cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.22750639.v1
title: Identification of SLC2A3 as a prognostic indicator correlated with the NF-κB/EMT axis and immune response in head and neck squamous cell carcinoma

description: SLC2A3 is an important member of the glucose transporter superfamily. It has been recently suggested that upregulation of SLC2A3 is associated with poor survival and acts as a prognostic marker in a variety of tumors. Unfortunately, the prognostic role of SLC2A3 in head and neck squamous cell carcinoma (HNSC) is less known. In the present study, we analyzed SLC2A3 expression in HNSC and its correlation with prognosis using TCGA and GEO databases. The results showed that SLC2A3 mRNA expression was higher in HNSC compared with adjacent normal tissues, which was validated with our 9 pairs of HNSC specimens. Moreover, high SLC2A3 expression predicted poor prognosis in HNSC patients. Mechanistically, GSEA revealed that high expression of SLC2A3 was enriched in epithelial-mesenchymal transition (EMT) and NF-κB signaling. In HNSC cell lines, SLC2A3 knockdown inhibited cell proliferation and migration. In addition, NF-κB P65 and EMT-related gene expression was suppressed upon SLC2A3 knockdown, indicating that SLC2A3 may play a preeminent role in the progression of HNSC through the NF-κB/EMT axis. Meanwhile, the expression of SLC2A3 was negatively correlated with immune cells, suggesting that SLC2A3 may be involved in the immune response in HNSC. The correlation between SLC2A3 expression and drug sensitivity was further assessed. In conclusion, our study demonstrated that SLC2A3 could predict the prognosis of HNSC patients and mediate the progression of HNSC via the NF-κB/EMT axis and immune responses.
DOI: 10.6084/m9.figshare.6497750
title: Western blot

description: Proteins
(30μg) extracted from cells were loaded and separated in 8% SDS-PAGE and then
transferred on nitrocellulose membranes. The membranes were blocked with 5%
non-fat milk and incubated with Anti-SP1 (1:1000, 9389, Cell Signaling
Technology, MA, USA) or Anti-CCR7 (1:1000, ab32527, Abcam, Cambridge, UK) in 5%
milk/PBS buffer at 4℃ overnight, followed by
incubation with goat anti-rabbit secondary antibody (A23720, Abbkine, Wuhan,
China) conjugated with DyLight fluorescent 680. After extensive wash with PBST
buffer, the band of protein was visualized under Odyssey CLx imaging system
(LI-COR, Inc., NE, USA).
DOI: 10.6084/m9.figshare.23273319.v1
title: Additional file 2 of Constructing ferroptosis-related competing endogenous RNA networks and exploring potential biomarkers correlated with immune infiltration cells in asthma using combinative bioinformatics strategy

description: Additional file 2: Table S2. List of miRNAs and mRNAs targeted by LUCAT1.
DOI: 10.6084/m9.figshare.23273322.v1
title: Additional file 3 of Constructing ferroptosis-related competing endogenous RNA networks and exploring potential biomarkers correlated with immune infiltration cells in asthma using combinative bioinformatics strategy

description: Additional file 3: Table S3. List of miRNAs and mRNAs targeted by MIR222HG.
DOI: 10.6084/m9.figshare.20652088.v1
title: Additional file 11 of Irradiation induces DJ-1 secretion from esophageal squamous cell carcinoma cells to accelerate metastasis of bystander cells via a TGF-β1 positive feedback loop

description: Additional file 11: Table S3. Clinicopathological data for 36 ESCC tissues and non-neoplastic ESCC tissue samples used for histological detections.
DOI: 10.6084/m9.figshare.22226455
title: Raw data for NM22061931A

description: Raw data for NM22061931A
DOI: 10.6084/m9.figshare.7546685
title: Dominant inflammatory profile of the placenta in a preterm labor mouse model

