cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14317428.v1
title: Effect of ethanol extracts of Antrodia cinnamomea on head and neck squamous cell carcinoma cell line

description: Head and neck squamous cell carcinoma (HNSCC) is one of the most common malignant tumors. Ethanol extract of Antrodia cinnamomea (EEA) has been widely studied for its health benefits including anticancer effects. The purpose of this study was to assess the effects of EEA on HNSCC. Cell proliferation, transwell, and wound healing assays were performed. The impact of EEA on tumor growth was investigated using a xenograft model. Expressions of migration-related proteins (MMP-2, MMP-9, TIMP-1, and TIMP-2) and apoptosis-related proteins (cleaved caspase-9 and cleaved PARP) were determined using western blot analysis. The results indicated that EEA significantly inhibited the capacities of proliferation, invasion, and migration of HNSCC cells in a dose-dependent manner. Cleaved caspase-9 and cleaved PARP expressions were increased in cells treated with an increasing concentration of EEA, which suggested that EEA induced apoptosis of HNSCC. MMP-2 and MMP-9 were downregulated when cells were administered EEA, while TIMP-1 and TIMP-2 were not affected, which uncovered the mechanisms mediating the EEA-induced inhibition on cell invasion and migration. The animal experiment also suggested that EEA inhibited tumor growth. Our study confirmed the inhibitive effects of EEA on cell proliferation, invasion, and migration of HNSCC in vitro and in vivo, providing the basis for further study of the application of EEA as an effective candidate for cancer treatment.
DOI: 10.6084/m9.figshare.14317436.v1
title: Treatment with β-elemene combined with paclitaxel inhibits growth, migration, and invasion and induces apoptosis of ovarian cancer cells by activation of STAT-NF-κB pathway

description: In this study, we aimed to analyze the anti-cancer effects of β-elemene combined with paclitaxel for ovarian cancer. RT-qPCR, MTT assay, western blot, flow cytometry, and immunohistochemistry were used to analyze in vitro and in vivo anti-cancer effects of combined treatment of β-elemene and paclitaxel. The in vitro results showed that β-elemene+paclitaxel treatment markedly inhibited ovarian cancer cell growth, migration, and invasion compared to either paclitaxel or β-elemene treatment alone. Results demonstrated that β-elemene+paclitaxel induced apoptosis of SKOV3 cells, down-regulated anti-apoptotic Bcl-2 and Bcl-xl gene expression and up-regulated pro-apoptotic P53 and Apaf1 gene expression in SKOV3 cells. Administration of β-elemene+paclitaxel arrested SKOV3 cell cycle at S phase and down-regulated CDK1, cyclin-B1, and P27 gene expression and apoptotic-related resistant gene expression of MDR1, LRP, and TS in SKOV3 cells. In vivo experiments showed that treatment with β-elemene+paclitaxel significantly inhibited ovarian tumor growth and prolonged the overall survival of SKOV3-bearing mice. In addition, the treatment inhibited phosphorylated STAT3 and NF-κB expression in vitro and in vivo. Furthermore, it inhibited migration and invasion through down-regulation of the STAT-NF-κB signaling pathway in SKOV3 cells. In conclusion, the data suggested that β-elemene+paclitaxel can inhibit ovarian cancer growth via down-regulation of the STAT3-NF-κB signaling pathway, which may be a potential therapeutic strategy for ovarian cancer therapy.
DOI: 10.6084/m9.figshare.16935524
title: Additional file 1 of Lupus susceptibility region containing CTLA4 rs17268364 functionally reduces CTLA4 expression by binding EWSR1 and correlates IFN-α signature

description: Additional file 1: Supplementary table 1. Demographical information of the cohorts. Supplementary table 2. Association results of SNPs in CTLA4-ICOS region and SLE susceptibility (1). Supplementary Table 3. Synthesized sequences for subcloning into pGL3-promoter. Supplementary Table 4. The sequences of the synthetic double-stranded oligonucleotides for protein mass spectrometry and EMSA. Supplementary table 5. Regulatory chromatin states from DNAse and histone ChIP-Seq (Roadmap Epigenomics Consortium, 2015) (2). Supplementary table 6. Single-Tissue eQTLs for rs17268364. Supplementary Figure 1. The correlation between mRNA expression of CTLA4 and rs17268364 genotypes. A. Healthy controls B. systemic lupus erythematosus patients without renal impairment. Supplementary Figure 2. The correlation between mRNA expression of ICOS and rs17268364 genotypes in SLE patients without renal impairment (A), lupus nephritis patients (B), and SLE patients (C). Supplementary Figure 3. Linkage disequilibrium (LD) heatmap of the 24 identified SLE-associated SNPs. The Linkage disequilibrium (LD) heatmap of the 24 identified SLE-associated SNPs was generated using genotype data of 103 Chinese Han Beijing individuals from 1000 genome project. The degrees of LD were estimated by CI method using Haploview4.2 (Cambridge, MA, USA) and a standard color scheme (D’/LOD) is used to display the LD pattern.
DOI: 10.6084/m9.figshare.16935540
title: Additional file 3 of Temporal expression study of miRNAs in the crown tissues of winter wheat grown under natural growth conditions

