bluuebunny/crossref_metadata_2025_split huggingface dataset:
Glycerol amendment enhances biosulfidogenesis in acid mine drainage-affected areas: An incubation column experiment
Authors: Ilin A. M. , van der Graaf C. M. , Yusta I. , Sorrentino A. , Sánchez-Andrea I. , Sánchez-España J. 
Published: August 2022

Microbial sulfate (SO42−) reduction in Acid Mine Drainage (AMD) environments can ameliorate the acidity and extreme metal concentrations by consumption of protons via the reduction of SO42− to hydrogen sulfide (H2S) and the concomitant precipitation of metals as metal sulfides. The activity of sulfate-reducing bacteria can be stimulated by the amendment of suitable organic carbon sources in these generally oligotrophic environments. Here, we used incubation columns (IC) as model systems to investigate the effect of glycerol amendment on the microbial community composition and its effect on the geochemistry of sediment and waters in AMD environments. The ICs were built with natural water and sediments from four distinct AMD-affected sites with different nutrient regimes: the oligotrophic Filón Centro and Guadiana acidic pit lakes, the Tintillo river (Huelva, Spain) and the eutrophic Brunita pit lake (Murcia, Spain). Physicochemical parameters were monitored during 18 months, and the microbial community composition was determined at the end of incubation through 16S rRNA gene amplicon sequencing. SEM-EDX analysis of sediments and suspended particulate matter was performed to investigate the microbially-induced mineral (neo)formation. Glycerol amendment strongly triggered biosulfidogenesis in all ICs, with pH increase and metal sulfide formation, but the effect was much more pronounced in the ICs from oligotrophic systems. Analysis of the microbial community composition at the end of the incubations showed that the SRB Desulfosporosinus was among the dominant taxa observed in all sulfidogenic columns, whereas the SRB Desulfurispora, Desulfovibrio and Acididesulfobacillus appeared to be more site-specific. Formation of Fe3+ and Al3+ (oxy)hydroxysulfates was observed during the initial phase of incubation together with increasing pH while formation of metal sulfides (predominantly, Zn, Fe and Cu sulfides) was observed after 1–5 months of incubation. Chemical analysis of the aqueous phase at the end of incubation showed almost complete removal of dissolved metals (Cu, Zn, Cd) in the amended ICs, while Fe and SO42− increased towards the water-sediment interface, likely as a result of the reductive dissolution of Fe(III) minerals enhanced by Fe-reducing bacteria. The combined geochemical and microbiological analyses further establish the link between biosulfidogenesis and natural attenuation through metal sulfide formation and proton consumption.
Myocarditis in SARS-CoV-2 infection vs. COVID-19 vaccination: A systematic review and meta-analysis
Authors: Voleti Navya , Reddy Surya Prakash , Ssentongo Paddy 
Published: August 2022

BackgroundThis study aimed to compare the incidence of myocarditis in COVID-19 vaccines and in severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) infection groups.MethodsElectronic databases (MEDLINE, Scopus, Cochrane Central Register of Controlled Trials, Cochrane Database of Systematic Reviews, and the WHO Global Literature on Coronavirus Disease) and trial registries were searched up to May 2022, for randomized controlled trials and observational cohort studies reporting the risk of myocarditis associated with the COVID-19 vaccines and the risk associated with SARS-CoV-2 infection. We estimated the effect of COVID-19 infection and vaccines on rates of myocarditis by random-effects meta-analyses using the generic inverse variance method. Meta-regression analyses were conducted to assess the effect of sex and age on the incidence of myocarditis.ResultsWe identified 22 eligible studies consisting of 55.5 million vaccinated cohorts and 2.5 million in the infection cohort. The median age was 49 years (interquartile range (IQR): 38–56), and 49% (IQR: 43 to 52%) were men. Of patients diagnosed with myocarditis (in both vaccination and COVID-19 cohort) 1.07% were hospitalized and 0.015% died. The relative risk (RR) for myocarditis was more than seven times higher in the infection group than in the vaccination group [RR: 15 (95% CI: 11.09–19.81, infection group] and RR: 2 (95% CI: 1.44-2.65, vaccine group). Of patients who developed myocarditis after receiving the vaccine or having the infection, 61% (IQR: 39–87%) were men. Meta-regression analysis indicated that men and younger populations had a higher risk of myocarditis. A slow decline in the rates of myocarditis was observed as a function of time from vaccination. The risk of bias was low.ConclusionIn this systematic review and meta-analysis, we found that the risk of myocarditis is more than seven fold higher in persons who were infected with the SARS-CoV-2 than in those who received the vaccine. These findings support the continued use of mRNA COVID-19 vaccines among all eligible persons per CDC and WHO recommendations.
Predictors of psychological and physiological measures of graduate student health during COVID-19
Authors: Marashi Maryam , Heisz Jennifer J. 
Published: August 2022

