bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of hydrological regime on Taxodium ascendens plant decomposition and nutrient dynamics in the Three Gorges Reservoir riparian zone
Authors: Chen Zhangting , Song Hong , Arif Muhammad , Li Changxiao 
Published: September 2022

Riparian plants are an integral part of the river ecosystem and have significant impacts on the water quality of the reservoir area. The special hydrological process of the riparian zone makes it possible to become a “source” or “sink” of organic matter and nutrients. This study quantifies the flooding period on the decomposition as well as nutrient dynamics of leaves from artificially regenerated Taxodium ascendens in the riparian zone of the Three Gorges Reservoir (TGR) in China. Five decomposition treatment groups were exposed to 10, 30, 60, 90, and 180 days of decomposition: conventional water (T1), mild drought stress (T2), saturated water content (T3), light flooding stress (T4), and severe flooding stress (T5). In T4 and T5, the decomposition rate of T. ascendens leaves was significantly higher than that of T1, T2, and T3. All the leaf C, N, P, and K concentrations at the end of the test were lower than their respective starting values. The concentrations of N and P in the overlying water decrease to various degrees due to decomposition. At the end of the study, the TN content was 1.34 times (T4) and 1.16 times (T5) higher than that of the control group, and the TP content was 3.97 times (T4) and 3.21 times (T5) higher than that of the control group. Leaf decomposition increases the content of N and P in the overlying water under flood conditions, which adversely affects the water environment. This study establishes a theoretical framework for understanding how hydrological processes affect leaf decomposition and nutrient release in riparian areas, providing a scientific basis for riparian zone management in TGR.
Pan-cancer analysis of CREB3L1 as biomarker in the prediction of prognosis and immunotherapeutic efficacy
Authors: Lin Zhengjun , Wu Yanlin , Xiao XunGang , Zhang Xianghong , Wan Jia , Zheng Tao , Chen Hongxuan , Liu Tang , Tang Xianzhe 
Published: September 2022

Background: CAMP response element binding protein 3-like 1 (CREB3L1) has been indicated as a critical biomarker and can modulate multifaced behaviors of tumor cells in diverse cancers. However, a systematic assessment of CREB3L1 in pan-cancer is of absence, and the predictive value of CREB3L1 in cancer prognosis, the tumor immune microenvironment and the efficacy of immunotherapy remains unexplored.Methods: CREB3L1 expression in 33 different cancer types was investigated using RNAseq data from The Cancer Genome Atlas (TCGA) database. The characteristics of CREB3L1 alternations were illustrated in cBioPortal database. The prognostic and clinicopathological value of CREB3L1 was analyzed through clinical data downloaded from the TCGA database. The potential role of CREB3L1 in the tumor immune microenvironment was illustrated by utilizing CIBERSORT and ESTIMATE algorithms, and TISIDB online database. The associations between CREB3L1 expression and tumor mutation burden (TMB), and microsatellite instability (MSI) were assessed by spearman’s rank correlation coefficient. Furthermore, Gene Set Enrichment Analysis (GSEA) was conducted to explore the potential biological functions and downstream pathways of CREB3L1 in different human cancers. The correlations of CREB3L1 expression with PD-1/PD-L1 inhibitors efficacy and drug sensitivity were also investigated.Results: The expression of CREB3L1 was abnormally high or low in several different cancer types, and was also strictly associated with the prognosis of cancer patients. CREB3L1 expression levels have a strong relationship with infiltrating immune cells, including regulatory T cells, CD8+ T cells, macrophages, B naïve cells, dendritic cells and mast cells. CREB3L1 expression was also correlated with the expression of multiple immune-related biomolecules, TMB, and MSI in several cancers. Moreover, CREB3L1 had promising applications in predicting the immunotherapeutic benefits and drug sensitivity in cancer management.Conclusions: Our results highlight the value of CREB3L1 as a predictive biomarker for the prognosis and immunotherapy efficacy in multiple cancers, and CREB3L1 seems to play key roles in the tumor immune microenvironment, suggesting the role of CREB3L1 as a promising biomarker for predicting the prognosis and immune-related signatures in diverse cancers.
Prognostic value of LECT2 and relevance to immune infiltration in hepatocellular carcinoma
Authors: Qin Jiangfeng , Sun Weijie , Zhang Hui , Wu Zihao , Shen Jiapei , Wang Wenhai , Wei Yuanyuan , Liu Yanyan , Gao Yufeng , Xu Honghai 
Published: September 2022

