bluuebunny/crossref_metadata_2025_split huggingface dataset:
Negative emission power plants: Techno-economic analysis of a biomass-based integrated gasification solid oxide fuel cell/gas turbine system for power, heat, and biochar co-production—part 2
Authors: Jaiganesh N. , Kuo Po-Chih , Champatan Vipin , Gopi Girigan , Kumar R. Ajith , Aravind P.V. 
Published: August 2022

In our previous work (Part I), we evaluated the thermodynamic models of the biomass-fed integrated gasification solid oxide fuel cell system with a carbon capture and storage (BIGFC/CCS) unit. In this work (Part II), the techno-economic analysis of the proposed negative emission power plants is carried out. Levelized cost of electricity, net present value (NPV), payback period, internal rate of return (IRR), and levelized cost of negative carbon (LCNC) are the key economic parameters evaluated. The results of a series of sensitivity analysis show the impact of gasification agents and stepwise increase in biochar co-production on the performance of the system. The total overnight cost is estimated to be 6197 $/kW and 5567 $/kW for the air and steam-oxygen gasification BIGFC/CCS systems, respectively. Steam-oxygen gasification is found to be more economically beneficial than air gasification one for all of the cases studied. Economically viable biochar co-production cases are identified to ascertain the influence of capital cost, operating cost, biomass cost, plant capacity factor, and tax. Moreover, the effect of the carbon credit scenario on the economic indicators is also reported. The results show that the most effective economic performance from the steam-oxygen gasification case reported an NPV of 3542 M$, an IRR of 24.2%, and a payback period of 3.3 years, with an LCNC of -322.5$/t of CO2. Compiling the results from Part I and Part II shows that it is easier to achieve negative emission using the steam-oxygen gasification of a BIGFC/CCS system. These results are expected to be helpful for stakeholders in identifying appealing negative emissions power plant projects for near and long-term future investments.
Nine-gene signature and nomogram for predicting survival in patients with head and neck squamous cell carcinoma
Authors: Yang Fan , Zhou Liu-qing , Yang Hui-wen , Wang Yan-jun 
Published: August 2022

Background: Head and neck squamous cell carcinomas (HNSCCs) are derived from the mucosal linings of the upper aerodigestive tract, salivary glands, thyroid, oropharynx, larynx, and hypopharynx. The present study aimed to identify the novel genes and pathways underlying HNSCC. Despite the advances in HNSCC research, diagnosis, and treatment, its incidence continues to rise, and the mortality of advanced HNSCC is expected to increase by 50%. Therefore, there is an urgent need for effective biomarkers to predict HNSCC patients’ prognosis and provide guidance to the personalized treatment.Methods: Both HNSCC clinical and gene expression data were abstracted from The Cancer Genome Atlas (TCGA) database. Intersecting analysis was adopted between the gene expression matrix of HNSCC patients from TCGA database to extract TME-related genes. Differential gene expression analysis between HNSCC tissue samples and normal tissue samples was performed by R software. Then, HNSCC patients were categorized into clusters 1 and 2 via NMF. Next, TME-related prognosis genes (p &lt; 0.05) were analyzed by univariate Cox regression analysis, LASSO Cox regression analysis, and multivariate Cox regression analysis. Finally, nine genes were selected to construct a prognostic risk model and a prognostic gene signature. We also established a nomogram using relevant clinical parameters and a risk score. The Kaplan–Meier curve, survival analysis, time-dependent receiver operating characteristic (ROC) analysis, decision curve analysis (DCA), and the concordance index (C-index) were carried out to assess the accuracy of the prognostic risk model and nomogram. Potential molecular mechanisms were revealed by gene set enrichment analysis (GSEA). Additionally, gene correlation analysis and immune cell correlation analysis were conducted for further enriching our results.Results: A novel HNSCC prognostic model was established based on the nine genes (GTSE1, LRRN4CL, CRYAB, SHOX2, ASNS, KRT23, ANGPT2, HOXA9, and CARD11). The value of area under the ROC curves (AUCs) (0.769, 0.841, and 0.816) in TCGA whole set showed that the model effectively predicted the 1-, 3-, and 5-year overall survival (OS). Results of the Cox regression assessment confirmed the nine-gene signature as a reliable independent prognostic factor in HNSCC patients. The prognostic nomogram developed using multivariate Cox regression analysis showed a superior C-index over other clinical signatures. Also, the calibration curve had a high level of concordance between estimated OS and the observed OS. This showed that its clinical net can precisely estimate the one-, three-, and five-year OS in HNSCC patients. The gene set enrichment analysis (GSEA) to some extent revealed the immune- and tumor-linked cascades.Conclusion: In conclusion, the TME-related nine-gene signature and nomogram can effectively improve the estimation of prognosis in patients with HNSCC.
Elevated insulin-like growth factor 2 mRNA binding protein 1 levels predict a poor prognosis in patients with breast carcinoma using an integrated multi-omics data analysis
Authors: Li Shiqi , Jiang Meixiu 
Published: August 2022