IntroductionThe COVID-19 pandemic brought on higher-than-normal levels of anxiety and depression, especially among graduate students whose academic trajectory was disrupted. However, not all graduate students were affected and therefore, it is important to identify potential protective factors.MethodWe recruited 61 graduate students whose research was directly impacted by the pandemic and examined their change in academic stressors since the onset of the pandemic. Hierarchical regression analyses were used to evaluate how perceived academic stressors brought on by the COVID-19 pandemic impacted anxiety, depression, and heart rate variability (HRV), and whether physical activity and trait resiliency independently buffered against the effects of stress.ResultsGraduate students who reported greater changes in academic stressors since the onset for the pandemic were more anxious and depressed. Moderate-intensity physical activity explained significant variance in anxiety whereas resiliency explained significant variance in both anxiety and depression. HRV was higher in males than females, aligning with sex differences in vulnerability to stress and mental illness.ConclusionOverall, the results suggest that resiliency and physical activity may offer unique protection against symptoms of anxiety and depression in graduate students experiencing increased academic stress during COVID-19. Institutions of higher education should consider investing in programs that encourage physical activity and promote resiliency by teaching mindfulness, stress management, and cognitive behavioral approaches.
Transcriptomic analysis shows that surgical treatment is likely to influence the endometrial receptivity of patients with stage III/IV endometriosis
Authors: Xiang Rui , Chen Peigen , Zeng Zhi , Liu Huijun , Zhou Juan , Zhou Chuanchuan , Peng Jintao , Zeng Haitao 
Published: August 2022

BackgroundEndometriosis negatively affects fertility, and it is a common disease in assisted reproductive practice. Surgical removal of endometriotic lesions is widely carried out to relieve symptoms and promote fertility. But it is not intensively investigated what changes in the secretory eutopic endometrium of patients with endometriosis after surgery.MethodsEighteen patients with stage III/IV endometriosis were included in the study, and they were divided into the untreated group and the treated group (6 vs. 12). Basic clinical data were compared, and transcriptomic data of the secretory eutopic endometrium were analyzed with DESeq2, Cytoscape, ClueGO, CluePedia, and Gene Set Enrichment Analysis (GSEA). CIBERSORT was used to calculate the relative abundance of 22 immune cells in the samples.ResultsWe determined 346 differentially expressed genes (DEGs) using DESeq2. These DEGs were used to enrich seven Gene Ontology terms including three associated with immune processes and one correlated to prostaglandin using ClueGO and CluePedia. GSEA enriched 28 Gene Ontology terms in the treated group mainly associated with immune and blood pressure regulation process. Compared to the untreated group, the relative abundance of resting CD4+ memory T cells [0.218 (0.069, 0.334) vs. 0.332 (0.181, 0.429), P = 0.022] and the even less abundant memory B cells [0.001 (0.000, 0.083) vs. 0.033 (0.007, 0.057), P = 0.049] are significantly decreased in the treated group.ConclusionSurgical treatment of stage III/IV endometriosis influences some genes and biological processes related to endometrial receptivity, but more evidence is needed.
What’s the difference between lung adenocarcinoma and lung squamous cell carcinoma? Evidence from a retrospective analysis in a cohort of Chinese patients
Authors: Wang Wen , Liu Hui , Li Guoli 
Published: August 2022

