bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of microRNAs as diagnostic biomarkers for atrial fibrillation: a systematic review and meta-analysis
Authors: Rizal Ardian , Waranugraha Yoga , Wikananda Adhika Prastya , Yuniadi Yoga 
Published: April 2023

BackgroundGenetic factors contribute to the AF pathophysiology by altering the structural and functional properties of proteins involved in different cellular activities. MicroRNAs (miRNAs), which take part in structural and electrical remodeling during the AF evolution, are important genetic elements that must be considered. The aim of study is to determine correlation between the expression of miRNAs and the development of AF, as well as to explain any potential importance of genetic factors in the AF diagnosis.Methods and ResultsOnline scientific databases, including Cochrane, ProQuest, PubMed, and Web of Science were used to conduct the literature search. The keywords were associated with or characterized the relationship between miRNAs and AF. The pooled sensitivity and specificity statistical parameters were analyzed using a random-effects model. The miRNAs had a combined sensitivity and specificity of 0.80 (95% CI = 0.70–0.87) and 0.75 (95% CI = 0.64–0.83) for the diagnosis of AF, respectively. The area under the SROC was 0.84 (95% CI = 0.81–0.87). The DOR was 11.80 (95% CI = 6.79–20.50). This study also revealed that miRNAs had a pooled PLR of 3.16 (95% CI = 2.24–4.45) and NLR of 0.27 (95% CI = 0.18–0.39) for the diagnosis of AF. The miR-425-5p demonstrated the highest sensitivity (0.96, 95% CI, 0.89–0.99).ConclusionThe meta-analysis revealed substantial connection between miRNA expression dysregulation and AF, supporting the potential diagnostic role of miRNAs. The miR-425-5p has potential role as a biomarker for AF.
Visual analysis of the research hotspots in neoadjuvant therapy for patients with gastric cancer
Authors: Chen Tianxing , Liu Yating , Gao Jing , Zhang Dekui 
Published: April 2023

ObjectiveThis study aimed to analyze the research hotspots and frontiers in the field of neoadjuvant therapy for patients with gastric cancer (GC) using bibliometric and identify its developmental trends.MethodsThe literature related to neoadjuvant therapy for GC systematically retrieved between 1991 and 2021. Bibliometric methods were used to analysis the research hotspots and trends by CiteSpace and VOS-viewer software.ResultsThe number of studies related to neoadjuvant therapies for GC showed an upward trend. Moreover, the current research directions were mostly focused on the clinical trials and applications of neoadjuvant therapies for GC. The frontier research directions included microsatellite instability, peritoneal metastasis, randomized controlled trials, multicenter studies, and regression analysis.ConclusionsThe interest and attention of researchers in this field are still growing. In the past five years, the literature related to neoadjuvant therapy and immunotherapy for gastric cancer has exploded. It is still an important period and a key stage for the development of neoadjuvant therapy for gastric cancer.
Identification of TREM2-positive tumor-associated macrophages in esophageal squamous cell carcinoma: implication for poor prognosis and immunotherapy modulation
Authors: Li Hongmu , Miao Yu , Zhong Leqi , Feng Songjie , Xu Yue , Tang Lu , Wu Chun , Zhang Xianzhou , Gu Ling , Diao Hengyi , Wang Huiyun , Wen Zhesheng , Yang Minglei 
Published: April 2023

