bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predicting risk factors for Epstein-Barr virus reactivation using Bayesian network analysis: a population-based study of high-risk areas for nasopharyngeal cancer
Authors: Zeng Zhiwen , Lin Kena , Li Xueqi , Li Tong , Li Xiaoman , Li Jiayi , Ning Zule , Liu Qinxian , Xie Shanghang , Cao Sumei , Du Jinlin 
Published: January 2025

Background and objectiveNasopharyngeal carcinoma (NPC) is a rare disease in most parts of the world, but it is highly prevalent in South China. Epstein-Barr virus (EBV) is one of the major risk factors for NPC. Hence, understanding the factors associated with the reactivation of EBV from the latent stage is crucial for preventing NPC. This study aimed to investigate the risk factors for EBV reactivation associated with NPC in high-prevalence areas in China using a Bayesian network (BN) model combined with structural equation modeling tools.MethodsThe baseline information for this study was derived from NPC screening data from a population-based prospective cohort in Sihui City, Guangdong Province, China. We divided the data into a training dataset and a test dataset. We then constructed an interaction networktionba BN prediction model to explore the risk factors for EBV reactivation, which was compared with a conventional logistic regression model.ResultsA total of 12,579 participants were included in the analyses, with 1596 participant pairs finally included after the use of a nested case-control study. The results of multivariable logistic regression showed that only being older than 60 years (OR = 1.718, 95% CI = 1.273,2.322) and being a current smoker (OR = 1.477, 95% CI = 1.167 - 1.872) were the risk factors for EBV reactivation. The results of the model constructed using BN showed that age and smoking were directly associated with EBV reactivation. In contrast, sex, education level, tea drinking, cooking, and family history of cancer were indirectly associated with EBV reactivation. Further, we predicted the risk of EBV reactivation using Bayesian inference and visualized the BN inference. Model prediction performance was evaluated using the test dataset. The results showed that the BN model slightly outperformed the traditional logistic regression model in all metrics.ConclusionsBN not only reflects the complex interaction between factors but also visualizes the prediction results. It has a promising application potential in the risk prediction of EBV reactivation associated with NPC.
Transcription factor KLF2 is associated with the dysfunctional status of NK cells and the prognosis of pediatric B-ALL patients
Authors: Wu Fang , Xu Huimin , Zhang Benshan 
Published: January 2025

BackgroundNatural killer cells, an important component of the innate immune system, can directly recognize and lyse virally infected or transformed cells. However, NK cells fail to restrain the growth of malignancies, such as B-cell acute lymphoblastic leukemia (B-ALL). The molecular genetics of NK cells in the B-ALL bone marrow microenvironment and the mechanisms underlying the inhibited function of NK cells at the single-cell level remain largely elusive.MethodsIn this study, we studied the frequency and absolute number of NK cells in peripheral blood samples collected from 43 healthy volunteers and 104 pediatric B-ALL patients diagnosed at Hunan Children’s Hospital. We also analyzed published single-cell RNA sequencing (scRNAseq) data from B-ALL and normal bone marrow samples using unsupervised clustering. Our findings were further validated using bulk transcriptomic data and clinical data from a cohort of 139 B-ALL bone marrow samples.ResultsWe found that the frequency and number of NK cells were significantly decreased in the bone marrow and peripheral blood of B-ALL patients. In-depth analysis of scRNAseq data identified 12 NK cell clusters. Among them, the C2 cluster, which is present in healthy bone marrow but reduced in B-ALL bone marrow, displays overexpression of a transcription factor KLF2 and a significant downregulation of the “leukocyte proliferation” pathway. Furthermore, we found that the expression of KLF2 in B-ALL at diagnosis was positively correlated with the percentage of leukemia cells and the positive rate of minimal residual disease (MRD), indicating that KLF2 is a marker of poor prognosis.ConclusionThere are dramatic differences at the single-cell level in the transcriptomics of NK cells between healthy donors and B-ALL patients. A transcription factor, KLF2, which is enriched in the C2 cluster of NK cells, has been suggested to regulate the proliferation of NK cells and is associated with poor prognosis of pediatric B-ALL.
Prognosis of premenopausal women with low-risk endometrial cancer but elevated CA125 levels
Authors: Song Jeong Min , Aiob Ala , Kim Kidong , Lee Kwang Beom , Kang Sokbom , Lee Chae Hyeong , Kim Se Ik , Kim Nam Kyeong , Jeong Dae Hoon 
Published: January 2025

