综合性期刊最新文献

{"title":"Identification of mitochondria-related biomarkers for acute respiratory distress syndrome.","authors":"Huang Hongyuan, Chen Mengchi, Liang Yingying, Zheng Xiaowen, Huang Qiaojuan, Liu Jianghua","doi":"10.1038/s41598-025-13448-8","DOIUrl":"https://doi.org/10.1038/s41598-025-13448-8","url":null,"abstract":"<p><p>Mitochondria-related genes (MRGs) are considered screening MRGs as biomarkers for important therapeutic targets, but their role in acute respiratory distress syndrome (ARDS) remains unclear. This study aimed to identify MRGs-related biomarkers for ARDS. Intersection of 2030 MRGs with 343 differentially expressed genes (DEGs) between sepsis-non-ARDS and sepsis-ARDS group yielded 20 MRGs-related DEGs enriched in mitochondrion-related pathways. Monocytes, T cells, natural killer (NK) T cells, NK cells, and innate lymphoid cells (ILCs) were screened as candidate key cell types. SLC2A1 and IFI27 were defined as biomarkers; naive B cells, resting NK cells, and naive CD4 T cells, as differential immune cells; and monocytes, as the key cell type, subdivided into the CD14 and CD16 subtypes. The sepsis-ARDS group exhibited enhanced CD14 Mono and B cells compared with the sepsis-non-ARDS group and CD16 had a higher percentage and score in the G2/M and S phases than CD14. IFI27 and SLC2A1 were mainly expressed differently in the CD14 monocytes in ARDS, and their mRNA expression levels in peripheral blood of the sepsis patients was upregulated compared with those of the healthy controls. Thus, our findings demonstrate that SLC2A1 and IFI27 represent novel MRGs-related diagnostic biomarkers for ARDS, providing theoretical references for its treatment.</p>","PeriodicalId":21811,"journal":{"name":"Scientific Reports","volume":"15 1","pages":"28221"},"PeriodicalIF":3.9,"publicationDate":"2025-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144768978","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Open access dataset integrating behavioral and EEG measures in Chinese spoken word production.","authors":"Chenghui Tan, Qingfang Zhang","doi":"10.1038/s41597-025-05671-9","DOIUrl":"https://doi.org/10.1038/s41597-025-05671-9","url":null,"abstract":"<p><p>Speech production involves the transformation of abstract phonemes into concrete phonetic units through phonological encoding, a process where syllables play a particularly crucial role in Mandarin Chinese as a tonal language. Studies suggest that syllables serve as the primary units for phonological encoding, as evidenced by the syllable effect, where shared syllables between words lead to faster and more efficient processing in native Mandarin speakers. However, there is a lack of publicly available datasets that simultaneously capture behavioral and electroencephalogram (EEG) to study this process. This dataset, collected from 87 native Mandarin speakers across four experiments on Chinese spoken word production, integrates behavioral and EEG data, providing insights into the temporal dynamics of syllable and phonemes processing in speech production. Analysis on the accuracy and response latencies derived from behavioral recordings, along with event-related potential analysis of EEG data, reveals the existence of syllable effect. These findings advance our understanding of phonological encoding in tonal languages and enable cross-linguistic comparisons.</p>","PeriodicalId":21597,"journal":{"name":"Scientific Data","volume":"12 1","pages":"1348"},"PeriodicalIF":6.9,"publicationDate":"2025-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144769006","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A mirrored pair of optimal non-decomposable entanglement witnesses for two qudits does exist.","authors":"Dariusz Chruściński, Anindita Bera, Joonwoo Bae, Beatrix C Hiesmayr","doi":"10.1038/s41598-025-10985-0","DOIUrl":"https://doi.org/10.1038/s41598-025-10985-0","url":null,"abstract":"<p><p>Two approaches can be utilized to handle the separability problem, finding out whether a