BackgroundIt is now understood that the effectiveness of checkpoint immunotherapy can be impaired by immunosuppressive tumor-associated macrophages (TAMs). Nonetheless, the impact of different TAM subpopulations on the antitumor immune response remains unclear, mainly due to their heterogeneity. Herein, we identified a novel TAM subpopulation in esophageal squamous cell carcinoma (ESCC) that might contribute to poor clinical outcomes and immunotherapy modulation.Methods and resultsWe analyzed two single-cell RNA sequencing (scRNA-seq) datasets (GSE145370 and GSE160269) of esophageal squamous cell carcinoma to identify a novel TREM2-positive TAM subpopulation characterized by upregulation of TREM2, C1QC, C1QB, C1QA, SPP1, and APOE. Quantitative real-time PCR (qRT-PCR) and enzyme-linked immunosorbent assay (ELISA) demonstrated that these genes were significantly overexpressed in ESCC. Multiplex immunofluorescence validated the infiltration of TREM2+ TAMs in ESCC tissues, which correlated with poorer overall survival (OS). The scRNA-seq analysis in dataset GSE120575 indicated significant enrichment of TREM2+ TAMs in melanoma patients (n=48) with poor immunotherapy response, which had an identical gene signature with TREM2+ TAMs from ESCC. Analysis of 29 bulk-RNA melanoma samples from dataset GSE78220 revealed that a gene signature of 40 genes associated with TREM2+ TAMs was upregulated in the transcriptome of melanomas that did not respond to anti-PD1 therapy. Validation in the TCGA ESCC cohort (n=80) showed that a high enrichment score of the TREM2+ TAM was associated with poor prognosis. In addition, 10 ESCC patients treated with anti-PD1 therapy suggested that patients who are not sensitive to immunotherapy have higher density of TREM2+TAMs infiltration.ConclusionOverall, TREM2+ TAM infiltration in ESCC is associated with poor prognosis and may serve as a biomarker for predicting outcomes and immunotherapy modulation in this patient population. modulation; single-cell RNA sequencing
Development of a high-resolution mass-spectrometry-based method and software for human leukocyte antigen typing
Authors: Wang Kun , Sun Zetao , Zhu Fei , Xu Yunping , Zhou Feng 
Published: April 2023

IntroductionThe human leukocyte antigen (HLA) system plays a critical role in the human immune system and is strongly associated with immune recognition and rejection in organ transplantation. HLA typing method has been extensively studied to increase the success rates of clinical organ transplantation. However, while polymerase chain reaction sequence-based typing (PCR-SBT) remains the gold standard, cis/trans ambiguity and nucleotide sequencing signal overlay during heterozygous typing present a problem. The high cost and low processing speed of Next Generation Sequencing (NGS) also render this approach inadequate for HLA typing.Methods and materialsTo address these limitations of the current HLA typing methods, we developed a novel typing technology based on nucleic acid mass spectrometry (MS) of HLA. Our method takes advantage of the high-resolution mass analysis function of MS and HLAMSTTs (HLA MS Typing Tags, some short fragment PCR amplification target products) with precise primer combinations.ResultsWe correctly typed HLA by measuring the molecular weights of HLAMSTTs with single nucleotide polymorphisms (SNPs). In addition, we developed a supporting HLA MS typing software to design PCR primers, construct the MS database, and select the best-matching HLA typing results. With this new method, we typed 16 HLA-DQA1 samples, including 6 homozygotes and 10 heterozygotes. The MS typing results were validated by PCR-SBT.DiscussionThe MS HLA typing method is rapid, efficient, accurate, and readily applicable to typing of homozygous and heterozygous samples.
The contrast in suspended particle dynamics at surface and near bottom on the river-dominated northern South China Sea shelf in summer: implication on physics and biogeochemistry coupling
Authors: Lee Jay , Liu James T. , Lin Yu-Shih , Chen Chen-Tung Arthur , Wang Bo-Shian 
Published: April 2023

