bluuebunny/crossref_metadata_2025_split huggingface dataset:
The construction of ceRNA prognostic regulatory network for ESCA by weighted gene co-expression network analysis and tumor-infiltrating immune cell analysis
Authors: Pang Feng , Bu Su , Liu Chunlai , Mei Yunqing , Zhou Dongsheng , Zhou Lei , Li Qingchuan 
Published: July 2022

Abstract
Esophageal cancer (ESCA) is the most common and aggressive tumor worldwide, and the long-term survival of ESCA patients remains poor. The competing endogenous RNAs (ceRNAs) hypothesis has been mostly applied in the study of molecular biological mechanisms of cancer occurrence and progression. However, studies on comprehensive analysis of lncRNA-miRNA-mRNA ceRNA prognostic regulatory network of ESCA based on high-throughput sequencing and the large-scale sample size is limited. Here, the expression profiles of lncRNAs and mRNAs were retrieved from both 555 Esophagus Mucosa (GTEx) as normal and 162 ESCA samples (TCGA). We applied the limma and edgeR packages to identify differentially expressed mRNAs and lncRNAs. We also applied the weighted gene co-expression network analysis (WGCNA) to identify differentially expressed pattern of mRNAs and lncRNAs. Then we further used MiRcode, starBase, miRTarBase, miRDB, and TargetScan to predict interactions between lncRNAs, miRNAs, and target mRNAs. Importantly, the 275 overlapped genes were analyzed by univariate and multivariate cox proportional hazard regression, and we set up a survival model for 5-year OS with 8 genes (SH3BP4+RUNX3+IGF2+COX20+TIAM2+BCAT1+NME2+HOXC8), of which the AUC was only 0.853 at 5th year. Finally, we constructed a ceRNA network including 99 lncRNAs, 4 miRNAs, and 6 mRNAs through these 8 genes. Consequently, these 6 hub genes might act as prognostic biomarkers and therapeutic targets of ESCA. Furthermore, BCAT1 may be involved in regulating immune cell infiltration and macrophage polarization, Ultimately, We verified that the expression of BCAT1 was significantly increased in Esophageal squamous cell carcinoma tissues, and its expression was correlated with DFS, which may provide new treatment strategies for ESCA.
Akebia saponin D acts via the PPAR-gamma pathway to reprogramme a pro-neurogenic microglia that can restore hippocampal neurogenesis in mice exposed to chronic mild stress
Authors: Zhang Jinqiang , Liu Qin , Su Dapeng , Li Liangyuan , Xiao Chenghong , Jiang Weike , You Zili , Zhou Tao 
Published: August 2022

Abstract

Using drugs to modulate microglial function may be an effective way to treat disorders such as depression that involve impaired neurogenesis. Akebia saponin D (ASD) can cross the blood-brain barrier and exert anti-inflammatory and neuroprotective effects, so we wondered whether it might influence adult hippocampal neurogenesis to treat depression. We exposed C57BL/6 male mice to chronic mild stress (CMS) as a model of depressive-like behaviors, then gave them ASD (40 mg/kg) intraperitoneally once daily for 3 weeks. We investigated the effects of ASD on microglial phenotype, hippocampal neurogenesis, and animal behavior. We found that CMS upregulated pro-inflammatory factors and downregulated anti-inflammatory factors in dentate gyrus of mice, while decreasing sucrose preference and prolonging immobility time in the forced swimming test. CMS also inhibited hippocampal neurogenesis. ASD treatment induced Arg-1+ microglia and increases brain-derived neurotrophic factor (BDNF) expression in the dentate gyrus of CMS mice, and partially reversed all these stress effects. Conditioned medium from microglia treated with ASD and lipopolysaccharide (LPS) strongly increased levels of phospho-TrkB in neural stem/progenitor cells (NSPCs), while promoting their proliferation, survival and neuronal differentiation. An antagonist of TrkB blocked the pro-neurogenic, anti-depressant effects of ASD. Furthermore, ASD activated peroxisome proliferator-activated receptor-gamma (PPAR-γ) in dentate gyrus of CMS mice as well as in primary microglial cultures treated with LPS. Blocking the PPAR-γ using GW9962 suppressed the ASD-reprogrammed Arg-1+ microglia and BDNF expression in dentate gyrus of CMS mice. Such blockade abolished the promoted effects of ASD-treated microglia on NSPC proliferation, survival and neurogenesis. The pro-neurogenic and anti-depressant effects of ASD were blocked by GW9962. These results suggested that ASD acts via the PPAR-γ pathway to induce a pro-neurogenic microglia in dentate gyrus of CMS mice that can increase BDNF expression and promote NSPC proliferation, survival, and neurogenesis. Our results justify further studies of ASD as a potential treatment for depression and may inspire new lines of research targeting the PPAR-γ pathway in disorders involving impaired neurogegammnesis.
A detailed description of the distress trajectory from pre to post treatment in breast cancer patients receiving neoadjuvant chemotherapy
Authors: Lacourt Tamara , Koncz Zsuzsa , Tullos Emily A , Tripathy Debu 
Published: July 2022

