bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of FOXP2 transcription factor on immune infiltration of thyroid cancer and its potential clinical value
Authors: Xu Lianghui , Yang Zheyu , Zhao Qiwu , Feng Haoran , Kuang Jie , Liu Zhuoran , Chen Linxie , Zhan Lin , Yan Jiqi , Cai Wei , Qiu Weihua 
Published: September 2022

BackgroundThe clinical outcomes are not always favorable in certain thyroid cancer patients. The effect of Forkhead-box family on immune cells infiltration and tumor microenvironment in thyroid cancer was explored. The role of FOXP2 in tumor invasion and recurrence was investigated consequently.MethodsTIMER and GEPIA were firstly employed to compare FOXPs expression in normal and cancer tissues from multiple human cancers. The results from database were confirmed by quantitative Real Time-PCR and Western blot in matched thyroid cancer and adjacent normal tissues, in addition to a panel of thyroid cancer cell lines and normal thyroid cell. GEPIA platform was employed to discover the possibility of FOXPs as prognostic indicator. TISIBD and UACLCAN were then employed to estimate the influence of FOXPs on lymph node metastasis and tumor staging. GEPIA analysis was initially employed to analyze correlation of FOXPs and tumor immune infiltrating cells, and TIMER dataset was then included for standardization according to tumor purity.ResultDifferent member of FOXPs showed divergence in expression in various cancer tissues. Lower FOXP1, FOXP2 and higher FOXP3, FOXP4 levels could be identified in thyroid cancer tissues when compared with matched normal tissue. There was an inverse correlation between FOXP2, FOXP4 and immune invasion, whereas FOXP1 and FOXP3 were positively correlated. FOXPs showed remarkable correlations with multiply immune cells. More importantly, only FOXP2 showed the significant effect on recurrence and tumor staging.ConclusionAs immune regulatory factor, the reduction of FOXP2 may affect tumor microenvironments and immune cells infiltration, enhance tumor immune escape, and promote recurrence of thyroid cancer. FOXP2 could be a new potential diagnostic and prognostic marker.
Identification and validation of autophagy-related gene expression for predicting prognosis in patients with idiopathic pulmonary fibrosis
Authors: Huang Guichuan , Xu Xin , Ju Chunrong , Zhong Nanshan , He Jianxing , Tang Xiao Xiao 
Published: September 2022

BackgroundIdiopathic pulmonary fibrosis (IPF) is a chronic, progressive, and fatal fibrotic pulmonary disease with unknow etiology. Owing to lack of reliable prognostic biomarkers and effective treatment measures, patients with IPF usually exhibit poor prognosis. The aim of this study is to establish a risk score prognostic model for predicting the prognosis of patients with IPF based on autophagy-related genes.MethodsThe GSE70866 dataset was obtained from the gene expression omnibus (GEO) database. The autophagy-related genes were collected from the Molecular Signatures Database (MSigDB). Gene enrichment analysis for differentially expressed genes (DEGs) was performed to explore the function of DEGs. Univariate, least absolute shrinkage and selection operator (LASSO), as well as multivariate Cox regression analyses were conducted to identify a multi-gene prognostic model. Receiver operating characteristic (ROC) curve was applied to assess the prediction accuracy of the model. The expression of genes screened from the prognostic model was validated in clinical samples and human lung fibroblasts by qPCR and western blot assays.ResultsAmong the 514 autophagy-related genes, a total of 165 genes were identified as DEGs. These DEGs were enriched in autophagy-related processes and pathways. Based on the univariate, LASSO, and multivariate Cox regression analyses, two genes (MET and SH3BP4) were included for establishing the risk score prognostic model. According to the median value of the risk score, patients with IPF were stratified into high-risk and low-risk groups. Patients in high-risk group had shorter overall survival (OS) than low-risk group in both training and test cohorts. Multivariate regression analysis indicated that prognostic model can act as an independent prognostic indicator for IPF. ROC curve analysis confirmed the reliable predictive value of prognostic model. In the validation experiments, upregulated MET expression and downregulated SH3BP4 expression were observed in IPF lung tissues and TGF-β1-activated human lung fibroblasts, which is consistent with results from microarray data analysis.ConclusionThese findings indicated that the risk score prognostic model based on two autophagy-related genes can effectively predict the prognosis of patients with IPF.
Clinical characteristics of new-onset acute kidney injury in patients with established acute respiratory distress syndrome: A prospective single-center post hoc observational study
Authors: Cui Xiaoyang , Huang Xu , Yu Xin , Cai Ying , Tian Ye , Zhan Qingyuan 
Published: September 2022

