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30 pages, 3080 KiB  
Article
Unsupervised Multimodal Community Detection Algorithm in Complex Network Based on Fractal Iteration
by Hui Deng, Yanchao Huang, Jian Wang, Yanmei Hu and Biao Cai
Fractal Fract. 2025, 9(8), 507; https://doi.org/10.3390/fractalfract9080507 (registering DOI) - 2 Aug 2025
Abstract
Community detection in complex networks plays a pivotal role in modern scientific research, including in social network analysis and protein structure analysis. Traditional community detection methods face challenges in integrating heterogeneous multi-source information, capturing global semantic relationships, and adapting to dynamic network evolution. [...] Read more.
Community detection in complex networks plays a pivotal role in modern scientific research, including in social network analysis and protein structure analysis. Traditional community detection methods face challenges in integrating heterogeneous multi-source information, capturing global semantic relationships, and adapting to dynamic network evolution. This paper proposes a novel unsupervised multimodal community detection algorithm (UMM) based on fractal iteration. The core idea is to design a dual-channel encoder that comprehensively considers node semantic features and network topological structures. Initially, node representation vectors are derived from structural information (using feature vectors when available, or singular value decomposition to obtain feature vectors for nodes without attributes). Subsequently, a parameter-free graph convolutional encoder (PFGC) is developed based on fractal iteration principles to extract high-order semantic representations from structural encodings without requiring any training process. Furthermore, a semantic–structural dual-channel encoder (DC-SSE) is designed, which integrates semantic encodings—reduced in dimensionality via UMAP—with structural features extracted by PFGC to obtain the final node embeddings. These embeddings are then clustered using the K-means algorithm to achieve community partitioning. Experimental results demonstrate that the UMM outperforms existing methods on multiple real-world network datasets. Full article
27 pages, 18859 KiB  
Article
Application of a Hierarchical Approach for Architectural Classification and Stratigraphic Evolution in Braided River Systems, Quaternary Strata, Songliao Basin, NE China
by Zhiwen Dong, Zongbao Liu, Yanjia Wu, Yiyao Zhang, Jiacheng Huang and Zekun Li
Appl. Sci. 2025, 15(15), 8597; https://doi.org/10.3390/app15158597 (registering DOI) - 2 Aug 2025
Abstract
The description and assessment of braided river architecture are usually limited by the paucity of real geological datasets from field observations; due to the complexity and diversity of rivers, traditional evaluation models are difficult to apply to braided river systems in different climatic [...] Read more.
The description and assessment of braided river architecture are usually limited by the paucity of real geological datasets from field observations; due to the complexity and diversity of rivers, traditional evaluation models are difficult to apply to braided river systems in different climatic and tectonic settings. This study aims to establish an architectural model suitable for the study area setting by introducing a hierarchical analysis approach through well-exposed three-dimensional outcrops along the Second Songhua River. A micro–macro four-level hierarchical framework is adopted to obtain a detailed anatomy of sedimentary outcrops: lithofacies, elements, element associations, and archetypes. Fourteen lithofacies are identified: three conglomerates, seven sandstones, and four mudstones. Five elements provide the basic components of the river system framework: fluvial channel, laterally accreting bar, downstream accreting bar, abandoned channel, and floodplain. Four combinations of adjacent elements are determined: fluvial channel and downstream accreting bar, fluvial channel and laterally accreting bar, erosionally based fluvial channel and laterally accreting bar, and abandoned channel and floodplain. Considering the sedimentary evolution process, the braided river prototype, which is an element-based channel filling unit, is established by documenting three contact combinations between different elements and six types of fine-grained deposits’ preservation positions in the elements. Empirical relationships are developed among the bankfull channel depth, mean bankfull channel depth, and bankfull channel width. For the braided river systems, the establishment of the model promotes understanding of the architecture and evolution, and the application of the hierarchical analysis approach provides a basis for outcrop, underground reservoir, and tank experiments. Full article
(This article belongs to the Section Earth Sciences)
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21 pages, 6621 KiB  
Article
Ecological Restoration Reshapes Ecosystem Service Interactions: A 30-Year Study from China’s Southern Red-Soil Critical Zone
by Gaigai Zhang, Lijun Yang, Jianjun Zhang, Chongjun Tang, Yuanyuan Li and Cong Wang
Forests 2025, 16(8), 1263; https://doi.org/10.3390/f16081263 (registering DOI) - 2 Aug 2025
Abstract
Situated in the southern hilly-mountain belt of China’s “Three Zones and Four Belts Strategy”, Gannan region is a critical ecological shelter belt for the Ganjiang River. Decades of intensive mineral extraction and irrational agricultural development have rendered it into an ecologically fragile area. [...] Read more.