description: <b>Objective:</b> Despite a growing association between inflammation and preterm labor, the underlying mechanisms explaining the development of preterm labor after infection are still poorly understood. Here, we use RNA-sequencing to characterize the transcriptome changes of placenta tissue in a preterm labor mouse model. <b>Materials and methods:</b> On day 15.5 of gestation, BALB/c mice received intrauterine injection of LPS to mimic preterm labor. A comprehensive catalog of genes was obtained using RNA-sequences and followed by bioinformatics analysis. The NOD-like receptor signaling pathway (Nod2, Cxcl1, Cxcl2, and IL-1β) and two downregulated genes (Ctsg and Snca) were selected for validating the results using qPCR analysis. <b>Results:</b> We identified 155 differentially expressed genes (DEGs), 84 biological processes and 45 pathways in the placenta using RNA-seq. Fifty-four biological processes could be categorized as immune-related processes and 33 pathways were mainly related to immune disease and infections. All genes were consistent between the RNA-seq and qPCR analyses. <b>Conclusions:</b> The dominant role for inflammatory biological processes and pathways in placenta can lead to preterm labor.
DOI: 10.6084/m9.figshare.20652094
title: Additional file 13 of Irradiation induces DJ-1 secretion from esophageal squamous cell carcinoma cells to accelerate metastasis of bystander cells via a TGF-β1 positive feedback loop

description: Additional file 13: Table S5. Probes for siRNAs and plasmid/primers for the luciferase reporter vectors and primers for RT-qPCR.
DOI: 10.6084/m9.figshare.20652100.v1
title: Additional file 15 of Irradiation induces DJ-1 secretion from esophageal squamous cell carcinoma cells to accelerate metastasis of bystander cells via a TGF-β1 positive feedback loop

description: Additional file 15: Table S7. The total proteins identified from the LC–MS/MS.
DOI: 10.6084/m9.figshare.20652085.v1
title: Additional file 10 of Irradiation induces DJ-1 secretion from esophageal squamous cell carcinoma cells to accelerate metastasis of bystander cells via a TGF-β1 positive feedback loop

description: Additional file 10: Table S2. Clinical data for 46 serum samples of ESCC patients receiving similar treatments, used for ELISA and survival analysis.
DOI: 10.6084/m9.figshare.20652100
title: Additional file 15 of Irradiation induces DJ-1 secretion from esophageal squamous cell carcinoma cells to accelerate metastasis of bystander cells via a TGF-β1 positive feedback loop

description: Additional file 15: Table S7. The total proteins identified from the LC–MS/MS.
DOI: 10.6084/m9.figshare.23273461.v1
title: Additional file 4 of Risk prediction for dermatomyositis-associated hepatocellular carcinoma

description: Additional file 4. HCC diffGeneExp.xlsx
DOI: 10.6084/m9.figshare.20652085
title: Additional file 10 of Irradiation induces DJ-1 secretion from esophageal squamous cell carcinoma cells to accelerate metastasis of bystander cells via a TGF-β1 positive feedback loop

description: Additional file 10: Table S2. Clinical data for 46 serum samples of ESCC patients receiving similar treatments, used for ELISA and survival analysis.
DOI: 10.6084/m9.figshare.23273458
title: Additional file 3 of Risk prediction for dermatomyositis-associated hepatocellular carcinoma

description: Additional file 3. DM diffGeneExp.xlsx.
DOI: 10.6084/m9.figshare.20652088
title: Additional file 11 of Irradiation induces DJ-1 secretion from esophageal squamous cell carcinoma cells to accelerate metastasis of bystander cells via a TGF-β1 positive feedback loop

description: Additional file 11: Table S3. Clinicopathological data for 36 ESCC tissues and non-neoplastic ESCC tissue samples used for histological detections.
DOI: 10.6084/m9.figshare.20652127.v1
title: Additional file 9 of Irradiation induces DJ-1 secretion from esophageal squamous cell carcinoma cells to accelerate metastasis of bystander cells via a TGF-β1 positive feedback loop

description: Additional file 9: Table S1. Clinical data for 177 ESCC serum samples used for ELISA.
DOI: 10.6084/m9.figshare.23273452.v1
title: Additional file 1 of Risk prediction for dermatomyositis-associated hepatocellular carcinoma

description: Additional file 1. Original data of DM.xlsx.
DOI: 10.6084/m9.figshare.20652091.v1
title: Additional file 12 of Irradiation induces DJ-1 secretion from esophageal squamous cell carcinoma cells to accelerate metastasis of bystander cells via a TGF-β1 positive feedback loop

description: Additional file 12: Table S4. List of antibodies for western blotting, immunofluorescence, immunohistochemistry or Co-immunoprecipitation analyses.
DOI: 10.6084/m9.figshare.23273458.v1
title: Additional file 3 of Risk prediction for dermatomyositis-associated hepatocellular carcinoma

description: Additional file 3. DM diffGeneExp.xlsx.
DOI: 10.6084/m9.figshare.20652091
title: Additional file 12 of Irradiation induces DJ-1 secretion from esophageal squamous cell carcinoma cells to accelerate metastasis of bystander cells via a TGF-β1 positive feedback loop

