bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vascular Calcification in Different Arterial Beds in Ex Vivo Ring Culture and in Vivo Rat Model
Authors: Muyor Karen , Laget Jonas , Cortijo Irene , Duranton Flore , Jover Bernard , Argilés Àngel , Gayrard Nathalie 
Published: March 2022

Abstract
Background.Vascular calcification is a risk factor for cardiovascular and kidney diseases. Medial calcification may differently affect the arterial tree depending on vessel location and smooth muscle injury. Objective.The aim was to map the anatomical distribution of vascular calcifications on different arteries and artery locations, in cultured artery rings (ex vivo) and in a rat model of elastocalcinosis (in vivo).Design and Results. Vascular calcification was assessed histologically (von Kossa staining of the media) and by calcium content measurement. Arteries of different sizes were harvested from untreated rats for ring culture and from the vitamin D3-nicotine (VDN) rat model for direct observation. When cultured in pro-calcifying conditions, thoracic aorta exhibited similar calcification from the arch to the diaphragm. Calcification increased in abdominal aorta along with the reduction in cross sectional area. Carotid and renal arteries exhibited similar ex vivo calcification. In VDN rats, calcification was greater in carotid artery than in aorta, and was accompanied by fibrosis and apoptosis. Ex vivo, calcification was increased by the induction of lesions on arteries.Conclusions.Along the vascular tree, calcification of the arterial wall increases with the narrowing of vessels in ex vivo ring culture and in vivo. The observed differences represent local susceptibility of the vessels to the calcifying processes.
Qingfei Tongluo formula mitigates Mycoplasma pneumoniae infection via PERK signaling pathway
Authors: Liu Xiuxiu , Wang Mingjing , Kan Qianna , Lin Yan , Jiang Zhiyan 
Published: March 2022

Abstract
Introduction: Mycoplasma pneumoniae pneumonia (MPP) is usually found in school-aged children and seems to relapse easily because of the resistance to antibiotics. Qingfei Tongluo formula (QTF) is clinical used Traditional Chinese Medicine to treat MPP. Our previous study demonstrated that QTF exhibited ameliorative effects on experimental MPP mice model. In this study, we tried to further explore the function and underlying mechanism of QTF in MPP. Methods: MP was applied to infect A549 cells and BALB/c mice to mimic MPP in vitro and in vivo. Cytokine release and reactive oxygen species (ROS) production were analyzed using Enzyme-linked immunosorbent assay (ELISA) assay and flow cytometry. Western blot analysis was used to detect the protein involved in endoplasmic reticulum (ER) stress. Results: We found that MP infection enhanced cytokine release and ER stress in vitro and in vivo, and these effects could be alleviated by QTF. Moreover, protein kinase RNA-like endoplasmic reticulum kinase (PERK) knockdown alleviated MP infection-induced cytokine release, ROS production, and ER stress in A549 cells. While PERK overexpression exhibited the opposite effects. Conclusions: QTF alleviated MP infection-induced cytokine release, ROS production, and ER stress via inhibiting PERK signaling pathway.
C2orf40 inhibits Metastasis and Regulates Chemo-resistance and Radio-resistance of Nasopharyngeal Carcinoma Cells by Influencing Cell Cycle and Activating the PI3K/AKT/mTOR Signaling Pathway
Authors: Xie Zuozhong , Li Wei , Ai Jingang , Xie Jun , Zhang Xiaowei 
Published: March 2022

