bluuebunny/crossref_metadata_2025 huggingface dataset:
Multi-Omics Analysis Reveals Immune Infiltration and Clinical Significance of Phosphorylation Modification Enzymes in Lung Adenocarcinoma
Authors: Long Deyu , Ding Yanheng , Wang Peng , Wei Lili , Ma Ketao
Published: January 2025

Protein phosphorylation is a dynamic and reversible modification involved in almost all cellular processes. Numerous investigations have shown that protein phosphorylation modification enzymes (PPMEs) that regulate protein phosphorylation play an important role in the occurrence and treatment of tumors. However, there is still a lack of effective insights into the value of PPMEs in the classification and treatment of patients with lung adenocarcinoma (LUAD). Here, four topological algorithms identified 15 hub PPMEs from a protein–protein interaction (PPI) network. This PPI network was constructed using 124 PPMEs significantly correlated with 35 cancer hallmark-related pathways. Our study illustrates that these hub PPMEs can affect the survival of patients with LUAD in the form of somatic mutation or expression perturbation. Consistency clustering based on hub PPMEs recognized two phosphorylation modification subtypes (namely cluster1 and cluster2) from LUAD. Compared with patients in cluster1, the survival prognosis of patients in cluster2 is worse. This disparity is probably attributed to the higher tumor mutation burden, the higher male proportion, and the more significant expression disturbance in patients in cluster2. Moreover, phosphorylation modification subtypes also have different characteristics in terms of immune activity, immune infiltration level, immunotherapy response, and drug sensitivity. We constructed a PSig scoring system by using a principal component analysis algorithm to estimate the level of phosphorylation modification in individual LUAD patients. Patients in the high and low PSig score groups demonstrated different characteristics in terms of survival rate, tumor mutation burden, somatic gene mutation rate, immune cell abundance, and sensitivity to immunotherapy and drug treatment. This work reveals that phosphorylation plays a non-negligible role in the tumor microenvironment and immunotherapy of LUAD. Evaluating the phosphorylation status of individual LUAD patients by the PSig score can contribute to enhancing our cognition of the tumor microenvironment and guiding the formulation of more effective personalized treatment strategies.
Oral Cancer-Derived miR-762 Suppresses T-Cell Infiltration and Activation by Horizontal Inhibition of CXCR3 Expression
Authors: Peng Hsuan-Yu , Chang Chia-Wei , Wu Ping-Hsiu , Li Li-Jie , Lin Yu-Lung , Hsiao Michael , Chang Jang-Yang , Chang Peter Mu-Hsin , Lee Hsin-Lun , Chang Wei-Min
Published: January 2025

Oral squamous cell carcinoma (OSCC) is an immune-cold tumor characterized by an immunosuppressive microenvironment with low cytotoxic activity to eliminate tumor cells. Tumor escape is one of the initial steps in cancer development. Understanding the underlying mechanisms of cancer escape can help researchers develop new treatment strategies. In this study, we prove the oral oncogenic miR-762 can suppress T-cell recruitment and cytotoxic activation in the tumor microenvironment (TME) through horizontal transmission from OSCC cells to adaptive immune T cells. Public database analysis and quantitative real-time polymerase chain reaction (qRT-PCR) were used to determine the prognosis and expression of miR-762 in OSCC. T-cell activation by flow cytometry, qRT-PCR, IL-12 secretion, and T-cell recruitment and cytotoxicity abilities were conducted in the miR-762 manipulation T-cell and OSCC-T-cell co-culture system. A luciferase reporter and CXCR3 protein expression were also carried out to validate the direct interaction between CXCR3 and microRNA (miR)-762. This horizontal transmission of miR-762 directly suppresses CXCR3 expression in T cells, inhibiting CXCR3-induced T-cell migration and downstream T-cell cytotoxic activity by disrupting AKT activation. Additionally, miR-762 transmission suppressed T-cell activation marker expression, T-cell proliferation, IL-12 secretion, and T-cell cytotoxicity. In conclusion, our findings reveal a novel miR-762/CXCR3 axis that regulates the immunosuppressive microenvironment in OSCC and may be a potential RNA-targeted therapeutic approach to restore the anti-tumor immune response in OSCC treatment.
Morin Reactivates Nrf2 by Targeting Inhibition of Keap1 to Alleviate Deoxynivalenol-Induced Intestinal Oxidative Damage
Authors: Zan Gengxiu , He Hui , Wang Xiaofan , Zhou Jiayi , Wang Xiuqi , Yan Huichao
Published: January 2025