Abstract
Purpose: To characterize the distress trajectory in patients with newly diagnosed, non-metastatic breast cancer from pre-neoadjuvant chemotherapy until 12 months after onset of treatment and to identify demographic and clinical predictors of distress in these patients. Methods: In a retrospective, longitudinal study, chart review data were abstracted for 252 eligible patients treated at a comprehensive cancer care center. The center screens for distress at least monthly with the Distress Thermometer; the highest distress score per month was included in the analyses. The growth trajectory was established using mixed modeling and predictors were added to the initial growth model in subsequent models. Results: Distress showed a cubic growth trajectory with highest distress prior to treatment onset followed by a steep decline in the first three months of treatment. A slight increase in distress was apparent over months 6-10. Being Hispanic was associated with a stronger increase in distress in the second half of the year (p=0.012). NACT was associated with lower distress and surgery with higher distress (both: p<0.001). Conclusions: Distress is at its peak prior to treatment onset and rapidly decreases once treatment has started. Oncologist should be aware that both completion of NACT and undergoing surgery are associated with increases in distress and Hispanic patients may be more at risk for an increase in distress at these times; this suggests that careful monitoring of distress during the treatment trajectory and in Hispanic patients in particular in order to provide timely support.
Assessment of Sex Bias in Housekeeping Gene Expression in Adipose Tissue Through the Massive Analysis of Transcriptomics Data
Authors: Guaita-Cespedes Maria , Grillo-Risco Rubén , Hidalgo Marta R. , Fernández-Veledo Sonia , Burks Deborah J. , Iglesia-Vayá María de la , Galán Amparo , Garcia-Garcia Francisco 
Published: July 2022

Abstract
Background: As the housekeeping genes generally involved in maintaining essential cell functions are typically assumed to exhibit constant expression levels across cell types, they are commonly employed as internal controls in gene expression studies. Nevertheless, multiple studies indicate that not all housekeeping genes display stable expression across cells and tissues and under various healthy and diseased conditions, which can introduce systematic errors into experimental results. The selection and validation of housekeeping genes as controls for each studied condition represent crucial steps in ensuring the validity of obtained results; however, up till now, sex has not been typically considered as a biological variable.Methods: In this study, we evaluate the expression profiles of six classical housekeeping genes (four metabolic: GAPDH, HPRT, PPIA, and UBC, and two ribosomal: 18S and RPL19) to determine expression stability in adipose tissues of Homo sapiens and Mus musculus and check sex bias and their overall suitability as internal controls. We also assess the stabile expression of genes included in distinct whole-transcriptome microarrays available from the Gene Expression Omnibus database to identify sex-unbiased housekeeping genes suitable for use as internal controls. We perform a novel computational strategy based on meta-analysis techniques to describe any sexual dimorphisms in mRNA expression stability.Results: Just above half of the considered studies informed properly about the sex of the samples. Found differences in the HKG expression stability in humans between female and male samples, with females presenting greater instability. The extensively used 18S gene displays sex-based variability in adipose tissue, although PPIA and RPL19 do not, and hence, represent robust housekeeping genes. All results generated during this study are readily available by accessing an open web resource (https://bioinfo.cipf.es/metafun-HKG) for consultation and reuse in further studies.Conclusions: This sex-based analysis proves that certain classical housekeeping genes fail to function adequately as controls when analyzing human adipose tissue considering sex as a variable. We confirm RPL19 and PPIA suitability as sex-unbiased human and mouse housekeeping genes derived from sex-specific expression profiles, and propose new ones such as RPS8 and UBB.
Aspirin use and risk of pancreatic ductal adenocarcinoma: A large case-control study
Authors: Sanat Zahra Momayez , Masoudi Sahar , Tabaeian Seidamir Pasha , Shorani Maryam Jameh , Soruri Majid , Pourshams Akram 
Published: July 2022

