bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of Transcriptional Pattern Related to Immune Cell Infiltration With Gene Co-Expression Network in Papillary Thyroid Cancer
Authors: Li Meiye , Zhang Jimei , Zhang Zongjing , Qian Ying , Qu Wei , Jiang Zhaoshun , Zhao Baochang 
Published: February 2022

BackgroundA growing body of evidence suggests that immune cell infiltration in cancer is closely related to clinical outcomes. However, there is still a lack of research on papillary thyroid cancer (PTC).MethodsBased on single-sample gene set enrichment analysis (SSGSEA) algorithm and weighted gene co-expression network analysis (WGCNA) tool, the infiltration level of immune cell and key modules and genes associated with the level of immune cell infiltration were identified using PTC gene expression data from The Cancer Genome Atlas (TCGA) database. In addition, the co-expression network and protein-protein interactions network analysis were used to identify the hub genes. Moreover, the immunological and clinical characteristics of these hub genes were verified in TCGA and GSE35570 datasets and quantitative real-time polymerase chain reaction (PCR). Finally, receiver operating characteristic (ROC) curve analysis was used to evaluate the diagnostic value of hub genes.ResultsActivated B cell, activated dendritic cell, CD56bright natural killer cell, CD56dim natural killer cell, Eosinophil, Gamma delta T cell, Immature dendritic cell, Macrophage, Mast cell, Monocyte, Natural killer cell, Neutrophil and Type 17 T helper cell were significantly changed between PTC and adjacent normal groups. WGCNA results showed that the black model had the highest correlation with the infiltration level of activated dendritic cells. We found 14 hub genes whose expression correlated to the infiltration level of activated dendritic cells in both TCGA and GSE35570 datasets. After validation in the TCGA dataset, the expression level of only 5 genes (C1QA, HCK, HLA-DRA, ITGB2 and TYROBP) in 14 hub genes were differentially expressed between PTC and adjacent normal groups. Meanwhile, the expression levels of these 5 hub genes were successfully validated in GSE35570 dataset. Quantitative real-time PCR results showed the expression of these 4 hub genes (except C1QA) was consistent with the results in TCGA and GSE35570 dataset. Finally, these 4 hub genes had diagnostic value to distinguish PTC and adjacent normal controls.ConclusionsHCK, HLA-DRA, ITGB2 and TYROBP may be key diagnostic biomarkers and immunotherapy targets in PTC.
Serum Cystatin C Levels Are Associated With Obesity in Adolescents Aged 14–17 Years
Authors: Huo Ying-Xiang , Wei Wei , Liu Yang , Ma Ya-Nan , Tao Jun-Min , Wang Ning-Ning , Li Xiao-Feng , Chen Xin 
Published: February 2022

BackgroundThe association between serum cystatin C levels and obesity has not been fully explored in adolescents. This study aimed to explore the association between serum cystatin C levels and obesity in adolescents of different sexes.MethodsWe conducted a cross-sectional study including 481 adolescents aged 14−17 years. Cystatin C level was measured by immunoassay. Health examinations data, biochemical parameters, and questionnaire information were collected. The restricted cubic spline model analyzed the association between cystatin C levels and obesity in boys and girls.ResultsBoys exhibited significantly higher cystatin C levels than girls, with a mean level of 0.97 ± 0.10 mg/L in boys and 0.86 ± 0.09 mg/L in girls (P &lt; 0.001). The restricted cubic spline model suggested that low or high cystatin C levels were associated with an increased risk of obesity in boys, whereas only higher cystatin C levels were associated with an increased risk of obesity in girls.ConclusionsA U-shaped correlation was observed between serum cystatin C levels and the risk of obesity in boys. However, in girls, the risk of obesity showed a trend of initially increase and then decrease with increasing cystatin C levels. Longitudinal studies should be conducted to further investigate the diagnostic potential of cystatin C in the progression of early obesity in adolescents of different sexes.
RNA Sequencing of Lake Charr Epidermal Mucus to Assess Molecular Effects of Diluted Bitumen Exposure in a Boreal Lake
Authors: Andrzejczyk Nicolette E. , Palace Vince P. , Hrenchuk Lee , Peters Lisa , Schlenk Daniel 
Published: February 2022

