syedzayyan/paper_mill_benchmark huggingface dataset:
Dysosma versipellis Extract Inhibits Esophageal Cancer Progression through the Wnt Signaling Pathway

In this study, we aim to investigate the effect of dysosma versipellis extract on biological behavior of esophageal cancer cells and its underlying mechanisms.Methods.A total of 30 balb/c nude mice (class spf) were equally and randomly divided into the control group, model group, and dysosma versipellis group.Cp-c cell of esophageal cancer was subcutaneously injected into the model group as well as the dysosma versipellis group, and the same amount of normal saline into the control group, in order to compare the tumorigenesis of nude mice of three groups.Wnt, β-catenin, and p-gsk3β/gsk3β expression in tumor tissues was detected using western blot.Cp-c cells in logarithmic growth were selected and divided into 4 groups, including the control group, podophyllotoxin group, wnt activator group, and combined group (mixture of podophyllotoxin and wnt activator).The cell viability, apoptosis, and invasion ability, wnt, β-catenin, and p-gsk3β/gsk3β expression level of cp-c cells in each group were detected via mtt assay, flow cytometry, transwell, and western blot, respectively.Results.The tumorigenesis rates of the control group, model group, and dysosma versipellis group were 0%, 90% (1 tumor-free mouse), and 80% (2 tumor-free mice), respectively.The tumor mass in the dysosma versipellis group was significant less than that in the model group.Based on the results of western blot, wnt, ß-catenin, and p-gsk3β/gsk3β expression of the dysosma versipellis group was lower than that of the control group.The in vitro viability test indicated that there was a significant difference in cell viability exhibited among four groups.Cell viability level in the 3 groups, including the combined group, blank group, and wnt activator group, was higher than the podophyllotoxin group at each time point.In vitro apoptosis assay revealed that significant differences in cell apoptosis exhibited among four groups.Cell apoptosis rate was higher in the podophyllotoxin group compared to the remaining three groups.The wnt activator group showed the lowest cell apoptosis rate.The in vitro invasion assay demonstrated that numbers of transmembrane cell in the 3 groups, involving the combined group, blank group, and wnt activator group, showed a higher level than the podophyllotoxin group.The results of western blot manifested that the podophyllotoxin group showed lower level of wnt, ß-catenin, and p-gsk3β/gsk3β expression compared to the other 3 groups.Conclusion.Podophyllotoxin in dysosma versipellis has an excellent antiesophageal cancer effect and is able to inhibit cell viability as well as invasion ability and promote apoptosis of esophageal cancer cells by inhibiting the wnt signaling pathway, which could be potentially used in future clinical treatment of esophageal cancer.

Journal: Evidence-Based Complementary and Alternative Medicine (2021)
Publication types: Research Article;
Identification of Four Metabolic Subtypes of Glioma Based on Glycolysis-Cholesterol Synthesis Genes

Based on alterations in gene expression associated with the production of glycolysis and cholesterol, this research classified glioma into prognostic metabolic subgroups.In this study, data from the cgga325 and the cancer genome atlas (tcga) datasets were utilized to extract single nucleotide variants (snvs), rna-seq expression data, copy number variation data, short insertions and deletions (in del) mutation data, and clinical follow-up information from glioma patients.Glioma metabolic subtypes were classified using the consensus cluster plus algorithm.This study determined four metabolic subgroups (glycolytic, cholesterogenic, quiescent, and mixed).Cholesterogenic patients had a higher survival chance.Genome-wide investigation revealed that inappropriate amplification of myc and tert was associated with improper cholesterol anabolic metabolism.In glioma metabolic subtypes, the m rna levels of mitochondrial pyruvate carriers 1 and 2 (mpc1/2) presented deletion and amplification, respectively.Differentially upregulated genes in the glycolysis group were related to pathways, including il-17, hif-1, and tnf signaling pathways and carbon metabolism.Downregulated genes in the glycolysis group were enriched in terpenoid backbone biosynthesis, nitrogen metabolism, butanoate metabolism, and fatty acid metabolism pathway.Cox analysis of univariate and multivariate survival showed that risks of glycolysis subtypes were significantly higher than other subtypes.Those results were validated in the cgga325 dataset.The current findings greatly contribute to a comprehensive understanding of glioma and personalized treatment.

