syedzayyan/paper_mill_benchmark huggingface dataset:
Impact of Light and Temperature on Growth, Intracellular and Extracellular Pigment, and Lovastatin Yield by Monascus ruber in Synthetic Medium

The development of alternate sources for the production of natural pigments has been targeted to overcome the utilization of artificial coloring, which is dangerous to human health and the environment.Dyes extracted from microbial sources are more important for beneficial food industry use, especially monascus spp.Produces several critical secondary metabolites such as lovastatin, g-amino butyric acids, monascodilone, monascorubramine, monascin, ankaflavin, rubropunctatin, and citrinin.Lovastatin is a fungal polyketide that inhibits the rate-limiting enzymes hmg-co a reductase, an essential precursor in cholesterol biosynthesis.The light source regulates fungi’ growth, metabolism, and reproduction and is necessary for fungi’ existence and distribution.The impact of different color lights (red, green, blue, yellow, and white, darkness) and different temperatures (27°c and 37°c) on extracellular and intracellular pigment yield, lovastatin production, and biomass of monascus ruber was studied, and appropriate incubation temperature and time enhance the intracellular, extracellular pigment, and biomass production.However, when exposed to other color lights, fungus growth and pigment yield are significantly reduced in monascus ruber.Then, fungi and pigment yield development is decreased when exposed to other color lights.It can be concluded that darkness influenced pigment production and biomass yield at both temperatures (27°c and 37°c).Similarly, the production of lovastatin and its concentration were analyzed by hplc.The highest concentration of lovastatin was obtained at 27°c when exposed to red color light (302.6 mg/ml for extracellular fermentation broth) and (86.7 mg/ml for intracellular fermentation broth).At 37°c, the highest concentration of lovastatin was obtained from (571.5 mg/ml extracellular fermentation broth) when exposed to darkness and (170.4 mg/ml intracellular fermentation broth) exposed to red color light.Thus, the result provides the knowledge to enable us to explore the pigments and lovastatin yield for functional foods and large-scale industrial applications.

Journal: Advances in Materials Science and Engineering (2022)
Publication types: Research Article;
Improvement of Cerebral Ischemia-Reperfusion Injury via Regulation of Apoptosis by Exosomes Derived from BDNF-Overexpressing HEK293

Brain‐derived neurotrophic factor (bdnf) provides neuroprotective effects towards therapeutic cerebral ischemia‐reperfusion (i/r) injury.This view has been proposed by more and more evidence.However, due to the lack of permeability of the blood‐brain barrier (bbb) as well as the brief half‐life in serum, clinical application is not widespread.To study the participation of exosomes containing bdnf in i/r, we isolated exosomes from bdnf‐overexpressing hek293.The protective outcomes of exosomes in hypoxia/reoxygenation (h/r) experiments were determined by the use of sy‐5y cells.Exosome‐bdnf therapy restrained h/r‐induced apoptosis by inhibition of the reducing levels of oxidative stress and calcium ions in the cells while maintaining stable levels of mitochondrial membrane potential in brain cells damaged by i/r.We then constructed a cerebral i/r injury model using sd rats to find the function of bdnf in exosome‐mediated neuroprotection.The in vivo experiments conducted established that exosomes from bdnf‐overexpressing hek293 cells improved cerebral i/r injury by concealing neuronal apoptosis.Findings gained demonstrated that bdnf is a part of preventing cerebral i/r injury due to exosome mediation by regulating the cellular internal environment and inhibiting apoptosis.

Journal: BioMed Research International (2021)
Publication types: Research Article;
Lagerstroemia speciosa Ameliorated Blood Pressure in LNAME Induced Hypertension in Experimental Rats through NO/cGMP and Oxidative Stress Modulation

Cardiovascular disease is the primary reason for chronic heart diseases and mortality worldwide.Hypertension (htn) is the utmost dominant risk factor for the evolution of several diseases.Herbal medicines, traditional medicinal herbs, and their extracts are widely utilized to treat and monitor htn.Herbal components have been shown to help relax arteries and lower oxidative stress.The current study assesses the probable role of herbal plant extract lagerstroemia speciosa (ls) in the lname induced htn in rats.Lname (50 mg/100 m l) in drinkable water was given to rats for five weeks.There was a significant upsurge in lname‐treated hypertensive rats’ blood pressure (bp).On treatment with ls, it ameliorates blood pressure.Further, ls also improved body weight, reduced heart weight, and heart hypertrophy.The no/c gmp concentration was lowered along with a substantial upsurge in the level of glutathione and a decline in mda level.The ls extract also reduced the inflammatory cytokine markers in the systemic circulation.In conclusion, thus, the extract of ls treatment can efficiently alleviate the bp, oxidative stress markers, and inflammation and improve no/c gmp concentration in lname induced htn in rats.