Transport of diluted bitumen (dilbit) from Canada’s oil sands region poses risk for leaks and spills of petroleum-derived contaminants into the environment. Exposure of fish to dilbit is known to cause cardiotoxicity, developmental deformities, and impairment in swim performance. However, previous studies have examined the toxicity of dilbit in laboratory settings which does not account for environmental and biological food-web variables that may alter exposure and/or toxicity of dilbit. Moreover, most methods of assessing organism health following oil exposure require lethal sampling. This work is a part of a larger set of experiments where dilbit spills were simulated within enclosures on a lake; the present study assesses the impacts of residual levels of dilbit that may have entered the surrounding lake environment from the enclosures following model spill cleanup. In order to understand the impacts of residual dilbit in an ecosystem setting without use of lethal sampling, epidermal mucus was collected and sequenced from lake charr (Salvelinus namaycush) exposed to residual dilbit in a boreal lake. While concentrations reached a maximum of 2.29 μg/L total polycyclic aromatic compounds (ΣPAC) within surface waters, surface water ΣPAC concentrations generally remained below 1 μg/L. Results of RNA sequencing were compared to sequencing data from mucus collected prior to dilbit additions. Differential gene expression and pathway analyses indicated dysregulation of genes associated with intermediary and energy metabolism as well as a trend in upregulation of cyp1a3 in epidermal mucus following dilbit exposure. Thus, results of the present study suggest that lake charr undergo consistent biological responses after exposure to residual levels of dilbit following a model spill, and that mRNA-based analysis of mucus may be a viable method for non-lethal oil exposure assessment. Overall, the results provide insight on the response of wild fish to very dilute dilbit exposures after a model spill cleanup.
Determination of CSF GFAP, CCN5, and vWF Levels Enhances the Diagnostic Accuracy of Clinically Defined MS From Non-MS Patients With CSF Oligoclonal Bands
Authors: Probert Fay , Yeo Tianrong , Zhou Yifan , Sealey Megan , Arora Siddharth , Palace Jacqueline , Claridge Timothy D. W. , Hillenbrand Rainer , Oechtering Johanna , Kuhle Jens , Leppert David , Anthony Daniel C. 
Published: February 2022

BackgroundInclusion of cerebrospinal fluid (CSF) oligoclonal IgG bands (OCGB) in the revised McDonald criteria increases the sensitivity of diagnosis when dissemination in time (DIT) cannot be proven. While OCGB negative patients are unlikely to develop clinically definite (CD) MS, OCGB positivity may lead to an erroneous diagnosis in conditions that present similarly, such as neuromyelitis optica spectrum disorders (NMOSD) or neurosarcoidosis.ObjectiveTo identify specific, OCGB-complementary, biomarkers to improve diagnostic accuracy in OCGB positive patients.MethodsWe analysed the CSF metabolome and proteome of CDMS (n=41) and confirmed non-MS patients (n=64) comprising a range of CNS conditions routinely encountered in neurology clinics.ResultsOCGB discriminated between CDMS and non-MS with high sensitivity (85%), but low specificity (67%), as previously described. Machine learning methods revealed CCN5 levels provide greater accuracy, sensitivity, and specificity than OCGB (79%, +5%; 90%, +5%; and 72%, +5% respectively) while glial fibrillary acidic protein (GFAP) identified CDMS with 100% specificity (+33%). A multiomics approach improved accuracy further to 90% (+16%).ConclusionThe measurement of a few additional CSF biomarkers could be used to complement OCGB and improve the specificity of MS diagnosis when clinical and radiological evidence of DIT is absent.
Immune Response Is Key to Genetic Mechanisms of SARS-CoV-2 Infection With Psychiatric Disorders Based on Differential Gene Expression Pattern Analysis
Authors: Xia Jing , Chen Shuhan , Li Yaping , Li Hua , Gan Minghong , Wu Jiashuo , Prohaska Clare Colette , Bai Yang , Gao Lu , Gu Li , Zhang Dongfang 
Published: February 2022

Existing evidence demonstrates that coronavirus disease 2019 (COVID-19) leads to psychiatric illness, despite its main clinical manifestations affecting the respiratory system. People with mental disorders are more susceptible to COVID-19 than individuals without coexisting mental health disorders, with significantly higher rates of severe illness and mortality in this population. The incidence of new psychiatric diagnoses after infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is also remarkably high. SARS-CoV-2 has been reported to use angiotensin-converting enzyme-2 (ACE2) as a receptor for infecting susceptible cells and is expressed in various tissues, including brain tissue. Thus, there is an urgent need to investigate the mechanism linking psychiatric disorders to COVID-19. Using a data set of peripheral blood cells from patients with COVID-19, we compared this to data sets of whole blood collected from patients with psychiatric disorders and used bioinformatics and systems biology approaches to identify genetic links. We found a large number of overlapping immune-related genes between patients infected with SARS-CoV-2 and differentially expressed genes of bipolar disorder (BD), schizophrenia (SZ), and late-onset major depressive disorder (LOD). Many pathways closely related to inflammatory responses, such as MAPK, PPAR, and TGF-β signaling pathways, were observed by enrichment analysis of common differentially expressed genes (DEGs). We also performed a comprehensive analysis of protein–protein interaction network and gene regulation networks. Chemical–protein interaction networks and drug prediction were used to screen potential pharmacologic therapies. We hope that by elucidating the relationship between the pathogenetic processes and genetic mechanisms of infection with SARS-CoV-2 with psychiatric disorders, it will lead to innovative strategies for future research and treatment of psychiatric disorders linked to COVID-19.
S100A12 as Biomarker of Disease Severity and Prognosis in Patients With Idiopathic Pulmonary Fibrosis
Authors: Li Yupeng , He Yaowu , Chen Shibin , Wang Qi , Yang Yi , Shen Danting , Ma Jing , Wen Zhe , Ning Shangwei , Chen Hong 
Published: February 2022