As a prevalent mycotoxin found in cereal foods and feed, deoxynivalenol (DON) disrupts the orderly regeneration of intestinal epithelial tissue by interfering with the intracellular antioxidant defense system. However, the potential of mulberry leaf-derived Morin, a natural flavonoid active substance with clearing reactive oxygen species (ROS), to mitigate DON-induced intestinal oxidative damage remains unclear. Our investigation demonstrates that Morin effectively reverses the decline in growth performance and repairs damaged jejunal structures and barrier function under DON exposure. Furthermore, the proliferation and differentiation of intestinal stem cells (ISCs) is enhanced significantly after Morin intervention. Importantly, Morin increases the levels of total antioxidant capacity (T-AOC), superoxide dismutase (SOD), and glutathione peroxidase (GSH-PX) in the serum and jejunal tissue, while reducing the accumulation of ROS and malondialdehyde (MDA). Molecular interaction analysis further confirms that Morin targets inhibition of Keap1 to activate the Nrf2-mediated antioxidant system. In summary, our results suggest that Morin alleviates the oxidative damage induced by DON by regulating the Keap1/Nrf2 pathway, thereby restoring the proliferation and differentiation activity of ISC, which provides new insights into Morin mitigating DON damage.
Signature Construction Associated with Tumor-Infiltrating Macrophages Identifies IRF8 as a Novel Biomarker for Immunotherapy in Advanced Gastric Cancer
Authors: Liao Wanqian , Wang Yu , Wang Rui , Fu Bibo , Chen Xiangfu , Ouyang Ying , Bai Bing , Jin Ying , Lu Yunxin , Liu Furong , Zhang Yang , Shi Dongni , Zhang Dongsheng
Published: January 2025

Advanced gastric cancer (AGC) is characterized by poor prognosis and limited responsiveness to immunotherapy. Tumor-associated macrophages (TAMs) play a pivotal role in cancer progression and therapeutic outcomes. In this study, we developed a novel gene signature associated with M1-like TAMs using data from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) to predict prognosis and immunotherapy response. This gene signature was determined as an independent prognostic indicator for AGC, with high-risk patients exhibiting an immunosuppressive tumor immune microenvironment (TIME) and poorer survival outcomes. Furthermore, Interferon regulatory factor 8 (IRF8) was identified as a key gene and validated through in vitro and in vivo experiments. IRF8 overexpression reshaped the suppressive TIME, leading to an increased presence of M1-like TAMs, IFN-γ+ CD8+ T cells, and Granzyme B+ CD8+ T cells. Notably, the combination of IRF8 overexpression and anti-PD-1 therapy significantly inhibited tumor growth in syngeneic mouse models. AGC patients with elevated IRF8 expression were found to be more responsive to anti-PD-1 treatment. These findings highlight potential biomarkers for prognostic evaluation and immunotherapy in AGC, offering insights that could guide personalized treatment strategies.
On the Synergistic Effects of Cold Atmospheric Pressure Plasma Irradiation and Electroporation on Cytotoxicity of HeLa Cells
Authors: Kitajima Nao , Makihara Kosuke , Kurita Hirofumi
Published: January 2025

Cold atmospheric plasma (CAP) treatment induces cancer cell death through the generation of reactive oxygen and nitrogen species (RONS). However, the efficacy of RONS delivery into cells remains limited by membrane permeability. Here, we investigated whether combining CAP with pulsed electric fields (PEFs) could enhance cancer cell death through increased intracellular RONS uptake. HeLa cells were treated with argon atmospheric pressure plasma jet (Ar-APPJ), PEF, or their combination. The combined treatment showed significantly enhanced cell death compared to single treatments. While PEF treatment alone induced membrane permeabilization, the combination with Ar-APPJ resulted in more pronounced and sustained membrane disruption, as evidenced by increased calcein leakage. This enhanced effect was attributed to Ar-APPJ-induced lipid peroxidation interfering with membrane resealing after PEF-induced electroporation. We also demonstrated that PEF-induced membrane electroporation facilitates the intracellular uptake of CAP-generated RONS. These findings provide mechanistic insights into the synergistic effects of combined CAP and PEF treatments, suggesting enhanced cell death via multiple pathways.
Multi-Omics Sequencing Dissects the Atlas of Seminal Plasma Exosomes from Semen Containing Low or High Rates of Sperm with Cytoplasmic Droplets
Authors: Zhang Zilu , Xu Xiaoxian , Chen Fumei , Liu Qingyou , Li Zhili , Zheng Xibang , Zhao Yunxiang
Published: January 2025

Sperm cytoplasmic droplets (CDs) are remnants of cytoplasm that can cause a number of problems if it not shed from the sperm after ejaculation. Exosomes can rapidly bind to sperm, but it is not clear whether exosomes can affect the migration and shedding of CDs. We first extracted and characterized seminal plasma exosomes from boar semen containing sperm with low or high rates of CDs. Then, the transcriptomic and proteomic detection of these exosomes were performed to analyze the differences between the two groups of seminal plasma exosomes. The results revealed that 486 differentially expressed genes (DEGs), 40 differentially expressed proteins (DEPs), and 503 differentially expressed lncRNAs (DElncRNAs) were identified between the low CD rate group and high CD rate group. Integrative multi-omics analysis showed that exosome components may affect migration and shedding of cytoplasmic droplets by influencing cytoskeletal regulation and insulin signaling, including regulation of the actin cytoskeleton, ECM–receptor interaction, axon guidance, insulin secretion, and the insulin signaling pathway. Overall, our study systematically revealed the DEGs, DEPs, and DElncRNAs in seminal plasma exosomes between low CD rate semen and high CD rate semen, which will help broaden our understanding of the complex molecular mechanisms involved in the shedding of CDs.
TMEM160 Promotes Tumor Growth in Lung Adenocarcinoma and Cervical Adenocarcinoma Cell Lines
Authors: Herrera-Quiterio Gloria Angelina , Valencia-González Heriberto Abraham , de la Cruz-López Karen Griselda , Fernández-Coto Diana Lashidua , Gil Jeovanis , Marko-Varga György , Morales-Gálvez Josué , Sánchez Nilda C. , Rodríguez-Bautista Rubén , Avilés-Salas Alejandro , Arrieta Oscar , García-Carrancá Alejandro , Encarnación-Guevara Sergio
Published: January 2025

