Frontiers in Genetics最新文献

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Retrospective analysis of inflammatory biomarkers and prognosis in non-small cell lung cancer without adenocarcinoma in situ.
IF 2.8 3区 生物学
Frontiers in Genetics Pub Date : 2025-03-18 eCollection Date: 2025-01-01 DOI: 10.3389/fgene.2025.1549602
Qing Zhao, Songping Cui, Bin Hu, Shuo Chen
{"title":"Retrospective analysis of inflammatory biomarkers and prognosis in non-small cell lung cancer without adenocarcinoma in situ.","authors":"Qing Zhao, Songping Cui, Bin Hu, Shuo Chen","doi":"10.3389/fgene.2025.1549602","DOIUrl":"https://doi.org/10.3389/fgene.2025.1549602","url":null,"abstract":"<p><strong>Background: </strong>Inflammatory biomarkers have shown prognostic value in Non-Small Cell Lung Cancer (NSCLC), but the inclusion of Adenocarcinoma <i>In Situ</i> (AIS) cases in previous studies may introduce bias. This study aims to evaluate the prognostic significance of inflammatory biomarkers in NSCLC while excluding AIS.</p><p><strong>Methods: </strong>This study included patients who received surgery for lung carcinoma from August 2016 and August 2019. We collected demographic, clinical, laboratory, and outcome information. Inflammatory biomarkers were analyzed using receiver operating characteristic (ROC) curves, Kaplan-Meier survival analysis, and Cox regression to assess their prognostic value.</p><p><strong>Results: </strong>Higher levels of inflammatory biomarkers correlated with poorer survival, with significant differences in overall survival (OS) between high- and low-expression groups. However, multivariate Cox regression identified age, tumor stage, and differentiation as independent prognostic factors, while biomarkers were not independently predictive.</p><p><strong>Conclusion: </strong>Inflammatory biomarkers have short-term prognostic value in invasive NSCLC, but traditional clinical and pathological factors remain key for long-term outcomes.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1549602"},"PeriodicalIF":2.8,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11959042/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143763743","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Genetic diversity and population structure of non-descript cattle in South African smallholder systems.
IF 2.8 3区 生物学
Frontiers in Genetics Pub Date : 2025-03-18 eCollection Date: 2025-01-01 DOI: 10.3389/fgene.2025.1535730
M P Ramoroka, M D MacNeil, F W C Neser, S F Lashmar, M L Makgahlela
{"title":"Genetic diversity and population structure of non-descript cattle in South African smallholder systems.","authors":"M P Ramoroka, M D MacNeil, F W C Neser, S F Lashmar, M L Makgahlela","doi":"10.3389/fgene.2025.1535730","DOIUrl":"https://doi.org/10.3389/fgene.2025.1535730","url":null,"abstract":"<p><p>The genetic background and characteristics of South African smallholder cattle populations remain largely unknown. These cattle exhibit remarkable adaptability to challenging environments with minimal inputs from farmers, making them a valuable genetic resource for sustainable farming. This study aimed to genetically characterize non-descript cattle kept in smallholding systems using single-nucleotide polymorphism (SNP) markers. A total of 188 non-descript smallholder beef cattle were sampled from seven South African provinces; Eastern Cape (n = 27), Free State (n = 28), Gauteng (n = 13), KwaZulu-Natal (n = 29), Limpopo (n = 34), North West (n = 44) and Northern Cape (n = 10). In addition, samples were obtained from Afrikaner (n = 42), Bonsmara (BON; n = 46), Boran (n = 20), Brahman (n = 96), Drakensberger (n = 25), Hereford (n = 31), Holstein (HOL; n = 29), Nguni (n = 59) and Shorthorn (n = 35) to serve as reference populations. Quality control of the original SNP data removed less informative animals and SNPs, which resulted in a final data set consisting of 185 animals and 119,392 SNPs. Principal coordinate analysis, ancestry, and genomic diversity statistics revealed moderate to high levels of diversity within smallholder cattle and substantial relationship with commercial beef cattle (i.e., Afrikaner, Bonsmara, Brahman, Drakensberger, Hereford, Holstein and Nguni). In North West province, there was tendency towards greater influence of Bonsmara, whereas in KwaZulu Natal the cattle were more closely related to Holstein. The smallholder populations were shown not to