Background: Previous studies have shown that Leukocyte cell-derived chemotaxin2 (LECT2) is associated with the development of HCC. However, there are still no studies with a comprehensive analysis of the role of LECT2 in hepatocellular carcinoma (HCC).Methods: TCGA data sets were used to analyze the expression of LECT2 in HCC. In addition, the prognostic value of LECT2 in HCC was also investigated. DriverDBv3 was used to analyze the Mutation, CNV, and methylation profiles of LECT2. And, validated by immunohistochemistry in 72 HCC samples. The prognostic value of LECT2 and the correlation with clinicopathological features were analyzed. The GO/KEGG enrichment analysis of LECT2 co-expression and gene set enrichment analysis (GSEA) was performed using the R software package. The PPI interaction network was constructed by Search Tool for the Retrieval of Interacting Genes (STRING) database. Immune infiltration was estimated by the XCELL, TIMER, QUANTISEQ, MCPCOUNTER, EPIC, CIBERSORT abs and CIBERSORT algorithms, and Spearman was used to analyzing their correlation with LECT2. Moreover, we analyzed the correlation of LECT2 expression with immune checkpoint molecules and HLA genes. Finally, we analyzed the IC50 values of six chemotherapeutic drugs by the pRRophetic package.Results: Reduced LECT2 expression levels found in HCC patients. Moreover, decreased levels of LECT2 were associated with poor overall survival, disease-free survival, disease-specific survival, and progression-free survival. Besides, methylation was significantly associated with LECT2 expression. The functional enrichment analysis revealed that LECT2 may affect HCC progression through various pathways such as JAK/STAT signaling pathway, cell cycle, and pathways in cancer. Additionally, the results showed that LECT2 expression was negatively correlated with immune infiltration of B cells, Neutrophil, Monocyte, Cancer-associated fibroblast, and Myeloid dendritic cell, and positively correlated with T cell CD8+ naive, Endothelial cell, and Hematopoietic stem cell. LECT2 expression was negatively correlated with multiple immune checkpoint molecules and HLA genes. Chemosensitivity analysis showed that chemosensitivity was lower in the LECT2 high expression group. We validated the prognostic value of LECT2 and analysis of clinicopathological features showed a lower TNM stage in the group with high expression of LECT2.Conclusion: Low expression of LECT2 in HCC is closely associated with poor prognosis, LECT2 may have potential clinical applications due to its unique immunological effects.
Genomic selection in United States dairy cattle
Authors: Wiggans George R. , Carrillo José A. 
Published: September 2022

The genomic selection program for dairy cattle in the United States has doubled the rate of genetic gain. Since 2010, the average annual increase in net merit has been $85 compared to $40 during the previous 5 years. The number of genotypes has been rapidly increasing both domestically and internationally and reached over 6.5 million in 2022 with 1,134,593 submitted in 2021. Evaluations are calculated for over 50 traits. Feed efficiency (residual feed intake), heifer and cow livability, age at first calving, six health traits, and gestation length have been added in recent years to represent the economic value of selection candidates more accurately; work is underway to develop evaluations for hoof health. Evaluations of animals with newly submitted genotypes are calculated weekly. In April 2019, evaluations were extended to crossbreds; to support that effort, evaluations are initially calculated on an all-breed base and then blended by an estimated breed composition. For animals that are less than 90% of one breed, the evaluation is calculated by weighting contributions of each of the five major dairy breeds evaluated (Ayrshire, Brown Swiss, Guernsey, Holstein, and Jersey) by the breed proportion. Nearly 200,000 animals received blended evaluations in July 2022. Pedigree is augmented by using haplotype matching to discover maternal grandsires and great-grandsires. Haplotype analysis is also used to discover undesirable recessive conditions. In many cases, the causative variant has been identified, and results from a gene test or inclusion on a genotyping chip improves the accuracy of those determinations for the current 27 conditions reported. Recently discovered recessive conditions include neuropathy with splayed forelimbs in Jerseys, early embryonic death in Holsteins, and curly calves in Ayrshires. Techniques have been developed to support rapid searches for parent-progeny relationships and identical genotypes among all likely genotypes, which substantially reduces processing time. Work continues on using sequence data to discover additional informative single nucleotide polymorphisms and to incorporate those previously discovered. Adoption of genotyping by sequencing is expected to improve flexibility of marker selection. The success of the Council on Dairy Cattle Breeding in conducting the genetic evaluation program is the result of close cooperation with industry and research groups, including the United States Department of Agriculture, breed associations, genotyping laboratories, and artificial-insemination organizations.
Diabetes exacerbated sepsis-induced intestinal injury by promoting M1 macrophage polarization via miR-3061/Snail1 signaling
Authors: Tan Fang , Cao Yuling , Zheng Lei , Wang Tao , Zhao Shuhua , Chen Jiong , Pang Changji , Xia Weiyi , Xia Zhengyuan , Li Ningning , Chi Xinjin 
Published: September 2022

