bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cuproptosis related genes associated with Jab1 shapes tumor microenvironment and pharmacological profile in nasopharyngeal carcinoma
Authors: Wang Liping , Wang Dujuan , Yang Liu , Zeng Xiaojiao , Zhang Qian , Liu Guohong , Pan Yunbao 
Published: December 2022

BackgroundNasopharyngeal carcinoma (NPC) is the most common subcategory of head and neck squamous cell carcinoma (HNSCC). This study focused on the roles of cuproptosis related genes and Jab1 in the tumor microenvironment of NPC and HNSCC.MethodsDifferential expression analysis of Jab1 and cuproptosis related genes in tumor cell enriched region (PanCK-expressing) and immune cell enriched region (CD45-expressing) of NPC microenvironment were performed by packages of R software. Survival analysis was performed using the survival and survminer packages. Corrplot package was used for correlation analysis. ConsensusClusterPlus package was used for cluster clustering among different regions of NPC, and functional enrichment analysis was performed using GSVA, GSEABase, clusterProfiler, org.Hs.eg.db and enrichplot packages. The pRRophetic package was used to predict drug sensitivity in NPC and HNSCC.ResultsRelationships exist between cuproptosis related genes and Jab1 in the NPC microenvironment. The expression of cuproptosis related genes and Jab1 differed between tumor cell enriched region and immune cell enriched region. AKT inhibitor VIII, Doxorubicin, Bleomycin and Etoposide showed higher sensitivity to tumor cell than immune cell. In the high Jab1 group, higher expression of ATP7A, DBT, DLD and LIAS were associated with better prognosis of HNSCC patients. In contrast, in the low Jab1 group, higher expression of these genes is associated with worse prognosis of HNSCC patients.ConclusionsPrognostic cuproptosis related genes and Jab1 provided a basis for targeted therapy and drug development.
Acoustic sampling of Antarctic krill with simulated underwater buoyancy gliders: Does the sawtooth dive pattern work?
Authors: Kinzey Douglas , Cossio Anthony M. , Reiss Christian S. , Watters George M. 
Published: December 2022

Autonomous underwater gliders may be viable adjuncts to or in some cases replacements for ship-based oceanographic sampling. Gliders and ships acoustically sample the water column differently, with ships sampling all depths simultaneously in a single vertical pulse and gliders sampling shorter vertical segments of the water column in an up and down, sawtooth pattern. We simulated gliders following this flight pattern to sample the densities at depth of Antarctic krill (Euphausia superba), a patchily-distributed crustacean that is targeted by an international fishery. Krill densities from ship-based surveys conducted between 2001 to 2011 were treated as the “true” population densities sampled by the simulated gliders. Depth-integrated densities estimated from the glider sampling were compared to the population densities for each year. Coverage probabilities (the proportion of population means within a standard deviation of the glider sample means) for gliders diving to 150 m were near 100% in most years, better than the nominal 68%. Gliders diving to a maximum depth of 150 m estimated the annual population means better than gliders diving deeper because shallow dives provided more samples for a given length of trackline. Modeling the zero and non-zero data as separate distributions (the delta approach), an alternative to the lognormal CV approach used in this study, resulted in less accurate estimates of krill population densities. These results suggest that the sawtooth flight pattern of gliders can produce density estimates of krill comparable to the annual time series of density estimates from ship-based surveys. Gliders may also be useful to survey other patchily-distributed pelagic organisms.
Graphene based microstrip patch antenna on photonic crystal substrate for 5G application
Authors: Kumar Chandan , Raghuwanshi Sanjeev Kumar , Kumar Vikram 
Published: December 2022

One of the strongest and thinnest substances known to exist is graphene. It can be efficiently used for antenna fabrication and significant benefits can be analyzed such as size miniaturization, gain and return loss enhancement, flexibility and increase in bandwidth, etc. In this paper, a graphene patch antenna has been designed and fabricated for 5G applications at 28.3 GHz. Different 5G frequency allocation throughout the world is shown in tabular form. Photonic crystal substrate is used to reduce surface wave loss which in turn, increases the radiation efficiency of the antenna. The ground plane is made up of copper, treated as a Perfect Electric Conductor Several unique properties of graphene are analyzed and shown. Then, a thin graphene sheet is used as a patch and an antenna is designed and fabricated. The patch has dimensions of 3.4 mm by 2.38 mm. The simulated return loss is maximum at −33.69 dB at 28.3 GHz, whereas for the measured design it is −26.31 dB at 28.04 GHz. It is observed that graphene can be a good alternative to existing conductors, especially at higher frequencies. The proposed antenna is designed and simulated using HFSS software.
Spatial patterns of dominant bacterial community components and their influential factors in the southern Qinling Mountains, China
Authors: Zhao Yonghua , Luo Manya , Zhou Yujie , Jia Xia , Kang Shuaizhi , Yang Shuyuan , Mu Qi 
Published: December 2022

