewed by 603
Abstract
Background/Objectives: Accipitridae mitogenomes exhibit unique structural variations, including duplicated control regions (CRs) that undergo gradual degeneration into pseudo-CRs, revealing a complex evolutionary landscape. However, annotation of this characteristic in a subset of accipitrid genomes is lacking. Due to the taxonomic diversity of Accipitridae [...] Read more.
Background/Objectives: Accipitridae mitogenomes exhibit unique structural variations, including duplicated control regions (CRs) that undergo gradual degeneration into pseudo-CRs, revealing a complex evolutionary landscape. However, annotation of this characteristic in a subset of accipitrid genomes is lacking. Due to the taxonomic diversity of Accipitridae and the presence of understudied species, comprehensive mitogenomic studies are essential. This study sought to expand and investigate the evolutionary characteristics of Accipitridae mitogenomes. Methods: A comparative analysis was conducted using the newly acquired complete mitogenomes of Haliastur indus and Accipiter badius poliopsis along with 22 available accipitrid mitogenomes. Codon usage, selective pressure, phylogenetic relationships, and structural variations were comparatively analyzed. Results: Accipitrid mitogenomes showed a strong AT bias with adenine preference. Most protein-coding genes (PCGs) were under purifying selection except for ND3, which underwent positive selection. The ATP8 gene exhibited relaxed purifying selection on codon usage patterns and showed high genetic variation. Selection for ATP8 and ND3 genes was specific to certain clades of accipitrids. Gene order re-examination revealed both non-degenerate CRs and highly degenerate CR2 fragments in the Accipitridae family. Non-degenerate CRs were found in early diverging species, such as Elanus caeruleus and Pernis ptilorhynchus orientalis, while more recent lineages had highly degenerate CR2 fragments with missing conserved element. Repeat motifs and sequence variations were observed in the functional CR. Conclusions: These findings suggest that ATP8 and ND3 genes reflect metabolic adaptations, while CRs indicate potential diversification of these accipitrid species. This study provides valuable insights into mitochondrial genome evolution within the Accipitridae family. Full article
(This article belongs to the Section Animal Genetics and Genomics)
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<p>Circular maps of (<b>a</b>) <span class="html-italic">H. indus</span> and (<b>b</b>) <span class="html-italic">A. badius poliopsis</span> mitochondrial genomes.</p>
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<p>Codon analysis results of 13 protein-coding genes (PCGs) from 24 species within the Accipitridae family: (<b>a</b>) neutrality plot; (<b>b</b>) effective number of codons (ENc) plot; and (<b>c</b>) box plot of ENc of 24 species in each PCGs.</p>
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<p>Mitochondrial gene order and collections of DNA sequence motifs found in both CR1 and CR2 regions.</p>
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<p>Nucleotide sequence alignment of the conserved sequence element in CR1. The upper schematic represents the avian control region, with conserved sequence boxes (F, E, D, C, and bird), CSBa, and CSBb in the central domain, shown in red. Conserved sequence elements in other domains are shown in grey. The boxed region highlights sequence variations with corresponding annotations.</p>
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15 pages, 6523 KiB  
Article
Complete Mitogenomes of Xinjiang Hares and Their Selective Pressure Considerations
by Ruijie Wang, Mayinur Tursun and Wenjuan Shan
Int. J. Mol. Sci. 2024, 25(22), 11925; https://doi.org/10.3390/ijms252211925 - 6 Nov 2024
Viewed by 389
Abstract
Comparative analysis based on the mitogenomes of hares in Xinjiang, China, is limited. In this study, the complete mitochondrial genomes of seven hare samples including four hare species and their hybrids from different environments were sequenced, assembled, and annotated. Subsequently, we performed base [...] Read more.