BackgroundMacrophages play important roles in diabetes and sepsis-related intestinal injury. Accumulating evidence suggests that microRNAs (miRNAs) act as the fundamental link between macrophage polarization and tissue injury. However, the underlying mechanisms of miRNAs in regulating macrophage polarization–related intestinal injury under diabetes and sepsis conditions remain unclear.MethodsThe cecal ligation and puncture (CLP)–induced sepsis models were established in male wild-type (WT) and diabetic mice. Clodronate liposome was used to deplete macrophage. H&amp;E staining, inflammatory cytokines [tumor necrosis factor–α (TNF-α), interleukin-1β (IL-1β), and IL-6], and intestinal mucosal barrier function markers [occludin, ZO-1, lipopolysaccharide (LPS), and intestinal fatty acid binding protein (iFABP)] were used to assess elevated intestinal damage. miRNA array, RNA-seq, and bioinformatic analysis were performed to detect the miRNA and messenger RNA (mRNA) expression and the potential regulation mechanism. In vitro, RAW264.7 cells were cultured in the absence or presence of high glucose and LPS, miR-3061 mimics, and Snail small interfering RNA stimulation, respectively, for further mechanism studies. Luciferase reporter assay was used to confirm the interplay between miRNA and its target genes.ResultsCompared with WT CLP mice, the diabetic CLP mice showed severe intestinal damage characterized by significant increases in Chui’s scores, expression of inflammatory cytokines (TNF-α, IL-1β, and IL-6), serum LPS and iFABP concentration, and significant reductions in tight junction protein occludin and ZO-1 levels. Macrophage depletion reversed the intestinal damage caused by CLP. The bioinformatic analysis revealed that miR-3061/Snail1 might be a potential regulation axis of macrophage polarization. Furthermore, high glucose and LPS stimulation increased M1 macrophage and reduced the levels of miR-3061, which was negatively associated with Snail1 in RAW264.7 cells. Mechanistic studies demonstrated that miR-3061 regulated macrophage polarization by targeting the Snail1 mRNA 3′‐untranslated region. Moreover, miR-3061 overexpression suppressed Snail1 expression and inhibited M1 macrophage and inflammatory cytokines.ConclusionThis study elucidated that diabetes exacerbated sepsis-induced intestinal injury by promoting M1 macrophage polarization and further demonstrated that the miR-3061/Sani1 axis may be the potential target of macrophage polarization.
Efficacy and safety of dietary polyphenol supplementation in the treatment of non-alcoholic fatty liver disease: A systematic review and meta-analysis
Authors: Yang Kailin , Chen Junpeng , Zhang Tianqing , Yuan Xiao , Ge Anqi , Wang Shanshan , Xu Hao , Zeng Liuting , Ge Jinwen 
Published: September 2022

