bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of the prognostic biomarkers associated with cancer stem cell characteristics and immune infiltration of Helicobacter pylori-induced gastric cancer
Authors: Chen Qili , Lv Xuemei , Zhou Shuqi , Yan Yuanyuan , Zhang Jing , Wei Minjie , He Miao , Liu XinLI 
Published: November 2021

Abstract
BackgroundChina is a country with a high incidence of gastric cancer, accounting for about half of the new cases in the world every year. The development of Gastric cancer (GC) is closely related to Helicobacter pylori (H. pylori) infection. Cancer stem cells (CSCs) play important roles in the survival, proliferation, metastasis and recurrence of tumors. However, the mechanism of CSCs and H. pylori-induced GC remains unclear.At the same time, the effect of tumor microenvironment on tumor stem cells and GC with H. pylori infection is also worth exploring. On the basis of the existing research on GC, it is still of great significance to further understand and explore the pathogenesis of GC through bioinformatics analysis.ResultsThere was higher mRNA expression-based stemness index (mRNAsi) in H. pylori (+) GC tumor tissue than in normal tissue. The clinical features of stage T and N were highly correlated with mRNAsi. The purple module was the most significant modules related to the mRNAsi by WGCNA and its key genes played played a major function related to tumor immunity, mainly involved in regulating the Jak-STAT signal pathway, Th17 cell differentiation pathway, and so on. These key genes were correlated with the high level of immune infiltration of CD8+ T cells, CD4+ T cells, macrophages, neutrophils and dendritic cells in GC via Tumor Immune Estimation Resource (TIMER). 28 genes were found to be closely related to the characteristics of gastric CSCs (GCSCs) associated with H. pylori infection. 13 genes were associated with lymph node metastasis in GC, which may lead to poor prognosis in patients.ConclusionThe characteristics of GCSCs were related to the interleukins signaling, cytokine signaling, Jak-STAT signaling pathway, which provides a new idea for screening therapeutic targets to inhibit the characteristics of GCSCs and a basis for the eradication of H. pylori and the prevention of GC.
Multiscale Graph Attention Neural Networks for Mapping Materials and Molecules beyond Short-Range Interatomic Correlations
Authors: Liu Yuanbin , Liu Xin , Cao Bingyang 
Published: November 2021

Abstract
Bringing advances of machine learning to chemical science is leading to a revolutionary change in the way of accelerating materials discovery and atomic-scale simulations. Currently, most successful machine learning schemes can be largely traced to the use of localized atomic environments in the structural representation of materials and molecules. However, this may undermine the reliability of machine learning models for mapping complex systems and describing long-range physical effects because of the lack of non-local correlations between atoms. To overcome such limitations, here we report a unified framework named the multiscale graph attention neural network to map materials and molecules into a generalizable and interpretable representation which combines local and non-local information of atomic environments from multiple scales. As an exemplary study, our model is applied to predict electronic structure properties of one class of technologically important reticular materials, i.e., metal-organic frameworks (MOFs) which have notable diversity in compositions and structures. Our model is trained on density functional theory calculated datasets and the results show that it achieves the state-of-the-art performance for such a challenging task. The clustering analysis further demonstrates that our model leads to a high-level identification of MOFs with spatial and chemical resolution, which would be capable of revealing new insights into complex systems and efficiently guiding the search for reticular materials with desired properties.
The Identification and Validation of EphA7 Hypermethylation, a Novel Biomarker, in Cervical Cancer
Authors: Zhang Wenfan , Cao Huiling , Zhao Jing , Yang Jinhao , Liang Zheng , Kang Xiaodong , Wang Rong 
Published: November 2021

Abstract
Background

Aberrant methylation of EphA7 has been reported in the process of carcinogenesis,but not including cervical cancer.Therefore,an integration study was performed to explore the association between EphA7 hypermethylation and cervical cancer and validate the potential value of EphA7 hypermethylation in the diagnosis of cervical cancer.
Results