given bipartite qudit state is separable or not: a direct procedure on the state space or the effective tool of entanglement witnesses (EWs). This contribution studies the structure of EWs. Exploiting the very concept of mirrored EWs, increasing the detection power, we show, in contrast to the conjecture in a recent paper (Bera et al. in Sci Rep 13:10733, 2023), there exist pairs of optimal EWs, which are both non-decomposible, i.e. can detect bound/PPT-entangled states in an optimal way. Since we show that the structure also extends to higher dimensions, our results reveal a further structure of entanglement witnesses.</p>","PeriodicalId":21811,"journal":{"name":"Scientific Reports","volume":"15 1","pages":"28205"},"PeriodicalIF":3.9,"publicationDate":"2025-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144769017","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Postoperative functional training program for vascularised Iliac flap donor site in jaw defect reconstruction based on the Delphi method.","authors":"Li Li, Qian He, Na Zhou, Zhaoxia Zhang, Xiaoming Lv, Jie Zhang","doi":"10.1038/s41598-025-13774-x","DOIUrl":"https://doi.org/10.1038/s41598-025-13774-x","url":null,"abstract":"<p><p>Vascularised iliac flaps (VIFs) are widely used for the reconstruction of jawbone defects; however, postoperative donor-site complications, such as gait disturbances, with an incidence of 13.9-50%, significantly impede patient recovery. Despite this, evidence-based rehabilitation protocols specific to VIFs remain lacking. Existing rehabilitation guidelines for hip surgeries are unsuitable owing to differences in surgical mechanisms. This study employed the Delphi method, engaging 20 multidisciplinary experts (oral and maxillofacial surgery: 5; orthopaedics: 7; rehabilitation: 6; nursing: 2). Through three rounds of anonymous consultations, and by integrating literature evidence with postoperative mobility assessments, we developed a phased, individualised progressive functional training (PFT) protocol featuring dynamic evaluation, coordinated activation of abdominal and hip muscle groups, and safe exercise strategies during head and neck immobilisation, while overcoming conventional hip rehabilitation limitations (e.g., restrictions on flexion < 90°, and bans on squatting or cross-legged sitting). PFT is structured into six progressive phases, with exercise intensity tailored to assessment outcomes. A single-centre randomised controlled trial (n = 62) demonstrated that PFT significantly accelerated lower limb functional recovery, improved hip mobility and balance, reduced donor-site pain, and enhanced quality of life (University of Washington Quality of Life questionnaire: F (1,60) = 17.262, P < 0.001), without increasing the risk of flap vascular compromise or iliac hematoma. The limitations of the study include the single-centre design and lack of cross-cultural validation. Future multicentre studies are required to enhance adaptability. This study establishes a foundational yet effective framework for post-VIF rehabilitation, guiding clinical practice and research advancements.</p>","PeriodicalId":21811,"journal":{"name":"Scientific Reports","volume":"15 1","pages":"28224"},"PeriodicalIF":3.9,"publicationDate":"2025-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144769039","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"RNA sequencing and immunohistochemistry jointly improve tumor biomarker interpretation.","authors":"Vladimir Kushnarev, Danil Stupichev, Suren Davitavyan, Kirill Kriukov, Basavaraja U Shanthappa, Anna Butusova, Sofia Menshikova, Anna Belozerova, Anastasia Shvyrkova, Arina Tkachuk, Olga Khatenkova, Linda Balabanian, Ekaterina Postovalova, Jochen K Lennerz, Funda Meric-Bernstam, Alexander Bagaev","doi":"10.1038/s41598-025-12780-3","DOIUrl":"https://doi.org/10.1038/s41598-025-12780-3","url":null,"abstract":"<p><p>This study aimed to assess the correlation between RNA sequencing (RNA-seq) and immunohistochemistry (IHC) in