Journal: BioMed Research International (2022)
Publication types: Research Article;
IL-32 Promotes the Radiosensitivity of Esophageal Squamous Cell Carcinoma Cell through STAT3 Pathway

This study is set out to determine the relationship between il‐32 and radiosensitivity of esophageal squamous cell carcinoma (escc).Methods .Western blot was adopted for measuring il‐32 expression in eca‐109 and te‐10 cells.Eca‐109 and te‐10 cells with interference or overexpression of il‐32 were treated with the presence or absence of x‐ray irradiation.Then, the use of cck8 assay was to detect proliferation ability, and effects of il‐32 expression on radiosensitivity of escc were tested by colony formation assay.The cell apoptosis was detected using flow cytometry.Stat3 and p‐stat expression, and apoptotic protein bax were detected by western blot.Results .Colony formation assay and cck8 assay showed that compared with the nc group without treatment, the growth of the escc cells, that is eca‐109 and te‐10, was significantly inhibited in the oe+ir group with highly expressed il‐32 and irradiation.In flow cytometry analysis, in eca‐109 and te‐10 cells, highly expressed il‐32 combined with irradiation significantly increased apoptosis compared with the control group.Highly expressed il‐32 has a synergistic effect with irradiation, inhibiting stat3 and p‐stat3 expression and increasing apoptotic protein bax expression.Conclusion .Il‐32 can improve the radiosensitivity of escc cells by inhibiting the stat3 pathway.Therefore, il‐32 can be used as a new therapeutic target to provide a new attempt for radiotherapy of escc.

Journal: BioMed Research International (2021)
Publication types: Research Article;
Identification of Molecular Biomarkers and Key Pathways for Esophageal Carcinoma (EsC): A Bioinformatics Approach

Esophageal carcinoma (es c) is a member of the cancer group that occurs in the esophagus; globally, it is known as one of the fatal malignancies.In this study, we used gene expression analysis to identify molecular biomarkers to propose therapeutic targets for the development of novel drugs.We consider es c associated four different microarray datasets from the gene expression omnibus database.Statistical analysis is performed using r language and identified a total of 1083 differentially expressed genes (degs) in which 380 are overexpressed and 703 are underexpressed.The functional study is performed with the identified degs to screen significant gene ontology (go) terms and associated pathways using the database for annotation, visualization, and integrated discovery repository (david).The analysis revealed that the overexpressed degs are principally connected with the protein export, axon guidance pathway, and the downexpressed degs are principally connected with the l13a‐mediated translational silencing of ceruloplasmin expression, formation of a pool of free 40s subunits pathway.The string database used to collect protein‐protein interaction (ppi) network information and visualize it with the cytoscape software.We found 10 hub genes from the ppi network considering three methods in which the interleukin 6 (il6) gene is the top in all methods.From the ppi, we found that identified clusters are associated with the complex i biogenesis, ubiquitination and proteasome degradation, signaling by interleukins, and notch‐hlh transcription pathway.The identified biomarkers and pathways may play an important role in the future for developing drugs for the es c.

Journal: BioMed Research International (2022)
Publication types: Research Article;
Identification of Biomarkers for Predicting Allograft Rejection following Kidney Transplantation Based on the Weighted Gene Coexpression Network Analysis