The Chromosome-Centric Human Proteome Project (C-HPP) is an international initiative. It aims to create a protein list expressed in human cells by each chromosomal and mitochondrial DNA to enhance our understanding of disease mechanisms, akin to the gene list generated by the Human Genome Project. Transmembrane protein 160 (TMEM160) is a member of the transmembrane proteins (TMEM) family. TMEM proteins have been implicated in cancer-related processes, including cell proliferation, migration, epithelial-mesenchymal transition, metastasis, and resistance to chemotherapy and radiotherapy. This study aimed to investigate the role of TMEM160 in non-small cell lung cancer and cervical cancer using cell lines, clinical samples, and xenograft studies. Our findings demonstrated that TMEM160 knockdown decreased the proliferation of lung and cervical cancer cell lines. We observed that TMEM160 is localized in the nucleus and cytoplasm and dynamic localization during mitosis of cancer cells and discovered a novel interaction between TMEM160 and nuclear proteins such as NUP50. Furthermore, the TMEM160 interactome was enriched in processes associated with apical junctions, xenobiotic metabolism, glycolysis, epithelial-mesenchymal transition, reactive oxygen species, UV response DNA, the P53 pathway, and the mitotic spindle. This study provides an initial understanding of the function of TMEM160 in lung and cervical cancer progression and clarifies the need to continue investigating the participation of TMEM160 in these cancers.
Characterization of Main Responsive Genes Reveals Their Regulatory Network Attended by Multi-Biological Metabolic Pathways in Paclobutrazol (PAC)-Modulated Grape Seed Development (GSD) at the Stone-Hardening Stage
Authors: Aziz Rana Badar , Wei Ji , Wu Qiqi , Song Siyan , Yang Hui , Chen Xinpeng , Wang Ying , Chao Ruiqiang , Baz Naila Mir , Chen Haitao , Song Yuxuan , Fang Jinggui , Wang Chen
Published: January 2025

Paclobutrazol (PAC) is a significant inhibitor of gibberellin biosynthesis that profoundly influences grape seed development (GSD) through the modulation of key molecular pathways. Here, we identified 6659 differentially expressed genes (DEGs) in GSD under PAC treatment, with 3601 up-regulated and 3058 down-regulated. An analysis of hormone-associated DEGs revealed that auxin-related genes (16) were the most up-regulated, followed by genes associated with brassinosteroid and ABA. In contrast, cytokinin- and gibberellin-related genes exhibited a suppressive response. PAC treatment also triggered extensive reprogramming of metabolic pathways, including 44 genes involved in starch and sucrose metabolism (24 up-regulated, 20 down-regulated), 101 cell wall-related genes (53 up-regulated, 48 down-regulated), and 110 transcription factors (77 up-regulated, 33 down-regulated). A cis-element analysis of the promoters of 76 hormone-responsive genes identified 14 types of hormone-responsive cis-elements, with ABRE being the most prevalent. Genes responsible for inactivating active hormones, such as ABA-VvPP2CA, IAA-VvGH3.1, and CK-VvARR9-1, were also identified. Concurrently, PAC negatively regulated hormone-active genes, including BR-VvXTH25, SA-VvTGA21-3, and JA-VvTIFY3B, leading to reduced levels of these hormones. PAC modulates GSD by mediating the dynamic balance of multi-hormone accumulations. Furthermore, development-related cis-elements such as the AACA-motif, AAGAA-motif, AC-I, AC-II, O2-site, as-1, CAT-box, CCAAT-box, circadian, GCN4-motif, RY-element, HD-Zip 1, HD-Zip 3, MSA-like, MYB-like sequence, MYB-binding site, and MYB recognition site, were found in key DEGs involved in starch and sucrose metabolism, cell wall remodeling, and epigenetic regulation. This indicates that these pathways are responsive to PAC modulation during GSD. Finally, we developed a comprehensive regulatory network to illustrate the PAC-mediated pathways involved in GSD. This network integrates multi-hormonal signaling, cell wall remodeling, epigenetic regulation, and transcription factors, highlighting PAC’s pivotal role in GSD. Our findings provide new insights into the complex mechanisms underlying PAC’s effects on grapevine development.
Relationship Between Systemic Inflammatory Response Exponents, Levels of ADAM10, ADAM17 Proteins and Selected Clinical Parameters in Patients with Colorectal Cancer: Original Research Study
Authors: Sikora-Skrabaka Magdalena , Walkiewicz Katarzyna Weronika , Waniczek Dariusz , Strzelczyk Joanna Katarzyna , Nowakowska-Zajdel Ewa
Published: January 2025