be unique, likely due to indiscriminate hybridization with the commercial breeds. Among the provinces, estimates of observed heterozygosity (H<sub>O</sub>) ranged from 0.328 ± 0.001 to 0.395 ± 0.001, while expected heterozygosity (H<sub>E</sub>) ranged from 0.326 ± 0.001 to 0.389 ± 0.000. Inbreeding levels were low, with (mean ± standard error) per-province inbreeding coefficients (F<sub>IS</sub>) ranging from -0.023 ± 0.009 to 0.133 ± 0.0254. The low F<sub>ROH</sub> (<0.05) across all populations indicate a more diverse population, which is less likely to express deleterious recessive traits. Estimates of the population differentiation fixation index (F<sub>ST</sub>) indicated greater genetic distance between animals from KwaZulu natal and Gauteng provinces (F<sub>ST</sub> = 0.083) and less distance between the animals from Eastern Cape and Free State provinces (F<sub>ST</sub> = 0.010), suggesting a closer genetic relationship probably as a result of the proximity of the latter provinces and hence trans-boundary use of bulls. These findings suggest indiscriminate crossbreeding in smallholder cattle within and across the provinces of South Africa. The results provide foundational information for the transfer of technology for targeted breeding programs to smallholder farmers.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1535730"},"PeriodicalIF":2.8,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11960657/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143763739","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Bioinformatics revealed biomarkers for diagnosis in kidney stones.
IF 2.8 3区 生物学
Frontiers in Genetics Pub Date : 2025-03-18 eCollection Date: 2025-01-01 DOI: 10.3389/fgene.2025.1542840
Ziqi He, Chao Song, Zhong Wang, Caitao Dong, Qinhong Jiang, Xi Yu, Guang Shan
{"title":"Bioinformatics revealed biomarkers for diagnosis in kidney stones.","authors":"Ziqi He, Chao Song, Zhong Wang, Caitao Dong, Qinhong Jiang, Xi Yu, Guang Shan","doi":"10.3389/fgene.2025.1542840","DOIUrl":"https://doi.org/10.3389/fgene.2025.1542840","url":null,"abstract":"<p><strong>Background: </strong>One of the most prevalent urinary illnesses is kidney stone formation, often known as nephrolithiasis. The precise processes of kidney stone remain poorly known after substantial investigation. In order to successfully prevent and cure stone formation and recurrence, additional research into the pathophysiology of stone formation is of paramount importance. Ferroptosis is linked to a variety of renal diseases and is a critical factor in the death of cells. However, little is known about how ferroptosis-related genes (FRGs) contribute to the development of kidney stones.</p><p><strong>Methods: </strong>The Ferroptosis Database and the Gene Expression Omnibus (GEO) database provided us with information on kidney stones and FRGs, respectively (FerrDb).</p><p><strong>Results: </strong>Eight DE-FRGs related to kidney stones were found in total, and they were all closely related to immune response and autophagy management. Following this, among the 8 DE-FRGs, LASSO and SVM-RFE algorithms chose FZD7, STK11, SUV39H1, and LCN2 as marker genes with suitable diagnostic capabilities. These marker genes may be involved in the control of the PPAR signaling pathway, mTOR signaling system, and fatty acid production of kidney stones, according to the functional enrichment analysis that followed. Additionally, 24 drugs that target two marker genes have been found. Despite this, the ceRNA networks have gained that the regulatory relationship between marker genes is rather complex. Additionally, the findings of the CIBERSORT investigation indicated that FZD7 and SUV39H1 may be linked to variations in the immune milieu of people who have kidney stones.</p><p><strong>Conclusion: </strong>We developed a diagnostic tool and provided information on the development of kidney stones. In order to confirm its diagnostic applicability for kidney stones, more studies are needed before it may be used in clinical practice.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1542840"},"PeriodicalIF":2.8,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11959007/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143763717","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Cotton under heat stress: a comprehensive review of molecular breeding, genomics, and multi-omics strategies.