Here, we performed an integration study to identify and validate the association between EphA7 methylation and cervical cancer. First, data on EphA7 methylation and expression in cervical cancer were extracted and analyzed via bioinformatics tools. The results showed that EphA7 promoter methylation levels were significantly increased in cervical cancer compared to normal tissues (P<0.001) and negatively correlated with EphA7 expression. Subsequently, these prediction results were confirmed in cell lines; moreover, CRISPR-based methylation perturbation tools (dCas9-Tet1/DNMT3a) were constructed to further demonstrate that DNA methylation participates in the regulation of EphA7 expression directly. Ultimately, the clinical value of EphA7 methylation in cervical cancer was validated in cervical tissues and Thinprep cytologic test (TCT) samples by methylation-specific PCR (MSP) and quantitative methylation-specific PCR (QMSP), respectively. Consistently, the methylation level and the positive rate of EphA7 gradually increased with severity from normal to cancer stages in TCT samples (P<0.01).
Conclusion

Above all, EphA7 presents hypermethylation in the cervical cancer,which is a potential biomarker in the diagnosis of cervical cancer.
Bone marrow mesenchymal stromal cells from acute myelogenous leukemiapatients exhibit aberrant gene expression profiles and secreted protein levels
Authors: Wu Jinxian , Liu Xiaoyan , Zhang Nan , Li Xinqi , Shen Hui , Liu Li , Huang Tingting , Xu Lihua , Zhou Fuling 
Published: November 2021

Abstract
Purpose: In hematopoietic malignancies, bone marrow mesenchymal stromal cells (BMSCs) are believed to promote tumor development through cellular and molecular abnormalities. However, there are several discrepancies among BMSCs in patients with acute myeloid leukemia (AML-MSCs) and healthy individuals (HD-MSCs) . Our aim was to analyze the differences in gene and protein levels between AML-MSCs and HD-MSCs, and to explore the role of AML-MSCs in the tumor microenvironment.Methods: We obtained MSCs from leukemia patients and healthy individuals and identified them by flow cytometry and differentiation. Transcriptome sequencing was performed on MSCs from leukemia patients and healthy individuals and label-free proteomics analysis was conducted on cultured supernatants of MSCs. Finally, we analyzed the results for bioinformatics analysis.Results: MSCs were preliminarily isolated and identified from AML patients and healthy controls. Through bioinformatics analysis, AML-MSCs and HD-MSCs showed great differences in Gene expression profiles and protein expression profiles of MSCs culture supernatants. Notably, inhibition of PI3K-Akt signal pathway can attenuate chemotherapy resistance of AML cells induced by MSC to AraC.Conclusions: Together, our findings suggest that Gene expression profiles and secreted protein levels of MSCs culture supernatants differed significantly between AML-MSCs and HD-MSCs, which should greatly facilitate the understanding of the role of MSCs in driving the development of acute myeloid leukemia and exploring new therapeutic strategies in future.
Research on the escape mechanism and influencing factors of harmful gas induced by blasting excavation in deep rock tunnel
Authors: Luo Yi , Gong Hangli , Qu Dengxing , Li Xinping , Hu Shaohua , Zhu Yingwei , Pu Qingsong 
Published: November 2021

Abstract
The escape of toxic and harmful gases is a common disaster effect in tunnel engineering. Frequent drilling and blasting excavation disturbances under high in-situ stress environment will inevitably lead to cumulative damage effect on surrounding rock, which will increase the permeability coefficient of surrounding rock, increase the risk of toxic and harmful gas escape, and seriously endanger construction safety. In this paper, based on real-time monitoring data of harmful gases during blasting and excavation of Yuelongmen Tunnel on Chengdu-Lanzhou Railway, this study summarized laws and distribution characteristics of harmful gas escape intensified by the blasting excavation, and the effectiveness of shotcreting and grouting for water blocking to inhibit gas escape is verified. Then, taking water-containing and gas-containing voids as carriers, considering the influence of different in-situ stress, explosion load and void parameters (including void pressure, void diameter and distance between void and tunnel), to carry out research on the escape mechanism of water-soluble (H 2 S) and insoluble (CH 4 ) toxic and harmful gases under the coupling effect of stress-seepage-damage. The relationship between the amount of harmful gas escaped and the damage degree of the surrounding rock of the tunnel is analyzed, and the functional relationship between it and the in-situ stress, explosion load and cave parameters is established. The results further demonstrate that the amount of escaped harmful gases, such as methane and H 2 S is closely related to lithology of surrounding rock, occurrence conditions of the deep rock mass, development degree of structural fractures and void parameters. The damage of surrounding rock caused by dynamic disturbance during blasting excavation is the main reason of aggravating harmful gas escape. The research results can provide a theoretical reference for preventing harmful gas from escaping in the similar engineering construction.
Identification of Tumor Specific Neoantigens and Their Implications in Dendritic Cell Immunotherapy Using Liquid Biopsy Results: Findings from an Observational Cohort Study
Authors: Myint Khin Zay Yar , Shimabuku Masanari , Horio Ruriko , Kaneda Munehisa , Shimizu Yoko , Taguchi Junichi 
Published: November 2021