Chronic inflammation is a confirmed risk factor for colorectal cancer (CRC). Indicators of systemic inflammatory response (SIR), such as neutrophil-to-lymphocyte ratio (NLR) or platelet-to-lymphocyte ratio (PLR), are easily accessible indicators of the generalized inflammatory response. At the molecular level, inflammation-related carcinogenesis involves proteins from the adamalysin family: ADAM10 and ADAM17. The aim of the study was to assess NLR and PLR and their relationship with selected clinical parameters in CRC patients, as well as the correlation between ADAM10 and ADAM17 in tumor tissue and matched surgical margins with NLR and PLR values. Tumor tissue material matched surgical margins, and blood was collected from 66 patients who underwent surgery because of CRC. The concentrations of ADAM10 and ADAM17 in the collected material were tested using the enzyme-linked immunosorbent assay (ELISA) method. SIR parameters (NLR, PLR) were also determined. The results were statistically analyzed and compared with selected clinical parameters. Results: The study showed that PLR was lower in patients with comorbid cardiovascular diseases (CVD). In patients who underwent preoperative treatment, both the NLR and PLR values were higher than in patients who underwent primary surgery. There was also a negative correlation between ADAM17 concentrations in the surgical margin and PLR values. In conclusion, the presence of additional diseases such as CVD or diabetes mellitus type 2 (DMT2) or the use of preoperative treatment should be taken into account when assessing SIR parameters in CRC patients. Moreover, no clear correlations have been found between ADAM10 and ADAM17 and SIR parameters.
Catalytic Performance of Oxydianiline-Derived Polybenzoxazine in the Cycloaddition of CO2 with Epoxides for Selective and Cleaner Production of Cyclic Carbonates
Authors: Shaikh Rafik Rajjak , Yazdanpanah Mohammad , Shaikh Isak Rajjak , Khan Rais Ahmad , Praserthdam Supareak , Praserthdam Piyasan
Published: January 2025

Benzoxazine-based polymer (PBZ) acts as a catalyst for converting CO2 into cyclic carbonates. PBZ-ODA was successfully synthesized and examined for its catalytic efficiency, proving to be effective under milder conditions with higher yields at room temperature without solvents. Various terminal monoepoxides showed good to excellent conversion rates, while epoxides with aromatic or bulky groups and second oxirane rings also were able to produce corresponding cyclic carbonates. Recyclability tests demonstrated that regenerated PBZ-ODA retained 93% of its catalytic activity. Overall, there was a low catalyst deactivation, as investigated by chemical experiments, SEM-EDX, TGA, FT-IR, XPS, XRD and NMR. The catalyst is reusable and suitable for use in flow or batch reactors.
Advances in Synthetic Immunology for Targeted Treatment of Systemic Autoimmune Diseases: Opportunities, Challenges, and Future Directions
Authors: Adytia Galih Januar , Sutanto Henry , Pratiwi Laras , Fetarayani Deasy
Published: January 2025

Systemic autoimmune diseases (SAIDs) affect millions worldwide, presenting significant clinical challenges due to their complex pathogenesis and limited treatment options. Traditional immunosuppressive therapies, while effective, often lack precision, leading to significant side effects and inadequate disease control. Recent advances in synthetic immunology offer promising avenues for precise, targeted interventions in SAIDs. This review examines the latest innovations in synthetic immunology for treating autoimmune diseases, focusing on engineered immune cells, synthetic biologics, and gene-editing technologies. It explores the therapeutic potential of these approaches to modulate immune tolerance, reduce systemic inflammation, and enhance patient-specific treatment efficacy. However, despite these promising developments, challenges remain, including immune system complexity, safety concerns, and regulatory hurdles that may hinder clinical translation. This review aims to consolidate current advancements, address existing barriers, and outline potential future directions for synthetic immunology in autoimmune disease management, highlighting synthetic immunology’s role in transforming the therapeutic landscape for SAIDs.
Homo-Chromophores in Cu(I)(XXX), (X3 = N3, C3, Cl3, S3, P3, Br3, or I3) Derivatives—Structural Aspects
Authors: Melník Milan , Mikušová Veronika , Mikuš Peter
Published: January 2025

The structural aspects of homo-chromophores in Cu(I)(XXX) complexes, where X3 = N3, C3, Cl3, S3, P3, Br3, or I3, are analyzed in this study. These copper(I) derivatives crystallize in five distinct crystal systems as follows: rhombohedral (1 example), trigonal (1 example), orthorhombic (4 examples), triclinic (5 examples), and monoclinic (15 examples). The angular distortion from regular trigonal geometry increases in the following order: Cu(ClClCl) < Cu(NNN) < Cu(PPP) < Cu(BrBrBr) < Cu(III) < Cu(CCC) < Cu(SSS). For Cu(I)(XX) complexes, the deviation from linear geometry increases in the order: Cu(SeSe) < Cu(SS) < Cu(OO) < Cu(ClCl) < Cu(NN) < Cu(CC) < Cu(PP) < Cu(BrBr). The structural parameters of Cu(I)(XXX) are examined, discussed, and compared with those of homonuclear Cu(I)(XX) complexes.
Design and Simulation of a Muon Detector Using Wavelength-Shifting Fiber Readouts for Border Security
Authors: Georgadze Anzori Sh.
Published: January 2025