description: Additional file 12: Table S4. List of antibodies for western blotting, immunofluorescence, immunohistochemistry or Co-immunoprecipitation analyses.
DOI: 10.6084/m9.figshare.22226902
title: φC31 -Mediated Cassette Exchange in Sf9 Insect Cells for Stable Expression

description:   
The raw data for the artical &lt; φC31 -Mediated Cassette Exchange in Sf9 Insect Cells for Stable Expression&gt;
DOI: 10.6084/m9.figshare.20652097.v1
title: Additional file 14 of Irradiation induces DJ-1 secretion from esophageal squamous cell carcinoma cells to accelerate metastasis of bystander cells via a TGF-β1 positive feedback loop

description: Additional file 14: Table S6. The whole transcriptome results detected by RNA-seq.
DOI: 10.6084/m9.figshare.19589268
title: Additional file 3 of VCP suppresses proteopathic seeding in neurons

description: Additional file 3.
DOI: 10.6084/m9.figshare.20652094.v1
title: Additional file 13 of Irradiation induces DJ-1 secretion from esophageal squamous cell carcinoma cells to accelerate metastasis of bystander cells via a TGF-β1 positive feedback loop

description: Additional file 13: Table S5. Probes for siRNAs and plasmid/primers for the luciferase reporter vectors and primers for RT-qPCR.
DOI: 10.6084/m9.figshare.19589274.v1
title: Additional file 4 of VCP suppresses proteopathic seeding in neurons

description: Additional file 4.
DOI: 10.6084/m9.figshare.20652097
title: Additional file 14 of Irradiation induces DJ-1 secretion from esophageal squamous cell carcinoma cells to accelerate metastasis of bystander cells via a TGF-β1 positive feedback loop

description: Additional file 14: Table S6. The whole transcriptome results detected by RNA-seq.
DOI: 10.6084/m9.figshare.7544885
title: An ultrasonic feeding mechanism for continuous aerosol generation from cohesive powders

description: The dispersion of dry, cohesive micro- and nanosized powders has wide applications ranging from medical and environmental science to manufacturing technology. Being able to disperse the dry powder at a stable concentration over periods of time (∼hour to several hours) is challenging to achieve, which we attempt to address with a novel dry powder dispersion technology. A portable, cost effective and simple dry powder dispersion device that uses ultrasonic energy for continuous feeding of aerosol particles to a de-agglomeration device is developed and tested with commercially available powders. The study is performed using 5 µm polyamide powder and rutile TiO<sub>2</sub> powders of 500, 100, and 30 nm mean size of primary particles. The ultrasonic dispersion device proved to be able to disperse all of these powders, which represent low-density material to high-density metal oxides, with stable concentration over periods that extend to an hour. From aerosol measurements to obtain the size distribution of various size particles, it is seen that the highly agglomerated powder particles are not easy to de-agglomerate as we go to the lower (nominal) sized powders because of the stronger inter-particle adhesion forces between nanoparticles compared to microparticles. The scanning electron microscopy (SEM) images of particles in their native powder state and those collected after the dispersion showed significant difference in the agglomeration of the powder particles, which suggests partial success of the turbulent jet de-agglomeration employed. Copyright © 2019 American Association for Aerosol Research
DOI: 10.6084/m9.figshare.7544885.v1
title: An ultrasonic feeding mechanism for continuous aerosol generation from cohesive powders

description: The dispersion of dry, cohesive micro- and nanosized powders has wide applications ranging from medical and environmental science to manufacturing technology. Being able to disperse the dry powder at a stable concentration over periods of time (∼hour to several hours) is challenging to achieve, which we attempt to address with a novel dry powder dispersion technology. A portable, cost effective and simple dry powder dispersion device that uses ultrasonic energy for continuous feeding of aerosol particles to a de-agglomeration device is developed and tested with commercially available powders. The study is performed using 5 µm polyamide powder and rutile TiO<sub>2</sub> powders of 500, 100, and 30 nm mean size of primary particles. The ultrasonic dispersion device proved to be able to disperse all of these powders, which represent low-density material to high-density metal oxides, with stable concentration over periods that extend to an hour. From aerosol measurements to obtain the size distribution of various size particles, it is seen that the highly agglomerated powder particles are not easy to de-agglomerate as we go to the lower (nominal) sized powders because of the stronger inter-particle adhesion forces between nanoparticles compared to microparticles. The scanning electron microscopy (SEM) images of particles in their native powder state and those collected after the dispersion showed significant difference in the agglomeration of the powder particles, which suggests partial success of the turbulent jet de-agglomeration employed. Copyright © 2019 American Association for Aerosol Research
DOI: 10.6084/m9.figshare.7020734
title: MOESM2 of Tumor-associated macrophages derived CCL18 promotes metastasis in squamous cell carcinoma of the head and neck