Abstract
Background：Nasopharyngeal carcinoma (NPC) is a malignant tumor of epithelial origin in head and neck with high incidence rate in Southern China. C2orf40 has been identified as a tumor suppressor gene in many cancers. However, the roles of C2orf40 in nasopharyngeal carcinoma has not been studied.Methods：In this study, a bioinformatics analysis was performed to identify the differentially expressed genes in NPC. The quantitative methylation levels was detected using pyrosequencing. qRT-PCR, western blotting, immunohistochemistry and immunofluorescence were used to detect the expression level of related RNA and proteins. Cell proliferation was detected using CCK-8 assay, and colony formation capability was detected using colony formation.assays. Cell migration and invasion were analyzed using wound-healing and Transwell assays, respectively. The apoptosis level of cells was assessed using TUNEL staining. Endogenous DNA damage and repair were assessed by the comet assay . Cell cycle analyses carried out by flow cytometry. Finally, We used a xenograft nude mouse to verify the roles of C2orf40 in chemoresistance and radioresistance in vivo.Results：We found that the C2orf40 expression was significantly downregulated in NPC tissues and inversely associated with a poor prognosis. In vivo and in vitro functional experiments confirmed that overexpression of C2orf40 significantly inhibited the migration and invasion of NPC cells, and promoted their sensitivity to radiotherapy and chemotherapy of NPC cells. Mechanically, the expression level of C2orf40 was negatively correlated with the expression levels of CCNE1 and CDK1. Overexpression of C2orf40 induced cell cycle arrest of NPC cells at G/M phase. In addition, C2orf40 can down-regulated the expression levels of homologous recombination-related proteins (BRCA1, BRCA2, RAD51, and CDC25A) and inhibited the activity of the PI3K/AKT/mTOR signaling pathway.Conclusion：The results clarified the biological functions and mechanisms of C2orf40, as a tumor suppressor gene, in NPC, and provided a potential molecular target for improving the sensitivity of NPC to radiotherapy and chemotherapy.
Dynamics of invariant solutions of mKdV-ZK arising in a homogeneous magnetised plasma
Authors: Kumar Raj , Verma Ravi Shankar 
Published: March 2022

Abstract
Classical Lie symmetry analysis is proposed to get similarity reductions of a nonlinear (3+1)-modified Korteweg de Vries-Zakharov-Kuznetsov equation. The equation is often used to control the type of weakly nonlinear ion-acoustic waves in a homogeneous magnetised electron-positron plasma. In a magnetised plasma including some hot and cold ions, such waves exist. Some more general types of analytical solutions to the equation are derived in this article. Through their animation profiles, the dynamics of electrostatic potential indicate elastic single soliton to multi solitons, elastic multi solitons, kink to stationary, bell-shaped to asymptotic. The solutions are confirmed by comparing the existing results.
Bioinformatics analysis of potential core genes for pilocytic astrocytoma
Authors: zhang siqi , Zeng Hongwu 
Published: March 2022

Abstract
Background
Pilocytic astrocytoma (PA) is the most common primary brain tumor of childhood. Due to its complicated pathogenesis, the choice and timing of adjuvant therapy after tumor treatment are controversial. This study explored and identified potential biomarkers for PA.
Materials and methods
To identify potential core genes in PA that may provide new therapeutic insights, we analyzed three gene chips (GSE50161, GSE66354, GSE86574) screened from the GEO database. Differentially expressed genes (DEG) from the tissues of PA and normal brain were screened using GEO2R. To determine the functional annotation and pathway of DEG, Gene Ontology (GO) and KEGG pathway enrichment analysis were conducted using DAVID database. Protein interactions of DEG were visualized using PPI network on Cytoscape software. Next, 10 Hub nodes were screened from the differentially expressed network using DMNC algorithm on CytoHubba software and subsequently identified as Hub genes. Finally, the relationship between Hub genes and the prognosis of PA patients was described using GEPIA2 survival analysis web tool.
Results
A total of 37 up-regulated and 144 down-regulated genes were identified through microarray analysis. Amongst the 10 Hub genes selected, SLC12A5 and RAB3C are associated with poor prognosis in a Pilocytic astrocytoma based on the survival analysis.
Conclusion
Our study suggests that low expression of SLC12A5 and RAB3C are associated with poor prognosis in PA patients, whether they can be used as a new therapeutic target for PA.
Bayesian Updating of Seismic Fragility Curves Through Experimental Tests
Authors: Tekeste Gidewon Goitom , Correia António A. , Costa Aníbal G. 
Published: March 2022