detecting key cancer biomarkers across solid tumors, and then, to establish RNA-seq thresholds that accurately reflect clinical IHC classifications. Expression levels of nine biomarkers-ESR1, PGR, AR, MKI67, ERBB2, CD274, CDX2, KRT7, and KRT20-were analyzed in 365 formalin-fixed, paraffin-embedded samples from breast, lung, gastrointestinal, and other solid carcinomas. Correlations between RNA-seq data and IHC scores were determined using Spearman's correlation coefficients, with RNA-seq cut-offs established to distinguish positive from negative IHC scores. The results revealed strong correlations for most biomarkers, with coefficients ranging from 0.53 to 0.89. RNA-seq thresholds were confirmed across internal and external cohorts, demonstrating high diagnostic accuracy (up to 98%) and precision in identifying biomarker expression levels. The analysis also highlighted the influence of tumor microenvironment and purity, particularly in the moderate correlation of 0.63 observed for PD-L1. Our study demonstrates that RNA-seq can serve as a robust complementary tool to IHC, offering objective and high-throughput biomarker assessment. The RNA-seq thresholds established provide a reliable method for determining biomarker positivity, supporting the integration of RNA-seq in clinical diagnostics to enhance precision, especially where tumor purity and microenvironment factors are significant.</p>","PeriodicalId":21811,"journal":{"name":"Scientific Reports","volume":"15 1","pages":"28264"},"PeriodicalIF":3.9,"publicationDate":"2025-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144769047","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Validation of the age, neutrophil to lymphocyte ratio, C reactive protein score on 28 day mortality in the National COVID cohort collaborative.","authors":"Benjamin J Sines, Kunal K Jakharia, Chih-Huan Lu, Leslie Appleton, Colleen Rice, William A Fischer, Shannon M Wallet, G Stephen DeCherney, Jason R Mock, M Bradley Drummond","doi":"10.1038/s41598-025-08822-5","DOIUrl":"https://doi.org/10.1038/s41598-025-08822-5","url":null,"abstract":"<p><p>Identifying patients at high mortality risk can improve outcomes in SARS-CoV-2 pneumonia (COVID-19). We validate a prognostic model for mortality in patients hospitalized with COVID-19 receiving dexamethasone using a retrospective multi-centered study. This is a retrospective cohort study using the National COVID Cohort Collaborative (NC3) including 9,708 adult patients admitted for COVID-19 who received dexamethasone within 24 h of admission and remained hospitalized for 72 h. Previous work from a single-center cohort informed selection of prognostic variables including Age, day 3 neutrophil-lymphocyte Ratio, and day 3 C-reactive protein level (ARC Score). Variables from the development cohort were analyzed in a training cohort, and the resulting model was tested in a validation cohort. Age and day 3 measures of the neutrophil-lymphocyte ratio and C-reactive protein level were included in a logistic regression model to predict 28-day mortality. The 28-day mortality in this patient population was 15.4%. The area under the curve for the ARC model was 0.77 (95% confidence interval, 0.74-0.79). The Age, neutrophil-lymphocyte Ratio, and C-reactive protein (ARC) score identifies COVID-19 patients with a high risk of mortality within 28 days of hospitalization using clinical information on day 3 of hospitalization. ARC scores perform well across all variants of concern.