IF 2.8 3区 生物学
Frontiers in Genetics Pub Date : 2025-03-18 eCollection Date: 2025-01-01 DOI: 10.3389/fgene.2025.1553406
Tahira Luqman, Manzoor Hussain, Syed Riaz Ahmed, Iram Ijaz, Zahra Maryum, Sahar Nadeem, Zafran Khan, Sana Muhy Ud Din Khan, Mohammad Aslam, Yongming Liu, Muhammad Kashif Riaz Khan
{"title":"Cotton under heat stress: a comprehensive review of molecular breeding, genomics, and multi-omics strategies.","authors":"Tahira Luqman, Manzoor Hussain, Syed Riaz Ahmed, Iram Ijaz, Zahra Maryum, Sahar Nadeem, Zafran Khan, Sana Muhy Ud Din Khan, Mohammad Aslam, Yongming Liu, Muhammad Kashif Riaz Khan","doi":"10.3389/fgene.2025.1553406","DOIUrl":"https://doi.org/10.3389/fgene.2025.1553406","url":null,"abstract":"<p><p>Cotton is a vital fiber crop for the global textile industry, but rising temperatures due to climate change threaten its growth, fiber quality and yields. Heat stress disrupts key physiological and biochemical processes, affecting carbohydrate metabolism, hormone signaling, calcium and gene regulation and expression. This review article explores cotton's defense mechanism against heat stress, including epigenetic regulations and transgenic approaches, with a focus on genome editing tools. Given the limitations of traditional breeding, advanced omics technologies such as GWAS, transcriptomics, proteomics, ionomics, metabolomics, phenomics and CRISPR-Cas9 offer promising solutions for developing heat-resistant cotton varieties. This review highlights the need for innovative strategies to ensure sustainable cotton production under climate change.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1553406"},"PeriodicalIF":2.8,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11959566/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143763736","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Structural characteristics of mitochondrial genome of Spirobo-lus walkeri (Spirobolida: Spirobolidae), and phylogenetic analysis of Diplopoda.
IF 2.8 3区 生物学
Frontiers in Genetics Pub Date : 2025-03-17 eCollection Date: 2025-01-01 DOI: 10.3389/fgene.2025.1566634
Wenwen Zhang, Shengjun Zhao, Lingna Li, Yingzhu Li, Hongyi Liu, Peng Cui
{"title":"Structural characteristics of mitochondrial genome of <i>Spirobo-lus walkeri</i> (Spirobolida: Spirobolidae), and phylogenetic analysis of Diplopoda.","authors":"Wenwen Zhang, Shengjun Zhao, Lingna Li, Yingzhu Li, Hongyi Liu, Peng Cui","doi":"10.3389/fgene.2025.1566634","DOIUrl":"10.3389/fgene.2025.1566634","url":null,"abstract":"<p><p>The phylogeny of Diplopoda, a group of ancient arthropod and an important component of modern terrestrial ecosystems, remains unclear. Here, the complete mitogenome of <i>Spirobolus walkeri</i> was determined. The newly sequenced complete mitogenome was circular DNA molecules with sizes of 14,879 bp. The mitogenome was composed of 37 genes and one control region. Negative AT-skews and positive GC-skews were found in whole mitogenome. The gene <i>COX1</i> used CGA as the start codon, while the other PCGs utilized ATN (A, T, G) as the start codons; however, the sequence of the stop codon was variable. The Ser2 exhibited the highest usage bias. All tRNAs have typical cloverleaf structures, except <i>trnS-AGC</i> and <i>trnM</i>. Phylogenetic analysis showed that <i>S. walkeri</i> and <i>Spirobolus bungii</i> shared a close relationship and that they were also closely related with <i>Narceus annularus</i>. This study helps resolve taxonomic ambiguities among morphologically similar species and provides data to support the establishment of evolutionary benchmarks for millipedes, including gene rearrangements and variations in tRNA structure.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1566634"},"PeriodicalIF":2.8,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11955670/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143752297","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Exploring the oncogenic role and prognostic value of CKS1B in human lung adenocarcinoma and squamous cell carcinoma.
