bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deficiency of histone H3K36 methyltransferase SETD2 inhibits proliferation and migration of hepatocellular carcinoma through ERK pathway
Authors: Yang Yi , Zhang Linlin , Munyurangabo Gustave , Jin Hua , He Shuyang , Jia Yachun , Zhang Peihua , Yu Xiao , Yang Dan , Kong Guangyao 
Published: November 2023

Abstract
Background
Hepatocellular carcinoma (HCC) is one of the leading cause of cancer-related death worldwide. SETD2, as the only known methyltransferase for catalyzing trimethylation of histone H3 lysine 36 (H3K36), has been reported to be associated with several cancers. However, the function of SETD2 in HCC is ambiguous. This work aims to research the function and mechanism of SETD2 in HCC based on bioinformation analysis and cell experiments.
Methods
SETD2 expression and its relationship with prognosis in LIHC patients were evaluated based on the Cancer Genome Atlas (TCGA) database, the effect of SETD2 silencing and overexpression on HCC cell lines was explored according to CCK-8 assay, colony formation assay and wound healing assay. RNA-seq analysis, western blot and chromatin immunoprecipitation (ChIP) assay were used to explore the potential mechanism of SETD2 in HCC.
Results
The results indicated that SETD2 expression was upregulated and high SETD2 expression was related to poor prognosis in HCC. SETD2 silencing inhibited the proliferation and migration, and SETD2 overexpression promoted the proliferation and migration in HCC cells. RNA-seq data revealed that differentially expressed genes were dramatically enriched in fibroblast growth factor receptor signaling pathway. FGFBP1, as a FGF-binding protein, ranked in the top 10 among the DEGs. The expression of FGFBP1 in SETD2 silencing BEL-7402 cells was significantly decreased. As the downstream effector of FGFR, ERK phosphorylation level had positive correlation with SETD2. Besides, H3K36me3 directly bound to the promoter of FGFBP1 confirmed by ChIP-qPCR.
Conclusions
Our findings highlight the promotion role of SETD2/H3K36me3 in HCC proliferation and migration via FGFR-ERK signal pathway. Our studies will advance our understanding of epigenetic dysregulation at HCC progression and provide a rationale for SETD2 as potential diagnostic biomarker and therapeutic target in HCC.
Natto (fermented soybeans)-induced anaphylaxis in a surfer with the possibility of sensitization to poly(γ-glutamic acid) from cutaneous exposure to jellyfish sting: A case report
Authors: Shigeno Ayami , Suzuki Tsuyoshi , Obayashi Masakazu , Asada Kei , Matsushima Satoru 
Published: November 2023

Abstract
Background
We report a case of anaphylaxis induced by natto (fermented soybeans) allergy that occurred following dermal sensitization from a jellyfish sting.
Case presentation:
A 49-year-old male presented to the emergency room complaining of an acute onset of erythema with pruritis that appeared while he was surfing. Given that his heart rate dropped to ~ 40 bpm without a decline in blood pressure or oxygen saturation, we suspected anaphylaxis and administered 0.5 mg of adrenaline intramuscularly. Immediately after the muscular adrenaline injection, his heart rate recovered to ~ 60–70 bpm.
Conclusions
The major allergen that induces natto allergy is poly(γ-glutamic acid) (PGA), which is present in its mucilage. Given that PGA is also produced by jellyfish tentacles, it can be inferred that the PGA sensitization occurred via dermal exposure to jellyfish PGA. This is an example of a food allergy induced by animal stings. As PGA is a high-molecular-weight polymer, natto allergy, despite being IgE-mediated, often presents with late-onset anaphylaxis, which typically develops half a day after digestion. PGA has a wide range of applications in pharmaceuticals, cosmetics, and foods. Patients may develop allergic symptoms and experience repeated anaphylaxis with no known cause. Therefore, it is important to obtain a detailed medical history and individually instruct patients suspected of being allergic to PGA to avoid PGA-containing products.
An iterative matrix uncertainty selector for high-dimensional generalized linear models with measurement errors
Authors: Nono Betrand Fesuh , Nguefack-Tsague Georges , Kegnenlezom Martin , Nguéma Eugène-Patrice Ndong 
Published: November 2023