BackgroundDietary polyphenol treatment of non-alcoholic fatty liver disease (NAFLD) is a novel direction, and the existing clinical studies have little effective evidence for its therapeutic effect, and some studies have inconsistent results. The effectiveness of dietary polyphenols in the treatment of NAFLD is still controversial. The aim of this study was to evaluate the therapeutic efficacy of oral dietary polyphenols in patients with NAFLD.MethodsThe literature (both Chinese and English) published before 30 April 2022 in PubMed, Cochrane, Medline, CNKI, and other databases on the treatment of NAFLD with dietary polyphenols was searched. Manual screening, quality assessment, and data extraction of search results were conducted strictly according to the inclusion and exclusion criteria. RevMan 5.3 software was used to perform the meta-analysis.ResultsThe RCTs included in this study involved dietary supplementation with eight polyphenols (curcumin, resveratrol, naringenin, anthocyanin, hesperidin, catechin, silymarin, and genistein) and 2,173 participants. This systematic review and meta-analysis found that 1) curcumin may decrease body mass index (BMI), Aspartate aminotransferase (AST), Alanine aminotransferase (ALT), Triglycerides (TG) total cholesterol (TC), and Homeostasis Model Assessment-Insulin Resistance (HOMA-IR) compared to placebo; and curcumin does not increase the occurrence of adverse events. 2) Although the meta-analysis results of all randomized controlled trials (RCTs) did not reveal significant positive changes, individual RCTs showed meaningful results. 3) Naringenin significantly decreased the percentage of NAFLD grade, TG, TC, and low-density lipoprotein cholesterol (LDL-C) and increased high-density lipoprotein cholesterol (HDL-C) but had no significant effect on AST and ALT, and it is a safe supplementation. 4) Only one team presents a protocol about anthocyanin (from Cornus mas L. fruit extract) in the treatment of NAFLD. 5) Hesperidin may decrease BMI, AST, ALT, TG, TC, HOMA-IR, and so on. 6) Catechin may decrease BMI, HOMA-IR, and TG level, and it was well tolerated by the patients. 7) Silymarin was effective in improving ALT and AST and reducing hepatic fat accumulation and liver stiffness in NAFLD patients.ConclusionBased on current evidence, curcumin can reduce BMI, TG, TC, liver enzymes, and insulin resistance; catechin can reduce BMI, insulin resistance, and TG effectively; silymarin can reduce liver enzymes. For resveratrol, naringenin, anthocyanin, hesperidin, and catechin, more RCTs are needed to further evaluate their efficacy and safety.
Prognostic stratification based on m5C regulators acts as a novel biomarker for immunotherapy in hepatocellular carcinoma
Authors: Liu Ping , Zhu Ziqing , Ma Jiayao , Wei Le , Han Ying , Shen Edward , Tan Xiao , Chen Yihong , Cai Changjing , Guo Cao , Peng Yinghui , Gao Yan , Liu Yongting , Huang Qiaoqiao , Gao Le , Li Yin , Jiang Zhaohui , Wu Wantao , Liu Yihan , Zeng Shan , Li Wei , Feng Ziyang , Shen Hong 
Published: September 2022

BackgroundImmunotherapy is a promising anti-cancer strategy in hepatocellular carcinoma (HCC). However, a limited number of patients can benefit from it. There are currently no reliable biomarkers available to find the potential beneficiaries. Methylcytosine (m5C) is crucial in HCC, but its role in forecasting clinical responses to immunotherapy has not been fully clarified.MethodsIn this study, we analyzed 371 HCC patients from The Cancer Genome Atlas (TCGA) database and investigated the expression of 18 m5C regulators. We selected 6 differentially expressed genes (DEGs) to construct a prognostic risk model as well as 2 m5C-related diagnostic models.ResultsThe 1-, 3-, and 5-year area under the curve (AUC) of m5C scores for the overall survival (OS) was 0.781/0.762/0.711, indicating the m5C score system had an ideal distinction of prognostic prediction for HCC. The survival analysis showed that patients with high-risk scores present a worse prognosis than the patients with low-risk scores (p&lt; 0.0001). We got consistent results in 6 public cohorts and validated them in Xiangya real-world cohort by quantitative real-time PCR and immunohistochemical (IHC) assays. The high-m5C score group was predicted to be in an immune evasion state and showed low sensitivity to immunotherapy, but high sensitivity to chemotherapy and potential targeted drugs and agents, such as sepantronium bromide (YM-155), axitinib, vinblastine and docetaxel. Meanwhile, we also constructed two diagnostic models to distinguish HCC tumors from normal liver tissues or liver cirrhosis.ConclusionIn conclusion, our study helps to early screen HCC patients and select patients who can benefit from immunotherapy. Step forwardly, for the less likely beneficiaries, this study provides them with new potential targeted drugs and agents for choice to improve their prognosis.
Collaborative reliance in medicine safety and quality regulation: Investigation of experiences in handling N-nitrosamine impurities among ZaZiBoNa participating countries
Authors: Shabangu Patience P. , Kuwana Rutendo J. , Dube Admire 
Published: September 2022