Abstract
Fragility curves, commonly derived using analytical methods, are important ingredients of seismic risk analysis of structures in the framework of performance-based earthquake engineering. Hence, the accurate estimation of realistic fragility functions is a decisive step in a reliable risk assessment. This paper proposes a Bayesian updating procedure applied to analytical fragility curves of reinforced concrete (RC) structures based on data from experimental tests, namely shaking table tests. The latter are commonly performed by progressively increasing the intensity of the input motion applied to the same test specimen. In this regard, the maximal benefit from the output of a shaking table test is sought here, aiming to convert n sequential stages of a shaking table test of a single virgin specimen into n equivalent shaking table tests that are performed on n virgin specimens. This is performed by modifying the intensity of the input motion applied during the stage-wise testing based on a damage index coefficient. The parametric studies performed to validate this objective reveal that the approach is more suitable for simple structures compared to large or complex structures. The ATC-58 and Markov Chain Monte Carlo (MCMC) approaches for Bayesian updating of fragility curves are also closely examined and compared. The proposed Bayesian updating is applied to a RC structure, where fragility curves that are derived from incremental dynamic analysis are updated using shaking table results. The updating is examined considering three damage state models, namely HAZUS, homogenized RC and strain-based damages states. This work also highlights the pitfalls of using a limited sample of experimental test data for updating less reliable priors. Besides, the MCMC-based approach is shown to be more robust in the presence of complex analytical fragilities than the ATC-58 approach.
Variations in the poly-histidine repeat motif of HOXA1 predispose individuals to bicuspid aortic valve
Authors: Odelin Gaëlle , Faucherre Adèle , Marchese Damien , Pinard Amelie , Faure Emilie , Herbane Marine , Théron Alexis , Avierinos Jean-François , Jopling Chris , Collod-Béroud Gwenaelle , Rezsohazy René , Zaffran Stephane 
Published: March 2022

Abstract
Bicuspid aortic valve (BAV) is the most common cardiovascular malformation (0.5–1.2% of the population) and is often associated with premature aortic valve stenosis or insufficiency, aortic aneurysm and other congenital cardiac heart defects. Although highly heritable, few causal mutations have been identified in BAV patients. Here, we report the association of novel variants in the transcription factor HOXA1 with BAV in humans. Targeted sequencing of HOXA1 in a cohort of 333 BAV patients identified rare indel variants in the homopolymeric histidine tract of HOXA1. In vitro analysis revealed that disruption of the histidine repeat motif causes a significant reduction in the half-life of the protein, and that these variants are associated with a defective transcriptional activity of the HOXA1 protein. Targeting the zebrafish hoxa1a ortholog in vivo resulted in aortic valve defects that could be rescued by expressing the wild-type human HOXA1. Furthermore, expression of HOXA1 Histidine variants in zebrafish also impacted aortic valve development indicating a dominant negative effect of these mutated proteins. Lastly, homozygous knockout mice for Hoxa1 develop a BAV phenotype, which is associated with a very small, rudimentary non-coronary leaflet. Genetic lineage analysis indicates that this defect is caused by a strong reduction of mesenchymal cells in the intercalated cushion due to a failure of neural crest cell migration toward the heart which is consistent with our transcriptomic analysis showing a down-regulation of premigratory and migratory neural crest markers in Hoxa1−/− compared with control embryos. Together, these findings indicate that variants causing HOXA1 dysfunction play a significant role in the genetic cause of BAV in humans.
Impact of KRAS mutations on clinical outcomes of patients with advanced non-squamous non-small cell lung cancer receiving anti PD1/PDL1 therapy.
Authors: Veccia Antonello , Dipasquale Mariachiara , Kinspergher Stefania , Monteverdi Sara , Girlando Salvatore , Barbareschi Mattia , Caffo Orazio 
Published: March 2022

Abstract
PurposeTo evaluate the impact of KRAS mutations on response and survival outcomes in mutated vs wild type KRAS advanced non squamous non small cell lung cancer patients treated with immune checkpoint inhibitors alone or in combination with chemotherapy. Patients and methodsWe retrospectively identified 119 patients, most of which (58%) were wild type. For each patient we evaluated overall survival (OS), progression free survival (PFS) and disease control rate (DCR). An exploratory analysis was performed among mutated patients to investigate the impact of specific KRAS mutations on response and survival outcomes. ResultsAfter a median follow-up of 10.3 months, the median OS was 14.9 months (95% CI 7.6 – 22.7) in wild type KRAS patients vs 14.7 months (95% CI 8.0 – 19.5) in mutated KRAS patients; p-value=0.529. No differences were also detected between two groups in terms of PFS and DCR. Patients with pG12C KRAS mutation reported survival and response outcomes that were not statistically different from those of patients with other KRAS mutations. ConclusionOur data confirmed that KRAS mutational status is not associated with survival and response outcomes in advanced non squamous NSCLC patients treated with immunotherapy alone or combined to chemotherapy.
Influence of Age on Long-term Net Survival Benefit for Early-stage MALT Lymphomas Treated With Radiotherapy: a SEER Database Analysis (2000-2015)
Authors: Wu Yunpeng , Liu Xin , Imber Brandon S. , Zhong Qiu-Zi , Yang Yong , Wu Tao , Chen Si-Ye , Chen Bo , Song Yong-Wen , Fang Hui , Jin Jing , Liu Yue-Ping , Jing Hao , Tang Yuan , Li Ning , Lu Ning-Ning , Wang Shu-Lian , Chen Fan , Yin Lin , Zhang Xi-Mei , Zhu Jingru , Tsang Richard , Yahalom Joachim , Hu Chen , Men Kuo , Deng Min , Xia Changfa , Li Ye-Xiong , Qi Shu-Nan 
Published: March 2022