Abstract
Various regularization methods through penalization of parameters have been proposed for variable selection in high-dimensional regression analysis with measurement errors. Most of these techniques require knowledge of the measurement error distribution whose estimation can be computationally expensive or even unfeasible. A measurement error distribution free correction based on Rosenbaum and Tsybakov’s matrix uncertainty selector (MUS ) and Taylor expansion for generalized linear models (GLMs), termed generalized matrix uncertainty selector (GMUS), and its lasso variant, called generalized matrix uncertainty lasso (GMUL) have been proposed. Validation of the methods was mostly based on simulations, hence performance on real datasets remains to be verified. In this paper, we propose an iterative matrix uncertainty selector (IMUS) for high-dimensional GLMs which does not require knowledge of the measurement error distribution.The approach is grounded on the Rosenbaum and Tsybakov’s MUS and the derivation of the linear model underlying the iterative re-weighted least squares estimate in a GLM. Theoretical justifications have been given, alongside numerical comparison with the GMUS and GMUL with Taylor expansion truncated at first order. Simulations results and practical applications on three microarray real datasets demonstrate the effectiveness of our proposed method, producing comparable results for covariate selection in simulations or sometimes superior results in terms of convergence and well-defined elbow for all real datasets relative to the other methods. The IMUS algorithm is easily adaptable to all families as per the glm function in the stats R package.
Deep Learning-Based Automatic Measurement of Prostate Volume Using Two- Dimensional Transrectal Ultrasound: A Pilot Study
Authors: Yoon Heechul , Park Gihun , Hwang Inhyeok , Choi Moon Hyung , Song Tai-kyong 
Published: November 2023

Abstract
Purpose
The aim of this study is to automatically measure the prostate volume based on two-dimensional transrectal ultrasound (TRUS) images using deep learning.
Methods
A total of 1,645 ultrasound images were collected from 110 patients and partitioned into training and testing datasets at a 10:1 ratio. We introduced a method for automated prostate volume measurement using deep learning techniques on 2-D TRUS images. Initially, we applied a VGG-19-based model to classify the cross-sectional TRUS images into two types – transverse and sagittal images. These two groups of the categorized images were respectively fed into a U-Net-based model for segmentation. From the U-Net-based model, we obtained segmented images that are used to measure the prostate’s length and volume via an ellipsoid method. The measured volumes from our model were quantitatively evaluated by radiologist-measured results; the classification network was assessed based on accuracy and the segmentation network was assessed using intersection over union metrics, respectively.
Results
The classification network showed an accuracy of 99.35%, and the segmentation network exhibited a mean intersection over union value of 90.88%. The average error rate between the measured volume of the proposed method and the volume measured by the clinical assessment is 9.17%.
Conclusions
We have demonstrated that 2-D TRUS images, obtained through routine clinical diagnosis of prostate, can be effective and reliable in measurement of prostate volumes through a deep-learning-based approach with the ellipsoid formula. Our method can potentially address the previous challenges related to patient-dependent prostate shapes, ambiguous brightness patterns in TRUS, and inconsistencies among different operators when performing manual measurements.
Risk factors of renal insufficiency in patients with chronic obstructive pulmonary disease; A systematic review and meta-analysis
Authors: QIAN CAI HUA , MAO WEI , LU CHEN 
Published: November 2023

Abstract

Background
Chronic obstructive pulmonary disease (COPD) is a progressive, systematic inflammatory disorder. Chronic kidney disease (CKD) is frequently associated with COPD. A number of risk factors of CKD have been investigated among patients living with COPD. Conversely, the findings of the previous studies are contradictory and inconsistent. The present systematic review and meta-analysis revealed the risk of chronic renal insufficiency among patients living with COPD and patients-related and management-related risk factors.
Methods
Literature searching of twelve databases was performed on 14 July 2023. All clinical studies comparing the patients-related, COPD-related, and management-related variables among patients with COPD who developed chronic renal insufficiency and control groups were eligible. Studies reported the potential predictors of chronic renal insufficiency among patients with COPD were included.
Results
This meta-analysis included nine studies, encompassing 64289 patients with COPD. Of them, 10217 patients developed CKD, while 54072 had no-CKD. The risk of CKD after COPD was 22.5% (event rate 0.225, 95%CI; 17.2, 0.289; p < 0.001). Elderly patients (MD;5.50 years ,95%CI; 2.99, 8.02; p < 0.001), hypertensive patients (RR; 1.47, 95%CI; 1.16, 1.85; P = 0.001), diabetic patients (RR; 2.27, 95%CI; 1.52 to 3.38; P < 0.001), and patients with peripheral vascular disease (RR; 1.52, 95%CI; 1.45, 1.6; P < 0.001) were at higher risk of CKD.
Conclusions
The present meta-analysis pointed out the considerable risk of CKD among patients with COPD. Elderly patients with hypertension, diabetes mellitus, stroke, or peripheral vascular diseases were at higher risk of CKD.
Bioactivity and Toxicity of Biogenic Nickel Oxide Nanoparticles Using Punica granatum Seed Extract
Authors: Hussein Mohamed A. , Abdelkarim Esraa A. , Elsamahy Tamer , Sobhy Mabrouk , Bayomi Rasha M. El , Hafez Abd-Elsalam E. 
Published: November 2023

