PLoS ONE最新文献

{"title":"Gene expression profiling and pathway analysis in acute myeloid leukaemia-normal karyotype patients.","authors":"Angeli Ambayya, Rozaimi Razali, Sarina Sulong, Yee Yee Yap, Veena Selvaratnam, Jameela Sathar, Rosline Hassan","doi":"10.1371/journal.pone.0328911","DOIUrl":"https://doi.org/10.1371/journal.pone.0328911","url":null,"abstract":"<p><p>Acute myeloid leukaemia-normal karyotype (AML-NK) exhibits heterogeneity in expression profiles, influencing the treatment response and survival outcome. Transcriptome sequencing allows a comprehensive analysis of differentially expressed genes (DEGs) and dysregulated pathways in AML-NK, shedding light on the molecular mechanisms and their implications in patients' management. DEG analyses utilising transcriptome sequencing were conducted using a customised DESeq2 pipeline on 51 AML-NK patients at diagnosis (DX), 12 AML-NK patients who attained first remission (CR1) and 12 healthy controls. The transcriptomic sequencing of AML-NK compared to healthy controls revealed 5,126 DEGs, comprising 85.8% coding genes and 14.2% non-coding elements across 37 pathway categories. The AML-NK DX versus CR1 identified 5,621 DEGs consisting of 84.7% coding genes and 15.3% non-coding elements affecting 20 categories of pathways. Gene set enrichment analysis in this study revealed consistent upregulation of proliferative pathways, including cell cycle and DNA replication. In contrast, immune-related pathways, such as cytokine-cytokine receptor interactions and MHC antigen presentation pathways, were downregulated. Overexpression of oncogenes (FLT3, MYB, DNMT3B, and MYCN) in DX vs CR1 samples reinforces their usefulness in minimal residual disease monitoring, especially in AML-NK with no genetic aberrations. These findings reiterate the known hallmarks of cancers and validate the transcriptomic dysregulation in the pathogenesis of AML-NK. The robustness of the transcriptome sequencing findings was confirmed by RT-qPCR validation of six genes that were not reported in AML-NK patients. The comprehensive analyses of pathways with dysregulation of a myriad of genes led to an understanding of AML-NK pathogenesis and highlighted the markers for minimal residual disease. In summary, this study performed the first transcriptome-wide analysis of AML-NK in a Malaysian cohort and underscored pathways that are candidates for therapeutic interventions.</p>","PeriodicalId":20189,"journal":{"name":"PLoS ONE","volume":"20 9","pages":"e0328911"},"PeriodicalIF":2.6,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145006428","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative techno-economic optimization of microgrid configurations using hybrid battery-hydrogen storage: NEOM case study, Saudi Arabia.","authors":"Abdullah M Alharbi, Ziad M Ali, Ahmed A Zaki Diab","doi":"10.1371/journal.pone.0326050","DOIUrl":"https://doi.org/10.1371/journal.pone.0326050","url":null,"abstract":"<p><p>Renewable energy systems are at the core of global efforts to reduce greenhouse gas (GHG) emissions and to combat climate change. Focusing on the role of energy storage in enhancing dependability and efficiency, this paper investigates the design and optimization of a completely sustainable hybrid energy system. Furthermore, hybrid storage systems have been used to evaluate their viability and cost-benefits. Examined under a 100% renewable energy microgrid framework, three setup configurations are as follows: (1) photovoltaic (PV) and Battery Storage System (BSS), (2) Hybrid PV/Wind Turbine (WT)/BSS, and (3) Integrated PV/WT/BSS/Electrolyzer/Hydrogen Tank/Fuel Cell (FC). Using its geographical solar irradiance and wind speed data, this paper inspires on an industrial community in Neom, Saudi Arabia. HOMER software evaluates technical and economic aspects, net present cost (NPC), levelized cost of energy (COE), and operating costs. The results indicate that the PV/BSS configuration offers the most sustainable solution, with a net present cost (NPC) of $2.42M and a levelized cost of electricity (LCOE) of $0.112/kWh, achieving zero emissions. However, it has lower reliability, as validated by the provided LPSP. In contrast, the PV/WT/BSS/Elec/FC system, with a higher NPC of $2.30M and LCOE of $0.106/kWh, provides improved energy dependability. The PV/WT/BSS system, with an NPC of $2.11M and LCOE of $0.0968/kWh, offers a slightly lower cost but does not provide the same level of reliability. The surplus energy has been implemented for hydrogen production. A sensitivity analysis was performed to evaluate the impact of uncertainties in renewable resource availability and economic parameters. The results demonstrate significant variability in system performance across different scenarios.