Abstract
BACKGROUND Given the lower incidence of lymphoma-related death but higher background mortality in patients with early-stage mucosa-associated lymphoid tissue (MALT) lymphoma, it is critically important to examine how age affects a treatment’s survival benefit. METHODS 9,467 patients with early-stage MALT lymphoma in the Surveillance, Epidemiology, and End Results (SEER) database treated between 2000-2015 were extracted and analyzed. Primary therapy was classified as radiotherapy (n = 3,407), chemotherapy (n = 1,294), and other/unknown treatments including observation (n = 4,766). Inverse probability of treatment weighting (IPTW) was conducted to balance baseline characteristics between groups. Relative survival (RS), standardized mortality ratio (SMR), and transformed Cox regression were conducted to compare survival differences between treatment modalities by controlling for the background mortality. Radiotherapy–age interaction was examined.RESULTS Across age-groups, early-stage MALT lymphoma patients were at lower risk of lymphoma-related death than death due to other causes. The 10-year overall survival (OS, 73.8%) and RS (96.6%) rates were significantly higher, and the SMR (1.14) significantly lower, with radiotherapy than with chemotherapy (OS, 61.7%; RS, 86.4%; SMR, 1.54; P < 0.001) or other/unknown treatments (OS, 61.1%; RS, 87.2%; SMR, 1.41; P < 0.001). By multivariable analysis and IPTW, radiotherapy remained an independent predictor of better RS (HR 0.81, 95%CI, 0.73-0.89; P < 0.001). A significant interaction between age and radiotherapy was identified for both RS (Pinteraction = 0.016) and OS (Pinteraction = 0.024), indicating greater benefit in young adults.CONCLUSION Radiotherapy can provide significant survival benefit in early-stage MALT lymphoma, especially in young adults.
lncRNA C9orf139 can regulate the progression of esophageal squamous carcinoma by mediating the miR-661/HDAC11 axis
Authors: Yang Xiaojie , Shen Zhimin , Zhang Weiguang , Lin Yukang , Li Liming , Chai Tianci , Zhang Peipei , Kang Mingqiang , Lin Jiangbo 
Published: March 2022

Abstract
Background: Increasing evidence indicated that long non-coding RNAs (lncRNAs) play multiple functions in the development of cancer and function as indicator of diagnosis and prognosis. This study was to investigate the roles lncRNA C9ORF139 in the progression of esophageal squamous carcinoma (ESCC). Methods: RT-qPCR analysis was employed to evaluate mRNA expressions. Western blot was performed to measure relevant protein level. Colony formation and CCK-8 assays were conducted to certify proliferative ability. Cell apoptosis and migration were measured using Annexin V-FITC and Transwell assay respectively. The underlying mechanism of lncRNA C9orf139 was surveyed by luciferase activity reporter assay and further verified using tumor xenograft in vivo. Protein-protein interaction network was built using STRING database.Results: C9orf139 was highly expressed in ESCC and significantly suppressed cell proliferation, promoted apoptosis and inhibited migration and invasion. C9orf139 could negatively regulate miR-661 expression. While HDAC11 expression was negatively regulated by miR-661. C9orf139/miR-661/HDAC11 axis was further involved in regulating the expression of NF-κB signaling pathway. The association between the C9orf139 knockdown and the reduced tumor growth and size was observed in vivo study. Conclusion: C9orf139 is highly expressed in ESCC, qualified to be used as a potential diagnostic and prognostic marker for pancreatic cancer. Its promotion of ESCC progression is achieved by mediating the miR-661/HDAC11 axis.
Building capacity in quantitative research and data storytelling to enhance knowledge translation: a training curriculum for peer researchers
Authors: Tian Jason M. Lo Hog , Watson James R. , Deyman Megan , Tran Billy , Kerber Paul , Nanami Kajiko , Norris Deborah , Samson Kim , Cioppa Lynne , Murphy Michael , Mcgee A. , Ajiboye Monisola , Chambers Lori A. , Worthington Catherine , Rourke Sean B. 
Published: March 2022