Comparative analysis based on the mitogenomes of hares in Xinjiang, China, is limited. In this study, the complete mitochondrial genomes of seven hare samples including four hare species and their hybrids from different environments were sequenced, assembled, and annotated. Subsequently, we performed base content and bias analysis, tRNA analysis, phylogenetic analysis, and amino acid sequence analysis of the annotated genes to understand their characteristics and phylogenetic relationship. Their mitogenomes are circular molecules (from 16,691 to 17,598 bp) containing 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and a control region, which are similar with other Lepus spp. worldwide. The relative synonymous codon usage analysis revealed that the adaptation of Lepus yarkandensis to its unique arid and hot environment might be associated with synthesizing amino acids like alanine, leucine, serine, arginine, and isoleucine and the terminator caused by the different usage of codons. Further, we utilized the MEME model and identified two positive selection genes (ND4, ND5) in Lepus tibetanus pamirensis and one (ND5) in L. yarkandensis that might be important to their adaptation to the plateau and dry and hot basin environments, respectively. Meanwhile, Lepus tolai lehmanni and Lepus timidus may have evolved different adaptive mechanisms for the same cold environment. This study explored the evolutionary dynamics of Xinjiang hares’ mitochondrial genomes, providing significant support for future research into their adaptation mechanisms in extreme environments. Full article
(This article belongs to the Special Issue Molecular Insights into Zoology)
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<p>Global distribution of the <span class="html-italic">Lepus</span> species samples analyzed in this study. The red and yellow areas represent China, and the yellow area represents Xinjiang, China (GS (2024) 0650). Blue represents hares cited in GenBank, and yellow represents the Xinjiang hares. 1. <span class="html-italic">L. tibetanus pamirensis</span>, 2. Yarkand–Desert hare, 3. <span class="html-italic">L. yarkandensis</span>, 4. <span class="html-italic">Lepus timidus</span>, 5. <span class="html-italic">L. tolai lehmanni</span>, 6. <span class="html-italic">L. tolai centrasiaticus</span>, 7. Yarkand–Tolai hare, 8. <span class="html-italic">L. alleni</span>, 9. <span class="html-italic">L. americanus</span>, 10. <span class="html-italic">L. townsendii</span>, 11. <span class="html-italic">L. granatensis</span>, 12. <span class="html-italic">L. europaeus</span>, 13. <span class="html-italic">L. oiostolus</span>, 14. <span class="html-italic">L. capensis</span>, 15. <span class="html-italic">L. coreanus</span>.</p>
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<p>Mitochondrial genomes of Xinjiang hare species. (<b>a</b>) Circular structure maps of the mitochondrial genomes of 7 Xinjiang hares (16,691–17,598 bp). (<b>b</b>) Whole length and the lengths of protein-coding, tRNA, and rRNA genes, and the <span class="html-italic">D-loop</span> in the mitochondrial genomes of Xinjiang hares. (<b>c</b>) Secondary structure prediction diagram of <span class="html-italic">tRNA-Ser</span>.</p>
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<p>Mitochondrial genome base composition. (<b>a</b>) <span class="html-italic">Lepus</span> species mitochondrial genome base content. (<b>b</b>) <span class="html-italic">Lepus</span> species mitochondrial genome base bias. (<b>c</b>) Xinjiang hares’ protein-coding genes’ AT skew. (<b>d</b>) Xinjiang hares’ protein-coding genes’ GC skew.</p>
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<p>The relative synonymous codon usage (RSCU) in <span class="html-italic">Lepus</span> species worldwide. The columns from left to right show <span class="html-italic">Lepus timidus</span>, <span class="html-italic">L. tolai lehmanni</span>, <span class="html-italic">L. tolai centrasiaticus</span>, <span class="html-italic">L. tibetanus pamirensis</span>, Yarkand–Tolai hare, Yarkand–Desert hare, <span class="html-italic">L. yarkandensis</span>, <span class="html-italic">L. coreanus</span>, <span class="html-italic">L. oiostolus</span>, <span class="html-italic">L. europaeus</span>, <span class="html-italic">L. capensis</span>, <span class="html-italic">L. townsendii</span>, <span class="html-italic">L. granatensis</span>, <span class="html-italic">L. americanus</span>, and <span class="html-italic">L. alleni</span>.</p>
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<p>Phylogenetic tree, generated by IQ-Tree, and mitochondrial genome structure. The seven Xinjiang hares are shaded yellow. Each of the rectangular blocks represents a specific PCG in the mitochondrial genome, while the gray elliptical areas indicate non-coding regions.</p>
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<p>Shared selection pressure results in the protein-coding genes in <span class="html-italic">Lepus</span> species. The Xinjiang hares are enclosed in the red box. The bottom part shows the positively selected sites (<span class="html-italic">p</span> &lt; 0.1). The gene location information of <span class="html-italic">L. alleni</span> was used as the reference sequence for the positively selected sites in the other species. The background color represents the amino acid properties. [Threonine (T); isoleucine (I); leucine (L); asparagine (N); valine (V); glutamine (Q); phenylalanine (F); tyrosine (Y); proline (P); alanine (A)].</p>
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21 pages, 2717 KiB  
Article
Impacting Elements of Metaverse Platforms’ Intentional Use in Cultural Education: Empirical Data Drawn from UTAUT, TTF, and Flow Theory
by Shan Hu, Geqi Xing and Jing Xin
Appl. Sci. 2024, 14(21), 9984; https://doi.org/10.3390/app14219984 - 31 Oct 2024
Viewed by 676
Abstract
This study aims to address the need for design guidelines in developing a cultural-heritage-based metaverse educational system. Using the UTAUT, the TTF model, and Flow Theory, a theoretical framework is constructed. Through qualitative research based on the GT, three user perception factors—presence, interactivity, [...] Read more.