To understand the process-response relations among physical forcing and biogeochemical properties of suspended particles (SPs) in the river-dominated northern South China Sea shelf, a 5-day shipboard observation was conducted at a fixed location on the dispersal pathway of the Zhujiang (Pearl) River plume (ZRP) in the summer of 2016. Instrumented moorings were deployed near the sampling site to record the flow and wave fields every 10 minutes. Hydrographic properties were measured hourly to identify different water masses. Water and SPs samples at the surface (3 m) and near the bottom (3 m above the bed) were taken every 3 h for the analyses of nutrients, chlorophyll-a (Chl-a), and particulate organic matter (POM including POC, PN, and δ13CPOC). Meanwhile, the grain-size composition of SPs and seafloor sediment were also analyzed. Results showed that monsoon winds drove cold upwelling and ZRP waters at the surface. Both the upwelling and ZRP regimes contained newly produced marine phytoplankton based on low POC/Chl-a ratio (PC ratio) and enriched δ13CPOC. However, SPs in the ZRP regime were smaller (&lt;153 µm), having denser particle bulk density, and less enriched δ13CPOC, indicating different bio-communities from the upwelling regime. EOF analysis of the surface data suggested that mixing processes and the dispersal of the ZRP regime were mainly controlled by far-field storm winds, tidal modulation, and strength of mixing. On the other hand, a bottom nepheloid layer (BNL) was observed, mainly consisting of SPs&lt;63 μm with higher bulk density than SPs at the surface. POM in the BNL was degraded and δ13CPOC-depleted according to the PC ratio and δ13CPOC. EOF analysis of the near-bottom data indicated that the dominant physical processes influencing the biogeochemical properties of SPs in the BNL were jointly the upwelling-associated lateral transport (first order) and tide-related resuspension (second order). Our study identified the contrast between the surface and near-bottom regimes with the coupling patterns among physical forcing and physiochemical properties of SPs using good constraints on particle dynamics and particle sources.
The impact of metakaolin on the hydration of tricalcium silicate: effect of C-A-S-H precipitation
Authors: Sowoidnich T. , Cölfen H. , Rößler C. , Damidot D. , Ludwig H.-M. 
Published: April 2023

Introduction:Metakaolin (MK) is used as supplementary cementitious material to reduce the CO2footprint of Portland cements. However, the early hydration of Portland cement (OPC) is often retarded due to its use. The present work investigates the mechanisms of this retardation. Focus is laid on the interaction of MK with the main clinker phase C3S (Ca3SiO5, pure form of alite) that is known to govern the kinetics of early hydration of OPC.Methods:Hydration reactions of MK and C3S were analysed by optical emission spectroscopy, electron microscopy, thermal analysis, X-ray diffraction and reaction calorimetry.Results:Results on MK showed that compared to sodium ions the presence of calcium ions reduced the maximum amounts of silicate and aluminate ions released into solution by MK. For MK + C3S mixtures, C-A-S-H was formed at the surfaces of both C3S and MK within minutes with a composition of (CaO)1.3(SiO2)0.8(Al2O3)0.2(H2O)2.7. The solubility constant of (CaO)1.3(SiO2)0.8(Al2O3)0.2(H2O)2.7was determined.Discussion:C-A-S-H appeared to be an unsuitable substrate for C-S-H nucleation. Therefore, its formation during early hydration is expected to play an important role in the retardation of C3S hydration. Indeed, when C-A-S-H seeds are formed, less C-S-H seeds are formed leading to lengthen the duration of the induction period. The presence of sulfate ions reduces the amount of C-A-S-H seeds as most aluminate ions are consumed to form ettringite. Consequently, sulfate ions induce an increase of the hydration kinetics such as observed in MK + C3S mixtures.
Pre-operative prognostic nutrition index and post-operative pneumonia in aneurysmal subarachnoid hemorrhage patients
Authors: Xu Manman , Zhang Liang , Wang Juan , Cheng Longyang , Chen Chunlei , Li Shaoya , Dai Haibin , Zhao Penglai , Hang Chunhua 
Published: April 2023