</p>","PeriodicalId":21811,"journal":{"name":"Scientific Reports","volume":"15 1","pages":"28254"},"PeriodicalIF":3.9,"publicationDate":"2025-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144769067","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Peptide-based rigid nanorod-reinforced gelatin methacryloyl hydrogels for osteochondral regeneration and additive manufacturing","authors":"Junjin Zhu, Yueting Wei, Guangmei Yang, Jiangnan Zhang, Jiayi Liu, Xin Zhang, Zhou Zhu, Junyu Chen, Xibo Pei, Dongdong Wu, Jian Wang","doi":"10.1038/s41467-025-62540-0","DOIUrl":"https://doi.org/10.1038/s41467-025-62540-0","url":null,"abstract":"<p>Enhancing the toughness of hydrogels for biomedical applications remains a challenge, as many toughening approaches often sacrifice biocompatibility or in situ applicability, thereby restricting their broader utility in biomedical contexts. Inspired by the intervertebral disk, here, we introduce a biocompatible toughening strategy using peptide-based rigid nanorods (PRNs) as backbone supports within gelatin methacryloyl (GelMA) hydrogels. PRNs are short polymers with exceptional rigidity, capable of covalent cross-linking with GelMA molecules at both ends. Photocuring nanorod-supported GelMA (NSG) molecules yields NSG hydrogels, which demonstrate great improvements in compressive strength (1018%) and toughness (508%) compared to untreated GelMA hydrogels, alongside enhanced structural integrity and fatigue resistance. We further demonstrate that NSG hydrogels are ideal for in situ repair of damaged osteochondral tissues and are highly compatible with additive manufacturing, owing to their good biocompatibility and photocurable properties. This strategy provides a potential pathway for developing highly biocompatible and tough hydrogels, significantly expanding their potential for biomedical applications.</p>","PeriodicalId":19066,"journal":{"name":"Nature Communications","volume":"30 1","pages":""},"PeriodicalIF":16.6,"publicationDate":"2025-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144763135","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Inhibition of epithelial cell YAP-TEAD/LOX signaling attenuates pulmonary fibrosis in preclinical models","authors":"Darcy Elizabeth Wagner, Hani N. Alsafadi, Nilay Mitash, Aurelien Justet, Qianjiang Hu, Ricardo Pineda, Claudia Staab-Weijnitz, Martina Korfei, Nika Gvazava, Kristin Wannemo, Ugochi Onwuka, Molly Mozurak, Adriana Estrada-Bernal, Juan Cala-Garcia, Katrin Mutze, Rita Costa, Deniz Bölükbas, John Stegmayr, Wioletta Skronska-Wasek, Stephan Klee, Chiharu Ota, Hoeke A. Baarsma, Jingtao Wang, John Sembrat, Anne Hilgendorff, Jun Ding, Andreas Günther, Rachel Chambers, Ivan Rosas, Stijn de Langhe, Naftali Kaminski, Mareike Lehmann, Oliver Eickelberg, Melanie Königshoff","doi":"10.1038/s41467-025-61795-x","DOIUrl":"https://doi.org/10.1038/s41467-025-61795-x","url":null,"abstract":"<p>Idiopathic pulmonary fibrosis (IPF) is a progressive and lethal disease characterized by excessive extracellular matrix deposition. Current IPF therapies slow disease progression but do not stop or reverse it. The (myo)fibroblasts are thought to be the main cellular contributors to excessive extracellular matrix production in IPF. Here we show that fibrotic alveolar type II cells regulate production and crosslinking of extracellular matrix via the co-transcriptional activator YAP. YAP leads to increased expression of Lysl oxidase (LOX) and subsequent LOX-mediated crosslinking by fibrotic alveolar type II cells. Pharmacological YAP inhibition via verteporfin reverses fibrotic alveolar type II cell reprogramming and LOX expression in experimental lung fibrosis in vivo and in human fibrotic tissue ex vivo. We thus identify YAP-TEAD/LOX inhibition in alveolar type II cells as a promising potential therapy for IPF patients.</p>","PeriodicalId":19066,"journal":{"name":"Nature Communications","volume":"26 1","pages":""},"PeriodicalIF":16.6,"publicationDate":"2025-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144763149","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The genomic history of Iberian horses since the last Ice Age","authors":"Jaime Lira Garrido, Gaétan Tressières, Lorelei Chauvey, Stéphanie Schiavinato, Laure Calvière-Tonasso, Andaine Seguin-Orlando, John Southon, Beth Shapiro, Clément Bataille, Julie Birgel, Stefanie Wagner, Naveed Khan, Xuexue Liu, José María Rodanés, Jesús V. Picazo Millán, Josep Giralt, Natàlia Alonso, Isidro Aguilera, Adriano Orsingher, Angela