Situated in the southern hilly-mountain belt of China’s “Three Zones and Four Belts Strategy”, Gannan region is a critical ecological shelter belt for the Ganjiang River. Decades of intensive mineral extraction and irrational agricultural development have rendered it into an ecologically fragile area. Consequently, multiple restoration initiatives have been implemented in the region over recent decades. However, it remains unclear how relationships among ecosystem services have evolved under these interventions and how future ecosystem management should be optimized based on these changes. Thus, in this study, we simulated and assessed the spatiotemporal dynamics of five key ESs in Gannan region from 1990 to 2020. Through integrated correlation, clustering, and redundancy analyses, we quantified ES interactions, tracked the evolution of ecosystem service bundles (ESBs), and identified their socio-ecological drivers. Despite a 31% decline in water yield, ecological restoration initiatives drove substantial improvements in key regulating services: carbon storage increased by 6.9 × 1012 gC while soil conservation rose by 4.8 × 108 t. Concurrently, regional habitat quality surged by 45% in mean scores, and food production increased by 2.1 × 105 t. Critically, synergistic relationships between habitat quality, soil retention, and carbon storage were progressively strengthened, whereas trade-offs between food production and habitat quality intensified. Further analysis revealed that four distinct ESBs—the Agricultural Production Bundle (APB), Urban Development Bundle (UDB), Eco-Agriculture Transition Bundle (ETB), and Ecological Protection Bundle (EPB)—were shaped by slope, forest cover ratio, population density, and GDP. Notably, 38% of the ETB transformed into the EPB, with frequent spatial interactions observed between the APB and UDB. These findings underscore that future ecological restoration and conservation efforts should implement coordinated, multi-service management mechanisms. Full article
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21 pages, 3870 KiB  
Article
The Impact of Drilling Parameters on Drilling Temperature in High-Strength Steel Thin-Walled Parts
by Yupu Zhang, Ruyu Li, Yihan Liu, Chengwei Liu, Shutao Huang, Lifu Xu and Haicheng Shi
Appl. Sci. 2025, 15(15), 8568; https://doi.org/10.3390/app15158568 (registering DOI) - 1 Aug 2025
Abstract
High-strength steel has high strength and low thermal conductivity, and its thin-walled parts are very susceptible to residual stress and deformation caused by cutting heat during the drilling process, which affects the machining accuracy and quality. High-strength steel thin-walled components are widely used [...] Read more.
High-strength steel has high strength and low thermal conductivity, and its thin-walled parts are very susceptible to residual stress and deformation caused by cutting heat during the drilling process, which affects the machining accuracy and quality. High-strength steel thin-walled components are widely used in aerospace and other high-end sectors; however, systematic investigations into their temperature fields during drilling remain scarce, particularly regarding the evolution characteristics of the temperature field in thin-wall drilling and the quantitative relationship between drilling parameters and these temperature variations. This paper takes the thin-walled parts of AF1410 high-strength steel as the research object, designs a special fixture, and applies infrared thermography to measure the bottom surface temperature in the thin-walled drilling process in real time; this is carried out in order to study the characteristics of the temperature field during the thin-walled drilling process of high-strength steel, as well as the influence of the drilling dosage on the temperature field of the bottom surface. The experimental findings are as follows: in the process of thin-wall drilling of high-strength steel, the temperature field of the bottom surface of the workpiece shows an obvious temperature gradient distribution; before the formation of the drill cap, the highest temperature of the bottom surface of the workpiece is distributed in the central circular area corresponding to the extrusion of the transverse edge during the drilling process, and the highest temperature of the bottom surface can be approximated as the temperature of the extrusion friction zone between the top edge of the drill and the workpiece when the top edge of the drill bit drills to a position close to the bottom surface of the workpiece and increases with the increase in the drilling speed and the feed volume; during the process of drilling, the highest temperature of the bottom surface of the workpiece is approximated as the temperature of the top edge of the drill bit and the workpiece. The maximum temperature of the bottom surface of the workpiece in the drilling process increases nearly linearly with the drilling of the drill, and the slope of the maximum temperature increases nearly linearly with the increase in the drilling speed and feed, in which the influence of the feed on the slope of the maximum temperature increases is larger than that of the drilling speed. Full article
(This article belongs to the Special Issue Machine Automation: System Design, Analysis and Control)
36 pages, 3621 KiB  
Review
Harnessing Molecular Phylogeny and Chemometrics for Taxonomic Validation of Korean Aromatic Plants: Integrating Genomics with Practical Applications
by Adnan Amin and Seonjoo Park
Plants 2025, 14(15), 2364; https://doi.org/10.3390/plants14152364 - 1 Aug 2025
Abstract
Plant genetics and chemotaxonomic analysis are considered key parameters in understanding evolution, plant diversity and adaptation. Korean Peninsula has a unique biogeographical landscape that supports various aromatic plant species, each with considerable ecological, ethnobotanical, and pharmacological significance. This review aims to provide a [...] Read more.