Abstract
Liquid biopsies can be a rapid, cost-effective and noninvasive alternative to tumor biopsies for detecting genetic mutations in somatic tumors. Genetic profiling of liquid biopsies can also be used to identify novel antigens for targeted therapy, provide updated information on disease prognosis and evaluate treatment efficacy. In this study, we aimed to examine mutations that could be identified in liquid biopsy and their potential implications for personalized dendritic cell immunotherapy using neoantigens. We analyzed the genomic profiles of 99 blood samples from 85 patients with 22 different types of cancer using two commercially available liquid biopsy tests before the patients underwent standard cancer treatment and dendritic cell immunotherapy. Nonsynonymous mutations were detected in more than 90% of the samples, with an average frequency of 3.6 mutations per sample. The tumor mutations were specific to each patient, as approximately 94.7% of the mutations were so unique that there was almost no duplication among the patients. Clonal evolution was observed in two patients just before or after chemotherapy, radiotherapy and immunotherapy. These findings indicate that liquid biopsy can be a potential surrogate for neoantigen-based immunotherapy and the importance of tailoring neoantigen-based immunotherapy in accordance with the liquid biopsy result in each treatment stage.
Acyl-CoA Medium-Chain Synthetase-3 Promotes Chemosensitivity of Ovarian Cancer through the Inhibition of PI3K/AKT Signaling Pathway
Authors: An Yuanyuan , Duan Hua 
Published: November 2021

Abstract
Introduction: Dysregulation of fatty acid metabolism often occurs in tumor, which mainly constitutes of fatty acid synthesis and oxidation. In recent years, studies found that fatty acid metabolism participated in regulation of tumor immune microenvironment, which further influenced the progress of cancer. Thus, it is important to explore the key fatty acid metabolism-related molecules, which not only affects the prognosis of ovarian cancer, but also shows a close correlation with immune microenvironment of cancer.Methods: Database from TCGA was used to explore the fatty acid metabolism-related molecules, which correlated with the prognosis of ovarian cancer using univariate and multivariate cox proportional regression model. Nomogram was constructed to predict the prognostic probability based on ACSM3 and clinicopathological parameters. GDSC database was used to investigate the chemosensitivity of ovarian cancer cells. The correlation between ACSM3 and immune status of ovarian cancer was analyzed by TIMER and TISIDB online tools. In addition, CCK8 assay was used to investigate the chemosensitivity of ovarian cancer cells, real time-PCR and western blot were used to investigate the expression of chemoresistance-related genes.Results: ACSM3 worked as an independent favorable prognostic molecule through univariate and multivariate cox regression analysis. For the use in clinical, nomogram was constructed, and higher expression of ACSM3 showed better prognosis. We found that ACSM3 could regulate PI3K/AKT signaling, and GDSC database showed that PI3K/AKT inhibitor could promote the chemosensitivity of ovarian cancer cells. In addition, the expression of ACSM3 showed significantly correlated with the immune status of ovarian cancer. In vitro experiments showed that ACSM3 can promote the chemosensitivity of ovarian cancer cells by inhibiting PI3K/AKT signaling pathway.Conclusion: Our results showed that ACSM3 acted as a favorable prognostic-related biomarker for ovarian cancer, which could promote chemosensitivity of ovarian cancer through inhibiting PI3K/AKT signaling pathway. This might be due to participate in regulating immune status of ovarian cancer microenvironment.
Relationship between training database size and structural connectivity in artificial neural networks: Do specific local connections improve prediction accuracy?
Authors: Park Min Sik 
Published: November 2021