Abstract
The biosynthesis of metal oxide nanoparticles has attracted attention because of their bioactivity, low cost, rapid reactivity, and simplicity. This study aims to synthesize and characterize the nickel oxide nanoparticles (NiO-NPs) by Punica granatum seed extract and evaluate their bioactivities and toxicity. The biosynthesized NiO-NPs physicochemical characteristics were explored using NTA, TGA, XRD, UV–Vis, and FT-IR, showing the formation of high-purity crystalline NPs with an average size of 10–60 nm. Furthermore, the antibacterial, antioxidant, and hemolytic activity of the biosynthesized NiO-NPs were explored. The results of this study showed that NiO-NPs possess a high antibacterial activity against Gram-negative (Pseudomonas aeruginosa and Escherichia coli) and Gram-positive bacteria (methicillin-resistant Staphylococcus aureus and Aerococcus viridans). However, the NiO-NPs inhibitory effect on Gram-positive bacteria was higher than on Gram-negative bacteria. Moreover, NiO-NPs also showed a DPPH, ABTS, and H2O2 radical scavenging activity with non-hemolytic activity at low concentrations (< 250 mg/L) in a dose-dependent manner. Regarding the toxicity of NiO-NPs, an enhanced effect on seed development of Vigna radiate at low concentrations (5 mg/L) was observed, which can be utilized as an alternative to conventional agrochemicals. Also, the cytotoxicity analysis was performed in the L-929 normal fibroblast cell line using MTT assay and IC50 (125.5 mg/L), indicating that the biosynthesized NiO-NPs are biocompatible at different concentrations. The obtained data showed that the bioactivity of NiO-NPs might be due to their small size, which generates various active sites because of their high surface area. Generally, P. granatum seed extract showed ability as an efficient reducing and capping agent for NiO-NPs biosynthesis and played a vital role in enhancing their bioactivity.
Risk factors and a nomogram for predicting cognitive frailty in Chinese patients with lung cancer receiving drug therapy: a single-center cross-sectional study
Authors: Li Jinping , Wang Yan , Zhai Minfeng , Qin Mengyuan , Zhao Dandi , Xiang Qian , Shao Zaoyuan , Wang Panrong , Lin Yan , Dong Yiting , Liu Yan 
Published: November 2023

Abstract
Purpose
To identify independent factors of cognitive frailty and construct a nomogram to predict cognitive frailty risk in patients with lung cancer receiving drug therapy.
Methods
This is a cross-sectional study that enrolled patients with lung cancer undergoing drug therapy from October 2022 to July 2023. The collected data includes general demographic characteristics, clinical data characteristics and assessment of tools for cognitive frailty and other factors. Logistic regression was harnessed to determine the influencing factors, R software was used to establish a nomogram model to predict the risk of cognitive frailty. The enhanced Bootstrap method was employed for internal verification of the model. The performance of the nomogram was evaluated by using calibration curves, the area under the receiver operating characteristic curve, and decision curve analysis.
Results
A total of 372 patients were recruited, with a CF prevalence of 56.2%. Age, education background, diabetes Mellitus, insomnia, sarcopenia, and nutrition status were identified as independent factors by multivariate logistic regression analysis. Then, a nomogram model was constructed and patients were classified into high- and low-risk groups with a cutoff value of 0.552. For the entire cohort, the result of Hosmer-Lemeshow good of fit test was χ2 = 3.685 (P = 0.884), the area under the curve was 0.764 (95%CI:0.716–0.812), and the calibration curves presented good concordance with actual observations, which were consistent in both the training set and the validation set. Additionally, decision curve analysis demonstrated that the application of this nomogram could help improve clinical outcomes.
Conclusions
The prevalence of cognitive frailty was higher in lung cancer patients receiving drug therapy. The nomogram could identify the risk of cognitive frailty intuitively and simply in patients with lung cancer, so as to provide references for early screening and intervention for cognitive frailty at the early phases of drug treatment.
Online evolution of a phased array for ultrasonic imaging by a novel adaptive data acquisition method
Authors: Lukacs Peter , Stratoudaki Theodosia , Davis Geo , Gachagan Anthony 
Published: November 2023