description: Additional file 3: Table S2. Expression of wheat new miRNAs in crown tissues.
DOI: 10.6084/m9.figshare.14317437
title: Notoginsenoside R1 upregulates miR-221-3p expression to alleviate ox-LDL-induced apoptosis, inflammation, and oxidative stress by inhibiting the TLR4/NF-κB pathway in HUVECs

description: Atherosclerosis (AS) is a common vascular disease, which can cause apoptosis of vascular endothelial cells. Notoginsenoside R1 (NGR1) is considered an anti-AS drug. MicroRNAs (miRNAs) are believed to play a vital role in cell apoptosis and angiogenesis. This study aimed to explore the mechanism of NGR1 for treating AS through miRNAs. Flow cytometry was used to detect the apoptosis rate. The levels of inflammatory cytokines interleukin (IL)-6 and IL-1β were detected using ELISA. Reactive oxygen species (ROS) and malondialdehyde (MDA) levels were measured using corresponding assay kits. Quantitative real-time polymerase chain reaction (qRT-PCR) assay was performed to detect miR-221-3p expression. Dual-luciferase reporter and RNA immunoprecipitation assays were carried out to examine the relationship between miR-221-3p and toll-like receptors 4 (TLR4). Also, western blot analysis was performed to determine the levels of TLR4 and nuclear factor kappa B (NF-κB) signaling pathway-related proteins. Oxidized low-density lipoprotein (ox-LDL) induced human umbilical vein endothelial cells (HUVECs) apoptosis, inflammation, and oxidative stress. NGR1 alleviated the negative effect of ox-LDL through promoting the expression of miR-221-3p in HUVECs. TLR4 was a target of miR-221-3p, and its overexpression could reverse the inhibition effects of miR-221-3p on apoptosis, inflammation, and oxidative stress. NGR1 improved miR-221-3p expression to inhibit the activation of the TLR4/NF-κB pathway in ox-LDL-treated HUVECs. NGR1 decreased ox-LDL-induced HUVECs apoptosis, inflammation, and oxidative stress through increasing miR-221-3p expression, thereby inhibiting the activation of the TLR4/NF-κB pathway. This study of the mechanism of NGR1 provided a more theoretical basis for the treatment of AS.
DOI: 10.6084/m9.figshare.16935546
title: Additional file 5 of Temporal expression study of miRNAs in the crown tissues of winter wheat grown under natural growth conditions

description: Additional file 5: Table S4. Expression of differentially expressed miRNAs in wheat crown tissues.
DOI: 10.6084/m9.figshare.14317437.v1
title: Notoginsenoside R1 upregulates miR-221-3p expression to alleviate ox-LDL-induced apoptosis, inflammation, and oxidative stress by inhibiting the TLR4/NF-κB pathway in HUVECs

description: Atherosclerosis (AS) is a common vascular disease, which can cause apoptosis of vascular endothelial cells. Notoginsenoside R1 (NGR1) is considered an anti-AS drug. MicroRNAs (miRNAs) are believed to play a vital role in cell apoptosis and angiogenesis. This study aimed to explore the mechanism of NGR1 for treating AS through miRNAs. Flow cytometry was used to detect the apoptosis rate. The levels of inflammatory cytokines interleukin (IL)-6 and IL-1β were detected using ELISA. Reactive oxygen species (ROS) and malondialdehyde (MDA) levels were measured using corresponding assay kits. Quantitative real-time polymerase chain reaction (qRT-PCR) assay was performed to detect miR-221-3p expression. Dual-luciferase reporter and RNA immunoprecipitation assays were carried out to examine the relationship between miR-221-3p and toll-like receptors 4 (TLR4). Also, western blot analysis was performed to determine the levels of TLR4 and nuclear factor kappa B (NF-κB) signaling pathway-related proteins. Oxidized low-density lipoprotein (ox-LDL) induced human umbilical vein endothelial cells (HUVECs) apoptosis, inflammation, and oxidative stress. NGR1 alleviated the negative effect of ox-LDL through promoting the expression of miR-221-3p in HUVECs. TLR4 was a target of miR-221-3p, and its overexpression could reverse the inhibition effects of miR-221-3p on apoptosis, inflammation, and oxidative stress. NGR1 improved miR-221-3p expression to inhibit the activation of the TLR4/NF-κB pathway in ox-LDL-treated HUVECs. NGR1 decreased ox-LDL-induced HUVECs apoptosis, inflammation, and oxidative stress through increasing miR-221-3p expression, thereby inhibiting the activation of the TLR4/NF-κB pathway. This study of the mechanism of NGR1 provided a more theoretical basis for the treatment of AS.
DOI: 10.6084/m9.figshare.14847786
title: HydroWASTE version 1.0