BackgroundWe assessed the incidence and clinical characteristics of acute kidney injury (AKI) in acute respiratory distress syndrome (ARDS) patients and its effect on clinical outcomes.MethodsWe conducted a single-center prospective longitudinal study. Patients who met the Berlin definition of ARDS in the medical ICU in China-Japan Friendship Hospital from March 1, 2016, to September 30, 2020, were included. AKI was defined according to the KDIGO clinical practice guidelines. Early and late AKI were defined as AKI occurring within 48 h after ARDS was diagnosed or after 48 h, respectively.ResultsOf the 311 ARDS patients, 161 (51.8%) developed AKI after ICU admission. Independent risk factors for AKI in ARDS patients were age (OR 1.027, 95% CI 1.009–1.045), a history of diabetes mellitus (OR 2.110, 95%CI 1.100–4.046) and chronic kidney disease (CKD) (OR 9.328, 95%CI 2.393–36.363), APACHE II score (OR 1.049, 95%CI 1.008–1.092), average lactate level in the first 3 days (OR 1.965, 95%CI 1.287–3.020) and using ECMO support (OR 2.359, 95%CI 1.154–4.824). Early AKI was found in 91 (56.5%) patients and late AKI was found in 70 (43.5%). Early AKI was related to the patient’s underlying disease and the severity of hospital admission, while late AKI was related to the application of nephrotoxic drugs. The mortality rate of ARDS combined with AKI was 57.1%, which was independently associated with shock (OR 54.943, 95%CI 9.751–309.573).ConclusionA significant number of patients with ARDS developed AKI, and the mortality rate for ARDS patients was significantly higher when combined with AKI. Therapeutic drug monitoring should be routinely used to avoid drug toxicity during treatment.
Patients’ knowledge about their involvement in clinical trials. A non-randomized controlled trial
Authors: Juan-Salvadores Pablo , Michel Gómez Marcela Sánchez , Jiménez Díaz Víctor Alfonso , Martínez Reglero Cristina , Iñiguez Romo Andrés 
Published: September 2022

BackgroundNowadays, good clinical practice should be established in human research. Patient’s rights and autonomy must be respected above the interest of the researcher, making mandatory to raise patient’s awareness on the implications of participating in a clinical study. Contrary to popular belief, this is not always the case. This means that, after signing the informed consent form, some patients have difficulties understanding their responsibilities as participants.Materials and methodsThis study is a prospective, multicenter, non-randomized controlled trial comparative survey conducted on patients enrolled in a clinical trial to evaluate and improve their understanding after an educational intervention was applied to the research staff.ResultsFemales were underrepresented in the clinical trials performed in this study, 21.5%. Most of the participants had a low educational level (74.4%). Around 5 and 10% of the research participants were not aware they were part of a clinical study, and more 24% just trusted in the medical decision to be enrolled. After the interventional education, the following items: “given time and resolution of the patient doubts” (p-value = 0.003), “enough written information” (p-value = 0.006), “explanation of the risks of participating in the study,” (p-value = 0.047) and understanding of the information provided to them showed an improvement regarding the study in which they were participating.ConclusionThe research participants understanding of their involvement in clinical trials is limited. An educational intervention on the research team can improve the process of empowerment and transit of information.
Intramammary infusion of matrine-chitosan hydrogels for treating subclinical bovine mastitis —effects on milk microbiome and metabolites
Authors: Zhang Hua , Wang Ziyue , Yao Hua , Jiang Linshu , Tong Jinjin 
Published: September 2022