IntroductionWomen with low-risk endometrial cancer, as defined by the Korean Gynecologic Oncology Group (KGOG) criteria, have a low risk of lymph node metastasis and an excellent prognosis without lymphadenectomy. However, it is unclear whether lymphadenectomy should be performed in premenopausal women who meet the KGOG criteria other than elevated cancer antigen 125 (CA125) levels, because the CA125 level can be elevated by benign conditions. We investigated the patterns of metastasis and recurrence to assess the value of lymphadenectomy in this population.MethodsPremenopausal women with endometrial cancer meeting the KGOG criteria, except for those with elevated CA125 levels, were eligible. The characteristics of the eligible women were collected from seven institutes in the Republic of Korea by reviewing their medical records. Recurrence-free survival (RFS) was estimated using the Kaplan–Meier method and compared using the log-rank test.ResultsSeventy-three patients were included. Of 62 women who underwent lymphadenectomy, only two (3.2%) had lymph node metastasis. Eighteen women (24.7%) received adjuvant therapy. At a median follow-up of 59 months, the 5-year RFS was 88.8%. Five women (7%) experienced recurrence, two had lymph node recurrence, and three had non-nodal recurrence. RFS was similar between the women who did and did not undergo lymphadenectomy (P=0.737).ConclusionPremenopausal women who had elevated CA125 levels but met all other KGOG criteria showed a low risk of lymph node metastasis and recurrence as well as a good prognosis. Therefore, lymphadenectomy can be omitted in this population.
Dermatomyositis following resection of thyroid and breast cancer: a case report and literature review
Authors: Yang Miaomiao , Liu Jiannan 
Published: January 2025

BackgroundDermatomyositis is an idiopathic inflammatory myopathy and occurs as a paraneoplastic syndrome. Here, we report an unusual case of dermatomyositis that developed in a patient after the resection of thyroid cancer and breast cancer. The intercorrelation between dermatomyositis and neoplastic disorders was discussed.Case presentationA 60-year-old female farmer was diagnosed with thyroid cancer and breast cancer and then developed dermatomyositis after two curative surgeries and adjuvant chemotherapy. Dermatomyositic symptoms occurred after the fifth cycle of adjuvant chemotherapy for breast cancer and deteriorated progressively. Case history, imaging, and laboratory data were reviewed. This patient subsequently received systemic immunosuppressant therapy and thus dermatomyositis gradually resolved.ConclusionsA combination of thyroid cancer and breast cancer is thought to be very rare, especially in patients who develop dermatomyositis after thyroidectomy and mastectomy. An extraordinary case was reported in this study. Potential mechanisms for the development of dermatomyositis and novel insights neoplastic autoimmune diseases were proposed.
SMARCA4-related Coffin-Siris syndrome in newborn: a case report and literature review
Authors: Wang Yuqian , Zhang Li , Zhu Jing , Yang Liu , Wang Chan , Zou Ning 
Published: January 2025

ObjectiveOur objective was to examine the clinical and genetic features of Coffin-Siris syndrome resulting from a pathogenic variant in the SMARCA4 gene.MethodsThe clinical data and molecular genetic test results of a newbron with Coffin-Siris syndrome involving a pathogenic variant in the SMARCA4 gene were retrospectively analyzed, and the related literatures were reviewed.ResultsA newborn exhibited inspiratory dyspnea following birth and developmental anomalies (coarse appearance, thick hair, long eyelashes, broad nasal tip, flat nasal bridge, thin upper lip, thick lower lip, digital anomalies, cleft palate, supraglottic laryngeal chondromalacia, stenosis of the left upper bronchus and hypotonia). Whole exome sequencing revealed a heterozygous missense variant in SMARCA4 gene (NM_003072.5 c.3127C &gt; T, p.Arg1043Trp). Parents did not find the above pathogenic variant, which was a new pathogenic variant. In addition to our case, we also retrieved 22 cases of Coffin-Siris Syndrome in SMARCA4 gene variation, which is a congenital multi-system dysfunction syndrome characterized by abnormal appearance and developmental retardation. The common otolaryngologic features of 23 patients with CSS in SMARCA4 gene variant included palate abnormalities, feeding difficulties, ear abnormalities and hearing loss.ConclusionCoffin-Siris syndrome is a rare genetic disease inherited in an autosomal-dominated manner. It is often associated with malformations in the otorhinolaryngologic system. This case has many common features with previously reported CSS cases with pathogenic variant in the SMARCA4 gene, which further characterizes the performance of the pathogenic variant, suggesting that palatal abnormalities may be a significant feature of the genotype. For patients with developmental abnormalities, whole-genome sequencing or whole-exome sequencing is particularly important to assist diagnosis. Currently, there is no known treatment for CSS, and individuals with CSS experience various complications affecting multiple systems.
A novel α-conotoxin [D1G, ΔQ14] LvIC decreased mouse locomotor activity
Authors: Wang Wen , Wang Meiting , Wang Huanbai , Xu Weifeng , Wang Conggang , Pei Jie , Li Xiaodan , Zhangsun Dongting 
Published: January 2025