Kidney transplantation is the promising treatment of choice for chronic kidney disease and end‐stage kidney disease and can effectively improve the quality of life and survival rates of patients.However, the allograft rejection following kidney transplantation has a negative impact on transplant success.Therefore, the present study is aimed at screening novel biomarkers for the diagnosis and treatment of allograft rejection following kidney transplantation for improving long‐term transplant outcome.In the study, a total of 8 modules and 3065 genes were identified by wgcna based on the gse46474 and gse15296 dataset from the gene expression omnibus (geo) database.Moreover, the results of gene ontology (go) annotation and kyoto encyclopedia of genes and genomes (kegg) pathway enrichment analysis showed that these genes were mainly involved in the immune‐related biological processes and pathways.Thus, 317 immune‐related genes were selected for further analysis.Finally, 5 genes (including cd200r1, vav2, faslg, sh2d1b, and rap2b) were identified as the candidate biomarkers based on the roc and difference analysis.Furthermore, we also found that in the 5 biomarkers an interaction might exist among each other in the protein and transcription level.Taken together, our study identified cd200r1, vav2, faslg, sh2d1b, and rap2b as the candidate diagnostic biomarkers, which might contribute to the prevention and treatment of allograft rejection following kidney transplantation.

Journal: BioMed Research International (2021)
Publication types: Research Article;
Hypoxia-Activated PI3K/Akt Inhibits Oxidative Stress via the Regulation of Reactive Oxygen Species in Human Dental Pulp Cells

In order to use stem cells as a resource for tissue regeneration, it is necessary to induce expansion in vitro .However, during culture, stem cells often lose functional properties and become senescent.Increasing evidence indicates that hypoxic preconditioning with physiological oxygen concentration can maintain the functional properties of stem cells in vitro .The purpose of the current study was to test the hypothesis that hypoxic preconditioning with physiological oxygen concentration can maintain the functional properties of stem cells in culture by reducing oxidative stress.In vitro studies were performed in primary human dental pulp cells (h dpcs).Reduced levels of oxidative stress and increased cellular “stemness” in response to physiological hypoxia were dependent upon the expression of reactive oxygen species (ros).Subsequently, rna-sequencing analysis revealed the increased expression of phosphoinositide 3-kinase (pi3k)/akt signaling in culture, a pathway which regulates oxidative stress.Furthermore, we found evidence that pi3k/akt signaling might affect intracellular ros production by negatively regulating expression of the downstream protein forkhead box protein o1 (foxo1) and caspase 3.Collectively, our data show that the pi3k/akt pathway is activated in response to hypoxia and inhibits oxidative stress in a ros-dependent manner.This study identified redox-mediated hypoxic preconditioning regulatory mechanisms that may be significant for tissue regeneration.

Journal: Oxidative Medicine and Cellular Longevity (2019)
Publication types: Research Article;
Hydroxyphenyl Butanone Induces Cell Cycle Arrest through Inhibition of GSK3β in Colorectal Cancer

Colorectal cancer (crc) is among the top three gastrointestinal malignancy in morbidity and mortality.The abnormal activation of wnt/ β ‐catenin pathway is considered to be a key factor in the occurrence and development of crc.Novel inhibitor discovery against key factor in wnt pathway is important for crc treatment and prevention.Methods .Cell proliferation was detected after hydroxyphenyl butanone treatment in human colorectal cancer hct116, lovo, and normal colonic epithelial ncm460 cells.Colony formation, cell invasion ability, and cell cycle were detected with and without gsk‐3 β knockdown.Results .Hydroxyphenyl butanone induces cycle arresting on g1‐s phase of colorectal cancer cell line through gsk3 β in wnt/ β ‐catenin pathway and inhibits malignant biological manifestations of cell proliferation, colony formation, and invasion.The inhibition in the high concentration group is stronger than that in the low concentration group, and the antitumor effect is different for different tumor cells.Under the same concentration of natural hydroxyphenyl butanone, the inhibition on normal colonic epithelial cells is significantly lower than that on tumor cells.The natural hydroxyphenyl butanone with medium and low concentration could promote the proliferation of normal colonic epithelial cells.Conclusion .This study illustrated natural hydroxyphenyl butanone as new inhibitor of gsk3 β and revealed the mechanisms underlying the inhibitory effects in colorectal cancer.