Journal: Computational and Mathematical Methods in Medicine (2022)
Publication types: Research Article;
Identification of Differentially Methylated Genes Associated with Clear Cell Renal Cell Carcinoma and Their Prognostic Values

Renal cell carcinoma (rcc) is a heterogeneous disease comprising histologically defined subtypes among which clear cell rcc (cc rcc) accounts for 70% of all rcc cases.Dna methylation constitutes a main part of the molecular mechanism of cancer evolution and prognosis.In this study, we aim to identify differentially methylated genes related to cc rcc and their prognostic values.Methods.The gse168845 dataset was downloaded from the gene expression omnibus (geo) database to identify differentially expressed genes (degs) between cc rcc tissues and paired tumor-free kidney tissues.Degs were submitted to public databases for functional and pathway enrichment analysis, protein-protein interaction (ppi) analysis, promoter methylation analysis, and survival correlation analysis.Results.In the setting of |log2fc| ≥ 2 and adjusted p value &lt;0.05 during differential expression analysis of the gse168845 dataset, 1659 degs between cc rcc tissues and paired tumor-free kidney tissues were sorted out.The most enriched pathways were “t cell activation” and “cytokine-cytokine receptor interaction.” after ppi analysis, 22 hub genes related to cc rcc stood out, among which cd4, ptprc, itgb2, tyrobp, birc5, and itgam exhibited higher methylation levels, and bub1b, cenpf, kif2c, and melk exhibited lower methylation levels in cc rcc tissues compared with paired tumor-free kidney tissues.Among these differentially methylated genes, tyrobp, birc5, bub1b, cenpf, and melk were significantly correlated with the survival of cc rcc patients ( p &lt; 0.001 ).Conclusion.Our study indicates the dna methylation of tyrobp, birc5, bub1b, cenpf, and melk may be promising results for the prognosis of cc rcc.

Journal: Journal of Environmental and Public Health (2023)
Publication types: Research Article;
Observation on the Effect of MRI Image Scanning on Knee Pain in Football Injury

To study the effect of football injury on knee pain based on mri image scanning, in this paper, a total of 31 knee injuries of 29 male professional football players from december 2012 to april 2015 were used as the experimental group.The players were 23.6 ± 3.5 years old and received professional football training time 15.3 ± 3.6 years; 31 outpatients of the same age group with acute knee joint acute injury were randomly selected as the control group; both groups were imaged with a 1.5 tmr scanner and knee joint standard array coil imaging, and 2 senior radiation surgeons evaluate knee cartilage, meniscus, ligaments, tendons, bone marrow, infrapatellar fat pad, and joint effusions.Pearson’s chi-squared test and nonparametric test for two independent samples were used for statistical testing of the evaluation results.The experimental results showed that there were significant differences in the incidence of articular cartilage, lateral collateral ligament, tendon or ligament injury, multiligament or tendon injury, and bone marrow edema between the two groups ( p &lt; 0.05 ).There was no significant difference in the incidence of medial collateral ligament injury, infrapatellar fat pad edema, and joint effusion.Mri shows that knee injuries in male professional football players often involve ligaments or tendons, mostly multiligament or tendon injuries.The lesions of articular cartilage and meniscus are more common and serious, and bone marrow edema is also more common in football injuries.Mri has high diagnostic accuracy for various clinical knee injuries, and it belongs to a noninvasive examination method.It can not only reflect the pathological changes and changes of the knee joints of patients but also provide information for the formulation of clinical programs and the judgment of prognosis, for timely, accurate, and comprehensive imaging reference.

Journal: Scanning (2022)
Publication types: Clinical Study;
Noscapine, an Emerging Medication for Different Diseases: A Mechanistic Review

Noscapine is a benzylisoquinoline alkaloid isolated from poppy extract, used as an antitussive since the 1950s, and has no addictive or euphoric effects.Various studies have shown that noscapine has excellent anti-inflammatory effects and potentiates the antioxidant defences by inhibiting nitric oxide (no) metabolites and reactive oxygen species (ros) levels and increasing total glutathione (gsh).Furthermore, noscapine has indicated antiangiogenic and antimetastatic effects.Noscapine induces apoptosis in many cancerous cell types and provides favourable antitumour activities and inhibitory cell proliferation in solid tumours, even drug-resistant strains, via mitochondrial pathways.Moreover, this compound attenuates the dynamic properties of microtubules and arrests the cell cycle in the g2/m phase.Noscapine can reduce endothelial cell migration in the brain by inhibiting endothelial cell activator interleukin 8 (il-8).In fact, this study aimed to elaborate on the possible mechanisms of noscapine against different disorders.