</p>","PeriodicalId":20189,"journal":{"name":"PLoS ONE","volume":"20 9","pages":"e0326050"},"PeriodicalIF":2.6,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145006430","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"How fake news can turn against its spreader.","authors":"Dorje C Brody, Tomooki Yuasa","doi":"10.1371/journal.pone.0331608","DOIUrl":"https://doi.org/10.1371/journal.pone.0331608","url":null,"abstract":"<p><p>When different information sources on a given topic are combined, they interact in a nontrivial manner for a rational receiver of these information sources. Suppose that there are two information sources, one is genuine and the other contains disinformation. It is shown that under the conditions that the signal-to-noise ratio of the genuine information source is sufficiently large, and that the noise terms in the two information sources are positively correlated, the effect of disinformation is reversed from its original intent. That is, the effect of disinformation on a receiver of both information sources, who is unaware of the existence of disinformation, is to generate an opposite interpretation. While the condition in which this phenomenon occurs cannot always be ensured, when it is satisfied, the effect provides an effective way of countering the impacts of disinformation.</p>","PeriodicalId":20189,"journal":{"name":"PLoS ONE","volume":"20 9","pages":"e0331608"},"PeriodicalIF":2.6,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145006410","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Iterative rolling difference-Z-score and machine learning imputation for wind turbine foundation monitoring.","authors":"Renjie Li, Xiangxing Lu, Jizhang Zhao, Weibing Chen, Huanwei Wei, Cong Liu","doi":"10.1371/journal.pone.0331213","DOIUrl":"https://doi.org/10.1371/journal.pone.0331213","url":null,"abstract":"<p><p>In engineering structure performance monitoring, capturing real-time on-site data and conducting precise analysis are critical for assessing structural condition and safety. However, equipment instability and complex on-site environments often lead to data anomalies and gaps, hindering accurate performance evaluation. This study, conducted within a wind farm reinforcement project in Shandong Province, addresses these challenges by focusing on anomaly detection and data imputation for weld nail strain, anchor cable axial force, and concrete strain. We propose an innovative iterative rolling difference-Z-score method for anomaly detection and a machine learning-based imputation framework combining linear interpolation with LightGBM. Experimental results show that the iterative rolling difference-Z-score method detects single-point and clustered anomalies with a Z-score threshold of 4, achieving robust performance even with 80% data loss. The imputation framework maintains low mean squared error (MSE) of 0.0214-0.0227 and root mean squared error (RMSE) of 0.14-0.15 for continuous missing data scenarios (60-200 points), with reliable reconstruction up to 50% data loss. This research provides a robust solution for ensuring the precision and integrity of wind farm monitoring data, enhancing long-term structural reliability in renewable energy applications.</p>","PeriodicalId":20189,"journal":{"name":"PLoS ONE","volume":"20 9","pages":"e0331213"},"PeriodicalIF":2.6,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145006413","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The spatial dynamics of urban vegetation and housing prices: Insights from pre- and post-pandemic Chicago using OLS and MGWR models.","authors":"Dasom Han, Chang Gyu Choi","doi":"10.1371/journal.pone.0330932","DOIUrl":"https://doi.org/10.1371/journal.pone.0330932","url":null,"abstract":"<p><p>This study examines the spatial dynamics of urban vegetation and its impact on housing prices in Chicago, analyzing data from both pre- and post-COVID-19 periods. Employing Ordinary Least Squares (OLS) and Multiscale Geographically Weighted Regression (MGWR) models, we assess how the effects of green spaces on property values vary across different neighborhoods. The OLS model generally indicates a positive correlation between increased vegetation and housing prices. In contrast, the MGWR model reveals that the benefits of urban green spaces to property values are not uniformly distributed and exhibit significant variability. Notably, in some South Side areas of Chicago, increases in green space correlate with declines in property values, a sensitivity that intensified post-pandemic, leading to notable price declines. Conversely, the North Side, characterized as a higher-income area, shows greater resilience to the impacts of both increased green spaces and the COVID-19 pandemic, with less susceptibility to economic downturns. This research underscores the intricate interplay between urban green spaces and economic factors, highlighting how local socio-economic conditions and urban planning strategies can influence the economic benefits of vegetation. The findings provide essential insights for urban policymakers and planners striving to promote sustainable development and equitable economic growth in urban environments.