BackgroundLung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) are the two most common subtypes of lung cancer. Previously, they were categorized into one histological subtype known as non-small cell lung cancer (NSCLC) and often treated similarly. However, increasing evidence suggested that LUAD and LUSC should be classified and treated as different cancers. But yet, detailed differences in clinical features between LUAD and LUSC have not been well described.MethodsA cohort of 142 Chinese patients with 111 LUAD and 31 LUSC cases were consecutively enrolled from April 2019 to October 2020 in Hunan Provincial People’s Hospital. The clinical features of the patients were retrospectively analyzed and compared in the terms of general information, clinicopathologic characteristics, imaging findings and laboratory data.ResultsIn comparison with LUAD, LUSC patients had a significantly higher proportion of males, smokers, drinkers, higher-stage cases. The mean tumor size in LUSC patients was significantly larger than that in LUAD patients. Compared with LUAD patients, more of patients with LUSC had cough, fever and abundant sputum symptoms. Besides that, more bacterial infections and fungal infections were found in LUSC patients than that in LUAD patients. Imaging data shows that ground-glass opacity and patchy shadows in radiological films were more frequent in LUAD patients than that in LUSC patients. In addition to initial laboratory data, LUSC patients had higher levels of leukocytes, platelets, and creatinine that of LUAD patients.ConclusionsTogether, these results suggested that there exist distinct differences between LUAD and LUSC subtypes; LUSC may be a more malignant type in comparison with LUAD. Our findings may have potential implications in clinical settings. However, further multicenter studies are needed to validate these findings in a larger sample size.
Identification of ferroptosis-associated biomarkers for the potential diagnosis and treatment of postmenopausal osteoporosis
Authors: Hu Yunxiang , Han Jun , Ding Shengqiang , Liu Sanmao , Wang Hong 
Published: August 2022

ObjectivePostmenopausal osteoporosis (PMOP) is one of the most commonly occurring conditions worldwide and is characterized by estrogen deficiency as well as persistent calcium loss with age. The aim of our study was to identify significant ferroptosis-associated biomarkers for PMOP.Methods and materialsWe obtained our training dataset from the Gene Expression Omnibus (GEO) database using GSE56815 expression profiling data. Meanwhile, we extracted ferroptosis-associated genes for further analysis. Differentially expressed ferroptosis-associated genes (DEFAGs) between OP patients and normal controls were selected using the “limma” package. We established a ferroptosis-associated gene signature using training models, specifically, random forest (RF) and support vector machine (SVM) models. It was further validated in another dataset (GSE56814) which also showed a high AUC: 0.98, indicating high diagnostic value. Using consensus clustering, the OP patient subtypes were identified. A ferroptosis associated gene (FAG)-Scoring scheme was developed by PCA. The important candidate genes associated with OP were also compared between different ferrclusters and geneclusters.ResultsThere were significant DEFAGs acquired, of which five (HMOX1, HAMP, LPIN1, MAP3K5, FLT3) were selected for establishing a ferroptosis-associated gene signature. Analyzed from the ROC curve, our established RF model had a higher AUC value than the SVM model (RF model AUC:1.00). Considering these results, the established RF model was chosen to be the most appropriate training model. Later, based on the expression levels of the five DEFAGs, a clinical application nomogram was established. The OP patients were divided into two subtypes (ferrcluster A, B and genecluster A, B, respectively) according to the consensus clustering method based on DEFAGs and differentially expressed genes (DEGs). Ferrcluster B and genecluster B had higher ferroptosis score than ferrcluster A and genecluster A, respectively. The expression of COL1A1 gene was significantly higher in ferrcluster B and gencluster B compared with ferrcluster A and gencluster A, respectively, while there is no statistical difference in term of VDR gene, COL1A2 genes, and PTH gene expressions between ferrcluster A and B, together with gencluster A and B.ConclusionsOn the basis of five explanatory variables (HMOX1, HAMP, LPIN1, MAP3K5 and FLT3), we developed a diagnostic ferroptosis-associated gene signature and identified two differently categorized OP subtypes that may potentially be applied for the early diagnosis and individualized treatment of PMOP. The ER gene, VDR gene, IL-6 gene, COL1A1 and COL1A2 genes, and PTH gene are important candidate gene of OP, however, more studies are still anticipated to further elucidate the relationship between these genes and ferroptosis in OP.
Numerical analysis of thermal transportation in nanodiamond and silver-based nanofluid using the Cattaneo–Christov heat flux model
Authors: Zuhra Samina , Sikander Waseem , Elkotb Mohamed Abdelghany , Tag-Eldin E. M. , Khattak Sana Gul , Yassen Mansour F. 
Published: August 2022

