bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unveiling Immunotherapy Evasion in Lung Cancer: The Role of Fanconi Anemia and Stemness Genes in Shaping an Immunosuppressive Microenvironment
Authors: Wu Haixia , Yu Yilin , Huang Hailun , Lin Gen , Wang Wei , Huang Jianyuan , Yu Zhaojun , Ye Deju , Chi Wu , Lin Xing 
Published: November 2024

ABSTRACTThe study aimed to investigate the fanconi anemia (FA)‐related and stemness‐related genes in lung cancer (LC) patients. Firstly, we identified stemness‐related genes through weighted gene co‐expression network analysis combined with TCGA database. Further combined stemness‐related genes with FA‐related genes to screen for prognostic‐related genes. Risk score was constructed from the screened genes and comprehensive bioinformatics analyses were performed. Finally, single‐cell data and in vitro experiment were used to validate our results. We screened a total of eight genes to construct a risk score. The risk score was an independent prognostic factor for LC. The validation results of multiple GEO databases were consistent with our results. Functional and pathway enrichment analysis showed that risk score was associated with cell cycle, DNA replication, DNA damage repair, and immune‐related pathways. The results showed to be related to the stem cell self‐renewal and proliferation. Besides, we also found that patients with higher risk scores had lower immune activity and function, and the effectiveness of immunotherapy might be poorer, with a higher rate of immune escape. Finally, our results revealed that SLC2A1 had the highest correlation with B cells in single‐cell data analysis, and we validated its correlation with B cells and its expression with FA‐related genes, tumor invasiveness, stemness, and drug sensitivity. Our research constructed a risk score based on FA‐related and tumor stemness‐related specific genes. In addition to accurately predicting the prognosis of patients with LC, the risk score may also serve as an innovative and viable predictor of immunotherapy response.
Permutation Tests to Identify Significant Constraint or Promotion Within Biological Scatterplots
Authors: Mills Anthony J. , van Mazijk Ruan 
Published: November 2024

ABSTRACTScatterplots of biological datasets often have no‐data zones, which suggest constraint or promotion of dependent variables. Although methods exist to estimate boundary lines—that is, to fit lines to the edges of scatters of data points—there are, to our knowledge, none available to assess the significance of the areal extents of no‐data zones. Accordingly, we propose a flexible boundary line definition paired with a permutation test of the magnitude of no‐data zones—rather than testing the shape or slope of the line as current methods do. Our proposed permutation test can be used with any method of defining a boundary line. We demonstrate our approach with empirical datasets, find no‐data zones that methods such as quantile regressions fail to detect, and discuss how our approach can quantify constraint and promotion relationships that are not always apparent with other statistics.
Functional R code is rare in species distribution and abundance papers
Authors: Kellner Kenneth F. , Doser Jeffrey W. , Belant Jerrold L. 
Published: November 2024

AbstractAnalytic reproducibility is important for scientific credibility in ecology, but the extent to which scientific literature meets this criterion is not well understood. We surveyed 497 papers published in 2018–2022 in 9 ecology‐related journals. We focused on papers that used hierarchical models to estimate species distribution and abundance. We determined if papers achieved two components of analytic reproducibility: (1) availability of data and code, and (2) code functionality. We found that 28% of papers made data and code available, and 7% of papers provided code that ran without errors. Our findings indicate that analytic reproducibility remains the exception rather than the rule in ecology literature. We recommend authors (1) test code in a separate clean environment; (2) simplify code structure; (3) minimize software packages used; and (4) minimize code run time. We suggest journals (1) validate authors' provided open data statements and URLs; (2) recommend that code and data be shared in a separate repository rather than as appendices; and (3) elevate the status of code and data during review. We suggest these guidelines can aid the ecology community by improving the scientific reproducibility and credibility of ecological research.
Co‐crystallization as a Strategy for Tuning Spin Crossover Properties of Mononuclear Mn(III) Schiff‐base Complexes
Authors: Chen Li‐Wen , Zhang Hao‐Zhe , Zhao Sheng‐Ze , Zhou Hua‐Wei , Li Yong‐Hua , Tang Chao , Wang Shi 
Published: November 2024