BackgroundIdiopathic pulmonary fibrosis (IPF) is one of interstitial lung diseases (ILDs) with poor prognosis. S100 calcium binding protein A12 (S100A12) has been reported as a prognostic serum biomarker in the IPF, but its correlation with IPF remains unclear in the lung tissue and bronchoalveolar lavage fluids (BALF).MethodsDatasets were collected from the Gene Expression Omnibus (GEO) database. Person correlation coefficient, Kaplan–Meier analysis, Cox regression analysis, functional enrichment analysis and so on were used. And single cell RNA-sequencing (scRNA-seq) analysis was also used to explore the role of S100A12 and related genes in the IPF.ResultsS100A12 was mainly and highly expressed in the monocytes, and its expression was downregulated in the lung of patients with IPF according to scRNA-seq and the transcriptome analysis. However, S100A12 expression was upregulated both in blood and BALF of patients with IPF. In addition, 10 genes were found to interact with S100A12 according to protein–protein interaction (PPI) network, and the first four transcription factors (TF) targeted these genes were found according to hTFtarget database. Two most significant co-expression genes of S100A12 were S100A8 and S100A9. The 3 genes were significantly negatively associated with lung function and positively associated with the St. George’s Respiratory Questionnaire (SGRQ) scores in the lung of patients with IPF. And, high expression of the 3 genes was associated with higher mortality in the BALF, and shorter transplant-free survival (TFS) and progression-free survival (PFS) time in the blood. Prognostic predictive value of S100A12 was more superior to S100A8 and S100A9 in patients with IPF, and the composited variable [S100A12 + GAP index (gender, age, and physiological index)] may be a more effective predictive index.ConclusionThese results imply that S100A12 might be an efficient disease severity and prognostic biomarker in patients with IPF.
Comparison Between Different Composite Resins Used for Clear Aligner Attachments: An In-Vitro Study
Authors: Gazzani Francesca , Bellisario Denise , Quadrini Fabrizio , Parrinello Francesca , Pavoni Chiara , Cozza Paola , Lione Roberta 
Published: February 2022

Attachments are specific features of clear aligner treatment designed to ensure the aligner’s retention and the predictability of tooth movements. The properties of composite resin used for their reproduction play a relevant role to preserve their integrity and shape over the time. Thus, the aim of the present evaluation was to compare the mechanical properties and the wear performance of two nanocomposite by means of mechanical and tribological tests. Twelve samples for both flowable nanocomposite (FNC) and conventional nanocomposite (CNC) were created. The two nanocomposites differ in terms of filler volume and viscosity of the mixture. The following tests were performed: thermal analysis and burning test; flat instrumented indentation test and a compression stress relaxation test; tribological analysis. Wear evaluation was performed by means of a contact probe surface profiler and a TayMap software for the 3D analysis. A customized step-sliding test was conducted to simulate the clinical application of materials with a polymethyl methacrylate (PMMA) ball used as counterpart. Wear evaluation of both resin surfaces and PMMA ball was performed. No differences were found in terms of polymeric nature and quantity of nanoparticles in the matrix. FNC showed lower density values (1.62 g/cm3 ± 0.02) and inorganic percentage residue (41%) than the CNC (respectively 1.95 g/cm3 ± 0.01 and 23%). Significant differences in terms of decrement of stress values, elastic modulus (1,114.12 ± 91.39 MPa), and stress relaxation rate (24.39% ± 3.23) were observed for the CNC when compared to the FNC (respectively, 835.04 ± 184.73 MPa and 40.19% ± 4.65). FNC showed higher values of dynamic friction coefficient (0.72 ± 0.017) and more worn and deeper profiles than the conventional ones. The step-sliding test with a PMMA ball confirmed a higher friction coefficient for FNC and a greater wear of the PMMA surfaces when used against flowable samples. Lower viscosity of FNC ensures a better adaptation during clinical attachment fabrication, whereas it has a negative impact on mechanical properties. CNC showed greater performance and resistance under mechanical stresses than the flowable ones, resulting in being more suitable for clinical needs.
Prevalence of Antibodies to SARS-CoV-2 Following Natural Infection and Vaccination in Irish Hospital Healthcare Workers: Changing Epidemiology as the Pandemic Progresses
Authors: Allen Niamh , Brady Melissa , Ni Riain Una , Conlon Niall , Domegan Lisa , Carrion Martin Antonio Isidro , Walsh Cathal , Doherty Lorraine , Higgins Eibhlin , Kerr Colm , Bergin Colm , Fleming Catherine 
Published: February 2022