Journal: Evidence-Based Complementary and Alternative Medicine (2021)
Publication types: Review Article;
Identification of 9 Gene Signatures by WGCNA to Predict Prognosis for Colon Adenocarcinoma

A risk assessment model for prognostic prediction of colon adenocarcinoma (coad) was established based on weighted gene co-expression network analysis (wgcna).Methods.From the cancer genome atlas (tcga) database, rna-seq data and clinical data of coad patients were retrieved.After screening of differentially expressed genes (degs), wgcna was performed to identify gene modules and screen those associated with coad progression.Then, via protein-protein interaction (ppi) network construction of module genes, hub genes were obtained, which were then subjected to the least absolute shrinkage and selection operator (lasso) and cox regression to build a hub gene-based prognostic scoring model.The receiver operating characteristic curve (roc curve) was plotted for the optimal cutoff (oco) of the risk score, based on which, patients were assigned to high or low-risk groups.Areas under the roc curve (aucs) were calculated, and model performance was visualized using kaplan–meier (km) survival curves and verified in the external dataset gse29621.Finally, the model’s independent prognostic value was evaluated by univariate and multivariate cox regression analyses, and a nomogram was built.Results.Totally 2840 degs were screened from coad dataset of tcga, including 1401 upregulated ones and 1439 downregulated ones, which were divided into 10 modules by wgcna.The eigenvalue of the black module was found to have a high correlation with coad progression.Ppi interaction networks were constructed for genes in the black module, and 34 hub genes were obtained by using the mcode plug-in.A lasso-cox regression approach was utilized to analyze the hub genes, and a prognostic risk score model based on the signatures of 9 genes (chek1, depdc1b, fanci, mcm10, ncapg, parpbp, plk4, rad51ap1, and rfc4) was constructed.Km analysis identified shorter overall lower survival in the high-risk group.The model was verified to have favorable predictive ability through training set and validation set.The nomogram, composed of tumor node metastasis (tnm) staging and risk score, was of good predictability.Conclusions.The coad prognostic risk model constructed upon the signatures of 9 genes (chek1, depdc1b, fanci, mcm10, ncapg, parpbp, plk4, rad51ap1, and rfc4) can effectively predict the survival status of coad patients.

Journal: Computational Intelligence and Neuroscience (2022)
Publication types: Research Article;
Citrus Genus and Its Waste Utilization: A Review on Health-Promoting Activities and Industrial Application

Citrus fruits such as oranges, grapefruits, lemons, limes, tangerines, and mandarins, whose production is increasing every year with the rise of consumer demand, are among the most popular fruits cultivated throughout the globe.Citrus genus belongs to the rutaceae family and is known for its beneficial effects on health for centuries.These plant groups contain many beneficial nutrients and bioactive compounds.These compounds have antimicrobial, anticancer, antidiabetic, antiplatelet aggregation, and anti-inflammatory activities.Citrus waste, generated by citrus-processing industries in large amounts every year, has an important economic value due to richness of bioactive compounds.The present review paper has summarized the application and properties of citrus and its waste in some fields such as food and drinks, traditional medicine practices, and recent advances in modern approaches towards pharmaceutical and nutraceutical formulations.