IF 2.8 3区 生物学
Frontiers in Genetics Pub Date : 2025-03-17 eCollection Date: 2025-01-01 DOI: 10.3389/fgene.2025.1449466
Md Solayman Hossain, Tariqul Islam Tusar, Nairita Ahsan Faruqui, Tanjim Ishraq Rahaman, Yasin Arafath Sharker, Shimran Saharia Santo, Abu Tayab Moin, Yusha Araf, Ibrahim Khalil Afif, Shoaib Saikat, Mohammad Jakir Hosen
{"title":"Exploring the oncogenic role and prognostic value of <i>CKS1B</i> in human lung adenocarcinoma and squamous cell carcinoma.","authors":"Md Solayman Hossain, Tariqul Islam Tusar, Nairita Ahsan Faruqui, Tanjim Ishraq Rahaman, Yasin Arafath Sharker, Shimran Saharia Santo, Abu Tayab Moin, Yusha Araf, Ibrahim Khalil Afif, Shoaib Saikat, Mohammad Jakir Hosen","doi":"10.3389/fgene.2025.1449466","DOIUrl":"10.3389/fgene.2025.1449466","url":null,"abstract":"<p><strong>Introduction: </strong>Lung cancer (LC) is a highly aggressive malignancy and remains a leading cause of cancer-related mortality worldwide. Non-small cell lung cancer (NSCLC), which includes adenocarcinoma (LUAD) and squamous cell carcinoma (LUSC), accounts for the majority of these deaths. Due to the lack of early clinical symptoms and late-stage diagnosis, there is an urgent need for precise and targeted therapeutic strategies. Cyclin-dependent kinase regulatory subunit 1B (<i>CKS1B</i>), a key regulator of the cell cycle, has been implicated in various human cancers. Emerging evidence suggests that its upregulation is associated with poor prognosis in NSCLC, highlighting its potential as a biomarker for early detection and targeted therapy.</p><p><strong>Methods: </strong>In this study, we conducted a comprehensive bioinformatics analysis to evaluate the role of <i>CKS1B</i> in LUAD and LUSC. Differential gene expression analysis, survival analysis, immune infiltration correlation, and pathway enrichment analysis were performed using publicly available transcriptomic datasets. Additionally, gene interaction networks were analyzed to assess the functional significance of <i>CKS1B</i> in lung cancer progression.</p><p><strong>Results: </strong>Our findings indicate a significant overexpression of <i>CKS1B</i> in LUAD and LUSC compared to normal lung tissues. Survival analysis demonstrated that higher <i>CKS1B</i> expression correlates with poor prognosis in NSCLC patients. Immune infiltration analysis revealed a potential role of <i>CKS1B</i> in modulating the tumor microenvironment, further supporting its relevance in lung cancer progression. Functional enrichment analysis highlighted its involvement in critical oncogenic pathways, including cell cycle regulation and immune modulation.</p><p><strong>Discussion: </strong>The results suggest that <i>CKS1B</i> serves as a potential biomarker for early detection and prognosis in NSCLC. Its association with immune response pathways underscores its possible role in immunotherapy. However, despite these promising findings, further in vivo and in vitro studies are necessary to validate <i>CKS1B</i>'s clinical applicability as a diagnostic and therapeutic target for lung cancer.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1449466"},"PeriodicalIF":2.8,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11955630/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143752292","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
weIMPUTE: a user-friendly web-based genotype imputation platform.