description: <br>
HydroWASTE is a spatially-explicit global database of 58,502 WWTPs and their characteristics. This database was developed by combining national and regional datasets with auxiliary information to derive or complete missing WWTP characteristics, including the amount of people served. A high-resolution river network with streamflow estimates (HydroATLAS: https://doi.org/10.6084/m9.figshare.9890531) was used to georeference WWTP outfall locations and calculate each plant’s dilution factor (i.e., the ratio of the natural discharge of the receiving waterbody to the WWTP effluent discharge).
Version 1.0 of HydroWASTE is fully described in Ehalt Macedo et al. 2022 (see references below).
There is 1 zipped data file containing:
1. HydroWASTE_v10.csv - database in csv format
2. README.txt - overview information about the database
<br>
Reference:
Ehalt Macedo, H., Lehner, B., Nicell, J., Grill, G., Li, J., Limtong, A., and Shakya, R.: Distribution and characteristics of wastewater treatment plants within the global river network, Earth Syst. Sci. Data, 14, 559–577, https://doi.org/10.5194/essd-14-559-2022, 2022.
DOI: 10.6084/m9.figshare.14317442.v1
title: Evaluation of factors for predicting risk of uveitis recurrence in Behcet's disease patients

description: This study aimed to investigate the predictive factors for uveitis recurrence (UR) risk in Behcet's disease (BD) patients. BD patients (n=164) with a history of uveitis were recruited, and demographic data, clinical features, and laboratory tests were recorded. Uveitis was defined as anterior uveitis, intermediate uveitis, posterior uveitis, panuveitis referring to the “International Uveitis Study Group recommendations for the evaluation of intraocular inflammatory disease”. In total, there were 70 UR patients and 94 non-UR patients. Compared to non-UR patients, UR patients appeared to be older and presented with increased uveitis occurrence rate and times within 3 months, oral ulcers occurrence rate, as well as higher concentrations of triglycerides (TG), total cholesterol (TC), low-density lipoprotein (LDL), and serum amyloid A (SAA). Multivariate logistic model disclosed that uveitis occurrence times within 3 months, oral ulcers, TG, LDL, and SAA independently predicted higher risk of UR. Furthermore, receiver operating characteristic curve analysis showed that the combination of uveitis occurrence times within 3 months, oral ulcers, TG, LDL, and SAA exhibited a high predictive value for UR risk with an area under the curve of 0.983 (95%CI: 0.969−0.998). In conclusion, uveitis occurrence times within 3 months, oral ulcers, TG, LDL, and SAA might be potential predictive factors for UR risk in BD patients, which can help in prevention and management of the disease.
DOI: 10.6084/m9.figshare.14317451
title: Knocking down LSD1 inhibits the stemness features of colorectal cancer stem cells

description: As a top leading cause of cancer death in many countries, colorectal cancer (CRC) has drawn increasing attention to the study of the pathological mechanism. According to the “cancer stem cell hypothesis”, malignancies originate from a small fraction of cancer cells that show self-renewal properties to initiate and sustain tumor growth and tumor metastasis. Therefore, these cancer stem cells (CSC) probably play important roles in tumor recurrence, metastasis, and drug resistance. Previous research reported that lysine-specific histone demethylase 1 (LSD1) maintains cancer stemness through up-regulating stemness markers SOX2 and OCT4. CD133 is believed to be the most robust surface marker for CRC stem cells, however the regulatory effect of LSD1 on stemness of CD133+ CRC has never been reported. In this study, our objectives included: 1) to isolate pure CD133+ and CD133− cells from SW620 cell line; 2) to investigate the effect of LSD1 on the characteristics of CD133+ stem cancer cells by knocking down the target gene. Results suggested that the SW620 cell line had both CD133+ and CD133− subsets. The CD133+ subset exhibited more CSC-like characteristics compared with the CD133− subset with higher viability, colony formation rate, migration and invasion rate, resistance to anti-cancer drugs, and apoptosis in vitro. The CD133+ also induced faster tumor formation and larger tumors in vivo. In the LSD1-knockdown CD133+ cells, the CSC-like characteristics had been all weakened. We conclude that LSD1 was important for CSCs to maintain their “stemness” features, which could be a potential therapeutic target of CRC.
DOI: 10.6084/m9.figshare.14317452.v1
title: Detoxification effects of long-chain versus a mixture of medium- and long-chain triglyceride-based fat emulsion on propafenone poisoning