BackgroundBovine metabolism undergoes significant changes during subclinical mastitis, but the relevant molecular mechanisms have not been elucidated. In this study we investigated the changes in milk microbiota and metabolites after intramammary infusion of matrine-chitosan hydrogels (MCHs) in cows with subclinical mastitis.MethodsInfusions were continued for 7 days, and milk samples were collected on days 1 and 7 for microbiome analysis by 16S rRNA gene sequencing and metabolite profiling by liquid chromatography-mass spectrometry.ResultsMCHs significantly decreased the somatic cell count on day 7 compared to day 1, and the Simpson index indicated that microbial diversity was significantly lower on day 7. The relative abundance of Aerococcus, Corynebacterium_1, Staphylococcus and Firmicutes was significantly decreased on day 7, while Proteobacteria increased. In the milk samples, we identified 74 differentially expressed metabolites. The MCHs infusion group had the most significantly upregulated metabolites including sphingolipids, glycerophospholipids, flavonoids and fatty acyls. The mammary gland metabolic pathways identified after MCHs treatment were consistent with the known antimicrobial and anti-inflammatory properties of matrine that are associated with glycerophospholipid metabolism and the sphingolipid metabolic signaling pathways.ConclusionThese insights into the immunoregulatory mechanisms and the corresponding biological responses to matrine demonstrate its potential activity in mitigating the harmful effects of bovine mastitis.
Remote diffusion-weighted imaging lesions and blood pressure variability in primary intracerebral hemorrhage
Authors: Xu Xuhua , Peng Shuangshuang , Zhou Yanli , Li Jiawen , Tong Lusha , Gao Feng 
Published: September 2022

ObjectiveThe aim of this study was to examine the association between remote diffusion-weighted imaging lesions (R-DWILs) and blood pressure variability (BPV) in patients with primary intracerebral hemorrhage (ICH).MethodsWe conducted a retrospective review of a consecutive cohort of 375 patients with primary ICH within 24 h onset. R-DWILs were defined as hyperintensity lesions in DWI remote from the hematoma. Blood pressure recordings were extracted up to 24 h post-admission. BPV was measured using SD, coefficient of variation (CV), and successive variation (SV).ResultsRemote DWI lesions were detected in 65 (17.3%) primary ICH patients. In multivariable logistic regression analysis, parameters of BPV were independently associated with R-DWILs, and the results remained consistent after being adjusted with mean SBP. SD, CV, and SV values in the highest quintile, showed 3- to 8-fold increased risk of R-DWILs, compared with the lowest quintile. ΔSBP demonstrated a significant difference in 2 different predictive models. Max SBP only dictated a significant difference in model 1. Mean SBP, admission SBP, and min SBP, failed to present an association with R-DWILs in model 1 or model 2.ConclusionOur results provided additional evidence that BPV is associated with the development of R-DWILs in primary ICH.
Characteristics of menstrual disorders and reproductive hormones in women with epilepsy at an Indonesian national referral hospital
Authors: Octaviana Fitri , Sumapraja Kanadi , Wiratman Winnugroho , Indrawati Luh Ari , Budikayanti Astri 
Published: September 2022

ObjectiveMenstrual disorders are more common in women with epilepsy than in those without epilepsy. This study aimed to examine the characteristics of reproductive function in women with epilepsy at an Indonesian national referral hospital.MethodsA case-control study was conducted from March 2020 to March 2021. Women with and without epilepsy aged ≥18 years were enrolled. All women were premenopausal before epilepsy diagnosis. Data on demographic characteristics, menstrual profiles, epileptic syndrome, seizure type, seizure frequency, etiology, localization, and anticonvulsant medication were collected. Hormone levels (follicle stimulating hormone, luteinizing hormone, prolactin, and estradiol) were measured.ResultsA total of 72 women with and 50 without epilepsy (controls) were included. Dysmenorrhea was more common in women with epilepsy than in those without (59.7 vs. 20%, p &lt; 0.001; odds ratio: 5.931 [95% confidence interval: 2.566–13.709]). Marriage rates were higher in women without epilepsy (82 vs. 45.8%, p &lt; 0.001). No difference was found in hormone levels between the groups. The frequency of seizures was associated with prolactin and estradiol levels (p &lt; 0.001). Polytherapy with clobazam was associated with menstrual cycle regularity. In women with epilepsy with menstrual disorders, valproic acid was associated with higher estradiol levels (p = 0.001) and lamotrigine with lower follicle stimulating hormone levels (p = 0.008).SignificanceWomen with epilepsy experienced more dysmenorrhea. A higher frequency of seizures associated with lower prolactin and estradiol levels. Polytherapy with clobazam was associated with irregular menstrual cycles, while valproic acid and lamotrigine was associated with estradiol and follicle stimulating hormone levels.
A new neurosurgical adjustable pressure suction apparatus with a mechanically controlled air inlet: the study of precise regulation and atraumatic suction
Authors: Nie Pan , Chen Mengxi , Zhang Jibo , Pan Meicheng , Gu Xiqian , Xu Chengshi , Li Zhengwei , Zhang Jianjian , Zhao Wenyuan , Li Xiang , Zhang Jie , Chen Jincao 
Published: September 2022