Abstract
Training of artificial neural networks is very expensive, as a large-size database is necessary. Moreover, it is usually difficult to find such large-size training databases. Hence, it will be interesting to design artificial neural networks that can be used for training with a small-size database, while maintaining a similar accuracy for prediction compared to fully connected neural networks. We studied neural networks with partial disconnections, additional bypass connections, and negative activation nodes, which are found in the neuronal systems of the human brain. By combining the fully connected neural network and the above three brain-like elements, we found that the modified neural network showed improved prediction accuracy of 13% compared to the fully connected one despite the small size of the training database. To analyze the improved neural network, the contribution of each node in the hidden layers affecting the total prediction accuracy of the neural networks was studied. We also found important local connections that improve the prediction accuracy, and discussed the design of a neural network with a small-size training database without reduction in prediction accuracy.
A Systematic Review and Meta-Analysis of HLA-Class-II Associations in Patients with IgG4 Autoimmunity
Authors: Panhuber Anja , Lamorte Giovanni , Bruno Veronica , Cetin Hakan , Bauer Wolfgang , Erber Astrid , Frommlet Florian , Koneczny Inga 
Published: November 2021

Abstract
Autoimmune diseases caused by pathogenic IgG4 subclass autoantibodies (IgG4-AID) include diseases like MuSK myasthenia gravis, pemphigus vulgaris or thrombotic thrombocytopenic purpura. Their etiology is still unknown. Polymorphisms in the human leukocyte antigen (HLA) gene locus, particularly in HLA-DRB1, are known genetic susceptibility factors for autoimmune diseases. We hypothesized a similar role for HLA polymorphisms in IgG4-AID and conducted a systematic review and meta-analysis with case-control studies on IgG4-AID based on MOOSE/ HuGENet guidelines. Genotype (G) and allele (A) frequencies of HLA-DQB1*05 (G: OR 3.8; 95% CI 2.44-5.9; p < 0.00001; A: OR 2.54; 95% CI 1.82-3.55; p < 0.00001) and HLA-DRB1*14 (G: OR 4.31; 95% CI 2.82-6.59; p < 0.00001; A: OR 4.78; 95% CI 3.52-6.49; p < 0.00001) and the HLA-DRB1*14-DQB1*05 haplotype (OR 6.3; 95% CI 3.28-12.09; p < 0.00001 / OR 4.98; 95% CI 3.8-6.53; p < 0.00001) were increased while HLA-DRB1*13 (G: OR 0.48; 95% CI 0.34-0.68; p < 0.0001; A: OR 0.46; 95% CI 0.34-0.62; p < 0.00001) was decreased in IgG4-AID patients. In conclusion, the HLA-DQB1*05, HLA-DRB1*14 alleles and the HLA-DQB1*05-DRB1*14 haplotype could be genetic risk factors that predispose for the production of pathogenic IgG4 autoantibodies and the HLA-DRB1*13 allele may protect from IgG4 autoimmunity.
The Effect of Simulated Seasonal Temperatures On Metarhizium Brunneum-Associated Mortality In Two Click Beetle Species, And A Degree-Day Infection Model
Authors: Kabaluk Todd , Ruau Sophie , Poon Anita 
Published: November 2021

Abstract
Wireworms (Coleoptera: Elateridae), the larvae of adult click beetles are subterranean and generalist crop pests that can be difficult to target. Targeting adult beetles, however, may be an effective method to lower wireworm populations. Metarhizium brunneum (Petch) kills click beetles but the mortality rate was expected to vary according to temperature. Using a thermal gradient plate to simulate daily oscillating temperatures for April, May, and June, the effectiveness of M. brunneum strains LRC112 and F52 in causing mortality to Agriotes obscurus (L.) and A. lineatus (L.) beetles was studied. Mortality was fastest in beetles exposed to June temperatures and slowest in those exposed to April temperatures, with differences among beetle species x M. brunneum strain combinations. Warmer temperatures resulted in more rapid mycelial outgrowth and conidiation in beetle cadavers, with only A. obscurus infected with M. brunneum LRC112 attaining near 100% conidiation. The number of degree days required to kill 50% of the beetles (LDD50) was least for A. obscurus infected with M. brunneum LRC112 (176) followed by A. obscurus x M. brunneum F52 (212), A. lineatus x M. brunneum LRC112 (215), and A. lineatus x M. brunneum F52 (292). Hypothetical calculations showed that M. brunneum exposure earlier in the season resulted in a longer LT50 but the earliest LT50 calendar date. Later M. brunneum exposure dates resulted in lower LT50’s, but later LT50 dates. This conceptual work demonstrates the importance of considering daily temperature oscillations, seasonality, and degree days in predicting the efficacy of entomopathogens to manage agricultural pests.
Primary Graviceptive System and Astasia: Case Report and Literature Review
Authors: Chen Ko-Ting , Huang Sheng-Yao , Chen Yi-Jye 
Published: November 2021