Abstract
Background
Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest cancers, with a five-year survival rate of approximately 5%. The incidence and mortality rates of PDAC are increasing, and the results of medical treatments remain unsatisfactory. Some conflicting evidence suggests that aspirin intake may reduce the risk of PDAC. This study aimed to evaluate the association between regular low-dose aspirin use (80-mg aspirin tablets, 5–7 tablets/week) and the risk of PDAC.
Methods
This prospective, hospital-based, case-control study was performed on 470 PDAC patients (case group) and 526 controls, who were matched in terms of sex and age, in Tehran, Iran from 2011 to 2018. The participants were interviewed regarding the patterns of aspirin use. Data are expressed as mean ± SD or frequency and percentage as appropriate. Differences in frequency between the case and control groups were evaluated based on the analysis of the contingency table (χ2 test and Fisher’s exact test). The propensity score models were designed to calculate the odds ratios (OR) and 95% confidence intervals (95% CIs) for PDAC with respect to aspirin use, adjusted for age, sex, smoking status, opium use, diabetes mellitus, place of residence, and family history of cancer in first-degree relatives.
Results
About 60% of PDAC patients were male in this study. Nearly 30% of PDAC patients had a family history of cancer in one of their first-degree relatives, 26% were smokers, 16% were opium users, and 15% had a history of diabetes. Aspirin was used by 22.5% of PDAC patients and 18.06% of the controls. Aspirin use (OR: 1.037, 95% CI: 0.95–1.12) was not associated with PDAC. A possible reduction in the risk of PDAC was reported in individuals who used aspirin for more than 10 years (OR: 0.927, 95% CI: 0.86–0.99).
Conclusion
Overall, aspirin use was not associated with a reduced risk of PDAC. Based on the results, long-term aspirin use may play a role in PDAC prevention.
Bioinformatic analysis of ferroptosis-related genes and immune cell infiltration in non-alcoholic fatty liver disease
Authors: zhang huan , Axinbai Malina , Zhao Yuqing , Wei Jiaoyang , Qu Tongshuo , Kong Jinmin , He Yongqiang , Zhang Liping 
Published: August 2022

Abstract
Background
The morbidity and mortality rates for non-alcoholic fatty liver disease (NAFLD) have been steadily increasing in recent years. Studies have shown that ferroptosis plays a significant role in the development of NAFLD, but the exact mechanism has not yet been clarified. This study aimed to identify and validate the potential ferroptosis-related genes involved in NAFLD development and to explore the underlying molecular mechanisms of the disease.
Methods
We downloaded microarray datasets GSE72756 and GSE24807 at the Gene Expression Comprehensive Database to identify deferentially expressed genes (DEGs) between samples from NAFLD and healthy individuals. Among these DEGs, we extracted DEGs related to ferroptosis. Another microarray dataset, GSE89632, was used to validate the ferroptosis-related gene expression. In addition, the protein-protein interaction (PPI) network of ferroptosis-related genes was developed utilizing the STRING online tool. The target genes were also analyzed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. Finally, competing endogenous RNA networks were constructed, and the CIBERSORT package was used to evaluate the infiltration of immune cells in NAFLD.
Results
We identified that five ferroptosis-related genes (SCP2, MUC1, DPP4, SLC1A4, and TF) could be promising diagnostic biomarkers for NAFLD. According to the GO and KEGG enrichment analyses, these ferroptosis-related genes are mainly involved in the metabolic process.NEAT1-miR-1224-5p-SCP2, NEAT1-miR-485-5p-MUC1, MALAT1-miR-485-5p-MUC1, and CNOT6-miR-145-5p-SLC1A4 are likely to be potential RNA regulatory pathways affecting the development of NAFLD. The principal component analysis (PCA) indicated that immune cell infiltration was significantly different between the two tissues.
Conclusions
This work identified five ferroptosis-related genes as potential biomarkers for diagnosing NAFLD. The revealed correlations between the expression levels of these genes and immune cell infiltration might shed light on the study of the molecular mechanism underlying the disease.
Dysregulation of PLOD2 promotes tumor metastasis and invasion in hepatocellular carcinoma
Authors: Li Keren , Niu Yi , Li Kai , Zhong Chengrui , Qiu Zhiyu , Yuan Yichuan , Shi Yunxing , Lin Zhu , Huang Zhenkun , Zuo Dinglan , Yuan Yunfei , Li Binkui 
Published: August 2022