Plant genetics and chemotaxonomic analysis are considered key parameters in understanding evolution, plant diversity and adaptation. Korean Peninsula has a unique biogeographical landscape that supports various aromatic plant species, each with considerable ecological, ethnobotanical, and pharmacological significance. This review aims to provide a comprehensive overview of the chemotaxonomic traits, biological activities, phylogenetic relationships and potential applications of Korean aromatic plants, highlighting their significance in more accurate identification. Chemotaxonomic investigations employing techniques such as gas chromatography mass spectrometry, high-performance liquid chromatography, and nuclear magnetic resonance spectroscopy have enabled the identification of essential oils and specialized metabolites that serve as valuable taxonomic and diagnostic markers. These chemical traits play essential roles in species delimitation and in clarifying interspecific variation. The biological activities of selected taxa are reviewed, with emphasis on antimicrobial, antioxidant, anti-inflammatory, and cytotoxic effects, supported by bioassay-guided fractionation and compound isolation. In parallel, recent advances in phylogenetic reconstruction employing DNA barcoding, internal transcribed spacer regions, and chloroplast genes such as rbcL and matK are examined for their role in clarifying taxonomic uncertainties and inferring evolutionary lineages. Overall, the search period was from year 2001 to 2025 and total of 268 records were included in the study. By integrating phytochemical profiling, pharmacological evidence, and molecular systematics, this review highlights the multifaceted significance of Korean endemic aromatic plants. The conclusion highlights the importance of multidisciplinary approaches including metabolomics and phylogenomics in advancing our understanding of species diversity, evolutionary adaptation, and potential applications. Future research directions are proposed to support conservation efforts. Full article
(This article belongs to the Special Issue Applications of Bioinformatics in Plant Science)
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19 pages, 1549 KiB  
Article
Divergence in Coding Sequences and Expression Patterns Among the Functional Categories of Secretory Genes Between Two Aphid Species
by Atsbha Gebreslasie Gebrekidan, Yong Zhang and Julian Chen
Biology 2025, 14(8), 964; https://doi.org/10.3390/biology14080964 (registering DOI) - 1 Aug 2025
Abstract
Disparities in the functional classification of secretory genes among aphid taxa may be attributed to variations in coding sequences and gene expression profiles. However, the driving factors that regulate sequence evolution remain unclear. This study aimed to investigate the differences in coding sequences [...] Read more.