</p>","PeriodicalId":20189,"journal":{"name":"PLoS ONE","volume":"20 9","pages":"e0330932"},"PeriodicalIF":2.6,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145006576","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An anchor-based YOLO fruit detector developed on YOLOv5.","authors":"He Honggang, Olarewaju Mubashiru Lawal, Yao Tan, Kui Cheng","doi":"10.1371/journal.pone.0331012","DOIUrl":"https://doi.org/10.1371/journal.pone.0331012","url":null,"abstract":"<p><p>Fruit detection using the YOLO framework has fostered fruit yield prediction, fruit harvesting automation, fruit quality control, fruit supply chain efficiency, smart fruit farming, labor cost reduction, and consumer convenience. Nevertheless, the factors that affect fruit detectors, such as occlusion, illumination, target dense status, etc., including performance attributes like low accuracy, low speed, and high computation costs, still remain a significant challenge. To solve these problems, a collection of fruit images, termed the CFruit image dataset, was constructed, and the YOLOcF fruit detector was designed. The YOLOcF detector, which is an improved anchor-based YOLOv5, was compared to YOLOv5n, YOLOv7t, YOLOv8n, YOLOv9, YOLOv10n, and YOLOv11n of YOLO variants. The study findings indicate that the computation costs in terms of params and GFLOPs of YOLOcF are lower than those of other YOLO variants, except for YOLOv10n and YOLOv11n. The mAP of YOLOcF is 0.8%, 1.1%, 1.3%, 0.7%, and 0.8% more accurate than YOLOv5n, YOLOv7t, YOLOv8n, YOLOv10n, and YOLOv11n, respectively, but 1.4% less than YOLOv9t. The detection speed of YOLOcF, measured at 323 fps, exceeds that of other YOLO variants. YOLOcF is very robust and reliable compared to other YOLO variants for having the highest R2 of 0.422 value from count analysis. Thus, YOLOcF fruit detector is lightweight for easy mobile device deployment, faster for training, and robust for generalization.</p>","PeriodicalId":20189,"journal":{"name":"PLoS ONE","volume":"20 9","pages":"e0331012"},"PeriodicalIF":2.6,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145006421","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic and economic efficiencies of alternative breeding schemes for improvement of local breeds in low-input production systems: The case of the Farta sheep in Northwest Ethiopia.","authors":"Abiy Shenkut Abebe, Kefyalew Alemayehu, Solomon Gizaw","doi":"10.1371/journal.pone.0331701","DOIUrl":"https://doi.org/10.1371/journal.pone.0331701","url":null,"abstract":"<p><p>Designing and implementing a sound breeding program is essential for sustainably improving livestock productivity. This study evaluated the efficiencies of three breeding schemes for sustainable genetic improvement of indigenous sheep in low-input production systems. The schemes were one-stage selection at six months (Scheme I) or yearling age (Scheme II) and two-stage selections with the first at six months and the second at the yearling age (Scheme III). Each scheme was assessed with three levels of selection proportions (5%, 10% and 20%) and four flock sizes (600, 1200, 1800 and 2400 breeding ewes). Selection responses were simulated using a deterministic approach employed in the SelAction software. For six-month weight, the annual predicted genetic gains ranged from 0.177 to 0.267 kg (Scheme I) and 0.157 to 0.233 kg (Scheme III). For yearling weight, simulated annual genetic gains were 0.268 to 0.399 kg (Scheme II) and 0.265 to 0.398 kg (Scheme III). The expected annual genetic gains for the number of lambs weaned per ewe bred (NLW) and fertility rate were generally small, but the estimates in Schemes II and III were higher compared to Scheme I. The annual economic responses estimated for Schemes I, II, and III ranged from US$0.393 to 0.591, 0.589 to 0.879 and 0.494 to 0.744, respectively. Notably, Scheme II yielded 34% and 16% higher economic returns than Schemes I and III, respectively. The results also revealed that varying the selection proportion significantly influenced the annual selection response, index accuracy, and inbreeding rate. Increasing the flock size had little effect on the genetic progress but significantly reduced the inbreeding rate. Given its genetic and economic benefits alongside operational feasibility, Scheme II, with a 5% selection proportion and a flock size of 1200 breeding ewes, is appropriate for the genetic improvement of indigenous sheep in low-input systems.</p>","PeriodicalId":20189,"journal":{"name":"PLoS ONE","volume":"20 9","pages":"e0331701"},"PeriodicalIF":2.6,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145006424","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bank complexity and core competence of commercial banks in Vietnam: The buffer role of corporate social responsibility.","authors":"Hung Quang Phung, Khoa Dang Duong, Phuc Huu Truong, Anh Quynh Pham, Hoa Thanh Phan Le","doi":"10.1371/journal.pone.0330723","DOIUrl":"https://doi.org/10.1371/journal.pone.0330723","url":null,"abstract":"<p><p>Based on stakeholder theory, socially responsible practices may help firms gain competitive advantages by lowering operational costs and enhancing their core competencies. From the perspective of the conglomerate hypothesis, we further suggest that CSR can act as a mechanism to reduce hidden risks, as firms, particularly banks, tend to diversify their activities more extensively. Using a sample of 26 commercial banks in Vietnam from 2010 to 2023, we test a set of hypotheses and find that engaging in CSR and diversifying operations are associated with lower risk exposure, greater financial stability, and improved asset quality. Moreover, the positive effects are more evident in large banks. In contrast, smaller banks may incur relatively higher costs when combining CSR efforts with operational complexity, potentially offsetting the benefits. Our study underscores the role of CSR as a foundation for income diversification and core competence enhancement, offering practical implications for policymakers in emerging countries to foster sustainable development in the banking sector.