IF 2.8 3区 生物学
Frontiers in Genetics Pub Date : 2025-03-17 eCollection Date: 2025-01-01 DOI: 10.3389/fgene.2025.1532464
Mingliang Li, Zhuo Li, Defu Liu, Qi Li, Xiaodong Hu, Jun Yu, Jian Lin, Chunguang Bi, Guanshi Ye, Helong Yu, You Tang
{"title":"weIMPUTE: a user-friendly web-based genotype imputation platform.","authors":"Mingliang Li, Zhuo Li, Defu Liu, Qi Li, Xiaodong Hu, Jun Yu, Jian Lin, Chunguang Bi, Guanshi Ye, Helong Yu, You Tang","doi":"10.3389/fgene.2025.1532464","DOIUrl":"10.3389/fgene.2025.1532464","url":null,"abstract":"<p><strong>Background: </strong>Genotype imputation is a critical preprocessing step in genome-wide association studies (GWAS), enhancing statistical power for detecting associated single nucleotide polymorphisms (SNPs) by increasing marker size.</p><p><strong>Results: </strong>In response to the needs of researchers seeking user-friendly graphical tools for imputation without requiring informatics or computer expertise, we have developed weIMPUTE, a web-based imputation graphical user interface (GUI). Unlike existing genotype imputation software, weIMPUTE supports multiple imputation software, including SHAPEIT, Eagle, Minimac4, Beagle, and IMPUTE2, while encompassing the entire workflow, from quality control to data format conversion. This comprehensive platform enables both novices and experienced users to readily perform imputation tasks. For reference genotype data owners, weIMPUTE can be installed on a server or workstation, facilitating web-based imputation services without data sharing.</p><p><strong>Conclusion: </strong>weIMPUTE represents a versatile imputation solution for researchers across various fields, offering the flexibility to create personalized imputation servers on different operating systems.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1532464"},"PeriodicalIF":2.8,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11955643/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143752303","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Case report: Novel homozygous ACVRL1 missense variant in a family with hereditary hemorrhagic telangiectasia and pulmonary arterial hypertension: findings suggest a hypomorphic allele.
IF 2.8 3区 生物学
Frontiers in Genetics Pub Date : 2025-03-14 eCollection Date: 2025-01-01 DOI: 10.3389/fgene.2025.1554624
Akash Mathavan, Akshay Mathavan, Urszula Krekora, Adityanarayan Rao, Marc S Zumberg, Jeb Justice, Pinar Bayrak-Toydemir, Jamie McDonald, Ali Ataya
{"title":"Case report: Novel homozygous <i>ACVRL1</i> missense variant in a family with hereditary hemorrhagic telangiectasia and pulmonary arterial hypertension: findings suggest a hypomorphic allele.","authors":"Akash Mathavan, Akshay Mathavan, Urszula Krekora, Adityanarayan Rao, Marc S Zumberg, Jeb Justice, Pinar Bayrak-Toydemir, Jamie McDonald, Ali Ataya","doi":"10.3389/fgene.2025.1554624","DOIUrl":"10.3389/fgene.2025.1554624","url":null,"abstract":"<p><p>Hereditary hemorrhagic telangiectasia (HHT) is an autosomal dominant vascular disorder caused by pathogenic variants in genes within the transforming growth factor beta (TGF-β) signaling pathway, such as <i>ACVRL1</i>, leading to haploinsufficiency. Homozygous variants in HHT-related genes are exceptionally rare and have not been reported in <i>ACVRL1</i>-related HHT to date. We report the first known instance of a novel homozygous missense variant in the <i>ACVRL1</i> gene (c.576C>G; p.Phe192Leu) identified in two siblings from a family of seven, in which three heterozygotes were also present. Comprehensive clinical evaluations revealed striking phenotypic differences between the homozygous and heterozygous family members. Both homozygous individuals exhibited early-onset pulmonary arterial hypertension and diffuse pulmonary arteriovenous malformations. One of them also demonstrated childhood-onset gastrointestinal bleeding-a manifestation unprecedented in HHT that typically has a late-adulthood onset. In contrast, the heterozygotes displayed either mild or equivocal features of HHT, supporting the classification of this variant as a hypomorphic allele. The novel missense variant is located within the intracellular glycine-serine (GS) domain of the protein, suggesting potential impacts on receptor regulation and downstream signaling. Although these findings expand the phenotypic spectrum of <i>ACVRL1</i>-related HHT, they remain limited to clinical observations. Experimental studies, including functional and molecular assays, are therefore essential to confirm the pathogenic impacts of this variant, validate its classification as a hypomorphic allele, and elucidate its effects on BMP-TGF-β signaling.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1554624"},"PeriodicalIF":2.8,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11949910/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143752285","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Corrigendum: Case report and literature review: delayed diagnosis of ARCL1B due to a newly reported homozygous mutation c.464A>C p. (Tyr155Ser) in the EFEMP2 gene.