Background and objectivePost-operative pneumonia (POP), a common complication, may be associated with prolonged hospitalization and long-term mortality in aneurysmal subarachnoid hemorrhage (aSAH) patients. This study aimed to explore the association between pre-operative prognostic nutrition index (PNI) and POP in aSAH patients.MethodsA total of 280 aSAH patients were enrolled from Nanjing Drum Tower Hospital. PNI was calculated as follows: [10 × albumin(gr/dl)] + [0.005 × absolute pre-operative lymphocyte count (per mm3)]. We utilized multivariate analyses, restricted cubic spline, net reclassification improvement (NRI), and integrated discrimination improvement (IDI) to elucidate the role of PNI in POP.ResultsPre-operative PNI levels in the POP group were higher, compared with the non-POP group (41.0 [39.0, 45.4] vs. 44.4 [40.5, 47.3], P = 0.001). When we included PNI as a categorical variable in the multivariate analysis, the levels of PNI were associated with POP (odds ratio, 0.433; 95% confidence interval, 0.253–0.743; P=0.002). In addition, when we included PNI as a continuous variable in the multivariate analysis, the PNI levels were also associated with POP (odds ratio, 0.942; 95% confidence interval, 0.892–0.994; P = 0.028). The level of albumin was also a predictor of the occurrence of POP, with a lower diagnostic power than PNI [AUC: 0.611 (95% confidence interval, 0.549–0.682; P = 0.001) for PNI vs. 0.584 (95% confidence interval, 0.517–0.650; P = 0.017) for albumin]. Multivariable-adjusted spline regression indicated a linear dose–response association between PNI and POP in aSAH participants (P for linearity = 0.027; P for non-linearity = 0.130). Reclassification assessed by IDI and NRI was significantly improved with the addition of PNI to the conventional model of POP in aSAH patients (NRI: 0.322 [0.089–0.555], P = 0.007; IDI: 0.016 [0.001–0.031], P = 0.040).ConclusionThe lower levels of pre-operative PNI may be associated with the higher incidence of POP in aSAH patients. Neurosurgeons are supposed to pay more attention to pre-operative nutrition status in aSAH patients.
Predictive model of recurrent ischemic stroke: model development from real-world data
Authors: Elhefnawy Marwa Elsaeed , Sheikh Ghadzi Siti Maisharah , Albitar Orwa , Tangiisuran Balamurugan , Zainal Hadzliana , Looi Irene , Sidek Norsima Nazifah , Aziz Zariah Abdul , Harun Sabariah Noor 
Published: April 2023

BackgroundThere are established correlations between risk factors and ischemic stroke (IS) recurrence; however, does the hazard of recurrent IS change over time? What is the predicted baseline hazard of recurrent IS if there is no influence of variable predictors? This study aimed to quantify the hazard of recurrent IS when the variable predictors were set to zero and quantify the secondary prevention influence on the hazard of recurrent ischemic stroke.MethodsIn the population cohort involved in this study, data were extracted from 7,697 patients with a history of first IS attack registered with the National Neurology Registry of Malaysia from 2009 to 2016. A time-to-recurrent IS model was developed using NONMEM version 7.5. Three baseline hazard models were fitted into the data. The best model was selected using maximum likelihood estimation, clinical plausibility, and visual predictive checks.ResultsWithin the maximum 7.37 years of follow-up, 333 (4.32%) patients had at least one incident of recurrent IS. The data were well described by the Gompertz hazard model. Within the first 6 months after the index IS, the hazard of recurrent IS was predicted to be 0.238, and 6 months after the index attack, it reduced to 0.001. The presence of typical risk factors such as hyperlipidemia [HR, 2.22 (95%CI: 1.81–2.72)], hypertension [HR, 2.03 (95%CI: 1.52–2.71)], and ischemic heart disease [HR, 2.10 (95%CI: 1.64–2.69)] accelerated the hazard of recurrent IS, but receiving antiplatelets (APLTs) upon stroke decreased this hazard [HR, 0.59 (95%CI: 0.79–0.44)].ConclusionThe hazard of recurrent IS magnitude differs during different time intervals based on the concomitant risk factors and secondary prevention.
Identifying the intervention mechanisms of polydatin in hyperuricemia model rats by using UHPLC-Q-Exactive Orbitrap mass spectroscopy metabonomic approach
Authors: Ge Xueli , Su Zhenguo , Wang Yuhao , Zhao Xue , Hou Kaifei , Zheng Shuna , Zeng Pengjiao , Shi Zhongqi , Hu Senhao , Wang Yuqing , Zhou Mengchen , Zhang Jiayu , Li Xiulian 
Published: April 2023