Journal: BioMed Research International (2021)
Publication types: Research Article;
Histopathological Investigations and Molecular Confirmation Reveal Mycobacterium bovis in One-Horned Rhinoceros (Rhinoceros unicorns)

Mycobacterium bovis causes tuberculosis in dairy and wild animals.Presence of tuberculosis in animals poses a threat not only to their herd mates but also for public.No reports are available about the clinical, pathological, and molecular investigation of naturally occurring tuberculosis (tb) due to m.Bovis in one‐horned rhinoceros.One‐horned female rhinoceros ( rhinoceros unicorns ) at the age of 41 years died in a public park in pakistan.Postmortem and other investigations were carried out to know the cause of death.The present study describes necropsy, histopathology, and molecular‐based confirmation of tb in a captive female rhinoceros that died of this infection.Clinically, the rhinoceros showed nonspecific clinical signs including anorexia, lethargy, dyspnoea, coughing, and sudden death.At necropsy, the trachea exhibited mild congestion and contained catarrhal exudate at the bronchial bifurcation.Macroscopic examination revealed characteristic tubercles on all parenchymatous organs.The lungs showed consolidation, grey hepatization, and contained granulomatous lesions packed with cheesy exudate.Histopathological examination showed severe pneumonic changes in the form of granulomatous inflammation consisting of lymphocytes, multinucleated giant cells, caseous materials, and mineralized foci surrounded by a fibrous capsule.Pcr amplicon of 500 bp confirmed the presence of m.Bovis in multiple hepatic and pulmonary tissue samples, as well as in uterine exudates.It was concluded that the presence of tuberculosis in rhinoceros may pose potential transmission risk to other animals and the application of practical tools to determine tb status in the rhinoceros is crucial.

Journal: BioMed Research International (2022)
Publication types: Research Article;
Histone Deacetylase9 Represents the Epigenetic Promotion of M1 Macrophage Polarization and Inflammatory Response via TLR4 Regulation

Atherosclerosis is a chronic inflammatory response mediated by various factors, where epigenetic regulation involving histone deacetylation is envisaged to modulate the expression of related proteins by regulating the binding of transcription factors to dna, thereby influencing the development of atherosclerosis.The mechanism of atherosclerosis by histone deacetylation is partly known; hence, this project aimed at investigating the role of histone deacetylase 9 (hdac9) in atherosclerosis.For this purpose, serum was separated from blood samples following clotting and centrifugation from atherosclerotic and healthy patients ( n = 40 each), and then, various tests were performed.The results indicated that toll‐like receptor 4 (tlr4) was not only positively correlated to the hdac9 gene, but was also upregulated in atherosclerosis, where it was also significantly upregulated in the atherosclerosis cell model of oxidized low‐density lipoprotein‐induced macrophages.Conversely, the tlr4 was significantly downregulated in instances of loss of hdac9 function, cementing the bridging relationship between hdac9 and macrophage polarization, where the hdac9 was found to upregulate m1 macrophage polarization which translated into the release of higher content of proinflammatory cytokines such as interleukin‐1beta (il‐1 β ) and tumor necrosis factor‐alpha (tnf‐ α ), which tend to significantly decrease following the deletion of tlr4.Hence, this study reports novel relation between epigenetic control and atherosclerosis, which could partly be explained by histone deacetylation.

Journal: BioMed Research International (2022)
Publication types: Research Article;
High Glucose Enhances Bupivacaine-Induced Neurotoxicity via MCU-Mediated Oxidative Stress in SH-SY5Y Cells

Bupivacaine, a typical local anesthetic, induces neurotoxicity via reactive oxygen species regulation of apoptosis.High glucose could enhance bupivacaine-induced neurotoxicity through regulating oxidative stress, but the mechanism of it is not clear.Mitochondrial calcium uniporter (mcu), a key channel for regulating the mitochondrial ca 2+ (m ca 2+ ) influx, is closely related to oxidative stress via disruption of m ca 2+ homeostasis.Whether mcu is involved in high glucose-sensitized bupivacaine-induced neurotoxicity remains unknown.In this study, human neuroblastoma (sh-sy5y) cells were cultured with high glucose and/or bupivacaine, and the data showed that high glucose enhanced bupivacaine-induced mcu expression elevation, m ca 2+ accumulation, and oxidative damage.Next, ru360, an inhibitor of mcu, was employed to pretreated sh-sy5y cells, and the results showed that it could decrease high glucose and bupivacaine-induced m ca 2+ accumulation, oxidative stress, and apoptosis.Further, with the knockdown of mcu with a specific small interfering rna (si rna) in sh-sy5y cells, we found that it also could inhibit high glucose and bupivacaine-induced m ca 2+ accumulation, oxidative stress, and apoptosis.We propose that downregulation expression or activity inhibition of the mcu channel might be useful for restoring the mitochondrial function and combating high glucose and bupivacaine-induced neurotoxicity.In conclusion, our study demonstrated the crucial role of mcu in high glucose-mediated enhancement of bupivacaine-induced neurotoxicity, suggesting the possible use of this channel as a target for curing bupivacaine-induced neurotoxicity in diabetic patients.