Background: Insulin-like growth factor 2 mRNA binding protein 1 (IGF2BP1) controls the cytoplasmic fate of certain mRNAs and is hypothesized to predict a poor patient prognosis in several malignant tumors. However, the prognostic relevance of IGF2BP1 in breast cancer remains debatable.Methods: We interrogated large publicly available datasets from the Gene Expression Omnibus (GEO), The Cancer Genome Atlas (TCGA), and cBioportal databases to analyze the genetic alterations in the expression levels of IGF2BP1 in patients with invasive breast carcinoma (BRCA), and to discern the prognostic value of IGF2BP1 in BRCA. We applied Gene Ontology (GO), the Kyoto Encyclopedia of Genes and Genome (KEGG), and gene set enrichment analysis (GSEA) to uncover a functional association between IGF2BP1 and BRCA using differentially expressed genes (DEGs), and we screened genes and proteins related to BRCA.Results: We determined that both genetic alterations in IGF2BP1 (approximately 10%) and an increase in IGF2BP1 mRNA levels were related to certain cancer subtypes and an unfavorable prognosis in BRCA patients, and we then established an OS nomogram upon our multivariate regression model. The DEGs and IGF2BP1-correlated genes/proteins that implied the involvement of cornification, keratinization, drug/xenobiotic metabolism by cytochrome P450, chemical carcinogenesis, cell interactions, and cell adhesion to the extracellular matrix (ECM) pathways with respect to the prognostic relevance of IGF2BP1.Conclusion: In summary, our results indicated that both genetic alterations in IGF2BP1 and increased levels of IGF2BP1 mRNA and protein predict a poor patient prognosis in BRCA patients.
Robust pyroptosis risk score guides the treatment options and predicts the prognosis of bladder carcinoma
Authors: Deng Dingshan , Liu Fenglian , Liu Zhi , Wu Zuowei , He Yunbo , Zhang ChunYu , Zu Xiongbin , Ou Zhenyu , Wang Yongjie 
Published: August 2022

BackgroundBladder carcinoma (BLCA) is a heterogeneous disease that makes it difficult to achieve proper individual treatment and predict prognosis. This study aimed to develop a risk score from a new perspective of pyroptosis and guide accurate treatment and prognosis prediction for BLCA.MethodsThe TCGA-BLCA cohort data were downloaded from The Cancer Genome Atlas database. Two external validation cohorts were collected from the Gene Expression Omnibus. Another independent validation cohort (the Xiangya cohort) was recruited from our hospital. The least absolute shrinkage and selector operation (LASSO) algorithm and Cox regression models were used to establish the pyroptosis risk score. Thereafter, we correlated the pyroptosis risk score with prognosis, tumor microenvironment (TME) immune hallmarks, and multiple treatments, including anticancer immunotherapy, chemotherapy, radiotherapy, and targeted therapy.ResultsThe pyroptosis risk score was an independent prognostic predictor of BLCA. We found that the activities of multiple steps of the anticancer immune response cycle, such as the release of cancer cell antigens, CD8 T cell recruitment, and NK cell recruitment, were significantly higher in the high-risk score group than in the low-risk score group. In addition, the infiltration levels of the corresponding tumor-infiltrating immune cells (TIICs), such as CD8 T cells and NK cells, were positively correlated with the pyroptosis risk score. Thus, BLCA with a high-risk score may be associated with inflamed phenotypes. Simultaneously, the expression of multiple immune checkpoints (such as PD-L1, CTLA-4, and PD-1) and enrichment scores of gene signatures positively correlated with immunotherapy response were positively correlated with the pyroptosis risk score. Therefore, patients with a high pyroptosis risk score may be more sensitive to immunotherapy. In addition, patients with high pyroptosis risk scores may be more sensitive to chemotherapeutic drugs, such as cisplatin, docetaxel, and paclitaxel. In addition, the pyroptosis risk score accurately predicted the molecular subtypes of BLCA, which were cross-validated in several independent systems.ConclusionsThis study developed and validated a robust pyroptosis risk score that can predict the clinical outcomes and TME immune phenotypes of BLCA. In summary, the pyroptosis risk score helps drive precision therapy in patients with BLCA.
Global scientific trends on the immunomodulation of mesenchymal stem cells in the 21st century: A bibliometric and visualized analysis
Authors: Wang Zhongqing , Sun Yuqiang , Shen Rou , Tang Xia , Xu Yingxin , Zhang Ye , Liu Yao 
Published: August 2022