This study aims to address the need for design guidelines in developing a cultural-heritage-based metaverse educational system. Using the UTAUT, the TTF model, and Flow Theory, a theoretical framework is constructed. Through qualitative research based on the GT, three user perception factors—presence, interactivity, and narrativity—are introduced as external variables to explore the relationship between these factors and users’ willingness to adopt the cultural heritage metaverse system. The study examines this relationship from the dual perspectives of user perception and technology acceptance. A scale was designed to test the theoretical model empirically, and 298 valid responses were collected through a structured process involving GT coding, pre-testing, and formal surveys. The findings indicate that interactivity, narrativity, and presence significantly enhance the flow experience, while factors such as performance expectancy, effort expectancy, social influence, facilitating conditions, technology–task fit, and flow positively influence users’ intention to adopt the system. Among these, technology–task fit emerged as the most influential factor. This integrated approach reduces subjectivity and bias in criteria determination, enhancing the objectivity and precision of cultural heritage metaverse system assessments and making the system more responsive to user needs. Full article
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<p>Refinement of user perception factors (coding results).</p>
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<p>Research model of users’ willingness to use the cultural education meta-universe system.</p>
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<p>Flow of the research methodology.</p>
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<p>Descriptive statistical information of the official questionnaire.</p>
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<p>Analysis of the path coefficients of the research model.</p>
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<p>Design strategy of cultural heritage education meta-universe system.</p>
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<p>Cross-Music lost instrument meta-universe system interface design.</p>
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12 pages, 870 KiB  
Systematic Review
Nutritional Indicators of Bone Nonunion: A Systematic Review
by Eleanor Christianson, Margaret Thomas, Sheila Sprague, Jessica Rivera, Andrew Chapple and Robert Zura
J. Clin. Med. 2024, 13(21), 6553; https://doi.org/10.3390/jcm13216553 - 31 Oct 2024
Viewed by 538
Abstract
Background/Objectives: Bone nonunion remains a clinical challenge in orthopedic surgery with significant impacts on mental and physical wellbeing for patients. There are several previously established risk factors of nonunion that are connected to nutrition, but this has yet to be substantially explored. [...] Read more.
Background/Objectives: Bone nonunion remains a clinical challenge in orthopedic surgery with significant impacts on mental and physical wellbeing for patients. There are several previously established risk factors of nonunion that are connected to nutrition, but this has yet to be substantially explored. This review seeks to assess all studies that present associations between nutrition and nonunion to understand the potential for clinical relevance in nonunion prevention. Methods: Case–control and cohort studies comparing nonunion risk based on nutritional factors were gathered through PubMed in July 2024. Data were extracted with dual verification through Covidence and assessed for bias using the Newcastle–Ottawa Scale. Results: A total of 21 studies were included in this literature review. Vitamin D deficiency was a significant risk factor of nonunion in six studies and not significant in six other studies. Albumin was significant in three of the five studies addressing this lab value. Iron deficiency anemia was significant in a study assessing its impact on nonunion. Calcium was not significant in the one study mentioned. ICD-10-coded malnutrition was significant in one of the two studies. Sarcopenia, nutritional care plans, and dietitian-diagnosed malnutrition were statistically significant clinical indicators for predicting nonunion, but food insecurity was insignificant. Conclusions: Vitamin D, calcium, albumin, iron deficiency anemia, sarcopenia, and clinically diagnosed malnutrition have all been associated with an increased risk of nonunion in observational studies and should be considered when preventing nonunion development. Full article
(This article belongs to the Special Issue Clinical Advances in Musculoskeletal Disorders)
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<p>PRISMA chart which summarizes the literature review process.</p>
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<p>An inclusion of nutrition in orthopedic practice. Several nutritional risk factors may impact initial fracture and risk of nonunion. Labs, questionnaires, and imaging can be used together to create a clinical picture. From there, surgical intervention and supportive nutritional care can prevent nonunion.</p>
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17 pages, 655 KiB  
Article
A Cross-Lingual Media Profiling Model for Detecting Factuality and Political Bias
by Chichen Lin, Yongbin Wang, Chenxin Li, Weijian Fan, Junhui Xu and Qi Wang
Appl. Sci. 2024, 14(21), 9837; https://doi.org/10.3390/app14219837 - 28 Oct 2024
Viewed by 561
Abstract
Media profiling offers valuable insights to enhance the objectivity and reliability of news coverage by providing comprehensive analysis, but the diversity in languages posed significant challenges to our identification of factuality and political bias of non-English sources. The limitation of existing media analysis [...] Read more.