AbstractWe present co‐crystallization as an approach to tuning spin crossover (SCO) properties of mononuclear Mn(III) Schiff‐base complexes. Complexes [Mn(5‐F‐sal‐N‐1,5,8,12)]ClO4 ⋅ 0.5carbazole (cocrystal 1 a) and [Mn(5‐F‐sal‐N‐1,5,8,12)]PF6 ⋅ 0.5carbazole (cocrystal 2 b) are synthesized by the co‐crystallization of their parent complexes ( [Mn(5‐F‐sal‐N‐1,5,8,12)]Y, Y=ClO4− (1); Y=PF6− (2) ) with the carbazole and they both exhibit HS electronic configurations between 2 and 300 K. While, the parent complex 1 shows a nearly complete SCO with T1/2=100 K and complex 2 maintains a high‐spin (HS) state. The introduction of carbazole as the third component has a great influence on cation‐anion crystal packing and finally the cooperative effects of the SCO complexes.
Solid‐State Ion Exchange of Organic Ammonium Cations in Molecular Crystals
Authors: Ito Mizuki , Manabe Jun , Inoue Katsuya , Qian Yin , Ren Xiao‐Ming , Akutagawa Tomoyuki , Nakamura Takayoshi , Nishihara Sadafumi 
Published: November 2024

AbstractArtificial ion channels and transporters designed to recognise and transport specific ions and molecules have been extensively studied. These biomimetic single‐crystal materials have gained particular attention for their potential to reveal the complex mechanisms of biological functions and to provide functionalities based on molecular design. In the present study, we found that Li+ ions in the ion channels of Li2([18]crown‐6)3[Ni(dmit)2]2(H2O)4 (1) crystals exchange with R‐NH3+ (R=Me, Et, nPr) ions in aqueous solution. After ion exchange, the resultant (R‐NH3+)([18]crown‐6)[Ni(dmit)2]− (1‐R, R=Me, Et, nPr) crystals are missing one [18]crown‐6 molecule per two cations compared to 1. During ion exchange, some of the [18]crown‐6 molecules, which constitute the channels, are released into the aqueous solution along with Li+ ions. The ion exchange of 1 in mixed aqueous solutions of organic ammonium cations shows selectivity for MeNH3+, which is attributed to the stability of the 1‐Me. These results demonstrate the potential for transporting molecular cations in channel structures composed of crown ethers, which will facilitate the development of transporters for drugs and other substances essential for biological functions.
Facile N‐Modification of NH‐Tetrazoles via Rh(II)‐Catalyzed N−H Insertion Involving Structurally Diverse Diazo Reagents
Authors: Radiupov Valentin , Kantin Grigory , Dar'in Dmitry 
Published: November 2024

AbstractA convenient method for the N‐modification of NH‐tetrazoles by the Rh(II)‐catalyzed insertion reaction of diazocarbonyl compounds into the N−H bond has been proposed. A wide range of structurally diverse diazo reagents (including heterocyclic ones) as well as tetrazoles with different substituents in the fifth position have been used to prepare 2,5‐disubstituted tetrazole derivatives in good and high yields and with high regioselectivity. It is shown that the regioselectivity of the reaction can decrease in the presence of electron withdrawing groups in the tetrazole, as well as in the presence of protic acids.
Secrecy Performance of Full‐Duplex Space‐Air‐Ground Integrated Networks in the Presence of Active/Passive Eavesdropper, and Friendly Jammer
Authors: Buyuksar Ayse Betul , Erdogan Eylem , Altunbas Ibrahim 
Published: November 2024

ABSTRACTIn this paper, a full‐duplex (FD) space‐air ground integrated network (SAGIN) system with passive and active eavesdroppers (PE/AE) and a friendly jammer (FJ) is investigated. The shadowing side information (SSI)‐based unmanned aerial vehicle relay node (URN) selection strategy is considered to improve signal‐to‐interference plus noise power ratio (SINR) at the ground destination unit. To quantify the secrecy performance of the considered scenario, outage probability (OP), interception probability (IP), and transmission secrecy outage probability (TSOP) are investigated in the presence of FJ and PE/AE. The results have shown that aerial AE is an important threat since it can severely degrade the OP of the main transmission link. Furthermore, the FJ can decrease the IP of the eavesdropper by causing interference with the cost of power consumption of URNs. Simulations are performed to verify the theoretical findings.
Novel Finite‐Volume Complete Flux Approximation Schemes for the Incompressible Navier–Stokes Equations
Authors: Pandey Chitranjan , ten Thije Boonkkamp J. H. M. , Rathish Kumar B. V. 
Published: November 2024