Disparities in the functional classification of secretory genes among aphid taxa may be attributed to variations in coding sequences and gene expression profiles. However, the driving factors that regulate sequence evolution remain unclear. This study aimed to investigate the differences in coding sequences and expression patterns of secretory genes between the rose grain aphid (Metopolophium dirhodum) and the pea aphid (Acrythosiphon pisum), with a particular focus on their roles in evolutionary adaptations and functional diversity. The study involved the rearing of aphids, RNA extraction, de novo transcriptome assembly, functional annotation, secretory protein prediction, and comparative analysis of coding sequences and expression patterns across various functional categories using bioinformatics tools. The results revealed that metabolic genes exhibited greater coding sequence divergence, indicating the influence of positive selection. Moreover, significant expression divergence was noted among functional categories, particularly in metabolic and genetic information processing genes, which exhibited higher variability. This study enhances our understanding of the molecular mechanisms that contribute to phenotypic and genetic diversity among aphid species. This study elucidates the relationship between variations in coding sequences and differences in gene expression among functional categories, thereby establishing a foundation for future studies on gene evolution in response to environmental pressures. Full article
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22 pages, 1945 KiB  
Review
A Bibliometric Analysis of Chrononutrition, Cardiometabolic Risk, and Public Health in International Research (1957–2025)
by Emily Gabriela Burgos-García, Katiuska Mederos-Mollineda, Darley Jhosue Burgos-Angulo, David Job Morales-Neira and Dennis Alfredo Peralta-Gamboa
Int. J. Environ. Res. Public Health 2025, 22(8), 1205; https://doi.org/10.3390/ijerph22081205 - 31 Jul 2025
Abstract
Introduction: Breakfast has emerged as a critical factor in preventing cardiovascular diseases, driven not only by its nutritional content but also by its alignment with circadian rhythms. However, gaps remain in the literature regarding its clinical impact and thematic evolution. Objective: [...] Read more.
Introduction: Breakfast has emerged as a critical factor in preventing cardiovascular diseases, driven not only by its nutritional content but also by its alignment with circadian rhythms. However, gaps remain in the literature regarding its clinical impact and thematic evolution. Objective: To characterize the global scientific output on the relationship between breakfast quality and cardiovascular health through a systematic bibliometric analysis. Methodology: The PRISMA 2020 protocol was applied to select 1436 original articles indexed in Scopus and Web of Science (1957–2025). Bibliometric tools, including R (v4.4.2) and VOSviewer (v1.6.19) were used to map productivity, impact, collaboration networks, and emerging thematic areas. Results: Scientific output has grown exponentially since 2000. The most influential journals are the American Journal of Clinical Nutrition, Nutrients, and Diabetes Care. The United States, United Kingdom, and Japan lead in publication volume and citations, with increasing participation from Latin American countries. Thematic trends have shifted from traditional clinical markers to innovative approaches such as chrononutrition, digital health, and personalized nutrition. However, methodological gaps persist, including a predominance of observational studies and an underrepresentation of vulnerable populations. Conclusions: Breakfast is a dietary practice with profound implications for cardiometabolic health. This study provides a comprehensive overview of scientific literature, highlighting both advancements and challenges. Strengthening international collaboration networks, standardizing definitions of a healthy breakfast, and promoting evidence-based interventions in school, clinical, and community settings are recommended. Full article
33 pages, 2962 KiB  
Review
Evolution of Data-Driven Flood Forecasting: Trends, Technologies, and Gaps—A Systematic Mapping Study
by Banujan Kuhaneswaran, Golam Sorwar, Ali Reza Alaei and Feifei Tong
Water 2025, 17(15), 2281; https://doi.org/10.3390/w17152281 - 31 Jul 2025
Abstract
This paper presents a Systematic Mapping Study (SMS) on data-driven approaches in flood forecasting from 2019 to 2024, a period marked by transformative developments in Deep Learning (DL) technologies. Analysing 363 selected studies, this paper provides an overview of the technological evolution in [...] Read more.