Journal: Evidence-Based Complementary and Alternative Medicine (2021)
Publication types: Review Article;
Hub Genes and Long Noncoding RNAs That Regulates It Associated with the Prognosis of Esophageal Squamous Cell Carcinoma Based on Bioinformatics Analysis

Through bioinformatics analysis methods, the public databases geo and tcga were used to research m rna and squamous cell carcinoma of the esophagus, construct a lnc rna-m rna network, and screen hub genes and lnc rnas related to prognosis.Method.Download esophageal squamous cell carcinoma-related m rna and lnc rna datasets geo and tcga public datasets, as well as clinical data, use bioinformatic tools to perform gene differential expression analysis on the datasets to obtain differentially expressing m rna (dem rna) and lnc rna (delnc rna), and plot volcano plots and cluster heatmaps.The differential intersection of differentially expressed dem rna and delnc rna was extracted by venn diagram and imported into cyto scape software, a regulatory network visualization software, to construct a lnc rna-m rna network and use cyto hubba and mcode plug-ins to screen hub genes and key lnc rnas.The dem rna in the network was imported into the gene and protein interaction retrieval database (string), gene-encoded protein–protein interactions (ppi) network maps were created, and the genes in the ppi network maps were submitted to go functional annotation and pathway enrichment analysis using kyoto encyclopedia of gene genomes (kegg) (kegg).The link between hub gene and prognosis was studied using the clinical data collected by tcga.Result.Retrieve the datasets gse23400 and gse38129 from the geo database and the esophageal squamous cell carcinoma-related m rnas from tcga databases and then obtain intersection.Differentially regulated genes revealed a correlation of 326 (up) with 191 (down) in terms of the differential intersection; for this study, we need to collect the gse130078 dataset from geo, as well as the lnc rnas from tcga databases that are connected to esophageal squamous cell cancer.There were 184 differentially up- and downregulated genes in the differential intersection.A differential intersection network of the differential intersection lnc rna-m rna network allowed us to identify the hub genes, including col5a2 (col3a1), col1a1 (col1a1), ctd-2171n6.1 (ctd-2171n6.1), and rp11-863p13.3 (rp11-863p13.3).The extracellular matrix, which is important in protein digestion and absorption, was shown to be the primary site of functional enrichment, as shown by go/kegg analysis.Squamous cell carcinoma of the mouth and throat is associated with a poor prognosis because of a change in the extracellular matrix structure caused by specific long noncoding rna (lnc rna) regulatory upregulation.Conclusion.For the purpose of predicting the prognosis of cancer of the esophagus, researchers studied the esophageal squamous cell carcinoma-related hub genes and important noncoding rnas (nc rnas).

Journal: Computational and Mathematical Methods in Medicine (2022)
Publication types: Research Article;
Huayu Tongluo Recipe Attenuates Renal Oxidative Stress and Inflammation through the Activation of AMPK/Nrf2 Signaling Pathway in Streptozotocin- (STZ-) Induced Diabetic Rats

Diabetic nephropathy (dn), a severe microvascular complication of diabetes, is one of the leading causes of end-stage renal disease.Huayu tongluo recipe (htr) has been widely used in the clinical treatment of dn in china, and its efficacy is reliable.This study aimed to explore the renoprotective effect of htr and the underlying mechanism.Male sprague-dawley rats were fed with high sugar and fat diet combined with an intraperitoneal injection of stz to establish the diabetic model.Rats in each group were respectively given drinking water, htr, and irbesartan by gavage for 16 weeks.24-hour urine samples were collected every 4 weeks to detect the content of total protein and 8-ohd g.Blood samples were taken to detect biochemical indicators and inflammatory markers at the end of 16th week.Renal tissue was collected to investigate pathological changes and to detect oxidative stress and inflammatory markers.Ampk/nrf2 signaling pathway and fibrosis-related proteins were detected by immunohistochemistry, immunofluorescence, real-time pcr, and western blot.24h urine total protein (24h utp), serum creatinine (scr), blood urea nitrogen (bun), total cholesterol (tc), and triglyceride (tg) were decreased in the rats treated with htr, while there was no noticeable change of blood glucose.Htr administration decreased malondialdehyde (mda) content and increased superoxide dismutase (sod) activity in kidneys, complying with reduced 8-ohd g in the urine.The levels of tnf-α, il-1β, and mcp1 and the expression of nuclear nfκb were also lower after htr treatment.Furthermore, htr alleviated pathological renal injury and reduced the accumulation of extracellular matrix (ecm).Besides, htr enhanced the ampk/nrf2 signaling and increased the expression of ho-1 while it inhibited the nox4/tgf-β1 signaling in the kidneys of stz-induced diabetic rats.Htr can inhibit renal oxidative stress and inflammation to reduce ecm accumulation and protect the kidney through activating the ampk/nrf2 signaling pathway in dn.