ABSTRACTWe construct novel flux approximation schemes for the semidiscretized incompressible Navier–Stokes equations by finite‐volume method on a staggered mesh. The calculation of the cell‐face fluxes has been done by solving appropriate local non‐linear boundary value problems (BVP). Consequently, the cell‐face fluxes are represented as the sum of a homogeneous and an inhomogeneous flux; the homogeneous part represents the contribution of convection and viscous‐friction, while the inhomogeneous part represents the contribution of the source terms. We derive three flux approximation schemes to include the impact of the source terms on the numerical fluxes. The first one is based on a homogeneous 1‐D local BVP without source. The second scheme is based on an inhomogeneous 1‐D local BVP considering only the pressure gradient term in the source. Finally, a complete flux scheme is derived which is based on an inhomogeneous 2‐D local BVP. It takes into account both the gradient of the cross‐flux and the pressure gradient in the source term. The numerical validation of the schemes is done for the benchmark lid‐driven cavity flow for considerably high numbers along with a numerical convergence test for the exact solution of the Taylor–Green vortex problem.
Periostin Induces Epithelial‐Mesenchymal Transition via p38‐MAPK Pathway in Human Renal Tubular Cells by High Glucose
Authors: Xiong Xiaoling , Feng Xing , Ding Yuqing 
Published: November 2024

ABSTRACTBackgroundPeriostin mediates inflammation and fibrosis by regulating extracellular matrix adhesion, migration, and differentiation in multiple organ diseases. Studies have shown periostin mainly located in the dilated mesangium, tubulointerstitial and fibrotic regions of the diabetic kidney disease, which was negatively correlated with renal function. However, the underlying mechanism remains poorly explored.MethodsThe expression of periostin in HK‐2 cells was investigated under high glucose and high concentration of TGF‐β1. The signaling pathway of periostin involved in epithelial‐mesenchymal transdifferentiation of HK‐2 cells was also validated. The expression of periostin were investigated by RT‐PCR, western blot analysis and immunofluorescence assays with different concentrations of glucose and TGF‐β1. The expression of E‐Cad, α‐SMA and p38 proteins were also detected. The effects of periostin, E‐Cad, and α‐SMA in high glucose were investigated by p38 inhibitors. To demonstrate the interaction among periostin, p38 and EMT markers, periostin under high glucose and high TGF‐β1 was knocked down, resulting p38 and phosphorylated p38 was evaluated.ResultsThe combined of high glucose (HG, 22 mmol/L) and high TGF‐β1 (10 ng/mL) upregulated the expression of periostin obviously, stimulating the expression of α‐SMA and p38 while inhibiting the expression of E‐Cad. p38 inhibitors reduced the expression of periostin and α‐SMA while promoted E‐Cad protein expression in HK‐2 cells under HG conditions. Additionally, p38‐MAPK signal pathway was involved in epithelial‐mesenchymal transition of human renal tubules in high glucose environment. Significant, knockdown periostin expression effectively inhibited the expression of p38 and phosphorylated p38 under the combination of HG and high TGF‐β1, verifying the interaction of periostin with the p38‐MAPK signaling pathway.ConclusionPeriostin, a downstream factor of TGF‐β1, is positively regulated by TGF‐β1 under HG condition, affecting the epithelial‐interstitial differentiation of HK‐2 cells via p38‐MAPK signaling pathway. Therefore, periostin may serve as a biomarker of renal fibrosis in diabetic kidney disease.
Prognostic impact of PD‐L1 expression in surgically resected EGFR‐mutant lung adenocarcinoma: A real‐world database study in Japan (CReGYT‐01 EGFR study)
Authors: Nomura Kotaro , Takada Kazuki , Kinoshita Fumihiko , Muto Satoshi , Matsubara Taichi , Kouki Yasunobu , Katsumata Shinya , Hamada Akira , Haratake Naoki , Fujino Kosuke , Yoshikawa Mao , Suzawa Ken , Shien Kazuhiko , Suda Kenichi , Ohara Shuta , Fukuda Shota , Suzuki Hiroyuki , Okamoto Tatsuro , Hirai Fumihiko , Aokage Keiju , Shiono Satoshi , Soh Junichi , Tsuboi Masahiro , Shimokawa Mototsugu , Ohde Yasuhisa 
Published: November 2024