IntroductionSoil bacteria not only maintain the biodiversity of forest ecosystems but also affect soil nutrient cycling and ecosystem function. Nonetheless, the spatial pattern and patchy distribution of dominant bacterial community components in soil are still rarely explored.MethodThe spatial pattern and distribution of the dominant bacterial community components and their influential factors were investigated using traditional statistics, geostatistics, and kriging spatial interpolation methods in the Huoditang region of the Qinling Mountains, China.ResultsThe dominant bacterial phyla were Proteobacteria, Acidobacteria, Chloroflexi, Rokubacteria, Actinobacteria, and Verrucomicrobia in this region. Among the bacterial phyla, Proteobacteria occupied an area of 2.56 km2(the greatest) in the highest patch category, followed by Planctomycetes. Moreover, among the lowest patch category, Firmicutes occupied the lowest area (11.93 km2). The results of kriging maps showed that the dominant bacterial group presented “peak,” “bimodal,” and “multimodal” distributions in Huoditang. Proteobacteria, Acidobacteria, Chloroflexi, Gemmatimonadetes, Nitrospirae, and ASV (amplicon sequence variants) had significant spatial autocorrelation (&lt; 0.68 km). Variance partitioning analysis confirmed that soil nutrients (36.5%) were the significant driving factors shaping the bacterial community structure, followed by environmental factors (28.2%) and topographic factors (7.8%). Furthermore, pH (9.1%), soil organic carbon (SOC, 6.6%), available phosphorus (AP, 4.7%), and elevation (3.9%) were the most important driving factors for the spatial distribution of bacterial community groups in the Huoditang Forest of the Qinling Mountains. The findings provide a new perspective for studying the spatial distribution characteristics and driving factors of dominant soil bacterial community components in subtropical forest ecosystems.
A positive feedback loop of the TAZ/β-catenin axis promotes Helicobacter pylori-associated gastric carcinogenesis
Authors: Xu Xinbo , Shu Chunxi , Wu Xidong , Ouyang Yaobin , Cheng Hong , Zhou Yanan , Wang Huan , He Cong , Xie Chuan , He Xingxing , Hong Junbo , Lu Nonghua , Ge Zhongming , Zhu Yin , Li Nianshuang 
Published: December 2022

BackgroundHelicobacter pylori infection is the strongest known risk factor for gastric cancer. The Hippo signaling pathway controls organ size and maintains tissue homeostasis by coordinately regulating cell growth and proliferation. Here, we demonstrate the interactive role of TAZ, the transcriptional coactivator of the Hippo pathway, and beta-catenin in promoting the pathogenesis of H. pylori infection.MethodsTAZ expression was evaluated in human gastric tissues and H. pylori-infected insulin–gastrin (INS-GAS) mice. Western blot, immunofluorescence, immunohistochemistry, and RT–PCR assays were performed. Coimmunoprecipitation was performed to examine the interaction between TAZ and β-catenin. TAZ and β-catenin were silenced using small interfering RNAs. HA-β-catenin and Flag-TAZ were constructed.ResultsIncreased TAZ was noted in human gastric cancer tissues compared to chronic gastritis tissues and in H. pylori-positive gastritis tissues compared to H. pylori-negative gastritis tissues. In addition, H. pylori infection induced TAZ expression and nuclear accumulation in the gastric tissue of INS-GAS mice and cultured gastric epithelial cells, which was dependent on the virulence factor CagA. Moreover, TAZ or β-catenin knockdown significantly suppressed H. pylori infection-induced cell growth, survival, and invasion. Furthermore, the interactive regulation of TAZ and β-catenin activation was revealed. Finally, β-catenin was required for H. pylori-induced TAZ activation.ConclusionThese findings suggest the existence of a positive feedback loop of activation between TAZ and β-catenin that could play an important role in CagA+ H. pylori infection-induced gastric carcinogenesis. TAZ inhibition represents a potential target for the prevention of H. pylori infection-associated gastric cancer.
Integration of network pharmacology and molecular docking to explore the molecular mechanism of Cordycepin in the treatment of Alzheimer’s disease
Authors: Ma Xiaoying , Zhao Ying , Yang Tao , Gong Na , Chen Xun , Liu Guoli , Xiao Jun 
Published: December 2022