Background and PurposeNicotinic acetylcholine receptors (nAChRs), which are expressed throughout the mammalian brain, mediate a variety of physiological functions. Despite their widespread presence, the functions of nAChRs are not yet fully understood. α-Conotoxins, which are peptides derived from the venom of marine cone snails, target different subtypes of nAChRs. Specifically, α-Conotoxins [D1G, ΔQ14] LvIC, identified from Conus lividus, have demonstrated strong activity on α6β4* nAChRs in vitro. However, the effects of [D1G, ΔQ14] LvIC have not been investigated in vivo. This study aims to examine the activities of [D1G, ΔQ14] LvIC and explore its potential mechanisms in vivo.MethodsThe study involved the injection of [D1G, ΔQ14] LvIC into the lateral cerebral ventricle (LV) of mice. Following this procedure, behavioral tests were conducted to assess changes in the mice’s behavior. To investigate the molecular alterations in the mice’s brains, untargeted metabolomics and label-free Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) were employed. Subsequently, Western blot (WB) and quantitative reverse transcription PCR (RT-qPCR) techniques were utilized to detect specific molecular changes induced by [D1G, ΔQ14] LvIC.ResultsThe injection of [D1G, ΔQ14] LvIC led to a decrease in locomotor activity in mice. This treatment also resulted in reduced expression of neuronal calcium sensor 1 (NCS-1) and neuroligin 3 (NLGN-3) in the prefrontal cortex (PFC), hippocampus (Hip), and caudate putamen (CPu). Both NCS-1 and NLGN-3 are crucial for neuronal development, synapse formation, and neuron activity, and their reduction is associated with decreased synapse strength. Despite these changes, results from the Morris water maze (MWM) indicated that [D1G, ΔQ14] LvIC did not impair the learning and memory abilities of the mice.ConclusionOur findings indicate that α-conotoxin [D1G, ΔQ14] LvIC significantly decreased locomotor activity in mice. Additionally, it altered gene expression primarily in areas related to neuronal development, synapse formation, and neuron activity, while also reducing synapse strength. This study first proposed that [D1G, ΔQ14] LvIC could modulate mice’s locomotor activity. However, further investigation is needed to understand the therapeutic effects of [D1G, ΔQ14] LvIC.
Astaxanthin mitigates doxorubicin-induced cardiotoxicity via inhibiting ferroptosis and autophagy: a study based on bioinformatic analysis and in vivo/vitro experiments
Authors: Yin Bowen , Ren Jingyi , Liu Xuanyi , Zhang Yadong , Zuo Jinshi , Wen Rui , Pei Huanting , Lu Miaomiao , Zhu Siqi , Zhang Zhenao , Wang Ziyi , Zhai Yanyi , Ma Yuxia 
Published: January 2025