IntroductionPolydatin is a biologically active compound found in mulberries, grapes, and Polygonum cuspidatum, and it has uric acid-lowering effects. However, its urate-lowering effects and the molecular mechanisms underlying its function require further study.MethodsIn this study, a hyperuricemic rat model was established to assess the effects of polydatin on uric acid levels. The body weight, serum biochemical indicators, and histopathological parameters of the rats were evaluated. A UHPLC-Q-Exactive Orbitrap mass spectrometry-based metabolomics approach was applied to explore the potential mechanisms of action after polydatin treatment.ResultsThe results showed a trend of recovery in biochemical indicators after polydatin administration. In addition, polydatin could alleviate damage to the liver and kidneys. Untargeted metabolomics analysis revealed clear differences between hyperuricemic rats and the control group. Fourteen potential biomarkers were identified in the model group using principal component analysis and orthogonal partial least squares discriminant analysis. These differential metabolites are involved in amino acid, lipid, and energy metabolism. Of all the metabolites, the levels of L-phenylalanine, L-leucine, O-butanoylcarnitine, and dihydroxyacetone phosphate decreased, and the levels of L-tyrosine, sphinganine, and phytosphingosine significantly increased in hyperuricemic rats. After the administration of polydatin, the 14 differential metabolites could be inverted to varying degrees by regulating the perturbed metabolic pathway.ConclusionThis study has the potential to enhance our understanding of the mechanisms of hyperuricemia and demonstrate that polydatin is a promising potential adjuvant for lowering uric acid levels and alleviating hyperuricemia-related diseases.
Bacterial lipopolysaccharide-related genes are involved in the invasion and recurrence of prostate cancer and are related to immune escape based on bioinformatics analysis
Authors: Che Bangwei , Zhang Wenjun , Li Wei , Tang Kaifa , Yin Jingju , Liu Miao , Xu Shenghan , Huang Tao , Yu Ying , Huang Kunyuan , Peng Zheng , Zha Cheng 
Published: April 2023

BackgroundThe composition of the tumor microbial microenvironment participates in the whole process of tumor disease. However, due to the limitations of the current technical level, the depth and breadth of the impact of microorganisms on tumors have not been fully recognized, especially in prostate cancer (PCa). Therefore, the purpose of this study is to explore the role and mechanism of the prostate microbiome in PCa based on bacterial lipopolysaccharide (LPS)-related genes by means of bioinformatics.MethodsThe Comparative Toxicogenomics Database (CTD) was used to find bacterial LPS- related genes. PCa expression profile data and clinical data were acquired from TCGA, GTEx, and GEO. The differentially expressed LPS-related hub genes (LRHG) were obtained by Venn diagram, and gene set enrichment analysis (GSEA) was used to investigate the putative molecular mechanism of LRHG. The immune infiltration score of malignancies was investigated using single-sample gene set enrichment analysis (ssGSEA). Using univariate and multivariate Cox regression analysis, a prognostic risk score model and nomogram were developed.Results6 LRHG were screened. LRHG were involved in functional phenotypes such as tumor invasion, fat metabolism, sex hormone response, DNA repair, apoptosis, and immunoregulation. And it can regulate the immune microenvironment in the tumor by influencing the antigen presentation of immune cells in the tumor. And a prognostic risk score and the nomogram, which were based on LRHG, showed that the low-risk score has a protective effect on patients.ConclusionMicroorganisms in the PCa microenvironment may use complex mechanism and networks to regulate the occurrence and development of PCa. Bacterial lipopolysaccharide-related genes can help build a reliable prognostic model and predict progression-free survival in patients with prostate cancer.
Radiotherapy planning in a prostate cancer phantom model with intraprostatic dominant lesions using stereotactic body radiotherapy with volumetric modulated arcs and a simultaneous integrated boost
Authors: Skrobala Agnieszka , Kruszyna-Mochalska Marta , Graczyk Kinga , Ryczkowski Adam , Fundowicz Magdalena , Milecki Piotr , Malicki Julian 
Published: April 2023