AbstractThe expression of programmed cell death‐ligand 1 (PD‐L1) and mutation in epidermal growth factor receptor (EGFR) are biomarkers used for perioperative treatment of lung adenocarcinoma. However, the clinical significance of PD‐L1 expression in surgically resected EGFR‐mutant lung adenocarcinoma remains unclear. We conducted a real‐world database of patients with surgically resected lung adenocarcinoma from 2015 to 2018 was constructed across 21 centers in Japan. The association among PD‐L1 expression, EGFR mutations, and prognosis was evaluated. Among 847 patients, PD‐L1 expression was negative (tumor proportion score [TPS] < 1%) in 429 (51%), weakly positive (TPS = 1%–49%) in 275 (32%), and strongly positive (TPS ≥50%) in 143 (17%) patients. EGFR mutations were detected in 331 (39%) patients. PD‐L1 expression was associated with poor recurrence‐free survival (RFS) (p < .001) in both EGFR‐mutant and wild‐type patients. However, in EGFR‐mutant patients, PD‐L1 expression was not associated with overall survival (OS) (p = .506). Multivariable analysis confirmed an association between PD‐L1 expression and RFS but not OS. Furthermore, in EGFR‐mutant patients treated with EGFR‐tyrosine kinase inhibitor (EGFR‐TKI) treatment post‐relapse, PD‐L1 expression was not associated with overall response rate (p = .714), disease control rate (p = .554), or progression‐free survival (p = .660). In conclusion, PD‐L1 expression predicted poor RFS‐independent EGFR status but did not show any association with OS in EGFR‐mutant patients. The efficacy of post‐relapse EGFR‐TKI treatment was independent of PD‐L1 expression. The significance of PD‐L1 expression in perioperative EGFR‐TKI therapy should be evaluated.
Unveiling microbial communities with EasyAmplicon: A user‐centric guide to perform amplicon sequencing data analysis
Authors: Yousuf Salsabeel , Luo Hao , Zeng Meiyin , Chen Lei , Ma Tengfei , Li Xiaofang , Zheng Maosheng , Zhou Xin , Chen Liang , Xi Jiao , Lu Hongye , Cao Huiluo , Ma Xiaoya , Bian Bian , Zhang Pengfan , Wu Jiqiu , Gan Renyou , Jia Baolei , Sun Linyang , Ju Zhicheng , Gao Yunyun , Malik Waqar Afzal , Ma Chuang , Lyu Hujie , Li Yahui , Hou Huiyu , Zhou Yuanping , Bai Defeng , Wang Yao , Yang Haifei , Xun Jiani , Du Shengda , Zhang Tianyuan , Wan Xiulin , Peng Kai , Xu Shanshan , Wen Tao , Chen Tong , Liu Yong‐Xin 
Published: November 2024

AbstractThe advent of next‐generation sequencing has revolutionized microbiome research, enabling in‐depth exploration of microbial communities through amplicon sequencing. The widespread adoption of sequencing across diverse fields, coupled with decreasing costs, underscores the critical need for validated, fully automated, reproducible, and adaptable analysis pipelines. However, analyzing these high‐throughput datasets often necessitates extensive bioinformatics expertize, hindering accessibility for many researchers. To address this challenge, in 2023 we developed EasyAmplicon, a comprehensive, user‐friendly pipeline that integrates popular tools such as USEARCH and VSEARCH, offering a streamlined workflow from raw data to results. Remarkably, EasyAmplicon has garnered significant recognition within a year, as evidenced by 127 citations to date. To further facilitate the researchers and enhance usability, we present a detailed protocol with a video recording that guides users through each step of the pipeline, including data preprocessing (quality filtering, chimera removal), amplicon sequence variant analysis, diversity analysis, and data visualization. The protocol is designed for ease of use, with each step documented, allowing researchers to execute the workflow without requiring complex scripting skills. The EasyAmplicon pipeline is freely available on GitHub (https://github.com/YongxinLiu/EasyAmplicon).
KRT80 in hepatocellular carcinoma plays oncogenic role via epithelial–mesenchymal transition and PI3K/AKT pathway
Authors: Hua Ruheng , Yan Xiyue , He Jun , Wu Nuwa , Yu Wangjianfei , Yu Pengfei , Qin Lei 
Published: November 2024

AbstractHepatocellular carcinoma (HCC), a globally prevalent form of cancer, is featured by aggressive growth and early metastasis. Elucidating the underlying mechanism and identifying the effective therapy are critical for advanced HCC patients. In the study, we detect that KRT80 was upregulated in HCC samples. HCC patients with higher KRT80 are associated with worse overall survival after surgery. Gain‐of and loss‐of function studies show that KRT80 enhanced HCC cells proliferation, migration, invasion, and angiogenesis, whereas its silencing abolishes the effects in vivo and in vitro. Mechanistic investigation shows that KRT80 may function as an independent prognostic risk factor and act as an oncogene by influencing EMT and modulating the PI3K/AKT signaling pathway. Together, these findings suggest that KRT80 may be a potential oncogene and a good indicator in predicting prognosis. Targeting KRT80 can offer new insights into the prevention and treatment of HCC.
Behavioral correlates of U.S. retail protein demand: The case of exercise‐driven protein consumption
Authors: Bina Justin D. , Tonsor Glynn T. 
Published: November 2024