BackgroundDoxorubicin (DOX), a widely employed chemotherapeutic agent in cancer treatment, has seen restricted use in recent years owing to its associated cardiotoxicity. Current reports indicate that doxorubicin-induced cardiotoxicity (DIC) is a complex phenomenon involving various modes of cell death. Astaxanthin (ASX), a natural carotenoid pigment, has garnered significant attention for its numerous health benefits. Recent studies have shown that ASX has a broad and effective cardiovascular protective effect. Our study aims to investigate the protective effects of ASX against DIC and elucidate its underlying mechanisms. This has substantial practical significance for the clinical application of DOX.MethodsBioinformatic analyses were conducted using transcriptomic data from the gene expression omnibus (GEO) database to identify key mechanisms underlying DIC. Network pharmacology was employed to predict the potential pathways and targets through which ASX exerts its effects on DIC. In vitro experiments, following pretreatment with ASX, H9C2 cells were exposed to DOX. Cell viability, injury and the protein expression levels associated with ferroptosis and autophagy were assessed. In the animal experiments, rats underwent 4 weeks of gavage treatment with various doses of ASX, followed by intraperitoneal injections of DOX every 2 days during the final week. Histological, serum, and protein analyses were conducted to evaluate the effects of ASX on DIC.ResultsThe bioinformatics analysis revealed that ferroptosis and autophagy are closely associated with the development of DIC. ASX may exert an anti-DIC effect by modulating ferroptosis and autophagy. The experimental results show that ASX significantly mitigates DOX-induced myocardial tissue damage, inflammatory response, oxidative stress, and damage to H9C2 cells. Mechanistically, ASX markedly ameliorates levels of ferroptosis and autophagy both in vitro and in vivo. Specifically, ASX upregulates solute carrier family 7 member 11 (SLC7A11) and glutathione peroxidase 4 (GPX4), while downregulating the expression of transferrin receptor 1 (TFRC), ferritin heavy chain (FTH1) and ferritin light chain (FTL). Additionally, ASX enhances the expression of P62 and decreases levels of Beclin1 and microtubule-associated proteins light chain 3 (LC3).ConclusionOur results indicate that ferroptosis and autophagy are critical factors influencing the occurrence and progression of DOX-induced cardiotoxicity. ASX can alleviate DIC by inhibiting ferroptosis and autophagy.
Chrysanthemum classification method integrating deep visual features from both the front and back sides
Authors: Chen Yifan , Yang Xichen , Yan Hui , Liu Jia , Jiang Jian , Mao Zhongyuan , Wang Tianshu 
Published: January 2025

IntroducionChrysanthemum morifolium Ramat (hereinafter referred to as Chrysanthemum) is one of the most beloved and economically valuable Chinese herbal crops, which contains abundant medicinal ingredients and wide application prospects. Therefore, identifying the classification and origin of Chrysanthemum is important for producers, consumers, and market regulators. The existing Chrysanthemum classification methods mostly rely on visual subjective identification, are time-consuming, and always need high equipment costs.MethodsA novel method is proposed to accurately identify the Chrysanthemum classification in a swift, non-invasive, and non-contact way. The proposed method is based on the fusion of deep visual features of both the front and back sides. Firstly, the different Chrysanthemums images are collected and labeled with origins and classifications. Secondly, the background area with less available information is removed by image preprocessing. Thirdly, a two-stream feature extraction network is designed with two inputs which are the preprocessed front and back Chrysanthemum images. Meanwhile, the incorporation of single-stream residual connections and cross-stream residual connections is employed to extend the receptive field of the network and fully fusion the features from both the front and back sides.ResultsExperimental results demonstrate that the proposed method achieves an accuracy of 93.8%, outperforming existing methods and exhibiting superior stability.DiscussionThe proposed method provides an effective and dependable solution for identifying Chrysanthemum classification and origin while offering practical benefits for quality assurance in production, consumer markets, and regulatory processes. Code and data are available at https://github.com/dart-into/CCMIFB.
Cryoimmobilized anther analysis reveals new ultrastructural insights into Rhynchospora (Cyperaceae) asymmetrical microsporogenesis
Authors: Rocha Danilo M. , Neumann Ulla , Nogueira Fernanda M. , Tsipas Georgios , Vanzela André L. L. , Marques André 
Published: January 2025