Media profiling offers valuable insights to enhance the objectivity and reliability of news coverage by providing comprehensive analysis, but the diversity in languages posed significant challenges to our identification of factuality and political bias of non-English sources. The limitation of existing media analysis research is its concentration on a singular high-resource language, and it hardly extends to languages beyond English. To address this, we introduce xMP, a dataset for zero-shot cross-lingual media profiling tasks. xMP’s cross-lingual test set encompasses 34 non-English languages and 18 language families, extending media profiling beyond English resources and allowing us to assess cross-lingual media profiling model performance. Additionally, we propose a method, named R-KAT, to enhance the model’s zero-shot cross-lingual transfer learning capability by building virtual multilingual embedding. Our experiments illustrate that our method improves the transferability of models in cross-lingual media profiling tasks. Additionally, we further discuss the performance of our method for different target languages. Our dataset and code are publicly available. Full article
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<p>Number of media outlets and articles in our cross-lingual test dataset.</p>
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<p>Label distribution heat maps of xMP. (<b>a</b>,<b>b</b>) are, respectively, the distribution of English and cross-lingual test datasets under the fine-grained label setting; (<b>c</b>,<b>d</b>) are, respectively, the distribution of English data and multilingual data under the coarse-grained label setting. The color intensity in the charts reflects the relative volume of media sources, with darker shades indicating a higher quantity.</p>
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18 pages, 8156 KiB  
Article
Characterization, Codon Usage Pattern and Phylogenetic Implications of the Waterlily Aphid Rhopalosiphum nymphaeae (Hemiptera: Aphididae) Mitochondrial Genome
by Aiyang Shi, Chenyang Li, Muhammad Farhan, Chunhao Xu, Yanjin Zhang, Hongye Qian, Shuai Zhang and Tianxing Jing
Int. J. Mol. Sci. 2024, 25(21), 11336; https://doi.org/10.3390/ijms252111336 - 22 Oct 2024
Viewed by 590
Abstract
The water lily aphid, Rhopalosiphum nymphaeae, is the only known aphid that can live in both terrestrial and aquatic conditions. In this study, the complete mitochondrial genome of R. nymphaeae was generated using Illumina sequencing technology. The typical circular DNA mitochondrial genome [...] Read more.
The water lily aphid, Rhopalosiphum nymphaeae, is the only known aphid that can live in both terrestrial and aquatic conditions. In this study, the complete mitochondrial genome of R. nymphaeae was generated using Illumina sequencing technology. The typical circular DNA mitochondrial genome of R. nymphaeae is 15,772 bp in length, with a high A+T content (84.34%). It contains 37 coding genes (13 protein-coding genes, 22 transport RNAs, and two ribosomal RNAs) and two non-coding regions (one control region and one repeat region). Enc-plot, PR2-bias, and neutrality plot analysis indicated that the codon usage of the protein-coding genes is mainly affected by natural selection. The evolution rate analysis (the ratio of nonsynonymous to synonymous, Ka/Ks) indicated that all the PCGs in R. nymphaeae are under a strong purifying selection. The control region has conserved structure elements, and two types of tandem repeat units exist. The length and sequence of the aphid-unique repeat region has high similarity with closely related species. Phylogenetic analyses determined by both maximum likelihood and Bayesian inference support the monophyly of Aphidinae, Aphidini, Aphidina, and Rhopalosiphina. However, the monophyly of the genera in Rhopalosiphina, such as Rhopalosiphum, is still not resolved. This study may help us to understand the phylogenetic relationship of aphids, and much more aphid data are needed in future studies. Full article