Trentacoste, Xavier Payà, Marta Morán, María Pilar Iborra Eres, Silvia Albizuri, Silvia Valenzuela Lamas, Imma Mestres Santandreu, Montserrat Duran Caixal, Jordi Principal, Jordi Farré Huguet, Xavier Esteve, Mireia Pedro Pasqual, Nohemi Sala, Adrián Pablos, Patricia Martín, Josep Maria Vergès, Rodrigo Portero, Pablo Arias, Roberto Ontañón Peredo, Cleia Detry, Cristina Luís, João Luís Cardoso, Aren M. Maeir, Maria J. Valente, Elena Grau, Vicent Estall i Poles, Joaquín Alfonso Llorens, Ana Miguélez González, Armelle Gardeisen, Michele Cupitò, Umberto Tecchiati, Daniel G. Bradley, Liora Kolska Horwitz, Esther Rodríguez González, Ariadna Nieto Espinet, Pere Bover, Rosa Ruiz Entrecanales, Ignasi Garcés Estallo, Joaquín Jiménez Fragoso, Sebastián Celestino, Ludovic Orlando","doi":"10.1038/s41467-025-62266-z","DOIUrl":"https://doi.org/10.1038/s41467-025-62266-z","url":null,"abstract":"<p>Horses have inhabited Iberia (present-day Spain and Portugal) since the Middle Pleistocene, shaping a complex history in the region. Iberia has been proposed as a potential domestication centre and is renowned for producing world-class bloodlines. Here, we generate genome-wide sequence data from 87 ancient horse specimens (median coverage = 0.97X) from Iberia and the broader Mediterranean to reconstruct their genetic history over the last ~26,000 years. Here, we report that wild horses of the divergent IBE lineage inhabited Iberia from the Late Pleistocene, while domesticated DOM2 horses, native from the Pontic-Caspian steppes, already arrived ~1850 BCE. Admixture dating suggests breeding practices involving continued wild restocking until at least ~350 BCE, with IBE disappearing shortly after. Patterns of genetic affinity highlight the far-reaching influence of Iberian bloodlines across Europe and north Africa during the Iron Age and Antiquity, with continued impact extending thereafter, particularly during the colonization of the Americas.</p>","PeriodicalId":19066,"journal":{"name":"Nature Communications","volume":"37 1","pages":""},"PeriodicalIF":16.6,"publicationDate":"2025-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144763434","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Assessing the real implications for CO2 as generation from renewables increases","authors":"Dhruv Suri, Jacques de Chalendar, Inês M. L. Azevedo","doi":"10.1038/s41467-025-59800-4","DOIUrl":"https://doi.org/10.1038/s41467-025-59800-4","url":null,"abstract":"<p>Wind and solar electricity generation account for 14% of total electricity generation in the United States and are expected to continue to grow in the next decade. While increased renewable penetration reduces system-wide emissions, the intermittent nature of these resources disrupts conventional thermal plant operations. Generation displacement exhibits a nonlinear relationship, as thermal units forced to operate at suboptimal levels experience efficiency penalties. Here we show that as renewable generation rises, thermal plants often operate sub-optimally, increasing emissions when forced to respond to variability. Using hourly emissions and generation data from California and Texas, we find that solar and wind energy significantly reduce expected emissions under normal operating conditions - by 92.6% in California and 91.1% in Texas. However, if renewables force plants to operate inefficiently, emissions from natural gas and coal plants could increase by 12% to 26%. These results highlight the complex interactions between renewable energy growth and thermal plant emissions, indicating that careful management of renewables integration is crucial to minimizing overall system-level CO₂ emissions, especially in electricity grids with inflexible thermal capacity.</p>","PeriodicalId":19066,"journal":{"name":"Nature Communications","volume":"148 1","pages":""},"PeriodicalIF":16.6,"publicationDate":"2025-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144766024","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}