Journal: Oxidative Medicine and Cellular Longevity (2019)
Publication types: Research Article;
Hemodynamic and Geometric Risk Factors for In-Stent Restenosis in Patients with Intracranial Atherosclerotic Stenosis

Problem.Investigating the importance of vessel geometry and hemodynamics in intracranial atherosclerotic stenosis (icas) might provide a more profound understanding about the underlying mechanisms of in-stent restenosis (isr).Methods.Severe icas patients managed with percutaneous transluminal angioplasty and stenting (ptas) were included in the retrospective cohort study and were divided into two groups according to whether isr occurred at follow-up (isr group and no-isr group).Computational fluid dynamics models were built based on digital subtraction angiography before and after ptas to simulate blood flow and quantify hemodynamic parameters.The associations between vessel geometry, hemodynamics, and isr in icas patients were investigated.Results.Among 39 patients, isr occurred in seven patients (17.95%) after a mean follow-up period of 6.69 ± 3.24 months.Stenting decreased vessel angulation (51.11° [40.07°–67.27°] vs.15.97° [0.00°–36.16°], p = 0.000 ) and vessel tortuosity (0.09 [0.06–0.13] vs.0.01 [0.00–0.03], p = 0.000 ).Meanwhile, the translational pressure ratio (pr) dramatically increased (0.07 [0.00–0.31] vs.0.62 [0.41–0.82], p = 0.000 ) with the wall shear stress ratio decreased (13.93 [8.37–40.30] vs.2.90 [1.69–4.48], p = 0.000 ).In the multivariate analysis, smaller δ tortuosity ( p = 0.038 ) was independently associated with the occurrence of isr, and smaller post-ptas translesional pr was also a predictive factor of marginal significance ( p = 0.059 ).Conclusion.Ptas decreased vessel angulation, vessel tortuosity, and translesional wall shear stress ratio while it increased translesional pressure ratio (pr) dramatically in icas patients.Smaller δ tortuosity was found to be a risk factor for isr, and smaller post-ptas translesional pr was also a predictive factor of marginal significance, indicating that both geometric and hemodynamic parameters played important roles in the occurrence of isr after ptas.

Journal: Oxidative Medicine and Cellular Longevity (2022)
Publication types: Research Article;
Human Schlafen 5 Inhibits Proliferation and Promotes Apoptosis in Lung Adenocarcinoma via the PTEN/PI3K/AKT/mTOR Pathway

Human schlafen 5 (slfn5) is reported to inhibit or promote the proliferation of several specific types of cancer cells by our lab and other researchers.We are curious about its implications in lung adenocarcinoma (luac), a malignant tumor with a high incidence rate and high mortality.Method .Lentiviral stable transfections of slfn5‐specific sh rna for knockdown and slfn5 full‐length coding sequence for overexpression were performed in luac cell for proliferation analysis in vitro and in vivo in nude mice.Clinical luac samples were collected for immunohistochemical analysis of slfn5 protein levels.Results .We found that knockdown of endogenous slfn5 upregulates cancer cell proliferation while inhibiting apoptosis.Besides, slfn5 inhibition on proliferation was also observed in a nude mouse xenograft model.In contrast, overexpression of exogenous slfn5 inhibited cell proliferation in vitro and in vivo and promoted apoptosis.As to the signaling pathway, we found phosphatase and tensin homolog on chromosome 10 (pten) was positively regulated by slfn5, while its downstream signaling pathway akt/mammalian target of rapamycin (m tor) was inhibited.Moreover, compared with adjacent normal tissues, slfn5 protein levels were markedly decreased in lung adenocarcinoma tissues.In conclusion, these suggest that human slfn5 plays inhibitory roles in luac progression through the pten/pi3k/akt/m tor pathway, providing a potential target for developing drugs for lung cancer therapy in the future.

Journal: BioMed Research International (2021)
Publication types: Research Article;