description: Additional file 2. Â GO Biological Process, Molecular Function, and Cellular Component for the DEGs
DOI: 10.6084/m9.figshare.7020785.v1
title: Additional file 4: of Heterogeneous mutation pattern in tumor tissue and circulating tumor DNA warrants parallel NGS panel testing

description: Table S3. Validation of ctDNA variants by ddPCR. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7020737.v1
title: Additional file 1: of Heterogeneous mutation pattern in tumor tissue and circulating tumor DNA warrants parallel NGS panel testing

description: Table S1. Clinical characteristics of enrolled NSCLC patients. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.23799894
title: Recognizing different types of Ocean Plate Stratigraphy at the southeastern South Qilian Accretionary Belt, northeastern Tibet Plateau

description: Table S1. Zircon LA-ICP-MS U-Pb isotopic data.
DOI: 10.6084/m9.figshare.23799894.v1
title: Recognizing different types of Ocean Plate Stratigraphy at the southeastern South Qilian Accretionary Belt, northeastern Tibet Plateau

description: Table S1. Zircon LA-ICP-MS U-Pb isotopic data.
DOI: 10.6084/m9.figshare.23799900
title: Recognizing different types of Ocean Plate Stratigraphy at the southeastern South Qilian Accretionary Belt, northeastern Tibet Plateau

description: Table S2. Major element (wt%) and trace element (ppm) data.
DOI: 10.6084/m9.figshare.23799900.v1
title: Recognizing different types of Ocean Plate Stratigraphy at the southeastern South Qilian Accretionary Belt, northeastern Tibet Plateau

description: Table S2. Major element (wt%) and trace element (ppm) data.
DOI: 10.6084/m9.figshare.22227043
title: Supplementary original data

description:  
The  ongoing climate change is predicted to induce more weather extremes  such as frequent drought and high-intensity precipitation events,  causing more severe drying-rewetting cycles in soil. However, it remains  largely unknown how these changes will affect soil nitrogen (N)-cycling  microbes and the emissions of potent greenhouse gas nitrous oxide (N<sub>2</sub>O).  Utilizing a field precipitation manipulation in a semi-arid grassland  on the Loess Plateau, we examined how precipitation reduction (ca. −30%)  influenced soil N<sub>2</sub>O and carbon dioxide (CO<sub>2</sub>)  emissions in field, and in a complementary lab-incubation with simulated  drying-rewetting cycles. Results obtained showed that precipitation  reduction stimulated plant root turnover and N-cycling processes,  enhancing soil N<sub>2</sub>O and CO<sub>2</sub> emissions in field, particularly after each rainfall event. Also, high-resolution isotopic analyses revealed that field soil N<sub>2</sub>O  emissions primarily originated from nitrification process. The  incubation experiment further showed that in field soils under  precipitation reduction, drying-rewetting stimulated N mineralization  and ammonia-oxidizing bacteria in favor of genera <em>Nitrosospira</em> and <em>Nitrosovibrio</em>, increasing nitrification and N<sub>2</sub>O  emissions. These findings suggest that moderate precipitation  reduction, accompanied with changes in drying-rewetting cycles under  future precipitation scenarios, may enhance N cycling processes and soil  N<sub>2</sub>O emissions in semi-arid ecosystems, feeding positively back to the ongoing climate change.
DOI: 10.6084/m9.figshare.20652127
title: Additional file 9 of Irradiation induces DJ-1 secretion from esophageal squamous cell carcinoma cells to accelerate metastasis of bystander cells via a TGF-β1 positive feedback loop

description: Additional file 9: Table S1. Clinical data for 177 ESCC serum samples used for ELISA.
DOI: 10.6084/m9.figshare.19603453
title: Additional file 3 of Factors associated with fetal karyotype in spontaneous abortion: a case-case study

description: Additional file 3: Supplemental Table 1. Association of fetal chromosomal abnormalities with parental characteristics (data not shown, n = 160).
DOI: 10.6084/m9.figshare.24324745
title: Hierarchical Neyman-Pearson Classification for Prioritizing Severe Disease Categories in COVID-19 Patient Data