BackgroundIn October 2020 SARS-CoV-2 seroprevalence among hospital healthcare workers (HCW) of two Irish hospitals was 15 and 4. 1%, respectively. We compare seroprevalence in the same HCW population 6 months later, assess changes in risk factors for seropositivity with progression of the pandemic and serological response to vaccination.MethodsAll staff of both hospitals (N= 9,038) were invited to participate in an online questionnaire and SARS-CoV-2 antibody testing in April 2021. We measured anti-nucleocapsid and anti-spike antibodies. Frequencies and percentages for positive SARS-CoV-2 antibodies were calculated and adjusted relative risks for participant characteristics were calculated using multivariable regression analysis.ResultsFive thousand and eighty-five HCW participated. Seroprevalence increased to 21 and 13%, respectively; 26% of infections were previously undiagnosed. Black ethnicity (aRR 1.7, 95% CI 1.3–2.2,p&lt; 0.001), lower level of education (aRR 1.4 for secondary level education, 95% CI 1.1–1.8,p= 0.002), living with other HCW (aRR 1.2, 95% CI 1.0–1.4,p= 0.007) were significantly associated with seropositivity. Having direct patient contact also carried a significant risk being a healthcare assistant (aRR 1.8, 95% CI 1.3–2.3,p&lt; 0.001), being a nurse (aRR 1.4, 95% CI 1.0–1.8,p= 0.022), daily contact with COVID-19 patients (aRR 1.4, 95% CI 1.1–1.7,p= 0.002), daily contact with patients without suspected or confirmed COVID-19 (aRR 1.3, 95% CI 1.1–1.5,p= 0.013). Breakthrough infection occurred in 23/4,111(0.6%) of fully vaccinated participants; all had anti-S antibodies.ConclusionThe increase in seroprevalence reflects the magnitude of the third wave of the pandemic in Ireland. Genomic sequencing is needed to apportion risk to the workplace vs. the household/community. Concerted efforts are needed to mitigate risk factors due to ethnicity and lower level of education, even at this stage of the pandemic. The undiagnosed and breakthrough infections call for ongoing infection prevention and control measures and testing of HCW in the setting of close contact. Vaccinated HCW with confirmed infection should be actively assessed, including SARS-CoV-2 whole genome sequencing (WGS), serology testing and assessment of host determinants, to advance understanding of the reasons for breakthrough infection.
Periodontitis and Subsequent Risk of Cataract: Results From Real-World Practice
Authors: Yeh Li-Jen , Shen Te-Chun , Sun Kuo-Ting , Lin Cheng-Li , Hsia Ning-Yi 
Published: February 2022

BackgroundPeriodontitis can lead to systemic inflammation and oxidative stress, contributing to the development of various diseases. Periodontitis could also be associated with several ocular diseases.MethodsWe conducted a retrospective population-based cohort study using the National Health Insurance Research Database of Taiwan to evaluate the risk of cataract in people with and without periodontitis. We established a periodontitis cohort and a non-periodontitis cohort, which included 359,254 individuals between 2000 and 2012. Age, gender, and enrolled year were matched. All participants were monitored until the end of 2013. Cox proportional hazard models were applied to estimate hazard ratios (HRs) and confidence intervals (CIs).ResultsPatients with periodontitis had a significantly higher risk to develop cataract than those without periodontitis [10.7 vs. 7.91 per 1,000 person-years, crude HR = 1.35 (95% CI = 1.32–1.39), and adjusted HR = 1.33 (95% CI = 1.30–1.36)]. The significant levels remained the same after stratifying by age, gender, presence of comorbidity, and use of corticosteroid. In addition, we found that diabetes mellitus and hyperlipidemia had a synergistic effect in the interaction of periodontitis and cataract development.ConclusionPatients with periodontitis have a higher risk of cataract development than those without periodontitis. Such patients may request frequent ocular health check-up. Further studies should be performed to confirm the association and to understand the mechanisms.
Classification of Hepatocellular Carcinoma Based on N6-Methylandenosine–Related lncRNAs Profiling
Authors: Yin Lu , Zhou Liuzhi , Gao Shiqi , Feng Yina , Zhu Hanzhang , Xiang Jingjing , Xu Rujun 
Published: February 2022