BackgroundAn essential surgical tool in neurosurgery is the suction tube. The skillful and accurate use of a suction tube facilitates the neurosurgical operation.ObjectiveThis study is to verify the practicality of an adjustable pressure suction tube (APS tube) and to explore the ideal APS tube diameter and tip negative pressure for different intracranial structures.MethodsAPS tubes were used to aspirate brain tissues and carotid arteries of rats. Laser speckle contrast imaging (LSCI) was used to record the blood flow velocity (BFV). We measured APS tube diameter, air inlet size, tip negative pressure and central negative pressure and calculated the correlation between them. In our department, intraoperative real-time parameters including APS tube diameter, length, air inlet size, and central negative pressure were recorded, and the tube tip negative pressure suitable for different intracranial structures and parts was calculated.ResultsAll experiments were carried out using APS tubes. Experiments on rats objectively reflected a severe structural damage to the brain and blood vessels by the suction tube, which might even result in an irreversible reduction in blood flow., Rat carotid arteries and brain tissue suffered severe damage when the tip negative pressure exceeded 33.4 ± 1.8 and 29.2 ± 2.0 kPa, respectively. BFV failed to return to the preoperative level 3 min after the operation (p &lt; 0.05), and this decrease was more pronounced when the suction tube diameter was large (p &lt; 0.05). The tip negative pressure was positively and negatively correlated with central negative pressure and the air inlet size, and was independent of APS tube diameter. A total of 50 operations including 39 tumor resection operations and 11 moyamoya disease bypass operations were recorded. Large-diameter APS tubes (3.5 mm) with an closed air inlet were frequently used to maintain a greater tip negative pressure before the incision of dura mater. When important structures such as motor cortex and brainstem were involved, 1.5- or 2.0-mm-diameter APS tubes were mostly used, and an air inlet was opened up to 0.7–2.1 mm to maintain a safe tip negative pressure (7.4–27.9 kPa).ConclusionAPS tubes with a mechanical knob provide stable and precise adjustment of the tip negative pressure, avoiding excessive negative pressure that causes serious damage to the intracranial structure. And, this allows the surgeon to hold the suction tube more freely and operate at any angle with an appropriate fulcrum near the incision to achieve efficient atraumatic suction and enhance surgical safety.
Metagenomics next-generation sequencing for the diagnosis of central nervous system infection: A systematic review and meta-analysis
Authors: Qu Chunrun , Chen Yu , Ouyang Yuzhen , Huang Weicheng , Liu Fangkun , Yan Luzhe , Lu Ruoyu , Zeng Yu , Liu Zhixiong 
Published: September 2022

ObjectiveIt is widely acknowledged that central nervous system (CNS) infection is a serious infectious disease accompanied by various complications. However, the accuracy of current detection methods is limited, leading to delayed diagnosis and treatment. In recent years, metagenomic next-generation sequencing (mNGS) has been increasingly adopted to improve the diagnostic yield. The present study sought to evaluate the value of mNGS in CNS infection diagnosis.MethodsFollowing the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) 2022 guidelines, we searched relevant articles published in seven databases, including PubMed, Web of Science, and Cochrane Library, published from January 2014 to January 2022. High-quality articles related to mNGS applications in the CNS infection diagnosis were included. The comparison between mNGS and the gold standard of CNS infection, such as culture, PCR or serology, and microscopy, was conducted to obtain true positive (TP), true negative (TN), false positive (FP), and false negative (FN) values, which were extracted for sensitivity and specificity calculation.ResultsA total of 272 related studies were retrieved and strictly selected according to the inclusion and exclusion criteria. Finally, 12 studies were included for meta-analysis and the pooled sensitivity was 77% (95% CI: 70–82%, I2 = 39.69%) and specificity was 96% (95% CI: 93–98%, I2 = 72.07%). Although no significant heterogeneity in sensitivity was observed, a sub-group analysis was conducted based on the pathogen, region, age, and sample pretreatment method to ascertain potential confounders. The area under the curve (AUC) of the summary receiver operating characteristic curve (SROC) of mNGS for CNS infection was 0.91 (95% CI: 0.88–0.93). Besides, Deek's Funnel Plot Asymmetry Test indicated no publication bias in the included studies (Figure 3, p &gt; 0.05).ConclusionOverall, mNGS exhibits good sensitivity and specificity for diagnosing CNS infection and diagnostic performance during clinical application by assisting in identifying the pathogen. However, the efficacy remains inconsistent, warranting subsequent studies for further performance improvement during its clinical application.Study registration numberINPLASY202120002
Key biomarkers and latent pathways of dysferlinopathy: Bioinformatics analysis and in vivo validation
Authors: Xie Yan , Li Ying-hui , Chen Kai , Zhu Chun-yan , Bai Jia-ying , Xiao Feng , Tan Song , Zeng Li 
Published: September 2022