Background and Purpose: Studying the effects of suction and injection on heat transportation in nanofluids for time-dependent boundary layer flow is a key topic in fluid dynamics. Aerodynamics and the sciences of space both make extensive use of these types of flow. In this research, nanodiamond and silver nanoparticles in water-type base-fluid nanofluids flow are analyzed under the effects of thermal radiation and non-Fourier theory.Methodology: A mathematical system having certain physical variations of the flow model is converted to a non-dimensional ordinary differential equation system via suitable similarity transformation variables. Then the flow model is numerically solved by RK4 and a shooting technique to describe the dynamics of the nanofluids under varied flow conditions. RK4 with the shooting approach gives a rapid result with high convergence accuracy. The relevant characteristics of physical quantities evaluated by an inclusive numerical scheme are observed for flow pattern, temperature distribution, and nanofluids concentration variations in the presence of suction and injection fluxes.Finding: According to the findings, both ND-H2O and Ag-H2O have outstanding thermal performance characteristics. The Ag-based nanofluid, however, has a better heat transfer capability. To validate the analysis, a graphical and tabular comparison is presented under specified assumptions. The key finding is that, with the injection effect, the heat flow rate is larger than with the suction effect. The unsteadiness parameter causes a drop in the velocity profile, whereas energy distribution rises with this parameter.
Identification of a 5-lncRNA-Based Signature for Immune Characteristics and Prognosis of Lung Squamous Cell Carcinoma and Verification of the Function of lncRNA SPATA41
Authors: Huan Sheng , Chen Miao , Sun Sumin , Zhong Yanling , Chen Yu , Ji Yihao , Yin Guoping 
Published: August 2022

Lung squamous cell carcinoma (LUSC) is one of the most lethal cancers worldwide. Traditional tumor-node-metastasis (TNM) staging system has many insufficiencies in predicting immune characteristics, overall survival (OS), and prognosis of LUSC. LncRNA is currently found involved in tumor development and effectively predicts tumor prognosis. We screened potential tumor-related lncRNAs for immune characteristics and constructed a nomogram combining lncRNA and traditional clinical indicators for prognosis prediction. We obtained the large-scale gene expression profiles of samples from 492 LUSC patients in The Cancer Genome Atlas database. SPATA41, AL034550.2, AP003721.2, AC106786.1, and AC078889.1 were finally screened to construct a 5-lncRNA-based signature. The risk score of the signature divided patients into subgroups of high-risk and low-risk with significant differences in OS. Their area under the curve (AUC) reached more than 0.70 in 1, 3, and 5 years. In addition, compared with the high-risk subgroup, the low-risk subgroup exhibited a remarkably favorable prognosis and TME score, along with a higher immune infiltration score and lower TIDE score. The signature also significantly related to chemotherapy response, especially in cisplatin, vinorelbine, and paclitaxel. Importantly, the nomogram we constructed had good reliability with the assessment of the calibration chart and consistency index (c-index). GO and KEGG enrichment analysis indicated that co-expression mRNAs of the 5 lncRNAs were mainly focused on RNA splicing, DNA replication, and protein serine/threonine kinase activity. Functional assays demonstrated that SPATA41, one of the five OS-related lncRNAs, regulated invasion, migration, proliferation, and programmed death in vitro. In summary, our 5-lncRNA-based signature has a good performance in predicting immune characteristics and prognosis of LUSC patients.
A novel prognostic signature based on cuproptosis-related lncRNA mining in colorectal cancer
Authors: Hou Dong , Tan Jia-nan , Zhou Sheng-ning , Yang Xu , Zhang Zhi-hong , Zhong Guang-yu , Zhong Lin , Yang Bin , Han Fang-hai 
Published: August 2022