Journal: Evidence-Based Complementary and Alternative Medicine (2021)
Publication types: Research Article;
Ginsenoside Rg1 Suppresses Non-Small-Cell Lung Cancer via MicroRNA-126-PI3K-AKT-mTOR Pathway

As one of the most common cause of cancer death in the world, lung cancer causes approximately 1.6 million deaths annually.Among them, nsclc accounts for approximately 85% of patients in whole lung cancer patients.Ginsenoside rg1 has been confirmed to play an important role in various diseases including cancer.As one of mi rnas, mi r-126 closely involves in pathogenesis of the several types of cancers including colorectal, prostate, bladder and gastric cancer, and so on.Thus, the present study aims to investigate effects of the ginsenoside rg1 on nsclc and underlying mechanism.In the study, two lung cancer cell lines including a549 and h1650 were used.It was found that expression of mi r-126 was decreased in pbmc of nsclc patients compared to healthy control.Expression of mi r-126 was decreased in cancer tissue compared to paracancerous tissues in nsclc patients.Importantly, it was found ginsenoside rg1 could inhibit growth of lung cancer cells.Mi r-126 kd remarkably increased the expression of apoptosis genes including caspase 3 and caspase 9 and decreased cell viability in lung cancer cells including a549 and h1650 cells.Interesting, in silico analysis indicated that mi r-126 could target pi3k signaling pathway, which was confirmed by wb assay.Kd of pi3kr2 compromised promotion of mi r-126 on cell apoptosis.Similarly, it was found that kd of m tor compromised promotion of mi r-126 on cell apoptosis.Inhibition of ginsenoside rg1 on growth of lung cancer cells was through mi r-126 and m tor.Thus, the present study confirmed that ginsenoside rg1 remarkably inhibit lung cancer, which is through micro rna-126-pi3k-akt-m tor pathway.

Journal: Evidence-Based Complementary and Alternative Medicine (2022)
Publication types: Research Article;
Fungal- and Algal-Derived Synthesis of Various Nanoparticles and Their Applications

Nanoparticles synthesis through biological mediated methods with a particular focus on the processes mediated by fungi and algae is discussed, which systematically reviews nanoparticle characterization, composition, synthesis methods, and, lastly but not least, the applications of nps across five different categories to provide a reference for future research.Most traditional methods to generate nanoparticles have certain limitations, like the toxicity of precursor materials, the need for high‐temperature management, and the high cost of synthesis, which ultimately hinders their utility in sectors.Greener synthesis through fungus and algae done through bioreduction by biomolecules or enzymes present in them is low‐energy, low‐cost, and needs a low‐temperature environment, providing a unique technique for the manufacture of various metallic nanoparticles utilized in an array of industries and healthcare.

Journal: Bioinorganic Chemistry and Applications (2022)
Publication types: Review Article;
Functional Localizers for Motor Areas of the Brain Using fMRI

Neuroimaging researchers increasingly take advantage of the known functional properties of brain regions to localize motor regions in the brain and investigate changes in their activity under various conditions.Using this noninvasive functional mri (f mri) method makes it possible to identify and localize brain activation.There are many localizers that can be used to identify brain areas, namely, motor areas such as functional localizer, anatomical localizer, or atlas mask.Eighteen right-handed participants were recruited for this research to test the reliability of five localizers for primary motor cortex (m1), supplementary motor area (sma), premotor cortex (pmc), motor cerebellum, and motor thalamus.Motor execution task, namely, hand clenching was used to activate m1, sma, and motor cerebellum.A combined action observation and motor imagery (aomi) task was used to functionally activate pmc.Finally, a mask based on talairach coordinates atlas was created and used to identify the motor thalamus.Our results show that all localizers were successfully activated in the desired regions of interest.Motor execution successfully activated m1, sma, and motor cerebellum.A novel localizer based on aomi was successfully activated in pmc, and the motor thalamus mask obtained from the thalamus mask was successfully implemented on each participant.In conclusion, all five localizers tested in this research were reliable and can be used for rt-f mri neurofeedback research to define the regions of interest.

Journal: Computational Intelligence and Neuroscience (2022)
Publication types: Research Article;