Cosmic ray muon tomography is a promising method for the non-invasive inspection of shipping containers and trucks. It leverages the highly penetrating cosmic muons and their interactions with various materials to generate three-dimensional images of large and dense objects, such as inter-modal shipping containers, which are typically opaque to conventional X-ray radiography techniques. One of the key tasks of customs and border security is verifying shipping container declarations to prevent illegal trafficking, and muon tomography offers a viable solution for this purpose. Common imaging methods using muons rely on data analysis of either muon scattering or absorption–transmission. We design a compact muon tomography system with dimensions of 3 × 3 × 3 m3, consisting of 2D position-sensitive detectors. These detectors include plastic scintillators, wavelength-shifting (WLS) fibers, and SiPMs. Through light transport modeling with GEANT4, we demonstrate that the proposed detector design—featuring 1 m × 1 m scintillator plates with 2 mm2 square-shaped WLS fibers—can achieve a spatial resolution of approximately 0.7–1.0 mm. Through Monte Carlo simulations, we demonstrate that combining muon scattering and absorption data enables the rapid and accurate identification of cargo materials. In a smuggling scenario where tobacco is falsely declared as paper towel rolls, this combined analysis distinguishes the two with 3 σ confidence at a spatial resolution of 1 mm (FWHM) for the muon detector, achieving results within a scanning time of 40 s for a 20-foot shipping container.
Study on Dynamic Response of Damping Type Composite Floor Slabs Considering Interlayer Interaction Influences
Authors: Sun Liangming , Xu Ting , Tian Feng , Zhang Yijie , Zhao Hanbing , Mahmood Aziz Hasan
Published: January 2025

In order to explore the vibration mechanism of vibration damping composite floor slabs and further enrich the theory of floor slab vibration calculation, the free vibration characteristics of vibration damped composite floor slabs and the dynamic response of vibration damped composite floor slabs under multi-source excitation is analyzed using first type Chebyshev polynomials to construct the displacement function and derive an analytical solution. The three-dimensional laminated theory is employed, considering the interlayer interaction. Based on the proposed method, the influences of loading types, positions, magnitudes, and frequencies on the vertical vibration of floor slabs are calculated. The study illustrates that, under the action of multi-source excitation, the displacement and acceleration responses calculated by the method proposed in this paper are always greater than those calculated by the single-plate theoretical solution. The dynamic responses of the vibration damping composite floor slab decrease with the increase of the thickness and elastic modulus of the vibration damping layer. Under different thicknesses of the vibration damping layer, the peak accelerations of the vibration damping composite floor slabs increase linearly with the growth of the load amplitude. In addition, the load movement path has a significant effect on the vibration response of the floor slab. When the moving load moves along the short side of the floor, the displacement response of the floor is generally greater than that along the long side of the floor.
iForal: Automated Handwritten Text Transcription for Historical Medieval Manuscripts
Authors: Matos Alexandre , Almeida Pedro , Correia Paulo L. , Pacheco Osvaldo
Published: January 2025

The transcription of historical manuscripts aims at making our cultural heritage more accessible to experts and also to the larger public, but it is a challenging and time-intensive task. This paper contributes an automated solution for text layout recognition, segmentation, and recognition to speed up the transcription process of historical manuscripts. The focus is on transcribing Portuguese municipal documents from the Middle Ages in the context of the iForal project, including the contribution of an annotated dataset containing Portuguese medieval documents, notably a corpus of 67 Portuguese royal charter data. The proposed system can accurately identify document layouts, isolate the text, segment, and transcribe it. Results for the layout recognition model achieved 0.98 mAP@0.50 and 0.98 precision, while the text segmentation model achieved 0.91 mAP@0.50, detecting 95% of the lines. The text recognition model achieved 8.1% character error rate (CER) and 25.5% word error rate (WER) on the test set. These results can then be validated by palaeographers with less effort, contributing to achieving high-quality transcriptions faster. Moreover, the automatic models developed can be utilized as a basis for the creation of models that perform well for other historical handwriting styles, notably using transfer learning techniques. The contributed dataset has been made available on the HTR United catalogue, which includes training datasets to be used for automatic transcription or segmentation models. The models developed can be used, for instance, on the eSriptorium platform, which is used by a vast community of experts.
The Complete Mitochondrial Genome of the Korean Endemic Polychaete Phyllodoce koreana (Lee & Jae, 1985) from Jindong Bay, Korea, with Additional Morphological and Ecological Features
Authors: Kim Dae-Hun , Ryu So Jin , Kim Jong Rae , Eyun Seong-il , Jeong Man-Ki
Published: January 2025

Phyllodoce koreana was first described in 1985 in Gwangyang Bay, a semi-enclosed bay in Korea affected by significant organic input from the Seomjin River and dredging activities near the Gwangyang Port. Since then, this Korean endemic species has received limited attention in taxonomic and ecological studies. Phyllodoce koreana is known for its resilience to mild disturbances but is vulnerable to severe environmental changes. In this study, P. koreana specimens were collected from organically polluted Asian stalked tunicate aquaculture farms at eight sites in Jindong Bay, a location with environmental conditions similar to those of Gwangyang Bay, over the course of five sampling events from March to November. Both bays experience benthic hypoxia in summer due to elevated water temperatures and organic matter accumulation. Phyllodocid specimens were primarily collected in March and November 2023, non-hypoxic periods, suggesting potential seasonal adaptations to environmental fluctuations. The morphological features of the collected specimens were consistent with the original description of P. koreana, confirming their identification. Additionally, we reported previously overlooked morphological details, contributing to a more comprehensive taxonomic understanding of the species. We also present, for the first time, the complete mitochondrial genome of this species, comprising 15,559 bp, which provides essential genetic data for future taxonomic and phylogenetic studies. The phylogenetic analysis of protein-coding genes shows that, among 17 related polychaete species, P. koreana (family Phyllodocidae) is closely related to the family Goniadidae. Future research should expand our knowledge of polychaete taxonomy by integrating additional mitochondrial genomes and investigating the role of conserved gene synteny within Polychaeta.
An Improved YOLOv9s Algorithm for Underwater Object Detection
Authors: Zhou Shize , Wang Long , Chen Zhuoqun , Zheng Hao , Lin Zhihui , He Li
Published: January 2025