Abstract
Purpose of ReviewAstasia refers to the inability to maintain upright posture during standing, despite having full motor strength. However, the pathophysiology and neural pathways of astasia remains unclear.Recent FindingsWe analyzed 26, including ours, non-psychogenic astasia patients in English literature. Seventy-three percent of them were man, 73% were associated with other neurologic symptoms and 62% of reported lesions were at right side. Contralateral lateropulsion was very common followed by retropulsion while describing astasia. Infarction (54%) was the most commonly reported cause. Thalamus (65%) was the most commonly reported location. Infarction being the mostly likely to recover (mean:10.6 days), while lesions at brainstem had longer time to recover (mean: 61.6 days).SummaryThe underlying interrupted pathway may be the primary graviceptive system, which composed of at least five unilateral and contralateral projection fibers from vestibular nuclei to thalamic nuclei, and thalamo-cortical projections including subcortical white matter tracts and cortical areas.
The Influence of The Marine Bacillus Cereus Mc-1 Over Carbon Steel, Stainless Corrosion And Copper Coupons
Authors: Moreira-Filho Paulo , Figueiredo Paloma de Paula da Silva , Capão Artur , Procópio Luciano 
Published: November 2021

Abstract
The present study evaluated the influence of the marine bacteria Bacillus cereus Mc-1 on the corrosion of 1020 carbon steel, 316L stainless steel, and copper alloy. The Mc-1 strain was grown in a modified ammoniacal citrate culture medium (CFA.ico-), CFA.ico- with sodium nitrate supplementation (NO3-), and CFA.ico- with sodium chloride supplementation (NaCl). The and mass loss and corrosion rate were evaluated after the periods of seven, 15, and 30 days. The results showed that in CFA.ico- and CFA.ico- medium added NO3- the corrosion rates of carbon steel and copper alloy were high when compared to the control. Whereas the medium was supplemented with NaCl, despite the rates being above the averages of the control system, they were considerably below the previous results. In general, the corrosion rates induced by Mc-1 on 316L coupons were below the results compared to carbon steel and copper alloy. When analyzing the corrosion rate measurements, regardless of the culture medium, the corrosion levels decreased consistently after 15 days, being below the levels evaluated after seven days of the experiment. Our analyzes suggest that B. cereus Mc-1 has different influences on corrosion in different metals and environmental conditions, such as the presence of NO3- and NaCl. These results can help to better understand the influence of this bacteria genus on the corrosion of metals in marine environments.
Performance Investigation of Electrochemical Assisted HClO/Fe2+ Process For The Treatment of Landfill Leachate
Authors: Ye Zhihong , Miao Fei , Zhang Hui 
Published: November 2021

Abstract
The feasibility of removal of COD and ammonia nitrogen (NH4+-N) from landfill leachate by electrochemical assisted HClO/Fe2+ process is demonstrated for the first time. The performance of active chlorine generation at the anode was evaluated in Na2SO4/NaCl media, and a higher amount of active chlorine was produced at greater chloride concentration and higher current density. The probe experiments confirmed the coexistence of hydroxyl radical (·OH) and Fe(IV)-oxo complex (FeIVO2+) in the HClO/Fe2+ system. The influence of initial pH, Fe2+ concentration and applied current density on COD and NH4+-N abatement was elaborately investigated. The optimum pH was found to be 3.0, and the proper increase in Fe2+ dosage and current density resulted in higher COD removal due to the accelerated accumulation of ·OH and FeIVO2+ in the bulk liquid phase. Whereas, the NH4+-N oxidation was significantly affected by the applied current density because of the effective active chlorine generation at high current, but was nearly independent of Fe2+ concentration. The reaction mechanism of electrochemical assisted HClO/Fe2+ treatment of landfill leachate was finally proposed. The powerful ·OH and FeIVO2+, in concomitance with active chlorine and M(·OH) were responsible for COD abatement and active chlorine played a key role in NH4+-N oxidation. The proposed electrochemical assisted HClO/Fe2+ process is a promising alternative for the treatment of refractory landfill leachate.