This paper presents a Systematic Mapping Study (SMS) on data-driven approaches in flood forecasting from 2019 to 2024, a period marked by transformative developments in Deep Learning (DL) technologies. Analysing 363 selected studies, this paper provides an overview of the technological evolution in this field, methodological approaches, evaluation practices and geographical distribution of studies. The study revealed that meteorological and hydrological factors constitute approximately 76% of input variables, with rainfall/precipitation and water level measurements forming the core predictive basis. Long Short-Term Memory (LSTM) networks emerged as the dominant algorithm (21% of implementations), whilst hybrid and ensemble approaches showed the most dramatic growth (from 2% in 2019 to 10% in 2024). The study also revealed a threefold increase in publications during this period, with significant geographical concentration in East and Southeast Asia (56% of studies), particularly China (36%). Several research gaps were identified, including limited exploration of graph-based approaches for modelling spatial relationships, underutilisation of transfer learning for data-scarce regions, and insufficient uncertainty quantification. This SMS provides researchers and practitioners with actionable insights into current trends, methodological practices, and future directions in data-driven flood forecasting, thereby advancing this critical field for disaster management. Full article
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26 pages, 6611 KiB  
Article
The Geochronology, Geochemical Characteristics, and Tectonic Settings of the Granites, Yexilinhundi, Southern Great Xing’an Range
by Haixin Yue, Henan Yu, Zhenjun Sun, Yanping He, Mengfan Guan, Yingbo Yu and Xi Chen
Minerals 2025, 15(8), 813; https://doi.org/10.3390/min15080813 (registering DOI) - 31 Jul 2025
Viewed by 28
Abstract
The southern Great Xing’an Range is located in the overlap zone of the Paleo-Asian Ocean metallogenic domain and the Circum-Pacific metallogenic domain. It hosts numerous Sn-polymetallic deposits, such as Weilasituo, Bianjiadayuan, Huanggang, and Dajing, and witnessed multiple episodes of magmatism during the Late [...] Read more.
The southern Great Xing’an Range is located in the overlap zone of the Paleo-Asian Ocean metallogenic domain and the Circum-Pacific metallogenic domain. It hosts numerous Sn-polymetallic deposits, such as Weilasituo, Bianjiadayuan, Huanggang, and Dajing, and witnessed multiple episodes of magmatism during the Late Mesozoic. The study area is situated within the Huanggangliang-Ganzhuermiao metallogenic belt in the southern Great Xing’an Range. The region has witnessed extensive magmatism, with Mesozoic magmatic activities being particularly closely linked to regional mineralization. We present petrographic, zircon U-Pb chronological, lithogeochemical, and Lu-Hf isotopic analyses of the Yexilinhundi granites. The results indicate that the granite porphyry and granodiorite were emplaced during the Late Jurassic. Both rocks exhibit high SiO2, K2O + Na2O, differentiation index (DI), and 10,000 Ga/Al ratios, coupled with low MgO contents. They show distinct fractionation between light and heavy rare earth elements (LREEs and HREEs), exhibit Eu anomalies, and have low whole-rock zircon saturation temperatures (Tzr), collectively demonstrating characteristics of highly fractionated I-type granites. The εHf(t) values of the granites range from 0.600 to 9.14, with young two-stage model ages (TDM2 = 616.0~1158 Ma), indicating that the magmatic source originated from partial melting of Mesoproterozoic-Neoproterozoic juvenile crust. This study proposes that the granites formed in a post-collisional/post-orogenic extensional setting associated with the subduction of the Mongol-Okhotsk Ocean, providing a scientific basis for understanding the relationship between the formation of Sn-polymetallic deposits and granitic magmatic evolution in the study area. Full article
(This article belongs to the Section Mineral Geochemistry and Geochronology)
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21 pages, 1893 KiB  
Article
Relationship Between Body Composition and Biomarkers in Adult Females with Breast Cancer: 1-Year Follow-Up Prospective Study
by Angélica Larrad-Sáinz, María Gemma Hernández Núñez, Ana Barabash Bustelo, Inés Gil Prados, Johanna Valerio, José Luis Espadas Gil, María Eugenia Olivares Crespo, María Herrera de la Muela, Blanca Bernaldo Madrid, Irene Serrano García, Ignacio Cristóbal García, Miguel Ángel Rubio-Herrera, Alfonso Luis Calle-Pascual, Juana María Brenes Sánchez and Pilar Matía-Martín
Nutrients 2025, 17(15), 2487; https://doi.org/10.3390/nu17152487 - 30 Jul 2025
Viewed by 189
Abstract
Background/Objectives: After diagnosis, it is common for women with breast cancer to gain weight, which is associated with worse clinical outcomes. However, traditional measures such as body weight, BMI, and waist circumference do not detect key changes in body composition, such as fat [...] Read more.