AbstractThe economic implications of the relationship between physical exercise and protein consumption are not well understood. Using consumer‐level expenditure data obtained from an open‐ended choice experiment and an Almost Ideal Demand System specification, demand for various retail protein goods is estimated separately for exercise‐focused individuals and all other individuals. Exercise‐focused individuals exhibit lower own‐price sensitivity for all goods (0.28–0.83 lower in magnitude) and lower expenditure elasticities for most goods (0.03–0.19 lower). Substitution patterns are similar between the behavioral groups. These results indicate substantially different demand schedules for those who exercise and a need for future studies to consider behavioral determinants of food demand.
Interpretable Machine Learning Algorithms Identify Inetetamab‐Mediated Metabolic Signatures and Biomarkers in Treating Breast Cancer
Authors: Xie Ning , Liao Dehua , Liu Binliang , Zhang Jiwen , Liu Liping , Huang Gang , Ouyang Quchang 
Published: November 2024

ABSTRACTBackgroundHER2‐positive breast cancer (BC), a highly aggressive malignancy, has been treated with the targeted therapy inetetamab for metastatic cases. Inetetamab (Cipterbin) is a recently approved targeted therapy for HER2‐positive metastatic BC, significantly prolonging patients' survival. Currently, there is no established biomarker to reliably predict or assess the therapeutic efficacy of inetetamab in BC patients.MethodsThis study harnesses the power of metabolomics and machine learning to uncover biomarkers for inetetamab in BC therapy. A total of 23 plasma samples from inetetamab‐treated BC patients were collected and stratified into responders and nonresponders. Ultra‐high‐performance liquid chromatography‐quadrupole time‐of‐flight mass spectrometry was utilized to analyze the metabolites in blood samples. A combination of univariate and multivariate statistical analyses was employed to identify these metabolites, and their biological functions were then ascertained by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. Finally, machine learning algorithms were employed to screen responsive biomarkers from all differentially expressed metabolites.ResultsOur finding revealed 6889 unique metabolites that were detected. Pathways like retinol metabolism, fatty acid biosynthesis, and steroid hormone biosynthesis were enriched for differentially expressed metabolites. Notably, two key metabolites associated with inetetamab response in BC were identified: FAPy‐adenine and 2‐Pyrocatechuic acid. There was some negative correlation between progress‐free survival (PFS) and their kurtosis content.ConclusionsIn summary, the identification of these two significant differential metabolites holds promise as potential biomarkers for evaluating and predicting inetetamab treatment outcomes in BC, ultimately contributing to the diagnosis of the disease and the discovery of prognostic markers.
Serinc5 Regulates Sequential Chondrocyte Differentiation by Inhibiting Sox9 Function in Pre‐Hypertrophic Chondrocytes
Authors: Hata Kenji , Wakamori Kanta , Hirakawa‐Yamamura Akane , Ichiyama‐Kobayashi Sachi , Yamaguchi Masaya , Okuzaki Daisuke , Takahata Yoshifumi , Murakami Tomohiko , Uzawa Narikazu , Yamashiro Takashi , Nishimura Riko 
Published: November 2024

ABSTRACTThe growth plate is the primary site of longitudinal bone growth with chondrocytes playing a pivotal role in endochondral bone development. Chondrocytes undergo a series of differentiation steps, resulting in the formation of a unique hierarchical columnar structure comprising round, proliferating, pre‐hypertrophic, and hypertrophic chondrocytes. Pre‐hypertrophic chondrocytes, which exist in the transitional stage between proliferating and hypertrophic stages, are a critical cell population in the growth plate. However, the molecular basis of pre‐hypertrophic chondrocytes remains largely undefined. Here, we employed scRNA‐seq analysis on fluorescently labeled growth plate chondrocytes for their molecular characterization. Serine incorporator 5 (Serinc5) was identified as a marker gene for pre‐hypertrophic chondrocytes. Histological analysis revealed that Serinc5 is specifically expressed in pre‐hypertrophic chondrocytes, overlapping with Indian hedgehog (Ihh). Serinc5 represses cell proliferation and Col2a1 and Acan expression by inhibiting the transcriptional activity of Sox9 in primary chondrocytes. Chromatin profiling using ChIP‐seq and ATAC‐seq revealed an active enhancer of Serinc5 located in intron 1, with its chromatin status progressively activated during chondrocyte differentiation. Collectively, our findings suggest that Serinc5 regulates sequential chondrocyte differentiation from proliferation to hypertrophy by inhibiting Sox9 function in pre‐hypertrophic chondrocytes, providing novel insights into the mechanisms underlying chondrocyte differentiation in growth plates.