description: In the present study, we aimed to compare the detoxifying effects of two fat emulsions containing either long-chain triglyceride or a mixture of medium-chain and long-chain triglycerides in the propafenone-poisoned rat model. Rats were randomly divided into 3 groups according to the fat emulsions used: long-chain triglyceride-based fat emulsion (LL) group; medium-chain and long-chain triglyceride-based fat emulsion (ML) group; normal saline (NS) group. Propafenone was continuously pumped (velocity=70 mg/kg per h) until the mean blood pressure dropped to 50% of basal level. Then, LL/ML fat emulsions or NS was intravenously infused instantly with a loading-dose (1.5 mL/kg) and a maintenance dose (0.25 mL/kg per min) for 1 h. Subsequently, the propafenone was added to plasma (3.5 μg/mL) in vitro, mixed with three doses of LL or ML (1, 2, or 4%). Finally, after centrifugation, the concentration of propafenone was measured. Rats treated with LL exhibited accelerated recovery, characterized by higher blood pressure and heart rate. Rats in both the LL and ML groups demonstrated decreased propafenone in plasma (time-points: 15, 25, and 60 min). However, rats that received LL showed lower propafenone in myocardial tissue at the end of detoxification treatment. Rats in the ML group had the lowest value of pH, the minimum content of HCO3-, and the highest production of lactic acid at the end. In the in vitro experiments, propafenone decreased more dramatically in the LL group compared to the ML group. Long-chain triglyceride fat emulsion had a better effect on treating propafenone poisoning in rats.
DOI: 10.6084/m9.figshare.6453071.v1
title: Optimal Subsampling for Large Sample Logistic Regression

description: For massive data, the family of subsampling algorithms is popular to downsize the data volume and reduce computational burden. Existing studies focus on approximating the ordinary least-square estimate in linear regression, where statistical leverage scores are often used to define subsampling probabilities. In this article, we propose fast subsampling algorithms to efficiently approximate the maximum likelihood estimate in logistic regression. We first establish consistency and asymptotic normality of the estimator from a general subsampling algorithm, and then derive optimal subsampling probabilities that minimize the asymptotic mean squared error of the resultant estimator. An alternative minimization criterion is also proposed to further reduce the computational cost. The optimal subsampling probabilities depend on the full data estimate, so we develop a two-step algorithm to approximate the optimal subsampling procedure. This algorithm is computationally efficient and has a significant reduction in computing time compared to the full data approach. Consistency and asymptotic normality of the estimator from a two-step algorithm are also established. Synthetic and real datasets are used to evaluate the practical performance of the proposed method. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.14317472.v1
title: Modulation of Wnt/β-catenin signaling in IL-17A-mediated macrophage polarization of RAW264.7 cells

description: Macrophages play pivotal roles in host defense and immune homeostasis, which have two major functional polarization states, the classically activated M1 and the alternatively activated M2. Interleukin (IL)-17A is an immune modulator able to shape macrophage phenotypes. Wnt/β-catenin is a developmental signaling pathway that plays crucial roles in morphogenesis and tissue homeostasis, which has also been recently demonstrated playing roles in immune regulation. A growing amount of evidence suggests that both Wnt and IL-17A signaling are involved in macrophage polarization. However, their interaction in macrophage polarization remains elusive. The aim of present study was to explore impacts of Wnt/β-catenin on IL-17A-mediated macrophage M1/M2 polarization in murine monocyte/macrophage-like cell line RAW264.7. Results revealed that IL-17A activated Wnt/β-catenin signaling and induced macrophage M1 polarization, but inhibited M2 polarization. In contrast, the activation of Wnt/β-catenin signaling led to the inhibition of M1 macrophage polarization but the promotion of M2 polarization. Importantly, the activation of Wnt/β-catenin also showed abilities to inhibit the IL-17A-induced M1 macrophage polarization while diminishing the IL-17A-inhibited M2 polarization. Molecular analysis further uncovered that the JAK/STAT signaling pathway was involved in the interaction of Wnt/β-catenin and IL-17A in the modulation of macrophage polarization. These results suggested that the Wnt/β-catenin signaling modulated IL-17A-altered macrophage polarization in part by regulating the JAK/STAT signaling pathway. This study thus revealed a novel function of Wnt/β-catenin signaling in regulating IL-17A-altered macrophage polarization.
DOI: 10.6084/m9.figshare.14317476
title: Hyaluronic acid versus dexamethasone for the treatment of recurrent aphthous stomatitis in children: efficacy and safety analysis