Abstract
Background
Many community-based HIV research studies incorporate principles of greater involvement and meaningful engagement of people living with HIV (GIPA/MEPA) by training people with HIV as peer researchers. Unfortunately, there are still some aspects of research (e.g., quantitative data analysis and interpretation) where many projects fall short in realizing GIPA/MEPA principles. To address these gaps, we developed an eight-week training course that aimed to build capacity around the understanding and interpretation of quantitative data and incorporating lived experience to increase the impact of the knowledge transfer and exchange phase of a study.
Methods
Peer researchers (n = 8) participated from British Columbia, Alberta, and Ontario and lessons learned from the training were implemented throughout the dissemination of research findings from the People Living with HIV Stigma Index study. This paper presents the curriculum and main training components, course evaluation results, and challenges and lessons learned. The manuscript was created in collaboration with and includes the perspectives of both the peer researchers involved in the training, as well the course facilitators.
Results
Throughout the course, peer researchers’ self-assessed knowledge and understanding of quantitative research and data storytelling improved and, through interactive activities and practice, they gained the confidence to deliver a full research presentation. This improved their understanding of research findings, which was beneficial for discussing results with community partners and study participants. The peer researchers also agreed that learning about integrating lived experience with quantitative data has helped them to make research findings more relatable and convey key messages in a more meaningful way.
Conclusions
Our training curriculum provides a template for research teams to build capacity in areas of research where peer researchers and community members are less often engaged. In doing so, we continue to uphold the principles of GIPA/MEPA and enhance the translation of research knowledge in communities most greatly affected.
AMPK/ULK1 and JNK/p38/ERK Regulate Serotonin (5‐hydroxytryptamine) -induced Autophagy in Hepatoma Cells
Authors: Wang Chao , Wang Yang , Li Shulin , Cui Xinhua , Song Yuli , Tang Xudong , Xu Hongyue , Shi Jin yang ,   Yunxiao Ma1, Zhou Hong , An Yanan , Shen Keshu , Yu Lu 
Published: March 2022

Abstract

It has been reported that serotonin (5-hydroxytryptamine, 5‐HT), autophagy and ROS are involved in the pathogenesis of cancer, here, we used HepG2 and Hep3B cells as model cells to investigate whether 5-HT could induce hepatoma cells autophagy and its possible mechanisms involved in ROS. First, the immunofluorescence results showed that 5-HT could induce the production of LC3 in hepatoma cells, and western blot results showed that 5-HT induced a complete autophagy process in hepatoma cells. Secondly, our results showed that 5-HT induced autophagy through the AMPK/ULK1 instead of the mTOR-dependent pathway in hepatoma cells. Thirdly, 5-HT also could stimulate autophagy through JNK/p38/ERK pathway activation in hepatoma cells. Finally, the DHR 123 assay showed that 5-HT could induce ROS production in hepatoma cells and the ROS scavenger NAC significantly inhibited the 5-HT-induced LC3 in hepatoma cells, this showed that ROS was necessary for 5-HT-induced autophagy in hepatoma cells. Therefore, we demonstrated that 5-HT induced autophagy in hepatoma cells, which was mediated by respective AMPK/ULK1 and JNK/p38/ERK pathways not by inhibiting phosphorylation of the mTOR pathway, and ROS participated in the occurrence of 5-HT-induced autophagy. This provided a theoretical basis for the important effects of 5-HT in the treatment or prevention of cancer, and provided new ideas for the development of new anti-cancer drugs targeting 5-HT receptors.
Tunable Plasmonic Band-Pass Filter Using Five Circular Ring Resonators.
Authors: HamidAbbasi  
Published: March 2022

Abstract
This paper investigates and builds a highly sensitive refractive index sensor based on the resonance system in plasmonic structure. The proposed sensor structure consists of two waveguides and five loops. The results show that the resonance wavelength changes significantly with increasing refractive index, which proves that this method is suitable for understanding and analyzing the behavior of resonance wavelength and refractive index. In this research, we examine the characteristics of measurement such as sensitivity and quality factor and competency form (FOM). Compared to replicon sensors based on a similar structure, this proposed sensor can accept a more flexible amplitude of wavelength and a wider range of refractive index. As a result of this approach, it can be used in areas such as biochemical and medical analysis.