BackgroundCordycepin is a nucleoside adenosine analog and an active ingredient isolated from the liquid fermentation of Cordyceps. This study sought to explore the mechanism underlying the therapeutic effect of Cordycepin against Alzheimer’s disease using network pharmacology and molecular docking technology.MethodsTCMSP, SYMMAP, CTD, Super-pred, SEA, GeneCards, DisGeNET database, and STRING platform were used to screen and construct the target and protein interaction network of Cordycepin for Alzheimer’s disease. The results of Gene Ontology annotation and KEGG pathway enrichment analysis were obtained based on the DAVID database. The Omicshare database was also applied in GO and KEGG pathway enrichment analysis of the key targets. The protein–protein interaction network was constructed using the STRING database, and the potential effective targets for AD were screened based on the degree values. The correlation between the potential targets of Cordycepin in the treatment of AD and APP, MAPT, and PSEN2 was analyzed using (GEPIA) databases. We obtained potential targets related to aging using the Aging Altas database. Molecular docking analysis was performed by AutoDock Vina and Pymol software. Finally, we validated the significant therapeutic targets in the Gene Expression Omnibus (GEO) database.ResultsA total of 74 potential targets of Cordycepin for treating Alzheimer’s disease were identified. The potential targets of Cordycepin for the treatment of AD mainly focused on Lipid and atherosclerosis (hsa05417), Platinum drug resistance (hsa01524), Apoptosis (hsa04210), and Pathways in cancer (hsa05200). Our findings suggest that the therapeutic effect of Cordycepin on AD is primarily associated with these biological processes. We obtained 12 potential therapeutic targets for AD using the degree value in Cytoscape. Interestingly, AKT1, MAPK8, BCL2L1, FOXO3, and CTNNB1 were not only significantly associated with pathogenic genes (APP, MAPT, and PSEN2) but also with longevity in Alzheimer’s Disease. Thus we speculated that the five target genes were potential core targets mediating the therapeutic effect of Cordycepin against AD. Moreover, molecular docking results analysis showed good binding affinity between Cordycepin and the five core targets. Overall, MAPK8, FOXO3 and CTNNB1 may have significant clinical and treatment implications.ConclusionNetwork pharmacology demonstrated that Cordycepin exerts a therapeutic effect against Alzheimer’s disease via multiple targets and signaling pathways and has huge prospects for application in treating neurodegenerative diseases.
Preservation of EEG spectral power features during simultaneous EEG-fMRI
Authors: Gallego-Rudolf Jonathan , Corsi-Cabrera María , Concha Luis , Ricardo-Garcell Josefina , Pasaye-Alcaraz Erick 
Published: December 2022

IntroductionElectroencephalographic (EEG) data quality is severely compromised when recorded inside the magnetic resonance (MR) environment. Here we characterized the impact of the ballistocardiographic (BCG) artifact on resting-state EEG spectral properties and compared the effectiveness of seven common BCG correction methods to preserve EEG spectral features. We also assessed if these methods retained posterior alpha power reactivity to an eyes closure-opening (EC-EO) task and compared the results from EEG-informed fMRI analysis using different BCG correction approaches.MethodElectroencephalographic data from 20 healthy young adults were recorded outside the MR environment and during simultaneous fMRI acquisition. The gradient artifact was effectively removed from EEG-fMRI acquisitions using Average Artifact Subtraction (AAS). The BCG artifact was corrected with seven methods: AAS, Optimal Basis Set (OBS), Independent Component Analysis (ICA), OBS followed by ICA, AAS followed by ICA, PROJIC-AAS and PROJIC-OBS. EEG signal preservation was assessed by comparing the spectral power of traditional frequency bands from the corrected rs-EEG-fMRI data with the data recorded outside the scanner. We then assessed the preservation of posterior alpha functional reactivity by computing the ratio between the EC and EO conditions during the EC-EO task. EEG-informed fMRI analysis of the EC-EO task was performed using alpha power-derived BOLD signal predictors obtained from the EEG signals corrected with different methods.ResultsThe BCG artifact caused significant distortions (increased absolute power, altered relative power) across all frequency bands. Artifact residuals/signal losses were present after applying all correction methods. The EEG reactivity to the EC-EO task was better preserved with ICA-based correction approaches, particularly when using ICA feature extraction to isolate alpha power fluctuations, which allowed to accurately predict hemodynamic signal fluctuations during the EEG-informed fMRI analysis.DiscussionCurrent software solutions for the BCG artifact problem offer limited efficiency to preserve the EEG spectral power properties using this particular EEG setup. The state-of-the-art approaches tested here can be further refined and should be combined with hardware implementations to better preserve EEG signal properties during simultaneous EEG-fMRI. Existing and novel BCG artifact correction methods should be validated by evaluating signal preservation of both ERPs and spontaneous EEG spectral power.
Association between probiotic, prebiotic, and yogurt consumption and chronic kidney disease: The NHANES 2010–2020
Authors: Liu Xiaoxian , Gao Wenyan , Yang Jie , Mao Genxiang , Lu Hong , Xing Wenmin 
Published: December 2022