Background/Objectives: After diagnosis, it is common for women with breast cancer to gain weight, which is associated with worse clinical outcomes. However, traditional measures such as body weight, BMI, and waist circumference do not detect key changes in body composition, such as fat redistribution or muscle loss. The objective of this exploratory study was to assess the evolution of body composition and muscle strength after one year of treatment, and their relationship with metabolic biomarkers. Methods: Prospective observational study in newly diagnosed breast cancer patients. Body composition was assessed using bioelectrical impedance analysis (BIA) and ultrasound (US); muscle strength was measured by handgrip dynamometry. Biomarkers analyzed included glucose, insulin, Homeostatic Model Assessment of Insulin Resistance (HOMA-IR), glycosylated hemoglobin (HbA1c), total cholesterol (and its fractions), triglycerides, C-reactive protein (CRP), 6-interleukin (IL-6), vitamin D, myostatin, and fibroblast growth factor 21 (FGF-21). Results: Sixty-one women (mean age 58 years) were included. After one year, fat mass and related parameters significantly increased, while skeletal muscle mass and muscle strength decreased. Sarcopenic obesity prevalence rose from 1.16% to 4.9%. No significant changes were found in biomarkers, but positive correlations were observed between fat parameters and insulin, HOMA-IR, and triglycerides, and negative correlations with HDL-cholesterol. Conclusions: BIA and US can detect unfavorable changes in body composition that are not reflected in conventional measurements. At one year post-diagnosis, women showed increased fat accumulation, muscle loss, and reduced strength, even without significant metabolic biomarker changes. Further research is warranted to elucidate the long-term clinical implications of these findings and the external validity in larger cohorts. Full article
(This article belongs to the Special Issue Body Composition and Nutritional Status in Cancer Patients)
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13 pages, 5465 KiB  
Article
Molybdenite Re-Os Isotopic Ages of Two Late Mesozoic Giant Mo Deposits in the Eastern Qinling Orogenic Belt, Central China
by Yuanshuo Zhang, Li Yang, Herong Gui, Dejin Wang, Mengqiu He and Jun He
Minerals 2025, 15(8), 800; https://doi.org/10.3390/min15080800 - 30 Jul 2025
Viewed by 186
Abstract
Precise Re-Os isotopic ages of the Jinduicheng and Donggou Mo deposits in the East Qinling orogenic belt can shed light on the controversies about multiple-stage pulses of mineralization and further elucidate the genesis and metallogenic process of the deposits. In this study, we [...] Read more.
Precise Re-Os isotopic ages of the Jinduicheng and Donggou Mo deposits in the East Qinling orogenic belt can shed light on the controversies about multiple-stage pulses of mineralization and further elucidate the genesis and metallogenic process of the deposits. In this study, we propose two major events of Mo mineralization in this orogenic belt occurring during the Late Mesozoic: the early stage of 156–130 Ma and late stage of 122–114 Ma. Results of molybdenite Re-Os isotopic analysis reveal that the Jinduicheng deposit formed at 139.2 ± 2.9 Ma, while the Donggou deposit exhibited two-stage mineralization at 115.4 ± 1.6 Ma and 111.9 ± 1.3 Ma. These isotopic ages align with the spatiotemporal evolution of coeval ore-barren granites exposed in eastern Qinling, pointing to a close genetic relationship between the magmatism and mineralization that was controlled by the same tectonic activity, likely in a post-collisional setting. This highlights the multiple-stage Mo mineralization and provides evidence for further understanding the geodynamics and metallogenic process in the eastern Qinling orogenic belt. Full article
(This article belongs to the Section Mineral Deposits)
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16 pages, 1974 KiB  
Review
MicroRNA528 and Its Regulatory Roles in Monocotyledonous Plants
by Hailin Fu, Liwei Zhang, Yulin Hu, Ziyi Liu, Zhenyu Wang, Fafu Shen and Wei Wang
Int. J. Mol. Sci. 2025, 26(15), 7334; https://doi.org/10.3390/ijms26157334 - 29 Jul 2025
Viewed by 117
Abstract
MicroRNA528 (miR528) is a microRNA found only in monocotyledonous (monocot) plants. It has been widely reported that miR528 is involved in the regulation of plant growth and development, such as flowering, architecture, and seed and embryogenic development, in addition to playing a crucial [...] Read more.