BackgroundSince the discovery of the immunomodulatory functions of mesenchymal stem cells (MSCs), their application in immunomodulation has attracted considerable attention, and an increasing number of studies have been conducted worldwide. Our research aimed to investigate the global status and trends in this field.MethodsPublications on the immunomodulatory functions of MSCs from 1 January 2000 to 7 March 2022 were retrieved from the Web of Science Core Collection. The data were studied and indexed using the bibliometric methodology. Visualization analysis, co-authorship, co-occurrence analysis, and publication trends in MSC immunomodulation were conducted using the VOSviewer software.ResultsIn total, 4,227 papers were included in the study. The number of publications and research interests has significantly increased globally. China published the highest number of related articles, while the US published articles with the highest number of citations. Stem Cell Research &amp; Therapy had the highest number of publications. Sun Yat-sen University, Shanghai Jiao Tong University, Harvard University, and Seoul National University were the most contributive institutions. Furthermore, the studies were divided into four research hotspots for MSC immunomodulation: MSC immunomodulation in regenerative medicine, the effects and mechanisms of MSC immunomodulation, MSC therapy for immune diseases, and the cell source of MSCs.ConclusionThis study indicates that the number of publications on MSC immunomodulation will increase in the future, and MSC immunomodulation mechanisms and clinical applications of MSC immunotherapy should be the next hotspots in this research field.
Coastal aquaculture farms for the sea cucumber Apostichopus japonicus provide spawning and first-year nursery grounds for wild black rockfish, Sebastes schlegelii: A case study from the Luanhe River estuary, Bohai bay, the Bohai Sea, China
Authors: Xu Min , Qi Zun-li , Liu Zun-lei , Quan Wei-min , Zhao Qi , Zhang Yun-ling , Liu Hui , Yang Lin-lin 
Published: August 2022

Aquaculture farms are known to attract wild organisms from nearby areas. Sea cucumber Apostichopus japonicus aquaculture farms in Bohai Bay, the Bohai Sea, China, might provide spawning and nursery grounds for wild black rockfish Sebastes schlegelii populations. To identify the above, we studied the variation in the numbers of S. schlegelii larvae (and length-categories as a percentage of the natural population) via ichthyoplankton surveys by months from January to October 2020, and assessed the food web structure and energy flow distribution of the farm and trophic links of S. schlegelii natural stock by using Ecopath modeling in July 2016 to August 2017. Larvae with a length between 3.90-5.80 mm were observed in the farm in May 2020, the juveniles with an estimated trophic level of 4.31. Juveniles used the farms as first-year nursery ground, and then they swam into deeper waters in August of the following year. MTI analysis showed increasing biomass of S. schlegelii might result in a decrease in the biomass of crustacea, and had positive and negative impacts on mollusk and Hexagrammos otakii biomass. We argued that aquacultural infrastructures constructed by artificial reefs could be used as a fisheries management tool to enhance S. schlegelii stocks and that monitoring of other marine organisms, such as oysters, Rapana venosa, Charybdis japonica, and Asterias spp. etc., was necessary to maintain sustainable exploitations of aquacultural farm ecosystems. A paucity of knowledge surrounding the interactions between aquaculture farms and wild organisms needs furthermore researches.
Metagenomics-based systematic analysis reveals that gut microbiota Gd-IgA1-associated enzymes may play a key role in IgA nephropathy
Authors: Liang Xiaolin , Zhang Simeng , Zhang Difei , Hu Liang , Zhang La , Peng Yu , Xu Yuan , Hou Haijing , Zou Chuan , Liu Xusheng , Chen Yang , Lu Fuhua 
Published: August 2022