BackgroundPrevious studies suggested that gut dysbacteriosis may promote the occurrence of chronic kidney disease (CKD), and probiotic, prebiotic, or yogurt supplements may alleviate CKD progression. This study aims to examine the association between probiotic, prebiotic, or yogurt supplements and the risk of CKD using the data from NHANES.MethodsThis study was designed to prospectively search data from the National Health and Nutrition Examination Survey (NHANES) (2011–2020). We examined dietary supplements and prescription medication labels to identify probiotic, or prebiotic product, and yogurt consumption during the dietary interview. The diagnosis of CKD was determined by the value of glomerular filtration rate (eGFR) and albumin creatinine ratio (ACR).ResultsThe study enrolled a total of 6,522 individuals. The prevalence of CKD was lower in the probiotic, prebiotic, or yogurt consumption group [age-adjusted odds ratio (OR): 0.77, 95% CI: 0.62–0.95, P = 0.02; multivariable-adjusted OR: 0.86, 95% CI: 0.69–1.07, P = 0.05]. Furthermore, 32% reduced risk was observed in the older group aged 55 years or older, and 32% reduced risk was also observed in the female population. Probiotic, or prebiotic, or yogurt supplements was associated a 12% reduction in moderate risk of CKD and an 11% reduction in very high risk of CKD.ConclusionOur results suggest that probiotic, prebiotic, or yogurt supplements may contribute to the prevention of CKD and relieve its progression risk, especially in the female population and older population who were aged 55 years or older.
Detecting plasma hsa_circ_0061276 in patients with gastric cancer by reverse transcription-digital polymerase chain reaction
Authors: Ruan Yao , Li Zhe , Xie Yaoyao , Sun Weiliang , Guo Junming 
Published: December 2022

BackgroundThe role of circular RNAs (circRNAs) in the occurrence of gastric cancer is still unclear. Therefore, the diagnostic value and mechanisms underlying hsa_circ_0061276 in the occurrence of gastric cancer were explored.MethodsReverse transcription-droplet digital polymerase chain reaction was used to detect the copy number of hsa_circ_0061276 in plasma from healthy individuals, as well as from patients with gastric precancerous lesions or early-stage or advanced gastric cancer. Plasmids overexpressing or knocking down hsa_circ_0061276 expression were transfected into gastric cancer cells. The effects on the growth, migration, and cell cycle distribution of gastric cancer cells were then analyzed. Finally, miRanda and RNAhybrid were used to explore the binding sites between hsa_circ_0061276 and microRNAs (miRNAs). A double luciferase reporter gene assay was used to confirm the miRNA sponge effect.ResultsThe results show that plasma hsa_circ_0061276 copy number showed a trend of a gradual decrease when comparing healthy controls to the early cancer group and advanced gastric cancer group. Overexpression of hsa_circ_0061276 inhibited the growth and migration of gastric cancer cells. Through bioinformatic analyses combined with cellular experiments, it was found that hsa_circ_0061276 inhibited the growth of gastric cancer by binding to hsa-miR-7705.ConclusionHsa_circ_0061276 may be a new biomarker for gastric cancer. The tumor suppressor role of hsa_circ_0061276 on gastric cancer likely occurs through a sponge effect on miRNAs such as hsa-miR-7705.
Preclinical profiles of SKB264, a novel anti-TROP2 antibody conjugated to topoisomerase inhibitor, demonstrated promising antitumor efficacy compared to IMMU-132
Authors: Cheng Yezhe , Yuan Xiaoxi , Tian Qiang , Huang Xiuying , Chen Yang , Pu Yuzhi , Long Hu , Xu Mingyu , Ji Yafei , Xie Jia , Tan Yuping , Zhao Xi , Song Hongmei 
Published: December 2022