MicroRNA528 (miR528) is a microRNA found only in monocotyledonous (monocot) plants. It has been widely reported that miR528 is involved in the regulation of plant growth and development, such as flowering, architecture, and seed and embryogenic development, in addition to playing a crucial role in response to various biotic and abiotic stresses, such as plant pathogens, salt stress, heat/cold stress, water stress, arsenic stress, oxidative stress, heavy-metal stress, and nutrient stress. Given that it is specific to monocot plants, to which the major staple food crops such as rice and wheat belong, a review of studies investigating its diverse functional roles and underlying mechanisms is presented. This review focuses on the processes in which miR528 and its targets are involved and examines their regulatory relationships with significant participation in plant development and stress responses. It is anticipated that more biological functions and evolutionary effects of miRNA targets will be elucidated with the increase in knowledge of miRNA evolution and examination of target mRNAs. Full article
(This article belongs to the Special Issue Latest Reviews in Molecular Plant Science 2025)
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27 pages, 5776 KiB  
Review
From “Information” to Configuration and Meaning: In Living Systems, the Structure Is the Function
by Paolo Renati and Pierre Madl
Int. J. Mol. Sci. 2025, 26(15), 7319; https://doi.org/10.3390/ijms26157319 - 29 Jul 2025
Viewed by 129
Abstract
In this position paper, we argue that the conventional understanding of ‘information’ (as generally conceived in science, in a digital fashion) is overly simplistic and not consistently applicable to living systems, which are open systems that cannot be reduced to any kind of [...] Read more.
In this position paper, we argue that the conventional understanding of ‘information’ (as generally conceived in science, in a digital fashion) is overly simplistic and not consistently applicable to living systems, which are open systems that cannot be reduced to any kind of ‘portion’ (building block) ascribed to the category of quantity. Instead, it is a matter of relationships and qualities in an indivisible analogical (and ontological) relationship between any presumed ‘software’ and ‘hardware’ (information/matter, psyche/soma). Furthermore, in biological systems, contrary to Shannon’s definition, which is well-suited to telecommunications and informatics, any kind of ‘information’ is the opposite of internal entropy, as it depends directly on order: it is associated with distinction and differentiation, rather than flattening and homogenisation. Moreover, the high degree of structural compartmentalisation of living matter prevents its energetics from being thermodynamically described by using a macroscopic, bulk state function. This requires the Second Principle of Thermodynamics to be redefined in order to make it applicable to living systems. For these reasons, any static, bit-related concept of ‘information’ is inadequate, as it fails to consider the system’s evolution, it being, in essence, the organized coupling to its own environment. From the perspective of quantum field theory (QFT), where many vacuum levels, symmetry breaking, dissipation, coherence and phase transitions can be described, a consistent picture emerges that portrays any living system as a relational process that exists as a flux of context-dependent meanings. This epistemological shift is also associated with a transition away from the ‘particle view’ (first quantisation) characteristic of quantum mechanics (QM) towards the ‘field view’ possible only in QFT (second quantisation). This crucial transition must take place in life sciences, particularly regarding the methodological approaches. Foremost because biological systems cannot be conceived as ‘objects’, but rather as non-confinable processes and relationships. Full article
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17 pages, 1398 KiB  
Article
Spatio-Temporal Dynamics, Driving Mechanisms, and Decoupling Evaluation of Farmland Carbon Emissions: A Case Study of Shandong Province, China
by Tao Sun, Ran Li, Zichao Zhao, Bing Guo, Meng Ma, Li Yao and Xinhao Gao
Sustainability 2025, 17(15), 6876; https://doi.org/10.3390/su17156876 - 29 Jul 2025
Viewed by 158
Abstract
Understanding the spatio-temporal evolution of farmland carbon emissions, disentangling their underlying driving forces, and exploring the decoupling relationship between these emissions and economic development are pivotal to advancing low-carbon and high-quality agricultural development in Shandong Province, China. Using the Logarithmic Mean Divisia Index [...] Read more.