Monitoring marine life through underwater object detection technology serves as a primary means of understanding biodiversity and ecosystem health. However, the complex marine environment, poor resolution, color distortion in underwater optical imaging, and limited computational resources all affect the accuracy and efficiency of underwater object detection. To solve these problems, the YOLOv9s-SD underwater target detection algorithm is proposed to improve the detection performance in underwater environments. We combine the inverted residual structure of MobileNetV2 with Simple Attention Module (SimAM) and Squeeze-and-Excitation Attention (SE) to form the Simple Enhancement attention Module (SME) and optimize AConv, improving the sensitivity of the model to object details. Furthermore, we introduce the lightweight DySample operator to optimize feature recovery, enabling better adaptation to the complex characteristics of underwater targets. Finally, we employ Wise-IoU version 3 (WIoU v3) as the loss function to balance the loss weights for targets of different sizes. In comparison with the YOLOv9s model, according to the experiments conducted on the UPRC and Brackish underwater datasets, YOLOv9s-SD achieves an improvement of 1.3% and 1.2% in the mean Average Precision (mAP), reaching 83.0% and 94.3% on the respective datasets and demonstrating better adaptability to intricate underwater environments.
Mesozoic–Paleozoic Structural Characteristics and Their Controlling Effects on Oil and Gas in the Kongnan Area of Bohai Bay Basin
Authors: Peng Daicheng , Yang Dong , Cheng Fei , She Xiaoyu , Tao Ze , Liu Yukun
Published: January 2025

The Bohai Bay Basin is a typical marginal basin with complex internal structures and abundant oil and gas resources, exhibiting unique marine geological characteristics and processes. Based on seismic profile interpretation and balanced cross-section techniques, this paper presents a comprehensive systematic study of the structural combination and tectonic evolution of the Neo-Mesozoic–Cenozoic superimposed basin in the southern Bohai Bay Basin. The research findings indicate that the area exhibits four types of structural properties, including compression, extension, strike-slip, and thrust structures, along with thirteen fundamental styles. Building upon this foundation, research has been conducted on the tectonic evolution and formation processes during the Mesozoic and Cenozoic eras. Based on the effective correlation between hydrocarbon generation and tectonic evolution phases, a three-phase model was proposed as “early anticline-controlled oil accumulation-primary reservoir formation, mid-stage fault adjustment-secondary reservoir formation, late-stage block modification-multiple phase petroleum accumulation”. Our model explains the composite reservoir system in the Neogene–Mesozoic era, characterized by multiple-stage structural oil and gas accumulation, coexistence of primary and secondary hydrocarbon, and various types of oil and gas reservoirs. This study elucidates the controlling effects of structural characteristics and evolution on oil and gas accumulation under marine geological conditions, providing a theoretical basis for the efficient development of oil and gas resources in marginal basins.
Optimization of Inbound and Outbound Vessel Scheduling in One-Way Channel Based on Reinforcement Learning
Authors: Zhen Rong , Sun Meng , Fang Qionglin
Published: January 2025

As the size and number of ships continue to grow, effective management of vessel scheduling has become more and more important for the efficient one-way channel port operation, whose characteristics significantly affect the safety and efficiency of ports. This paper presents a reinforcement-learning-based approach to optimize the scheduling of vessels in a one-way channel, aiming to quickly identify a scheduling solution that enhances port operational efficiency. This method models the vessel scheduling problem in a one-way channel by incorporating navigational constraints, safety requirements, and vessel-specific characteristics. Using the Q-learning algorithm to minimize vessel wait times, it identifies an optimal scheduling solution. Experiments were conducted using real data from the Dayao Bay Pier of Dalian Port to validate the rationality and effectiveness of the proposed model and algorithm. The results show that the reinforcement learning approach achieved approximately a 16% improvement in solution quality compared to the genetic algorithm (GA) while requiring only half the computation time. Additionally, it reduced delay times by over 40% relative to the traditional FCFS strategy, indicating superior overall performance. This research presents an efficient, intelligent approach to vessel scheduling, providing a theoretical foundation for further advancements in this field and enhancing decision support for vessel scheduling in one-way channels with practical implications.
An Improved Thermoeconomic Diagnosis Method: Applying to Marine Diesel Engines
Authors: Xu Nan , Yang Longbin , Guo Yu , Chang Lei , Zhang Guogang , Zhang Jundong
Published: January 2025