Background: IgA nephropathy (IgAN) is the most common type of glomerulonephritis in Asia. Its pathogenesis involves higher expression of galactose-deficient IgA1 (Gd-IgA1) and dysregulated intestinal mucosal immunity. The objective of this study was to explore whether specific gut microbiota and associated enzymes affect Gd-IgA1 in IgAN.Methods: This study carried out shotgun metagenomic sequencing with Illumina on fecal samples collected from 20 IgAN patients (IgAN group) and 20 healthy controls (HCs group) who were recruited from January 2016 to December 2018 at the Second Clinical College of Guangzhou University of Chinese Medicine. Differences analysis in gut microbiota was performed to determine the overall microbiota composition, the representative enterotypes, and the microbiota abundance. Correlations between gut microbiota and clinical indicators were assessed by Spearman’s analysis. Moreover, the functional prediction of microbial communities and the quantitative calculation of enzymes encoded by microbiome were performed using the MetaCyc pathway and the bioBakery three platform, respectively.Results:Bacteroides plebeius and Bacteroides vulgatus levels were higher, while Prevotella copri and Alistipes putredinis levels were lower in the IgAN group compared to HCs group. Enterotype I characterized by Bacteroides was closely related to the IgAN patients. Moreover, Bacteroides fragilis, Flavonifractor plautii and Ruminococcus gnavus were characteristic bacteria enriched in IgAN patients. Spearman’s correlation analysis found that Eggerthella lenta and Ruminococcus bromii were positively correlated with urine protein-creatinine ratio, while Ruminococcus gnavus showed a direct association with red blood cells in urine, and Bacteroides vulgatus and Ruminococcus gnavus were positively correlated with eGFR. These results indicated that intestinal dysbacteriosis occurred in IgAN patients and was associated with clinical and biochemical features. In addition, MetaCyc pathway analysis predicted microbiota-related metabolic pathways, including the biosynthesis of amino acids and glycans, were associated with the IgAN group. Microbial enzymes analysis highlighted that Gd-IgA1-associated α-galactosidase and α-N-acetyl-galactosaminidase secreted by Flavonifractor plautii were enriched in IgAN patients.Conclusion: These findings suggested that α-galactosidase and α-N-acetyl-galactosaminidase secreted by Flavonifractor plautii might be related to the production of Gd-IgA1, indicating that enzymes originated from abnormal intestinal microbiota may contribute to the production of Gd-IgA1 and play an important role in the pathogenesis of IgAN.
Exploring the role of non-coding RNAs as potential candidate biomarkers in the cross-talk between diabetes mellitus and Alzheimer’s disease
Authors: Ghiam Shokoofeh , Eslahchi Changiz , Shahpasand Koorosh , Habibi-Rezaei Mehran , Gharaghani Sajjad 
Published: August 2022

BackgroundRecent research has investigated the connection between Diabetes Mellitus (DM) and Alzheimer’s Disease (AD). Insulin resistance plays a crucial role in this interaction. Studies have focused on dysregulated proteins to disrupt this connection. Non-coding RNAs (ncRNAs), on the other hand, play an important role in the development of many diseases. They encode the majority of the human genome and regulate gene expression through a variety of mechanisms. Consequently, identifying significant ncRNAs and utilizing them as biomarkers could facilitate the early detection of this cross-talk. On the other hand, computational-based methods may help to understand the possible relationships between different molecules and conduct future wet laboratory experiments.Materials and methodsIn this study, we retrieved Genome-Wide Association Study (GWAS, 2008) results from the United Kingdom Biobank database using the keywords “Alzheimer’s” and “Diabetes Mellitus.” After excluding low confidence variants, statistical analysis was performed, and adjusted p-values were determined. Using the Linkage Disequilibrium method, 127 significant shared Single Nucleotide Polymorphism (SNP) were chosen and the SNP-SNP interaction network was built. From this network, dense subgraphs were extracted as signatures. By mapping each signature to the reference genome, genes associated with the selected SNPs were retrieved. Then, protein-microRNA (miRNA) and miRNA-long non-coding RNA (lncRNA) bipartite networks were built and significant ncRNAs were extracted. After the validation process, by applying the scoring function, the final protein-miRNA-lncRNA tripartite network was constructed, and significant miRNAs and lncRNAs were identified.ResultsHsa-miR-199a-5p, hsa-miR-199b-5p, hsa-miR-423-5p, and hsa-miR-3184-5p, the four most significant miRNAs, as well as NEAT1, XIST, and KCNQ1OT1, the three most important lncRNAs, and their interacting proteins in the final tripartite network, have been proposed as new candidate biomarkers in the cross-talk between DM and AD. The literature review also validates the obtained ncRNAs. In addition, miRNA/lncRNA pairs; hsa-miR-124-3p/KCNQ1OT1, hsa-miR-124-3p/NEAT1, and hsa-miR-124-3p/XIST, all expressed in the brain, and their interacting proteins in our final network are suggested for future research investigation.ConclusionThis study identified 127 shared SNPs, 7 proteins, 15 miRNAs, and 11 lncRNAs involved in the cross-talk between DM and AD. Different network analysis and scoring function suggested the most significant miRNAs and lncRNAs as potential candidate biomarkers for wet laboratory experiments. Considering these candidate biomarkers may help in the early detection of DM and AD co-occurrence.
Change of mortality of patients with acute ischemic stroke before and after 2015
Authors: Park Sang-Won , Lee Ji Young , Heo Nam Hun , Han James Jisu , Lee Eun Chae , Hong Dong-Yong , Lee Dong-Hun , Lee Byung Cheol , Lim Young Wha , Kim Gui Ok , Lee Man Ryul , Oh Jae Sang 
Published: August 2022