Abstract
Ultrasonic imaging using ultrasonic phased arrays has an enormous impact in science, medicine and society and is a widely used modality in many application fields. The maximum amount of information which can be captured by an array is provided by the data acquisition method capturing the complete data set of signals from all possible combinations of ultrasonic generation and detection elements of a dense array. However, capturing this complete data set requires long data acquisition time, large number of array elements and transmit channels and produces a large volume of data. All these reasons make such data acquisition unfeasible due to the existing phased array technology or non-applicable to cases requiring fast measurement time. This paper introduces the concept of an adaptive data acquisition process, the Selective Matrix Capture (SMC), which can adapt, dynamically, to specific imaging requirements for efficient ultrasonic imaging. SMC is realised experimentally using Laser Induced Phased Arrays (LIPAs), that use lasers to generate and detect ultrasound. The flexibility and reconfigurability of LIPAs enable the evolution of the array configuration, on-the-fly. The SMC methodology consists of two stages: a stage for detecting and localising regions of interest, by means of iteratively synthesising a sparse array, and a second stage for array optimisation to the region of interest. The delay-and-sum is used as the imaging algorithm and the experimental results are compared to images produced using the complete generation-detection data set. It is shown that SMC, without a priori knowledge of the test sample, is able to achieve comparable results, while preforming ∼10 times faster data acquisition and achieving ∼ 10 times reduction in data size.
Comparison of liver resection and radiofrequency ablation in long-term survival among patients with early-stage hepatocellular carcinoma: A meta-analysis of randomized trials and high-quality propensity score- matched studies
Authors: Hu Lingbo , Lin Jiangying , Wang Aidong , Shi Xingpeng , Qiao Yingli 
Published: November 2023

Abstract
Background
Whether radiofrequency ablation (RFA) and liver resection (LR) are comparable treatments for early-stage hepatocellular carcinoma (HCC) is controversial. We conducted this study to provide ample clinical evidence for the argument.
Methods
The PubMed, Embase, Web of Science, and Cochrane Library databases were systematically searched to identify randomized controlled trials (RCTs) and propensity score-matched (PSM) studies that compared long-term outcomes of both RFA and LR for patients with early-stage HCC. The hazard ratios (HRs) with 95% confidence intervals (95% CI) of overall survival (OS) and disease-free survival (DFS) were calculated.
Results
Thirty-six studies consisting of six RCTs and thirty PSM studies were included in this study, and a total of 7,384 patients were involved, with 3,694 patients being treated with LR and 3,690 patients with RFA. Meta-analysis showed that LR provided better OS and DFS than RFA (HR: 1.22, 95% CI: 1.13–1.31; HR: 1.56, 95% CI: 1.39–1.74, respectively). A sensitivity analysis indicated that the results were stable. For the subgroup of patients with BCLC 0 stage, RFA and LR resulted in similar OS and DFS. For the subgroup of patients with single tumor sizes less than 3 cm, RFA reached similar OS (HR: 1.19, 95% CI: 0.90–1.58) but worse DFS compared with LR (HR: 1.45, 95% CI: 1.11–1.90). For the subgroup of ablation margin larger than 0.5cm, LR still resulted in better OS than RFA (HR: 1.29, 95% CI: 1.09–1.53), while the ablation margin was larger than 1cm, both RFA and LR resulted in similar OS. The modality of RFA was also a factor that affected results. Subgroup analysis showed that patients receiving ultrasound-guided RFA had worse OS and DFS than LR (HR: 1.24, 95% CI: 1.14–1.36; HR: 1.44, 95% CI: 1.25–1.66, respectively).
Conclusions
Meta-analysis showed that LR provided better OS and DFS for patients with early-stage HCC. However, RFA and LR had similar effects on long-term survival in patients with BCLC 0 stage HCC. RFA and LR had similar effects on OS in patients with solitary HCC less than 3cm or when the ablation margin was larger than 1cm. The effects of different modalities of RFA on long-term survival are needed for further assessment.
Determination of HLA class II risk alleles and prediction of self/non-self epitopes contributing Hashimotoˈs thyroiditis in a group of Iranian patients
Authors: Shirizadeh Ata , Borzouei Shiva , Razavi Zahra , Taherkhani Amir , Faradmal Javad , Solgi Ghasem 
Published: November 2023