Thermoeconomic diagnosis methods are designed to identify faulty components and evaluate the economic implications of these faults. However, these diagnostic techniques often struggle to filter out interference from induced factors during the diagnosis process. When multiple components malfunction simultaneously, these methods may fail to effectively identify all the faulty components. To address these challenges, this article introduces an improved thermoeconomic diagnosis method that integrates the traditional diagnosis method with the operational characteristic curves of the components. This improved method facilitates a more precise differentiation between the impacts of faults on each component, categorizing them into intrinsic and induced parts. The intrinsic part arises from the component’s inherent failure, while the induced part results from interactions among different components or adjustments made by the control system. The improved method generates fault diagnosis indicators and economic assessment indicators based on this classification, allowing for the identification of faulty components and the evaluation of the economic consequences of these faults. The proposed method was tested on a MAN 6S50 MC-C8 diesel engine and validated under two real operating conditions, where multiple faults were intentionally introduced in various components. The results demonstrated that the new method accurately identified all faulty components within the marine diesel engine and assessed the economic impacts of these faults.
Targeting Metabolic Vulnerabilities to Combat Drug Resistance in Cancer Therapy
Authors: Khan Taranatee , Nagarajan Manojavan , Kang Irene , Wu Chunjing , Wangpaichitr Medhi
Published: January 2025

Drug resistance remains a significant barrier to effective cancer therapy. Cancer cells evade treatment by reprogramming their metabolism, switching from glycolysis to oxidative phosphorylation (OXPHOS), and relying on alternative carbon sources such as glutamine. These adaptations not only enable tumor survival but also contribute to immune evasion through mechanisms such as reactive oxygen species (ROS) generation and the upregulation of immune checkpoint molecules like PD-L1. This review explores the potential of targeting metabolic weaknesses in drug-resistant cancers to enhance therapeutic efficacy. Key metabolic pathways involved in resistance, including glycolysis, glutamine metabolism, and the kynurenine pathway, are discussed. The combination of metabolic inhibitors with immune checkpoint inhibitors (ICIs), particularly anti-PD-1/PD-L1 therapies, represents a promising approach to overcoming both metabolic and immune evasion mechanisms. Clinical trials combining metabolic and immune therapies have shown early promise, but further research is needed to optimize treatment combinations and identify biomarkers for patient selection. In conclusion, targeting cancer metabolism in combination with immune checkpoint blockade offers a novel approach to overcoming drug resistance, providing a potential pathway to improved outcomes in cancer therapy. Future directions include personalized treatments based on tumor metabolic profiles and expanding research to other tumor types.
Investigation of Diverse Urban Carbon Emission Reduction Pathways in China: Based on the Technology–Organization–Environment Framework for Promoting Socio-Environmental Sustainability
Authors: Jiang Haiyan , Lu Jiaxi , Zhang Ruidong , Xiao Xi
Published: January 2025

In the context of global carbon emissions and climate change, identifying context-specific low-carbon pathways for urban areas is critical for achieving socio-environmental sustainability. This study applies the technology–organization–environment (TOE) framework to examine the driving mechanisms and the diversity in carbon reduction pathways across 81 cities in China. Utilizing partial least squares structural equation modeling (PLS-SEM) and necessary condition analysis (NCA), this research assesses the roles of technological, organizational, and environmental drivers in urban carbon reduction. Fuzzy-set qualitative comparative analysis (fsQCA) is employed to uncover distinct carbon reduction pathways and causal asymmetries between cities. The findings reveal that technological, organizational, and environmental factors significantly drive carbon reduction, with technological and organizational factors playing the central roles. Environmental factors exert primarily indirect effects, interacting with technological and organizational drivers. This study categorizes cities into three distinct carbon reduction models: cities with high carbon-neutral potential primarily leverage technological innovation and energy efficiency optimization; cities with moderate potential integrate technology and policy, emphasizing green landscape planning to achieve balanced development; and cities with lower carbon reduction potential are mainly policy-driven, constrained by technological and resource limitations. This study underscores the role of computational modeling in providing valuable insights for the development of context-tailored carbon reduction strategies. It highlights the synergetic interactions among technological, organizational, and environmental factors, offering essential guidance for advancing sustainable development planning and facilitating the low-carbon transition of cities and communities.
Six Decades of Rural Landscape Transformation in Five Lebanese Villages
Authors: Yehya Abed Al Kareem , Nguyen Thanh Thi , Wiehle Martin , Zurayk Rami , Buerkert Andreas
Published: January 2025

During the last six decades, Lebanon’s landscapes have undergone significant regime shifts whose causes are under-investigated. Using land cover maps from 1962 and satellite imagery from 2014 and 2023 in five randomly selected villages across Lebanon’s major agroecological zones (AEZs), we identified salient trends in the urbanization-driven transformation of land use and land cover (LULC). Household socio-economic characteristics and environmental pressures were analyzed as independent variables influencing land use decisions. Logistic regression (LR) was employed to assess the significance of these variables in shaping farmers’ choices to transition toward “perennialization”—namely fruit tree monocropping or protected agriculture. The LR results indicate that education reduced the likelihood of “perennialization” by 45% (p < 0.001). Farm size positively influenced “perennialization” (p < 0.01), suggesting that land availability encourages this agricultural practice. In contrast, water availability negatively affects “perennialization” (p < 0.01), though farmers may still opt to irrigate by purchasing water during shortages. Our findings underline the complex interplay of socio-economic and environmental dynamics and historical events in shaping Lebanon’s rural landscapes and they offer insights into similar transformations across the Middle East and North Africa (MENA) region.
Preface to “Recent Developments in Language Testing and Assessment”
Authors: Tsagari Dina , Bøhn Henrik
Published: January 2025