AimIn the treatment of prostate cancer with radiation therapy, the addition of a simultaneous integrated boost (SIB) to the dominant intraprostatic lesions (DIL) may improve local control. In this study, we aimed to determine the optimal radiation strategy in a phantom model of prostate cancer using volumetric modulated arc therapy for stereotactic body radiotherapy (SBRT-VMAT) with a SIB of 1-4 DILs.MethodsWe designed and printed a three-dimensional anthropomorphic phantom pelvis to simulate individual patient structures, including the prostate gland. A total of 36.25 Gy (SBRT) was delivered to the whole prostate. The DILs were irradiated with four different doses (40, 45, 47.5, and 50 Gy) to assess the influence of different SIB doses on dose distribution. The doses were calculated, verified, and measured using both transit and non-transit dosimetry for patient-specific quality assurance using a phantom model.ResultsThe dose coverage met protocol requirements for all targets. However, the dose was close to violating risk constraints to the rectum when four DILs were treated simultaneously or when the DILs were located in the posterior segments of the prostate. All verification plans passed the assumed tolerance criteria.ConclusionsModerate dose escalation up to 45 Gy seems appropriate in cases with DILs located in posterior prostate segments or if there are three or more DILs located in other segments.
Noninvasive positive-pressure ventilation for children with acute asthma: a meta-analysis of randomized controlled trials
Authors: Dai Jiajia , Wang Libo , Wang Fang , Wang Lu , Wen Qingfen 
Published: April 2023

BackgroundNoninvasive positive-pressure ventilation (NPPV) can be effective in children with acute asthma. However, clinical evidence remains limited. The objective of the meta-analysis was to systematically assess NPPV's effectiveness and safety in treating children with acute asthma.MethodsRelevant randomized controlled trials were obtained from electronic resources, including PubMed, Embase, Cochrane's Library, Wanfang, and CNKI databases. The influence of potential heterogeneity was taken into account before using a random-effect model to pool the results.ResultsA total of 10 RCTs involving 558 children with acute asthma were included in the meta-analysis. Compared to conventional treatment alone, additional use of NPPV significantly improved early blood gas parameters such as the oxygen saturation (mean difference [MD]: 4.28%, 95% confidence interval [CI]: 1.51 to 7.04, p = 0.002; I2 = 80%), partial pressure of oxygen (MD: 10.61 mmHg, 95% CI: 6.06 to 15.16, p &lt; 0.001; I2 = 89%), and partial pressure of carbon dioxide (MD: −6.29 mmHg, 95% CI: −9.81 to −2.77, p &lt; 0.001; I2 = 85%) in the arterial blood. Moreover, NPPV was also associated with early reduced respiratory rate (MD: −12.90, 95% CI: −22.21 to −3.60, p = 0.007; I2 = 71%), improved symptom score (SMD: −1.85, 95% CI: −3.65 to −0.07, p = 0.04; I2 = 92%), and shortened hospital stay (MD: −1.82 days, 95% CI: −2.32 to −1.31, p &lt; 0.001; I2 = 0%). No severe adverse events related to NPPV were reported.ConclusionsNPPV in children with acute asthma is associated with improved gas exchange, decreased respiratory rates, a lower symptom score, and a shorter hospital stay. These results suggest that NPPV may be as effective and safe as conventional treatment for pediatric patients with acute asthma.