Abstract
One of the probable hypotheses for the onset of autoimmunity is molecular mimicry. This study aimed to determine the HLA-II risk alleles for developing Hashimotoˈs thyroiditis (HT) in order to analyze the molecular homology between candidate pathogen-derived epitopes and potentially self-antigens (TPO) based on the presence of HLA risk alleles. HLA-DRB1/-DQB1 genotyping was performed in 100 HT patients and 330 ethnically matched healthy controls to determine the predisposing/protective HLA alleles for HT disease in our population. Then, insilico analysis was carried out to examine the sequence homology between epitopes derived from autoantigens and four potentially relevant pathogens and their binding capacity for HLA risk alleles based on peptide docking analysis. We identified HLA-DRB1*03:01, *04:02, *04:05 and *11:04 as predisposing alleles and DRB1*13:01 as potentially predictive allele for HT disease. Also, DRB1*11:04 ~ DQB1*03:01 (Pc = 0.002, OR:3.97) and DRB1*03:01 ~ DQB1*02:01 (Pc = 0.004, OR:2.24) haplotypes conferred a predisposing role for HT. Based on logistic regression analysis, carrying risk alleles increased the risk of HT development 4.5 times in our population (P = 7.09E-10). Also, ROC curve analysis revealed a high predictive power of those risk alleles in discrimination of susceptible from healthy individuals (AUC: 0.70, P = 6.6E-10). Analysis of peptide sequence homology between epitopes of TPO and epitopes derived from four candidate microorganisms revealed a homology between envelop glycoprotein D of herpes virus and sequence 151–199 of TPO with remarkable binding capacity to HLA-DRB1*03:01 allele. Our findings indicate the increased risk of developing HT in those individual carrying HLA risk alleles which can also be related to herpes virus infection.
Clinical characteristics and risk factors for plastic bronchitis in children with severe Mycoplasma pneumoniae pneumonia: a retrospective observational study
Authors: Mu Shiyin , Zou Yingxue , Guo Yongsheng , Huang Bing , Zhai Jia 
Published: November 2023

Abstract

Background: Plastic bronchitis (PB) is a rare, underdiagnosed and potentially fatal condition that should not be overlooked in children, particularly in children with severe Mycoplasma pneumoniae pneumonia (SMPP). Therefore, we explored the risk factors for PB in children with SMPP and the diagnostic value for PB.
Methods: We retrospectively evaluated children with a clinical diagnosis of SMMP who were treated with bronchoscopy at Tianjin Children's Hospital from January 1, 2017, to December 31, 2021. According to the bronchoscopy and pathological examination results, the patients were divided into the PB group and the non-PB group. The clinical manifestations, laboratory data, imaging findings and treatments were analysed.
Results: Data from a total of 306 children with SMMP, including 109 children in the PB group and 197 children in the non-PB group, were reviewed. Procalcitonin (PCT), lactate dehydrogenase (LDH), aspartate aminotransferase (AST), interleukin-6 (IL-6) and bronchial lavage fluid MP-DNA copy number levels were higher (P<0.05) while platelet (PLT) levels were lower (P<0.05) in the PB group. In addition, the incidence of pleural effusion, atelectasis, wheezing symptoms and hypoxemia in the PB group was significantly higher than that in the non-PB group (P<0.05). Multivariate logistic regression analysis showed that pleural effusion (odds ratio [OR], 3.148; 95% confidence interval [CI], 1.795-5.521; P<0.001), PLT (OR, 0.584; 95% CI, 0.439-0.776; P<0.001), and LDH (OR, 5.265; 95% CI, 1.488-18.630; P=0.011) were independent predictors of PB in children with SMPP. Receiver operating characteristic (ROC) curve analysis showed that the cut-off values for PLT and LDH in the diagnosis of PB were 242*109/L [sensitivity 57.80%; specificity 69.04%; area under the curve (AUC) 0.648; P<0.001] and 542 U/L (sensitivity 58.72%; specificity 64.97%; AUC 0.646, P<0.001), respectively. Children in the PB group had longer hospital stays and corticosteroid use durations than those in the non-PB group (P<0.05).
Conclusions: The PLT level (≤242*109/L), LDH level (>542 U/L) and pleural effusion were risk factors for PB in children with SMPP. This provides a basis for the early identification of PB in children with SMPP.