The field of language testing and assessment (LTA) has evolved significantly [...]
PI-Effects in South Bantu: Consonant Changes Due to a Preceding Front Close Vowel
Authors: Wills Jeffrey
Published: January 2025

An important set of sound changes affected the South Bantu languages through the impact of front vowels on following consonants, most notably under the form of the class 5 nominal prefix *i-. These consonant changes are well known, but their extent has been underestimated, as the substantial data in this paper show. There is not even a standard name for these changes, which are here called “Preceding-I effects”. This paper offers a detailed study of the relevant conditioning factor, calling attention to the understudied category of hiatus resolution in the history of Bantu languages. Although the reflexes in individual languages vary and levelling often reduced the number of surviving examples, indications of systematic PI-effects in all the subgroups of the South Bantu branch contrast with other Bantu branches and suggest a common conditioning factor was present in Proto-South-Bantu.
Morpho-Physiological Adaptations of Rice Cultivars Under Heavy Metal Stress: A Systematic Review and Meta-Analysis
Authors: Espinola Esmeth C. , Cabreros Monica Maricris N. , Redillas Mark Christian Felipe R.
Published: January 2025

Soil contamination, including in rice fields, arises from a variety of natural processes and anthropogenic activities, leading to an accumulation of heavy metals. While extensive research has addressed the bioaccumulation of heavy metals in rice, only limited systematic reviews have examined their specific impact on the morpho-physiological traits of rice plants. This review aims to provide a comprehensive synthesis of current studies detailing the rice cultivars, types of heavy metals investigated, study designs, sampling locations, and experimental sites while systematically analyzing the morphological and physiological responses of rice cultivars to heavy metal stress. Studies show that morphological traits generally exhibit a decline under heavy metal exposure. Physiologically, rice cultivars tend to show decreased total chlorophyll and carotenoid levels, along with increased levels of malondialdehyde (MDA), hydrogen peroxide (H₂O₂), and antioxidant enzymes such as superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), ascorbate peroxidase (APX), and proline. These findings suggest that plant genotype, type of heavy metal, and intensity of stress significantly modulate the morphological and physiological responses of rice, highlighting critical areas for further research in heavy metal stress tolerance in rice cultivars.
Stability of Expanded Austenite During Annealing in Vacuum
Authors: Mändl Stephan , Oh Hyemin , Hristov Daniel , Manova Darina
Published: January 2025

In situ X-ray diffraction has been used to investigate the stability of expanded austenite during annealing in vacuum for the austenitic stainless steel 316Ti, the super-austenitic stainless steel 904L, and the duplex steel 318LN. Expanded austenite has been formed using plasma immersion ion nitriding before. Time-of-flight secondary ion mass spectrometry before and after annealing yielded complementary information regarding nitrogen depth profiles and CrN precipitation using cluster analysis. The decay of expanded austenite during annealing was found to be thermally activated with an activation energy of 1.8 ± 0.3 eV, starting within five minutes at 550 °C and taking more than two hours below 450 °C. The decay occurs simultaneously throughout the whole nitrogen-containing zone—and not at the surface as during nitriding. Nitrogen diffusion occurring in parallel slightly complicates the data analysis. Further transmission electron microscopy investigations are necessary to understand the microstructure after annealing in vacuum. The limit for operating hard and wear-resistant expanded austenite layers at elevated temperatures of up to 350 °C is given, however, by nitrogen diffusion and not the decay into CrN.
Flexural Strength, Fatigue Behavior, and Microhardness of Three-Dimensional (3D)-Printed Resin Material for Indirect Restorations: A Systematic Review
Authors: Abad-Coronel Cristian , Durán Urdiales Daniela , Benalcázar Arias María Verónica , Córdova Andrea Karina , Medina María Sol , Bravo Torres Wilson
Published: January 2025

The purpose of this systematic review was to evaluate three mechanical properties of 3D-printed resins for indirect restorations according to published scientific evidence. This systematic review was conducted according to the PRISMA statement (preferred reporting elements for systematic reviews and meta-analyses). The search was performed by two investigators, (DD) and (VB), and a third (AC) resolved disagreements. Articles were searched in four digital databases: PubMed, EBSCO, Lilacs, and Science Direct, starting on 18 February 2024. As 3D-printing technology has shown significant advances in the last 5 years, the review was conducted with a publication year range between 2019 and 2024, in English language and included in vitro articles on the mechanical properties of flexural strength, fatigue behavior, and microhardness of 3D-printed materials for temporary or definitive restorations. MeSH terms and free terms were used for the titles and abstracts of each article. Finally, the QUIN tool was used to assess the risk of bias. In the main search, 227 articles were found, of which 20 duplicates were excluded, leaving 207 articles; of these, titles and abstracts were read, and 181 that did not meet the eligibility criteria were eliminated; of the remaining 26 articles, 1 article was eliminated for not presenting quantitative results. Regarding publication bias, 6 of the 25 articles had a low risk of bias, 18 had a medium risk of bias, and 1 had a high risk of bias. It may be concluded that 3D-printed resins have lower flexural strength, fatigue behavior, and microhardness than other resin types used for the fabrication of temporary and permanent restorations. The type of 3D printer and polymerization time could be factors that significantly affect the flexural strength, fatigue behavior and microhardness of 3D-printed resins. Based on existing evidence, it should be considered that additive technology has promising future prospects for temporary and permanent dental restorations.