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<p>Circular maps of the mitogenomes of <span class="html-italic">Rhopalosiphum nymphaeae</span>.</p>
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<p>Relative synonymous codon usage (RSCU) of the <span class="html-italic">Rhopalosiphum nymphaeae</span> mitochondrial genome. The amino acid frequencies are marked above the bars.</p>
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<p>Enc-plot, Parity Rule 2 bias, and Neutrality plot analysis of <span class="html-italic">Rhopalosiphum nymphaeae</span> mitochondrial genome. (<b>A</b>) Enc-plot analysis of concatenate of 13 PCGs from 17 Aphidinae species; (<b>B</b>) Enc-plot analysis of individual PCGs of <span class="html-italic">R. nymphaeae</span>; (<b>C</b>) Parity Rule 2 (PR2) bias of three <span class="html-italic">Rhopalosiphum</span> species; (<b>D</b>) Neutrality plots analysis of three <span class="html-italic">Rhopalosiphum</span> species, the diagonal line was shown in black line.</p>
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<p>(<b>A</b>) Nucleotide diversity of 13 PCGs in aphid mitochondrial genomes. (<b>B</b>) Evolutionary rates (the ratio of nonsynonymous to synonymous, Ka/Ks) of 13 mitochondrial PCGs among 17 Aphidinae species. Ka/Ks values were shown as black dots, and different letters above the columns indicate a significant difference of Ka/Ks values among 13 PCGs (mean ± SEM, <span class="html-italic">p</span> &lt; 0.05).</p>
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<p>Predicted secondary structures of 22 tRNAs in <span class="html-italic">Rhopalosiphum nymphaeae</span>.</p>
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<p>(<b>A</b>) The lead sequence is shown in the green box; the purple and blue boxes with Roman numerals indicate the tandem repeat units I and II, respectively; the A+T rich region is shown in the white box; the poly-thymidine stretch is shown in the orange box; the yellow box indicates the steam-loop region. (<b>B</b>) The secondary structure of the lead sequence and the stem-loop region. (<b>C</b>) The secondary structure of the repeat region. (<b>D</b>) The sequence alignment among the entire length of the <span class="html-italic">R. nymphaeae</span> repeat region, the full length of <span class="html-italic">R. rufiabdominalis</span> repeat region and the repeat unit sequence of <span class="html-italic">S. graminum.</span> Numbers showed the base positions from 5′ to 3′.</p>
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<p>Phylogeny of aphids inferred from the mitochondrial genomes. (<b>A</b>) Bayesian tree. The values at node indicate posterior probabilities. (<b>B</b>) Maximum-likelihood tree. The values at the nodes indicate bootstrap probabilities. Tree scale is shown at the lower-left conner. <span class="html-italic">Rhopalosiphum nymphaeae</span> mitochondrial genome in this study was marked with a red star.</p>
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19 pages, 7246 KiB  
Article
Comparative Genomics of Eight Complete Chloroplast Genomes of Phyllostachys Species
by Guolei Li, Guohua Liu and Changlai Liu
Forests 2024, 15(10), 1785; https://doi.org/10.3390/f15101785 - 11 Oct 2024
Viewed by 825
Abstract
(1) Background: The genus Phyllostachys belongs to the subfamily Bambusoideae within the family Gramineae. Bamboos of this genus are distinguished by their remarkable genetic traits, including exceptional resistance to both cold and drought conditions. These species possess considerable economic, ecological, and aesthetic value, [...] Read more.
