cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19502390.v1
title: Additional file 2 of Physiological adjustment of pomegranate pericarp responding to sunburn and its underlying molecular mechanisms

description: Additional file 2: Supplementary Table 2. The transcriptome sequencing results of control and sunburned pomegranate fruits.
DOI: 10.6084/m9.figshare.6395237.v1
title: Additional file 1: of Microarray analysis of long non-coding RNA expression profiles in monocytic myeloid-derived suppressor cells in Echinococcus granulosus-infected mice

description: Table S1. Primers used in qPCR detection of selected lncRNAs. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7968056.v1
title: Additional file 7: of Comparative analysis of sequencing technologies for single-cell transcriptomics

description: Table S5. Single-cell library statistics computed from randomly downsampled 1 million paired-end sequencing reads for mESCs and K562 using plate-based Smart-seq2 protocol and sequenced across HiSeq4000 and BGISEQ-500 platforms. (CSV 82 kb)
DOI: 10.25549/usctheses-c3-599885
title: etd-RuizSusana-3651~042
DOI: 10.6084/m9.figshare.19502396.v1
title: Additional file 4 of Physiological adjustment of pomegranate pericarp responding to sunburn and its underlying molecular mechanisms

description: Additional file 4: Supplementary Table 4. Quantity and function of differently expressed transcription factors between healthy and sunburned pomegranate pericarps.
DOI: 10.6084/m9.figshare.19502399
title: Additional file 5 of Physiological adjustment of pomegranate pericarp responding to sunburn and its underlying molecular mechanisms

description: Additional file 5: Supplementary Table 5. Primers designed for the qRT-PCR expression analysis.
DOI: 10.6084/m9.figshare.19502387.v1
title: Additional file 1 of Physiological adjustment of pomegranate pericarp responding to sunburn and its underlying molecular mechanisms

description: Additional file 1: Supplementary Table 1. Differentially accumulated metabolites in sunburned compared with healthy pomegranate pericarps.
DOI: 10.6084/m9.figshare.19502393
title: Additional file 3 of Physiological adjustment of pomegranate pericarp responding to sunburn and its underlying molecular mechanisms

description: Additional file 3: Supplementary Table 3. Differentially expressed genes in the control and sunburned pomegranate pericarps.
DOI: 10.6084/m9.figshare.7968050.v1
title: Additional file 6: of Comparative analysis of sequencing technologies for single-cell transcriptomics

description: Table S4. Single-cell library statistics computed from raw paired-end sequencing reads for mESCs and K562 using plate-based Smart-seq2 protocol and sequenced across HiSeq4000 and BGISEQ-500 platforms. (CSV 87 kb)
DOI: 10.6084/m9.figshare.6395258
title: Additional file 1: of Integrative analysis of DNA methylation and gene expression reveals hepatocellular carcinoma-specific diagnostic biomarkers

description: Methylation information for 109 CpGs in different HCC datasets. (XLSX 26Â kb)
DOI: 10.6084/m9.figshare.6395276.v1
title: Additional file 3: of Microarray analysis of long non-coding RNA expression profiles in monocytic myeloid-derived suppressor cells in Echinococcus granulosus-infected mice

description: Table S3. Significantly and differentially expressed mRNAs in M-MDSCs. (XLSX 83 kb)
DOI: 10.6084/m9.figshare.7968056
title: Additional file 7: of Comparative analysis of sequencing technologies for single-cell transcriptomics

description: Table S5. Single-cell library statistics computed from randomly downsampled 1 million paired-end sequencing reads for mESCs and K562 using plate-based Smart-seq2 protocol and sequenced across HiSeq4000 and BGISEQ-500 platforms. (CSV 82 kb)
DOI: 10.6084/m9.figshare.7968215
title: Additional file 10: of Development of a core SNP arrays based on the KASP method for molecular breeding of rice

description: Table S10. Subset 8 of SNPs from Zhao et al. (2011) & Yonemaru et al. (2014). (XLSX 12 kb)
DOI: 10.6084/m9.figshare.6395258.v1
title: Additional file 1: of Integrative analysis of DNA methylation and gene expression reveals hepatocellular carcinoma-specific diagnostic biomarkers

description: Methylation information for 109 CpGs in different HCC datasets. (XLSX 26Â kb)
DOI: 10.6084/m9.figshare.6395261
title: Additional file 2: of Microarray analysis of long non-coding RNA expression profiles in monocytic myeloid-derived suppressor cells in Echinococcus granulosus-infected mice

description: Table S2. Significantly and differentially expressed lncRNAs in M-MDSCs. (XLSX 49 kb)
DOI: 10.6084/m9.figshare.6395261.v1
title: Additional file 2: of Microarray analysis of long non-coding RNA expression profiles in monocytic myeloid-derived suppressor cells in Echinococcus granulosus-infected mice

description: Table S2. Significantly and differentially expressed lncRNAs in M-MDSCs. (XLSX 49 kb)
DOI: 10.6084/m9.figshare.7968245.v1
title: Additional file 3: of Development of a core SNP arrays based on the KASP method for molecular breeding of rice