IF 2.8 3区 生物学
Frontiers in Genetics Pub Date : 2025-03-13 eCollection Date: 2025-01-01 DOI: 10.3389/fgene.2025.1589037
Lixue Ouyang, Fan Yang, Hongyu Duan, Chuan Wang
{"title":"Corrigendum: Case report and literature review: delayed diagnosis of ARCL1B due to a newly reported homozygous mutation c.464A>C p. (Tyr155Ser) in the EFEMP2 gene.","authors":"Lixue Ouyang, Fan Yang, Hongyu Duan, Chuan Wang","doi":"10.3389/fgene.2025.1589037","DOIUrl":"https://doi.org/10.3389/fgene.2025.1589037","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.3389/fgene.2024.1453195.].</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1589037"},"PeriodicalIF":2.8,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11947943/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729732","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
CLMT: graph contrastive learning model for microbe-drug associations prediction with transformer.
IF 2.8 3区 生物学
Frontiers in Genetics Pub Date : 2025-03-12 eCollection Date: 2025-01-01 DOI: 10.3389/fgene.2025.1535279
Liqi Xiao, Junlong Wu, Liu Fan, Lei Wang, Xianyou Zhu
{"title":"CLMT: graph contrastive learning model for microbe-drug associations prediction with transformer.","authors":"Liqi Xiao, Junlong Wu, Liu Fan, Lei Wang, Xianyou Zhu","doi":"10.3389/fgene.2025.1535279","DOIUrl":"10.3389/fgene.2025.1535279","url":null,"abstract":"<p><p>Accurate prediction of microbe-drug associations is essential for drug development and disease diagnosis. However, existing methods often struggle to capture complex nonlinear relationships, effectively model long-range dependencies, and distinguish subtle similarities between microbes and drugs. To address these challenges, this paper introduces a new model for microbe-drug association prediction, CLMT. The proposed model differs from previous approaches in three key ways. Firstly, unlike conventional GCN-based models, CLMT leverages a Graph Transformer network with an attention mechanism to model high-order dependencies in the microbe-drug interaction graph, enhancing its ability to capture long-range associations. Then, we introduce graph contrastive learning, generating multiple augmented views through node perturbation and edge dropout. By optimizing a contrastive loss, CLMT distinguishes subtle structural variations, making the learned embeddings more robust and generalizable. By integrating multi-view contrastive learning and Transformer-based encoding, CLMT effectively mitigates data sparsity issues, significantly outperforming existing methods. Experimental results on three publicly available datasets demonstrate that CLMT achieves state-of-the-art performance, particularly in handling sparse data and nonlinear microbe-drug interactions, confirming its effectiveness for real-world biomedical applications. On the MDAD, aBiofilm, and Drug Virus datasets, CLMT outperforms the previously best model in terms of Accuracy by 4.3%, 3.5%, and 2.8%, respectively.</p>","PeriodicalId":12750,"journal":{"name":"Frontiers in Genetics","volume":"16 ","pages":"1535279"},"PeriodicalIF":2.8,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11936976/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143718589","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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