description: The objective of this study was to compare the safety and efficacy of 0.2% hyaluronic acid (HA) topical gel and dexamethasone topical ointment in the treatment of recurrent aphthous ulcers (RAU) in children. This retrospective observational study included 104 patients who had more than two episodes of oral aphthous ulcers per year and were treated with HA (n=52) or dexamethasone (n=52) from August 15, 2014 to September 3, 2018. Therapy efficacy was evaluated based on the ulcer size and pain score before versus 7 days after either therapy. The paired t-test, chi-squared test, and independent t-test were utilized for statistical analyses. There was no significant difference in ulcer size or pain score between the HA and dexamethasone groups, on day 1 or day 7. Both treatments were tolerated well and no side effects were reported. No significant differences in body temperature, respiration rate, pulse, or systolic/diastolic blood pressure were observed between the start (day 1) and end of treatment (day 7), for either treatment. HA and dexamethasone showed similar efficacy in reducing ulcer size and pain scores, and were tolerated equally well in children with RAU. Future high-quality studies with larger numbers of patients are needed to confirm our findings.
DOI: 10.6084/m9.figshare.14317428
title: Effect of ethanol extracts of Antrodia cinnamomea on head and neck squamous cell carcinoma cell line

description: Head and neck squamous cell carcinoma (HNSCC) is one of the most common malignant tumors. Ethanol extract of Antrodia cinnamomea (EEA) has been widely studied for its health benefits including anticancer effects. The purpose of this study was to assess the effects of EEA on HNSCC. Cell proliferation, transwell, and wound healing assays were performed. The impact of EEA on tumor growth was investigated using a xenograft model. Expressions of migration-related proteins (MMP-2, MMP-9, TIMP-1, and TIMP-2) and apoptosis-related proteins (cleaved caspase-9 and cleaved PARP) were determined using western blot analysis. The results indicated that EEA significantly inhibited the capacities of proliferation, invasion, and migration of HNSCC cells in a dose-dependent manner. Cleaved caspase-9 and cleaved PARP expressions were increased in cells treated with an increasing concentration of EEA, which suggested that EEA induced apoptosis of HNSCC. MMP-2 and MMP-9 were downregulated when cells were administered EEA, while TIMP-1 and TIMP-2 were not affected, which uncovered the mechanisms mediating the EEA-induced inhibition on cell invasion and migration. The animal experiment also suggested that EEA inhibited tumor growth. Our study confirmed the inhibitive effects of EEA on cell proliferation, invasion, and migration of HNSCC in vitro and in vivo, providing the basis for further study of the application of EEA as an effective candidate for cancer treatment.
DOI: 10.6084/m9.figshare.6453071
title: Optimal Subsampling for Large Sample Logistic Regression

description: For massive data, the family of subsampling algorithms is popular to downsize the data volume and reduce computational burden. Existing studies focus on approximating the ordinary least-square estimate in linear regression, where statistical leverage scores are often used to define subsampling probabilities. In this article, we propose fast subsampling algorithms to efficiently approximate the maximum likelihood estimate in logistic regression. We first establish consistency and asymptotic normality of the estimator from a general subsampling algorithm, and then derive optimal subsampling probabilities that minimize the asymptotic mean squared error of the resultant estimator. An alternative minimization criterion is also proposed to further reduce the computational cost. The optimal subsampling probabilities depend on the full data estimate, so we develop a two-step algorithm to approximate the optimal subsampling procedure. This algorithm is computationally efficient and has a significant reduction in computing time compared to the full data approach. Consistency and asymptotic normality of the estimator from a two-step algorithm are also established. Synthetic and real datasets are used to evaluate the practical performance of the proposed method. Supplementary materials for this article are available online.