(1) Background: The genus Phyllostachys belongs to the subfamily Bambusoideae within the family Gramineae. Bamboos of this genus are distinguished by their remarkable genetic traits, including exceptional resistance to both cold and drought conditions. These species possess considerable economic, ecological, and aesthetic value, finding extensive use in forestry and landscape design across China. (2) Methods: This study employed Illumina’s second-generation sequencing technology to sequence the chloroplast genomes of eight Phyllostachys species, followed by their assembly and annotation. (3) Results: The chloroplast genomes of the genus exhibit a characteristic tetrad structure with an average sequence length of 139,699 bp and an average GC content of 38.9%. A total of 130 genes have been annotated across eight bamboo species, comprising 75 protein-coding genes, 28 tRNA genes, and four rRNA genes. Global alignment and nucleotide polymorphism analyses indicate that the chloroplast genome of Phyllostachys is highly conserved overall. The boundaries of the four chloroplast regions are relatively conserved and exhibit minimal differences. Among these regions, three coding region genes—atpH, trnQ-UUG, and petB—and five non-coding regions—rpl32-trnL-UAG, rpl14-rpl16, rpl22-rps19, rps12-clpP, and trnR-UCU-trnM-CAU—exhibit high polymorphism and can be used as potential hotspot areas for subsequent research. A total of 266 simple sequence repeat (SSR) loci were identified by SSR analysis in the chloroplast genomes of eight bamboo species; the largest number of mononucleotide repeats was 154, predominantly consisting of A/T. Codon bias in the chloroplast genomes of the eight bamboo species indicates a preference for codons ending with A and U. Additionally, the UUA codon, which encodes leucine (Leu), is positioned between codons encoding phenylalanine (Phe), lysine (Lys), leucine (Leu), serine (Ser), and tyrosine (Tyr), indicating certain differences among these species. (4) Conclusions: This study aims to offer novel insights into the population genetics, phylogenetic relationships, and evolutionary patterns of Phyllostachys. Full article
(This article belongs to the Section Genetics and Molecular Biology)
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<p>Map of <span class="html-italic">Phyllostachys</span> chloroplast genome. Genes are color-coded based on their function, as shown in the legend. The inner circle indicates the inverted repeat boundaries and the genome’s GC content. The arrows indicate the direction of gene transcription.</p>
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<p>Comparisons of LSC, SSC, and IR region boundaries among the plastomes of <span class="html-italic">Phyllostachys</span> species. Genes adjacent to the junctions are shown as blocks of different colors.</p>
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<p>Sequence identity plots among chloroplast genomes of <span class="html-italic">P. edulis</span>, <span class="html-italic">P. nigra</span>, <span class="html-italic">P. nigra</span> var. <span class="html-italic">henonis</span>, <span class="html-italic">P. nigra</span> var. <span class="html-italic">punctata</span>, <span class="html-italic">P. aureosulcata spectabilis</span>, <span class="html-italic">P. heteroclada</span>, <span class="html-italic">P. vivax aureocanlis</span>, and <span class="html-italic">P. vivax</span> ‘Huangwenzhu’ with <span class="html-italic">P. edulis</span> (NC_015817) as a reference. Annotated genes are displayed along the top. The vertical scale represents the percent identity between 50 and 100%. Genome regions are color-coded as exon, intron, and conserved non-coding sequences (CDS).</p>
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<p>Nucleotide polymorphism analysis of chloroplast Genomes in the <span class="html-italic">Phyllostachys</span>. (<b>A</b>) Nucleotide polymorphism of intergenic region. (<b>B</b>) Nucleotide polymorphism of gene region. Window length: 600 bp; step size: 100 bp; <span class="html-italic">X</span>-axis: position of the midpoint of a window; <span class="html-italic">Y</span>-axis: nucleotide diversity of each window. Regions with high nucleotide polymorphism have been labeled with values. The red marker indicates the region with the highest nucleotide polymorphism.</p>
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<p>Analysis of SSRs in eight <span class="html-italic">Phyllostachys</span> chloroplast genomes. (<b>A</b>) Number of SSR repeat types. (<b>B</b>) Number of identified SSR motifs in different repeat types. (<b>C</b>) Number of identified SSRs in IGS, CDS, and intron regions. (<b>D</b>) Number of identified SSRs in LSC, SSC, and IR regions. (<b>E</b>) Number of SSRs by length.</p>
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<p>Analysis of large repeat sequences in eight <span class="html-italic">Phyllostachys</span> chloroplast genomes. (<b>A</b>) A total of five repeat types. (<b>B</b>) Number of tandem repeats in LSC, SSC, and IR regions. (<b>C</b>) Number of tandem repeats by length. (<b>D</b>) Number of dispersed repeats in IGS, CDS, and intron regions. (<b>E</b>) Number of dispersed repeats in LSC, SSC, and IR regions. (<b>F</b>) Number of dispersed repeats by length.</p>
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<p>RSCU value of eight chloroplast genomes of <span class="html-italic">Phyllostachys</span> species. Different colors represent various types of codons.</p>
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<p>Neutrality plot analysis of eight chloroplast genomes of <span class="html-italic">Phyllostachys</span> species.</p>
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<p>ENC-plot analysis of eight chloroplast genomes of <span class="html-italic">Phyllostachys</span> species.</p>
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<p>PR2-plot analysis of eight chloroplast genomes of <span class="html-italic">Phyllostachys</span> species.</p>
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