Understanding the spatio-temporal evolution of farmland carbon emissions, disentangling their underlying driving forces, and exploring the decoupling relationship between these emissions and economic development are pivotal to advancing low-carbon and high-quality agricultural development in Shandong Province, China. Using the Logarithmic Mean Divisia Index (LMDI) and Tapio decoupling model, this study conducted a comprehensive analysis of panel data from 16 cities in Shandong Province spanning 2004–2023. This research reveals that the total farmland carbon emissions in Shandong Province followed a trajectory of “initial fluctuating increase and subsequent steady decline” during the study period. The emissions peaked at 29.4 million tons in 2007 and then declined to 20.2 million tons in 2023, representing a 26.0% reduction compared to the 2004 level. Farmland carbon emission intensity in Shandong Province showed an overall downward trend over the period 2004–2023, with the 2023 intensity registering a 68.9% decline compared to 2004. The carbon emission intensity, agricultural structure, and labor effects acted as inhibiting factors on farmland carbon emissions in Shandong Province, while the economic development effect exerted a positive driving impact on the growth of such emissions. Over the 20-year period, these four factors cumulatively contributed to a reduction of 2.1 × 105 tons in farmland carbon emissions. During 2004–2013, the farmland carbon emissions in Zaozhuang, Yantai, Jining, Linyi, Dezhou, Liaocheng, and Heze showed a weak decoupling state, while in 2014–2023, the farmland carbon emissions and economic development in all cities of Shandong Province showed a strong decoupling state. In the future, it is feasible to reduce farmland carbon emissions in Shandong Province by improving agricultural resource utilization efficiency through technological progress, adopting advanced low-carbon technologies, and promoting the transformation of agricultural industrial structures towards “high-value and low-carbon” designs. Full article
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24 pages, 5785 KiB  
Article
Phylogenetic Reassessment of Murinae Inferred from the Mitogenome of the Monotypic Genus Dacnomys Endemic to Southeast Asia: New Insights into Genetic Diversity Erosion
by Zhongsong Wang, Di Zhao, Wenyu Song and Wenge Dong
Biology 2025, 14(8), 948; https://doi.org/10.3390/biology14080948 - 28 Jul 2025
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Abstract
The Millard’s rat (Dacnomys millardi), a threatened murid endemic to Southeast Asian montane rainforests and the sole member of its monotypic genus, faces escalating endangered risks as a Near Threatened species in China’s Biodiversity Red List. This ecologically specialized rodent exhibits [...] Read more.
The Millard’s rat (Dacnomys millardi), a threatened murid endemic to Southeast Asian montane rainforests and the sole member of its monotypic genus, faces escalating endangered risks as a Near Threatened species in China’s Biodiversity Red List. This ecologically specialized rodent exhibits diagnostic morphological adaptations—hypertrophied upper molars and cryptic pelage—that underpin niche differentiation in undisturbed tropical/subtropical forests. Despite its evolutionary distinctiveness, the conservation prioritization given to Dacnomys is hindered due to a deficiency of data and unresolved phylogenetic relationships. Here, we integrated morphological analyses with the first complete mitogenome (16,289 bp in size; no structural rearrangements) of D. millardi to validate its phylogenetic placement within the subfamily Murinae and provide novel insights into genetic diversity erosion. Bayesian and maximum likelihood phylogenies robustly supported Dacnomys as sister to Leopoldamys (PP = 1.0; BS = 100%), with an early Pliocene divergence (~4.8 Mya, 95% HPD: 3.65–5.47 Mya). Additionally, based on its basal phylogenetic position within Murinae, we propose reclassifying Micromys from Rattini to the tribe Micromyini. Codon usage bias analyses revealed pervasive purifying selection (Ka/Ks < 1), constraining mitogenome evolution. Genetic diversity analyses showed low genetic variation (CYTB: π = 0.0135 ± 0.0023; COX1: π = 0.0101 ± 0.0025) in fragmented populations. We propose three new insights into this genetic diversity erosion. (1) Evolutionary constraints: genome-wide evolutionary conservation and shallow evolutionary history (~4.8 Mya) limited mutation accumulation. (2) Anthropogenic pressures: deforestation-driven fragmentation of habitats (>20,000 km2/year loss since 2000) has reduced effective population size, exacerbating genetic drift. (3) Ecological specialization: long-term adaptation to stable niches favored genomic optimization over adaptive flexibility. These findings necessitate suitable conservation action by enforcing protection of core habitats to prevent deforestation-driven population collapses and advocating IUCN reclassification of D. millardi from Data Deficient to Near Threatened. Full article
(This article belongs to the Section Genetics and Genomics)
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