</p>","PeriodicalId":20189,"journal":{"name":"PLoS ONE","volume":"20 9","pages":"e0330723"},"PeriodicalIF":2.6,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145006412","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unlocking the power of L1 regularization: A novel approach to taming overfitting in CNN for image classification.","authors":"Ramla Sheikh, Fazli Wahid, Sikandar Ali, Ahmed Alkhayyat, Yingling Ma, Jawad Khan, Youngmoon Lee","doi":"10.1371/journal.pone.0327985","DOIUrl":"https://doi.org/10.1371/journal.pone.0327985","url":null,"abstract":"<p><p>Convolutional Neural Networks (CNNs) stand as indispensable tools in deep learning, capable of autonomously extracting crucial features from diverse data types. However, the intricacies of CNN architectures can present challenges such as overfitting and underfitting, necessitating thoughtful strategies to optimize their performance. In this work, these issues have been resolved by introducing L1 regularization in the basic architecture of CNN when it is applied for image classification. The proposed model has been applied to three different datasets. It has been observed that incorporating L1 regularization with different coefficient values has distinct effects on the working mechanism of CNN architecture resulting in improving its performance. In MNIST digit classification, L1 regularization (coefficient: 0.01) simplifies feature representation and prevents overfitting, leading to enhanced accuracy. In the Mango Tree Leaves dataset, dual L1 regularization (coefficient: 0.001 for convolutional and 0.01 for dense layers) improves model interpretability and generalization, facilitating effective leaf classification. Additionally, for hand-drawn sketches like those in the Quick, Draw! Dataset, L1 regularization (coefficient: 0.001) refines feature representation, resulting in improved recognition accuracy and generalization across diverse sketch categories. These findings underscore the significance of regularization techniques like L1 regularization in fine-tuning CNNs, optimizing their performance, and ensuring their adaptability to new data while maintaining high accuracy. Such strategies play a pivotal role in advancing the utility of CNNs across various domains, further solidifying their position as a cornerstone of deep learning.</p>","PeriodicalId":20189,"journal":{"name":"PLoS ONE","volume":"20 9","pages":"e0327985"},"PeriodicalIF":2.6,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145006523","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Frankenstein, thematic analysis and generative artificial intelligence: Quality appraisal methods and considerations for qualitative research.","authors":"Tanisha Jowsey, Peta Stapleton, Shawna Campbell, Alexandra Davidson, Cher McGillivray, Isabella Maugeri, Megan Lee, Justin Keogh","doi":"10.1371/journal.pone.0330217","DOIUrl":"https://doi.org/10.1371/journal.pone.0330217","url":null,"abstract":"<p><strong>Objective: </strong>To determine accuracy and efficiency of using generative artificial intelligence (GenAI) to undertake thematic analysis.</p><p><strong>Introduction: </strong>With the increasing use of GenAI in data analysis, testing the reliability and suitability of using GenAI to conduct qualitative data analysis is needed. We propose a method for researchers to assess reliability of GenAI outputs using deidentified qualitative datasets.</p><p><strong>Methods: </strong>We searched three databases (United Kingdom Data Service, Figshare, and Google Scholar) and five journals (PlosOne, Social Science and Medicine, Qualitative Inquiry, Qualitative Research, Sociology Health Review) to identify studies on health-related topics, published prior to whereby: humans undertook thematic analysis and published both their analysis in a peer-reviewed journal and the associated dataset. We prompted a closed system GenAI (Microsoft Copilot) to undertake thematic analysis of these datasets and analysed the GenAI outputs in comparison with human outputs. Measures include time (GenAI only), accuracy, overlap with human analysis, and reliability of selected data and quotes.</p><p><strong>Results: </strong>Five studies were identified that met our inclusion criteria. The themes identified by human researchers and Copilot showed minimal overlap, with human researchers often using discursive thematic analyses (40%) and Copilot focusing on thematic analysis (100%). Copilot's outputs often included fabricated quotes (58% SD = 45%) and none of the Copilot outputs provided participant spread by theme. Additionally, Copilot's outputs primarily drew themes and quotes from the first 2-3 pages of textual data, rather than from the entire dataset. Human researchers provided broader representation and accurate quotes (79% quotes were correct, SD = 27%).</p><p><strong>Conclusions: </strong>Based on these results, we cannot recommend the current version of Copilot for undertaking thematic analyses. This study raises concerns about the validity of both human-generated and GenAI-generated qualitative data analysis and reporting.</p>","PeriodicalId":20189,"journal":{"name":"PLoS ONE","volume":"20 9","pages":"e0330217"},"PeriodicalIF":2.6,"publicationDate":"2025-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145006493","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}