Abstract
Background: Metastasis is a major factor associated with high recurrence and mortality in hepatocellular carcinoma patients while the underlying mechanism of metastasis remains elusive. In our study, PLOD2 was shown to be involved in the process of metastasis in HCC. Methods: TCGA database and HCC tissue microarrays were used to evaluate the expression of genes. In vitro migration, invasion, in vivo subcutaneous tumor model and in vivo lung metastasis assays were used to determine the role of PLOD2 in tumor growth and metastasis in HCC. RNA sequencing and gene set enrichment analysis were performed to uncover the downstream factor of PLOD2 in HCC cells. A luciferase reporter assay was performed to evaluate the interaction between PLOD2 and IRF5.Results: The expression of PLOD2 in HCC tissues was higher than that in adjacent tissues, and increased PLOD2 expression was often found in advanced tumors and was correlated with poor prognosis in HCC patients. In vitro experiments, knockdown of PLOD2 reduced the migration and invasion of human HCC cells. Loss of PLOD2 suppressed human HCC growth and metastasis in a subcutaneous tumor model and a lung metastasis model. BIRC3 was proven to be the downstream factor of PLOD2 in human HCC cells. In addition, PLOD2 was transcriptionally regulated by IRF5 in HCC cells. Conclusion: High expression of PLOD2 was regulated by IRF5, which was correlated with the poor survival of HCC patients. PLOD2 enhanced HCC metastasis via BIRC3, suggesting that PLOD2 might be a valuable prognostic biomarker for HCC treatment.
Microbiological characteristics of bread dough and nutritional quality of “ Tabnen-naow ”, ethnic artisan bread in Burkina Faso
Authors: TAPSOBA François , OUEDRAOGO Nicolas , KAGAMBEGA Boureima , OUEDRAOGO Ali , ZONGO Oumarou , NIKIEMA Fulbert , SAVADOGO Aly 
Published: July 2022

Abstract
This study aimed to evaluate the microbiological characteristics of bread dough and nutritional quality of “Tabnen-naow”, an ethnic artisan bread larged consumed in Burkina Faso. Originate from Boussé, this bread is spreading to the outskirts of Ouagadougou for several reasons such as the increase in the price of industrial bread and especially the supposed low glycemic index of artisanal bread. For purpose, Surveys were conducted among artisan bakers on 5 artisan bread production units in Ouagadougou using survey forms in order to take out the production diagram. The microbiological characteristics of bread dough were evaluated using microbiology standard methods. Lastly, nutritional quality of ethnic artisan bread was determined usind standard techniques. All The bakers were male, between 22 and 34 years old with an average age of 27.8 ± 5.1 years. They all used wheat flour mainly (80%) from the Grand Moulin du Faso (GMF). The baker's dough fermentation used dry or lyophilized yeasts and were carried out at ambient temperature. The interest microorganisms (yeasts, lactic acid bacteria) were present in all the samples of bread dough. The yeast (2.5 108 CFU/g) and lactic acid bacteria were abundant in yeast (2.5 108 CFU/g) apart from the one bread dough which had a low lactic acid bacterial load. The ethnic artisan bread contains carbohydrates (88.20-89.05%), proteins (9.60–10.60%) and minerals such as iron (11.56 to 89.27 mg / kg), calcium (00.00-290.03 mg / kg and zinc (69.18 ± 36.74 to 389.10 ± 32.89 mg / kg). The nutritional composition showed that ethnic artisan bread can contribute significantly to the nutritional diet and food security.
Generalized Properties of Generalized Fuzzy sets GFScom and Its Application
Authors: Zhang Shengli , Chen Jing 
Published: August 2022

Abstract
We further continually develop the theory of a generalized fuzzy set with contradictory, opposite and medium negation (GFScom) . The generalized properties (including convexity and concavity) of GFScom are discussed. By introducing GFScom to Mamdani fuzzy systems, we propose new constructive approaches from any (infinite) input-output data pairs to approximate any continuous function on a compact set to a desired degree of accuracy, and investigate the approximation error bounds for the classes of the constructed fuzzy systems. Furthermore, the new better sufficient conditions for this class of fuzzy systems to be universal approximators are provided. For Mamdani fuzzy systems, the novel conditions require a smaller number of known fuzzy sets than all previously published classical conditions. Finally, we illustrate several cases and compare the new results to published error bounds through numerical cases.
An emerging disease on young apple trees associated with crown and collar canker and necrosis caused by Cytospora balanejica sp. nov. in Iran
Authors: Azizi Razmig , Ghosta Youbert , Ahmadpour Abdollah 
Published: August 2022