BackgroundDysferlinopathy refers to a group of muscle diseases with progressive muscle weakness and atrophy caused by pathogenic mutations of the DYSF gene. The pathogenesis remains unknown, and currently no specific treatment is available to alter the disease progression. This research aims to investigate important biomarkers and their latent biological pathways participating in dysferlinopathy and reveal the association with immune cell infiltration.MethodsGSE3307 and GSE109178 were obtained from the Gene Expression Omnibus (GEO) database. Based on weighted gene co-expression network analysis (WGCNA) and differential expression analysis, coupled with least absolute shrinkage and selection operator (LASSO), the key genes for dysferlinopathy were identified. Functional enrichment analysis Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were applied to disclose the hidden biological pathways. Following that, the key genes were approved for diagnostic accuracy of dysferlinopathy based on another dataset GSE109178, and quantitative real-time polymerase chain reaction (qRT-PCR) were executed to confirm their expression. Furthermore, the 28 immune cell abundance patterns in dysferlinopathy were determined with single-sample GSEA (ssGSEA).Results1,579 differentially expressed genes (DEGs) were screened out. Based on WGCNA, three co-expression modules were obtained, with the MEskyblue module most strongly correlated with dysferlinopathy. 44 intersecting genes were recognized from the DEGs and the MEskyblue module. The six key genes MVP, GRN, ERP29, RNF128, NFYB and KPNA3 were discovered through LASSO analysis and experimentally verified later. In a receiver operating characteristic analysis (ROC) curve, the six hub genes were shown to be highly valuable for diagnostic purposes. Furthermore, functional enrichment analysis highlighted that these genes were enriched mainly along the ubiquitin-proteasome pathway (UPP). Ultimately, ssGSEA showed a significant immune-cell infiltrative microenvironment in dysferlinopathy patients, especially T cell, macrophage, and activated dendritic cell (DC).ConclusionSix key genes are identified in dysferlinopathy with a bioinformatic approach used for the first time. The key genes are believed to be involved in protein degradation pathways and the activation of muscular inflammation. And several immune cells, such as T cell, macrophage and DC, are considered to be implicated in the progression of dysferlinopathy.
White matter tract changes in pediatric posterior fossa brain tumor survivors after surgery and chemotherapy
Authors: Tanedo Jeffrey , Gajawelli Niharika , Guo Sharon , Baron Nelson Mary , Lepore Natasha 
Published: September 2022

BackgroundSurvivors of pediatric posterior fossa brain tumors are susceptible to the adverse effects of treatment as they grow into adulthood. While the exact neurobiological mechanisms of these outcomes are not yet understood, the effects of treatment on white matter (WM) tracts in the brain can be visualized using diffusion tensor (DT) imaging. We investigated these WM microstructural differences using the statistical method tract-specific analysis (TSA). We applied TSA to the DT images of 25 children with a history of posterior fossa tumor (15 treated with surgery, 10 treated with surgery and chemotherapy) along with 21 healthy controls. Between these 3 groups, we examined differences in the most used DTI metric, fractional anisotropy (FA), in 11 major brain WM tracts.ResultsLower FA was found in the splenium of the corpus callosum (CC), the bilateral corticospinal tract (CST), the right inferior frontal occipital fasciculus (IFOF) and the left uncinate fasciculus (UF) in children with brain tumors as compared to healthy controls. Lower FA, an indicator of microstructural damage to WM, was observed in 4 of the 11 WM tracts examined in both groups of children with a history of posterior fossa tumor, with an additional tract unique to children who received surgery and chemotherapy (left UF).ConclusionsOur findings indicate that a history of tumor in the posterior fossa and surgical resection may have effects on the WM in other parts of the brain.