Background: Colorectal cancer (CRC) is a common malignant tumor that affects the large bowel or the rectum. Cuproptosis, recently discovered programmed cell death process, may play an important role in CRC tumorigenesis. Long non-coding RNAs (lncRNAs) can alter the proliferation of colorectal cancer cells through the control and activation of gene expression. To date, cuproptosis-related lncRNAs, have not been investigated as potential predictive biomarkers in colorectal cancer.Methods: The mRNA and lncRNA expression data of colorectal cancer were gathered from The Tumor Genome Atlas (TCGA) database, and Pearson correlation analysis and univariate Cox regression analysis were used to identify the lncRNAs with differential prognosis. Colorectal cancer was classified using consistent clustering, and the clinical significance of different types, tumor heterogeneity, and immune microenvironment differences was investigated. The differential lncRNAs were further screened using LASSO regression to develop a risk scoring model, which was then paired with clinicopathological variables to create a nomogram. Finally, the copy number changes in the high-risk and low-risk groups were compared.Results: Two clusters were formed based on the 28 prognostic cuproptosis-related lncRNAs, and the prognosis of cluster 2 was found to be significantly lower than that of cluster 1. Cluster 1 showed increased immune cell infiltration and immunological score, as well as strong enrichment of immune checkpoint genes. Next, LASSO regression was used to select 11 distinctive lncRNAs, and a risk score model was constructed using the training set to distinguish between high and low-risk groups. Patients in the high-risk group had a lower survival rate than those in the low-risk group, and both the test set and the total set produced consistent results. The AUC value of the ROC curve revealed the scoring model’s efficacy in predicting long-term OS in patients. Moreover, the model could be used as an independent predictor when combined with a multivariate analysis of clinicopathological features, and our nomogram could be used intuitively to predict prognosis.Conclusion: Collectively, we developed a risk model using 11 differential lncRNAs and demonstrated that the model has predictive value as well as clinical and therapeutic implications for predicting prognosis in CRC patients.
Immunogenicity of COVID-19 vaccines in patients with diabetes mellitus: A systematic review
Authors: Boroumand Amir Bahador , Forouhi Mahtab , Karimi Farzaneh , Moghadam Arman Soltani , Naeini Leila Ghanbari , Kokabian Pajman , Naderi Delaram 
Published: August 2022

PurposeTo evaluate the immunogenicity of COVID-19 vaccines in patients with diabetes mellitus (DM) through a systematic approach.MethodA comprehensive search was conducted in PubMed, Scopus, and Web of Science with no time restrictions. The search was based on the three main concepts: Covid-19, Vaccine immunogenicity and Diabetes Mellitus.ResultsAfter excluding irrelevant studies, 16 studies remained for the quantitative assay. Among the sixteen studies, eleven had controls. Type of diabetes was specifically mentioned in six studies (T2DM; n=4, T1DM and T2DM; n=2). Twelve of the included studies were conducted on the immunogenicity of vaccines that included mRNA vaccines (i.e. BNT162b2 and mRNA-1273) in DM, five studies included vector-based vaccines (i.e. Ad5-nCoV and ChAdOx1-S), and five studies assessed the immunogenicity of vaccines in DM, including inactivated vaccines (i.e. BBV-152, CoronaVac, Sinopharm or SinoVac). Most of the current studies indicate lower antibody response in patients with DM compared to individuals without DM, after the second dose of vaccine and irrespective of vaccine type. Several studies have shown that higher age and higher BMI are associated with lower antibody response, while optimum glycemic control and higher GFR are associated with higher antibody response among patients with DM.ConclusionImmunogenicity of the vaccines has mostly been reported to be lower among patients with DM compared to healthy controls. There are also few studies assessing variables that significantly affect this association, including age, type of diabetes, BMI, glycemic control and eGFR. Investigating these associations could help us provide the most advantageous condition for patients with DM before, during and after vaccination for optimum antibody response. Many unresolved issues concerning potential factors affecting vaccine immunogenicity, including type of vaccine, numbers of administered doses, re-vaccination intervals and hyperglycemia in patients with DM need to be addressed through future research.