IntroductionAdvances in the diagnosis and management of acute ischemic stroke (AIS) and the increased use of mechanical thrombectomy (MT) have improved the quality of care and prognosis of patients with AIS since 2015. We investigated the changing trends in mortality of patients with AIS in Korea before and after 2015.Materials and methodsA retrospective cohort study was conducted using combined anonymized data from the Acute Stroke Assessment Registry of Korea and the Health Insurance Review &amp; Assessment Service database. Patients with ischemic stroke with precise onset time and initial National Institute of Health Stroke Scale records were included.ResultsPatients receiving MT treatment increased from 256 (2.7%) pre-2015 to 1,037 (3.9%) post-2015 (p &lt; 0.001). Overall mortality significantly decreased from pre-2015 to post-2015. In pre-2015, intravenous thrombolysis (IVT) administered within 2 h significantly reduced 3-month mortality when compared with non-IVT. While, in post-2015, IVT administered within 2 h significantly reduced the 3-month, 1-year, 2-year, and 4-year mortality (p &lt; 0.05). MT only reduced 1-year mortality pre-2015; however, MT significantly reduced the 3-month, 1-year, and 2-year mortality post-2015 (p &lt; 0.05). Post-stroke antiplatelet and anticoagulant drugs significantly reduced the 3-month, 1-year, 2-year, and 4-year mortality post-2015.DiscussionSince 2015, faster IVT has significantly reduced the short- and long-term mortality in patients with AIS; MT reduced the 3-month, 1-year, and 2-year mortality. Post-stroke antithrombotic medication has significantly lowered the 2- and 4-year mortality since 2015.ConclusionsChanging trends in AIS management since 2015 have improved the prognosis of patients with AIS.
A single-center retrospective study with 1-year follow-up after CEA in patients with severe carotid stenosis with contralateral carotid artery occlusion
Authors: Yuan Wanzhong , Huo Ran , Ma Kaiming , Han Yunfeng , Yin Xiaoliang , Yang Jun , Zhao Xihai , Wang Tao 
Published: August 2022

ObjectiveTo analyze the risk factors associated with adverse events after carotid endarterectomy (CEA) in patients with unilateral severe carotid stenosis and contralateral occlusion.MethodsPatients were recruited for CEA between August 2014 and February 2020. CEA was performed under general anesthesia. The carotid clamp time (CCT; long CCT: &gt;20 min) is defined as the period between clamp-on and clamp-off for the stenotic carotid artery. The perioperative factors and postoperative adverse events were recorded. All patients were followed up for 1 year after CEA.ResultsSixty subjects (65.8 ± 7.2 years; 54 males) were included. Patients with adverse events had significantly longer CCT than those without adverse events (60% vs. 40%, P = 0.013). Univariate logistic regression analysis showed that a history of diabetes was significantly associated with adverse events (OR, 0.190; 95% CI, 0.045–0.814; P = 0.025); long CCT was significantly associated with adverse events (OR, 8.500; 95% CI, 1.617–44.682; P = 0.011). After adjusting for confounding factors, including age, sex, BMI, diabetes, PSV, long CCT, non–use of shunt, and history of stroke or TIA, the associations between diabetes and adverse events (OR, 0.113; 95% CI, 0.013–0.959; P = 0.046) were statistically significant; the associations between long CCT and adverse events (OR, 1.301; 95% CI, 1.049–1.613; P = 0.017) were statistically significant.ConclusionsA longer carotid clamp time (&gt;20 min) and a history of diabetes may increase the risk of adverse events in patients with unilateral severe carotid stenosis and contralateral occlusion after CEA. With good preoperative evaluation and intraoperative monitoring, the use of shunts may not be needed intraoperatively in patients with unilateral severe carotid stenosis and contralateral occlusion.