IntroductionThe presence of N-nitrosamine impurities in medicines raised concerns globally as they are genotoxic and probable human carcinogens. A review of N-nitrosamine impurities in medicines provides an opportunity for National Regulatory Authorities (NRAs) to ensure that corrective and preventive actions are applied so that safe and good quality medicines are made available to the public. This study aimed to investigate the experiences on reviews conducted by NRAs from various Southern African Development Community countries which participate in the regional work-sharing forum, ZaZiBoNa, on the quality and safety data due to the presence of N-nitrosamine impurities in medicines.MethodsA comparative, descriptive study using mixed methods was conducted. Purposive sampling was applied in selecting research participants based on their participation status in the ZaZiBoNa initiative. A standardized questionnaire structured into five parts was completed by ZaZiBoNa focal persons/nominated individuals to determine the experience of each NRA in addressing the safety and quality issues related to the presence of N-nitrosamine impurities in the affected medicines. Profiled medicines included sartans, ranitidine, metformin, rifampicin, and rifapentine.ResultsSartan medicines had been reviewed by all countries participating in the ZaZiBoNa initiative. Although most NRAs have yet to conduct reviews on other profiled medicines, evaluations have been implemented to ensure access to safe and good quality medicines within the region. Most countries experienced challenges in communicating with applicants or marketing authorization holders (MAHs) on reviewing N-nitrosamine impurities in their medicines. The majority of NRAs agree that there is a need for further collaboration efforts to review N-nitrosamine impurities in medicines.ConclusionThe review of N-nitrosamine impurities in the profiled medicines by NRAs within the region has demonstrated the importance of enhanced regulatory oversight to safeguard against the risks associated with medicines. Collaborative reliance on the review of the safety and quality of medicine, continuous monitoring, implementation and review of processes, testing methods, and regular engagements with stakeholders could be essential in ensuring adequate control of N-nitrosamine impurities in medicines.
Peripheral interleukin-6-associated microglial QUIN elevation in basolateral amygdala contributed to cognitive dysfunction in a mouse model of postoperative delirium
Authors: Mu Jing-Lan , Liu Xiao-Dong , Dong Ye-Hong , Fang Ying-Ying , Qiu Shi-Da , Zhang Fu , Liu Ke-Xuan 
Published: September 2022

BackgroundDeveloping effective approaches for postoperative delirium has been hampered due to the lack of a pathophysiologically similar animal model to offer insights into the pathogenesis. The study, therefore, aimed to develop a delirium-like mouse model and explore the underlying mechanism.MethodsThe three cycles of 10-min clamp following 5-min reopening of the superior mesenteric artery (SMA) were performed in adult male C57BL/6 mice to induce a delirium-like phenotype. Composite Z score calculated based on the results of Open Field, Y Maze and Buried Food Tests was employed to assess the delirium phenotype in mice. Microglia activities were monitored by immunofluorescence staining and comprehensive morphological analysis. Systemic administration of minocycline (MINO), IL-6 antibody or IL-6 neutralizing antibody, was applied to manipulate microglia. The expressions of Indoleamine 2,3-dioxygenase-1 (IDO-1) and quinolinic acid (QUIN) were examined by RT-PCR and High-Performance Liquid Chromatography/Mass Spectrometry, respectively. Cytokines were measured using fluorescence activated cell sorting method.ResultsThe repeated ischemia/reperfusion (I/R) surgery caused significant anxiety (P &lt; 0.05) and cognition decline in working memory and orientation (P &lt; 0.05) in mice at postoperative 24 h. The composite Z score, indicating an overall disturbance of brain function, fluctuated over 24 h after I/R surgery (P &lt; 0.001). Immunofluorescent staining showed that the percentage of microglia in the basolateral amygdala (BLA) (P &lt; 0.05) was reactivated after I/R surgery and was negatively correlated with dwell time at Y maze (R = −0.759, P = 0.035). Inhibiting microglia activities by MINO reduced QUIN productions (P &lt; 0.01) that improved cognitive deficits (P &lt; 0.05). The peripheral IL-6 might cause IL-6 elevation in the BLA. Systemic administration of IL-6 antibodies suppressed I/R-induced IL-6 elevations (P &lt; 0.05), microglial reactivations (P &lt; 0.05), IDO-1 expressions (P &lt; 0.01), and neuroactive metabolite QUIN productions (P &lt; 0.05) in the BLA, resulting in a recovery of cognitive deficits (P &lt; 0.05). Injection of IL-6 exerted opposite effects.ConclusionThe repeated intestinal I/R surgery-induced mouse model is a simple and reproducible one of postoperative delirium. Peripheral IL-6-associated microglial QUIN elevations in the BLA contributed to cognitive dysfunction in the model of postoperative delirium.