PurposeThe aim of this study was to improve the intratumoral accumulation of an antibody–drug conjugate (ADC) and minimize its off-target toxicity, SKB264, a novel anti-trophoblast antigen 2 (TROP2) ADC that was developed using 2-methylsulfonyl pyrimidine as the linker to conjugate its payload (KL610023), a belotecan-derivative topoisomerase I inhibitor. The preclinical pharmacologic profiles of SKB264 were assessed in this study.MethodsThe in vitro and in vivo pharmacologic profiles of SKB264, including efficacy, pharmacokinetics–pharmacodynamics (PK-PD), safety, and tissue distribution, were investigated using TROP2-positive cell lines, cell-derived xenograft (CDX), patient-derived xenograft (PDX) models, and cynomolgus monkeys. Moreover, some profiles were compared with IMMU-132.ResultsIn vitro, SKB264 and SKB264 monoclonal antibody (mAb) had similar internalization abilities and binding affinities to TROP2. After cellular internalization, KL610023 was released and inhibited tumor cell survival. In vivo, SKB264 significantly inhibited tumor growth in a dose-dependent manner in both CDX and PDX models. After SKB264 administration, the serum or plasma concentration/exposure of SKB264 (conjugated ADC, number of payload units ≥1), total antibody (Tab, unconjugated and conjugated mAb regardless of the number of the payload units), and KL610023 in cynomolgus monkeys increased proportionally with increasing dosage from 1 to 10 mg/kg. The linker stability of SKB264 was significantly enhanced as shown by prolonged payload half-life in vivo (SKB264 vs. IMMU-132, 56.3 h vs. 15.5 h). At the same dose, SKB264’s exposure in tumor tissue was 4.6-fold higher than that of IMMU-132.ConclusionsCompared with IMMU-132, the longer half-life of SKB264 had a stronger targeting effect and better antitumor activity, suggesting the better therapeutic potential of SKB264 for treating TROP2-positive tumors.
The significance of time interval between perioperative SOX/XELOX chemotherapy and clinical decision model in gastric cancer
Authors: Chen Jun-Bing , Liu Zi-Ning , Wang Yin-Kui , Shan Fei , Li Shuang-Xi , Jia Yong-Ning , Xue Kan , Miao Ru-Lin , Li Zhe-Min , Wu Zhou-Qiao , Ying Xiang-Ji , Zhang Yan , Li Zi-Yu , Ji Jia-Fu 
Published: December 2022

IntroductionTo investigate the influences of time interval between multimodality therapies on survival for locally advanced gastric cancer (LAGC) patients, 627 patients were included in a retrospective study, and 350 who received neoadjuvant chemotherapy (NACT) based on SOX (S-1 plus Oxaliplatin)/XELOX (Capecitabine plus Oxaliplatin) treatment, radical surgery, and adjuvant chemotherapy (AC) from 2005.01 to 2018.06 were eligible for analyses.MethodsThree factors were used to assess influences, including time interval from NACT accomplishment to AC initiation (PECTI), time to surgery after NACT accomplishment (TTS), and time to adjuvant chemotherapy after surgery (TAC).ResultsConcerning PECTIs, 99 (28.29%) experienced it within 9 weeks, 188 (53.71%) within 9–13 weeks, 63 (18.00%) over 13 weeks. Patients’ 5-year overall survival (OS) significantly decreased as trichotomous PECTI increased (78.6% vs 66.7% vs 55.7%, P = .02). Analogously, there was a significant decrease for dichotomous TTS (within vs over 5 weeks) in OS (P = .03) and progression free survival (PFS) (P = .01) but not for dichotomous TAC (within vs over 6 weeks) in OS and PFS (P = .40). Through multivariate Cox analyses, patients with PECTI over 13 weeks had significantly worse OS (P = .03) and PFS (P = .02). Furthermore, extended TTS had significantly worse OS and PFS but insignificantly worse OS and PFS than extended TAC. Therefore, gastric patients receiving perioperative SOX/XELOX chemotherapy and surgery with extended PECTI over 9 weeks or TTS over 5 weeks would have a negative correlation with PFS and OS, and worse when PECTI over 13 weeks. Nomograms (including PECTI, ypT, ypN, Area Under Curve (AUC) = 0.81) could predict patient survival probability and guide intervention with net benefit.DiscussionIn control of PECTI, TTS could be extended appropriately, and shortened TAC might make a remedy, and delayed TAC might be allowed when TTS was shortened.