HCC is one of the most common types of malignancies worldwide and the fourth-leading cause of cancer deaths. Thus, there is an urgent need to search for novel targeted therapies in HCC. 186 m6a-related lncRNAs were screened for subsequent analysis. Two distinct m6A modification clusters were identified to be associated with the overall prognosis in TCGA-LIHC based on the m6A-related lncRNAs profiling, followed by univariate Cox regression analysis. In addition, four m6A-related lncRNAs prognostic signatures were developed and validated that could predict the OS of HCC patients, followed by univariate Cox regression, LASSO regression, and multivariate Cox regression analysis. Moreover, four m6A-related lncRNAs were identified to be related to HCC prognosis. ESTIMATE was used to evaluate the stromal score, immune score, ESTIMATE score, and tumor purity of each HCC sample. ssGSEA was performed to identify the enrichment levels of 29 immune signatures in each sample. Finally, quantitative real-time polymerase chain reaction shown that KDM4A-AS1, BACE1-AS, and NRAV expressions were upregulated in HCC patients. We proved that our m6A-related lncRNAs signature had powerful and robust ability for predicting OS of different HCC subgroups.
Melatonin Treatment for Sleep Disorders in Parkinson's Disease: A Meta-Analysis and Systematic Review
Authors: Ma Hongxia , Yan Junqiang , Sun Wenjie , Jiang Menghan , Zhang Yongjiang 
Published: February 2022

ObjectiveThe efficacy of melatonin on sleep disorders in Parkinson's disease (PD) is still unclear. The purpose of this study was to investigate the efficacy of melatonin on sleep disorders in PD by summarizing evidence from randomized clinical trials (RCTs).MethodsPubMed, Cochrane Library, EMBASE, and Web of Science databases were searched for studies published before 20 August 2021. Results were analyzed using Review Manager 5.2 software. We used Trial Sequential Analysis (TSA) software to avoid false-positive results caused by random errors.ResultsWe included 7 studies in this systematic review and meta-analysis. The results of the meta-analysis showed that compared with placebo, the subjective sleep quality of patients with PD significantly improved after melatonin treatment (MD = −2.19, 95% CI: −3.53 to −0.86, P = 0.001). In the systematic review, we qualitatively analyzed the efficacy of melatonin on the objective sleep quality of patients with PD, and the results showed that melatonin exerted a positive effect with good safety and tolerability. However, there was no significant improvement in excessive daytime sleepiness assessed by the Epworth Sleepiness Scale (ESS).ConclusionWe found that melatonin can significantly improve the subjective and objective sleep quality of patients with PD with good safety and tolerability. Melatonin could be considered an effective treatment for insomnia in patients with PD.
Toward a Feasible Solution for Removing Toxic Mercury and Chromium From Water Using Copper Oxide Nanoparticles
Authors: Raul Prasanta K. , Das Bodhaditya , Umlong Iohborlang M. , Devi Rashmi Rekha , Tiwari Gaurav , Kamboj Dev Vrat 
Published: February 2022

Objective: Water contaminated with heavy metals causes serious environmental issues for people. Mercury and chromium are considered to be extremely toxic for public health. Diversified technologies have been introduced to purify contaminated water; however, only a few become successful in reducing mercury and chromium below the permissible limit of drinking water (0.001 and 0.05 ppm, respectively, WHO/BIS Guidelines). Our main aim was to synthesize suitable nanoscale materials to make water potable by removing mercury and chromium from contaminated water while keeping essential elements as per the WHO/BIS guidelines.Methods: Copper(II) oxide nanomaterials are synthesized following a wet chemical process as per earlier reported procedures. Nanoparticles with average diameter of 10–20 nm are formed. XRD confirms the formation of orthorhombic CuO nanoparticles.Results: The nanoparticles are efficient in removing mercury from 200 ppb to less than 50 ppb (75%) and chromium from 200 ppb to less than 16 ppb (92%) over a wide range of pH.Conclusion: The nanomaterials have great potential in removing toxic heavy metals from contaminated water. The materials can be applied to integrated water purification systems to produce potable water.