Abstract
Apple is the most important fruit tree in West Azarbaijan province of Iran. However, a disease with crown and collar canker and necrosis was observed in three young apple orchards in Urmia, affected 15% and 1% of ‘Red Delicious’ and ‘Golden Delicious’ cultivars, respectively. A fungus with typical characteristics of the asexual morph of Cytospora was regularly isolated from the diseased tissues. Morphological characteristics and phylogenetic analysis inferred from the combined dataset of the ITS–rDNA, parts of LSU, tef1-α, rpb2 and act1 genes revealed that the isolates represent a new species of Cytospora, described herein as Cytospora balanejica sp. nov.. Pathogenicity of all isolates was confirmed on the cv. ‘Red Delicious’ based on Koch’s postulates. Also, the reaction of 12 apple cultivars was assessed against five selected isolates with higher virulence. Results showed that except cv. ‘Braeburn’ which did not produce any symptoms of infection, the other 11 cultivars showed characteristic symptoms including sunken and discolored bark and wood. The mean length of discolored area was different among the 11 so-called susceptible cultivars, hence cvs. ‘M4’ and ‘Golden delicious’ had the highest and the lowest lesion length, respectively. Moreover, the aggressiveness of five tested isolates was varied and the isolates BA 2–4 and BA 3–1 had the highest and lowest aggressiveness, respectively. Based on our observations on the potential ability of the fungus in causing the disease on young and actively growing apple trees, it will be a serious threat to apple cultivation and industry.
Inspection of defects in friction stir welded Al -7075 alloy using computer tomography
Authors: Delgado-Pamanes Miguel , Santana Carlos , Flores-Pinedo Rafael , Cabriales Roberto , Zambrano-Robledo Patricia , Reyes-Osorio Luis A. 
Published: July 2022

Abstract
The identification of defects is of great interest in the high-quality manufacturing of advance materials. The evaluation of tunnel defects in Al-7075 sheets processed by friction stir welding (FSW) using computed tomography (CT) and finite element method is explored in this work. The effect of axial force and temperature generated during the FSW was assessed. Four rotary speeds were evaluated (1600, 1700,1800 and 1900 rpm), each at two different welding speeds (15 and 30 mm/min). These joints are CT-scanned reconstructing the voxels from the X-Ray images. NEO insights software is used for measurement and evaluation of the voxel data from sectioned zones within the welded joints. It was selected a voxel size of 46 mm, a spot size of 59 mm and a magnification of 4.35 using a Cu filter of 0.5mm. The distance from the x-axis of the X-Ray source was 300 mm. The conditions are observed to differ between each welded joint. The 3D images of the welds showed the forms, places, and levels of the detected defects. The tunnel defects were detected at 2 mm form the bottom edge of the weld plates, and the tendency for the defects were reduce for 1900 rpm based on CT scans. The numerical results of FSW revealed that with higher rotational speed, the heat generated, and strain were increased, while the stress was lowered for higher welding speeds. The coupling of CT and numerical results provide an in-depth understanding of material flow and defect formation during friction process.
Efficient lipid production using food waste hydrolysate by Schizochytrium sp. HBW10 isolated from Northern China
Authors: Li Xiaofang , Zhang Yong , Yin Zhe , Zhang Dingding , Li Xinyang , Wang Qiuzhen 
Published: July 2022

Abstract
Marine oleaginous thraustochytrids had attracted increasing attention for their great potential in producing physiological active substances using a wide range of industrial and agricultural waste. Food waste containing abundant nutrients was considered as an excellent feedstock for microbial fermentation. In this study, a thraustochytrid strain Schizochytrium sp. HBW10, was isolated from seawater of Bohai Bay in Northern China for the first time. Further lipid production characteristics of S. sp. HBW10 was investigated utilizing sulfuric acid hydrolysate of food waste (FWH) from two different restaurants (FWH1 and FWH2) with the initial pH adjusted by NaOH or NaHCO 3 . Results showed the highest total fatty acids (TFAs) concentration was observed in FWH2 medium with 50% content level on the fifth day, reaching up to 0.34 g/L. Higher initial pH promoted the growth and saturated fatty acids (SFAs) accumulation of S. sp. HBW10, achieving nearly 100% of sum of saturated and monounsaturated fatty acids (SMUFAs) in TFAs with initial pH7 and pH8 in FWH1 medium. Moreover, continuous CO 2 release in the culture medium provided by NaHCO 3 solution was beneficial for TFAs production, especially linolic acid (C18:2), a functional substance used in the chemical and pharmaceutical industries, which was doubled compared with the FWH1NaOH group on the fifth day. This work demonstrated a possible way for lipid production by thraustochytrids using food waste hydrolysate with higher initial pH (pH7~ pH8) adjusted by NaHCO 3 .