description: COVID-19 has a spectrum of disease severity, ranging from asymptomatic to requiring hospitalization. Understanding the mechanisms driving disease severity is crucial for developing effective treatments and reducing mortality rates. One way to gain such understanding is using a multi-class classification framework, in which patients’ biological features are used to predict patients’ severity classes. In this severity classification problem, it is beneficial to prioritize the identification of more severe classes and control the “under-classification” errors, in which patients are misclassified into less severe categories. The Neyman-Pearson (NP) classification paradigm has been developed to prioritize the designated type of error. However, current NP procedures are either for binary classification or do not provide high probability controls on the prioritized errors in multi-class classification. Here, we propose a hierarchical NP (H-NP) framework and an umbrella algorithm that generally adapts to popular classification methods and controls the under-classification errors with high probability. On an integrated collection of single-cell RNA-seq (scRNA-seq) datasets for 864 patients, we explore ways of featurization and demonstrate the efficacy of the H-NP algorithm in controlling the under-classification errors regardless of featurization. Beyond COVID-19 severity classification, the H-NP algorithm generally applies to multi-class classification problems, where classes have a priority order. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.24324745.v1
title: Hierarchical Neyman-Pearson Classification for Prioritizing Severe Disease Categories in COVID-19 Patient Data

description: COVID-19 has a spectrum of disease severity, ranging from asymptomatic to requiring hospitalization. Understanding the mechanisms driving disease severity is crucial for developing effective treatments and reducing mortality rates. One way to gain such understanding is using a multi-class classification framework, in which patients’ biological features are used to predict patients’ severity classes. In this severity classification problem, it is beneficial to prioritize the identification of more severe classes and control the “under-classification” errors, in which patients are misclassified into less severe categories. The Neyman-Pearson (NP) classification paradigm has been developed to prioritize the designated type of error. However, current NP procedures are either for binary classification or do not provide high probability controls on the prioritized errors in multi-class classification. Here, we propose a hierarchical NP (H-NP) framework and an umbrella algorithm that generally adapts to popular classification methods and controls the under-classification errors with high probability. On an integrated collection of single-cell RNA-seq (scRNA-seq) datasets for 864 patients, we explore ways of featurization and demonstrate the efficacy of the H-NP algorithm in controlling the under-classification errors regardless of featurization. Beyond COVID-19 severity classification, the H-NP algorithm generally applies to multi-class classification problems, where classes have a priority order. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.7547642
title: MOESM3 of Comprehensive evaluation of fuel properties and complex regulation of intracellular transporters for high oil production in developing seeds of Prunus sibirica for woody biodiesel

description: Additional file 3: Table S3. Genes annotated for mitochondrial metabolite transporters in developing P. sibirica seeds. They mainly involved in ATP synthesis, TCA cycle and oil mobilization.
DOI: 10.6084/m9.figshare.7547651.v1
title: MOESM5 of Comprehensive evaluation of fuel properties and complex regulation of intracellular transporters for high oil production in developing seeds of Prunus sibirica for woody biodiesel

description: Additional file 5: Table S5. Genes annotated for transporters of ER membrane in developing P. sibirica seeds. They included ATP transporter (ER-ANT1) and nucleotide sugar transporter (AtUTr1).
DOI: 10.6084/m9.figshare.24849200
title: CiRS-7 Enhances the Liquid-liquid Phase Separation of miRISC and Promotes DNA Damage Repair

description: Noncoding RNAs have been found to play important roles in DNA damage repair, whereas the participation of circRNA remains undisclosed. Here, we characterized ciRS-7, a circRNA containing over 70 putative miR-7-binding sites, as an enhancer of miRISC condensation and DNA repair. Both <i>in vivo</i> and <i>in vitro</i> experiments confirmed the condensation of TNRC6B and AGO2, two core protein components of human miRISC. Moreover, overexpressing ciRS-7 largely increased the condensate number of TNRC6B and AGO2 in cells, while silencing ciRS-7 reduced it. Additionally, miR-7 overexpression also promoted miRISC condensation. Consistent with the previous report that AGO2 participated in RAD51-mediated DNA damage repair, the overexpression of ciRS-7 significantly promoted irradiation-induced DNA damage repair by enhancing RAD51 recruitment. Our results uncover a new role of circRNA in liquid-liquid phase separation and provide new insight into the regulatory mechanism of ciRS-7 on miRISC function and DNA repair.