IntroductionThe Cyperaceae family is distinguished by holocentric chromosomes and a distinctive microsporogenesis process, which includes inverted meiosis, asymmetric tetrad formation, selective cell death, and the formation of pseudomonad pollen. Despite significant advances, the ultrastructural details of these processes remain poorly understood.MethodsThis study provides a detailed analysis of microsporogenesis in Rhynchospora pubera using high-pressure freezing, freeze substitution, and transmission electron microscopy, significantly enhancing ultrastructural resolution.Results and discussionOur findings reveal that intracellular organization differs from model species Arabidopsis thaliana and drives nuclear selection, with endoplasmic reticulum vesicles organizing meiotic spindles. Microtubules attach to centromeres located deep within holocentric chromosomes, while extensive cytoplasmic connections facilitate material exchange until callose deposition encloses meiocytes. Lipid distribution contributes to cell asymmetry, resulting in the characteristic asymmetric tetrads. Following meiosis, cytoskeletal elements coordinate nuclear migration and cell plate formation. Pseudomonads exhibit reconfigurations in the endomembrane system, particularly involving the endoplasmic reticulum, which supports functional cell differentiation. Complementary histochemical analyses corroborate these findings, providing insights into the cellular processes governing Rhynchospora microsporogenesis. These findings contribute to a deeper understanding of the developmental processes of Cyperaceae pollen, thereby facilitating future investigations of the underlying molecular mechanisms.
An improved ShuffleNetV2 method based on ensemble self-distillation for tomato leaf diseases recognition
Authors: Ni Shuiping , Jia Yue , Zhu Mingfu , Zhang Yizhe , Wang Wendi , Liu Shangxin , Chen Yawei 
Published: January 2025

IntroductionTimely and accurate recognition of tomato diseases is crucial for improving tomato yield. While large deep learning models can achieve high-precision disease recognition, these models often have a large number of parameters, making them difficult to deploy on edge devices. To address this issue, this study proposes an ensemble self-distillation method and applies it to the lightweight model ShuffleNetV2.MethodsSpecifically, based on the architecture of ShuffleNetV2, multiple shallow models at different depths are constructed to establish a distillation framework. Based on the fused feature map that integrates the intermediate feature maps of ShuffleNetV2 and shallow models, a depthwise separable convolution layer is introduced to further extract more effective feature information. This method ensures that the intermediate features from each model are fully preserved to the ensemble model, thereby improving the overall performance of the ensemble model. The ensemble model, acting as the teacher, dynamically transfers knowledge to ShuffleNetV2 and the shallow models during training, significantly enhancing the performance of ShuffleNetV2 without changing the original structure.ResultsExperimental results show that the optimized ShuffleNetV2 achieves an accuracy of 95.08%, precision of 94.58%, recall of 94.55%, and an F1 score of 94.54% on the test set, surpassing large models such as VGG16 and ResNet18. Among lightweight models, it has the smallest parameter count and the highest recognition accuracy.DiscussionThe results demonstrate that the optimized ShuffleNetV2 is more suitable for deployment on edge devices for real-time tomato disease detection. Additionally, multiple shallow models achieve varying degrees of compression for ShuffleNetV2, providing flexibility for model deployment.
Multi-omics analysis of hexaploid triticale that show molecular responses to salt stress during seed germination
Authors: Wang Dongxia , Li Jiedong , Li Shiming , Fu Jiongjie , Liu Baolong , Cao Dong 
Published: January 2025

The development of a salt-tolerant hexaploid triticale cultivar offers an economical and efficient solution for utilizing marginal land. Understanding how hexaploid triticales respond to salt stress is essential if this goal is to be achieved. A genome-wide association study (GWAS), along with transcriptome and proteome analyses, were used in the present study to determine the molecular responses to salt stress in hexaploid triticale. In total, 81 marker-trait associations for 10 salt-tolerance traits were identified in 153 hexaploid triticale accessions, explaining 0.71% to 56.98% of the phenotypic variation, and 54 GWAS-associated genes were uncovered. A total of 67, 88, and 688 differential expression genes were co-expressed at both the transcriptomic and proteomic levels after 4, 12, and 18 h of salt stress, respectively. Among these differentially expressed genes, six appeared in the coincident expression trends for both the transcriptomic and proteomic levels at the seed germination stage. A total of nine common KEGG pathways were enriched at both the transcriptomic and proteomic levels at 4, 12, and 18 h. After integrating GWAS-target genes with transcriptomics and proteomics approaches that the candidate gene late embryogenesis abundant protein 14 (LEA14) was up-regulated at the transcriptomic and proteomic levels. LEA14 contained important stress-responsive cis-acting regulatory elements that could be dynamically regulated by the binding of transcription factors (TFs). This suggested that LEA14 was a key gene associated with salt tolerance in hexaploid triticale and could respond quickly to salt stress. This study improved understanding about the potential molecular mechanisms associated with hexaploid triticale salt tolerance and contributed to the breeding of salt-tolerant germplasms and the utilization of saline soils.