description: Table S3. Subset 1 of SNPs from Kurokawa et al. (2016). (XLSX 12 kb)
DOI: 10.6084/m9.figshare.7968254
title: Additional file 5: of Development of a core SNP arrays based on the KASP method for molecular breeding of rice

description: Table S5. Subset 3 of SNPs. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.7968260
title: Additional file 6: of Development of a core SNP arrays based on the KASP method for molecular breeding of rice

description: Table S6. Subset 4 of SNPs. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.6395300
title: Additional file 3: of Integrative analysis of DNA methylation and gene expression reveals hepatocellular carcinoma-specific diagnostic biomarkers

description: Prediction performance of specific CpGs in distinguishing HCC from normal tissue and other tumors. (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.7968074.v1
title: Additional file 9: of Comparative analysis of sequencing technologies for single-cell transcriptomics

description: Table S7. Metadata for all single-cell libraries profiled in this manuscript. Each cell is labeled with a sample id (accession number), protocol, place of experiment, read type, and sequencing platform.
DOI: 10.25549/usctheses-c3-589684
title: etd-ChiuCathle-3452~016
DOI: 10.6084/m9.figshare.6395315.v1
title: Additional file 4: of Integrative analysis of DNA methylation and gene expression reveals hepatocellular carcinoma-specific diagnostic biomarkers

description: Primers of CpGs or genes in BSP and gene expression experiments. BSP and qPCR data of fresh frozen tissues from ten HCC patients. (XLSX 14Â kb)
DOI: 10.6084/m9.figshare.7968230.v1
title: Additional file 1: of Development of a core SNP arrays based on the KASP method for molecular breeding of rice

description: Table S1. Primers for sequencing and genotyping. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.18978380.v1
title: Identification of a ferroptosis-related gene signature for predicting the prognosis of cholangiocarcinoma

description: Cholangiocarcinoma (CCA) is a highly intractable malignancy with poor prognosis. Ferroptosis, a newly explored type of programmed cell death, plays a critical role in the initiation and progression of a tumor. Herein, we aimed to identify a ferroptosis-related risk model to evaluate the prognosis of CCA. Differentially expressed genes (DEGs) were retrieved from three GEO cohorts. Univariate and LASSO analysis were employed to build a ferroptosis-related gene signature. Next, the predictive value was assessed in a training and a validation cohort. Metascape Online analysis, ESTIMATE and CIBERSORT algorithms, and ssGSEA were employed to perform the functional analysis between different risk groups. Finally, the expression of prognostic genes was validated with RT-qPCR. We identified 51 differentially expressed ferroptosis genes and established the prognostic signature containing five ferroptosis-related genes. The K-M curves and the ROC curves revealed a favorable predictive efficacy of the prognostic signature. Functional enrichment analysis indicated that immune-related responses were greatly enriched between different risk groups. Five prognostic genes were also differentially expressed in CCA cell lines. We developed a novel ferroptosis-related gene signature for CCA with high predictive accuracy. The analysis of the immune infiltration status may provide a potential therapeutic alternative to CCA.
DOI: 10.6084/m9.figshare.7968221.v1
title: Additional file 11: of Development of a core SNP arrays based on the KASP method for molecular breeding of rice

description: Table S11. KASP assay primers used in the study. (XLSX 39 kb)
DOI: 10.6084/m9.figshare.7968236
title: Additional file 2: of Development of a core SNP arrays based on the KASP method for molecular breeding of rice

description: Table S2. List of the rice germplasm used in this study. (XLSX 39 kb)
DOI: 10.25549/usctheses-c3-577218
title: etd-CardenasMi-3510_110
DOI: 10.6084/m9.figshare.21382979.v1
title: Additional file 7 of Profiling ATM regulated genes in Drosophila at physiological condition and after ionizing radiation

description: Additional file 7: Table S4. Differentially expressed protein-coding genes in atm mutated flies after X-ray irradiation.
DOI: 10.25549/usctheses-c3-601265
title: etd-GaddisMala-3657~46
DOI: 10.6084/m9.figshare.6395336
title: Additional file 2: of Comparative mitogenomics supports synonymy of the genera Ligula and Digramma (Cestoda: Diphyllobothriidae)

description: Table S2. The list of cestode species and outgroups used for comparative mitogenomic and phylogenetic analyses, and accession number, A+T content and skewness of different elements of each mitogenome. (XLSX 19 kb)
DOI: 10.6084/m9.figshare.7968188.v1
title: Additional file 1: of Novel parent-of-origin-specific differentially methylated loci on chromosome 16

description: Table S1. Overview of available genomic information for upd(16). Table S2. Differentially methylated regions identified in blood-based analysis (n = 1579), sorted by number of differentially methylated sites. Table S3. Differentially methylated regions identified in lung-based analysis (n = 8), sorted by number of differentially methylated sites contained. (XLSX 589 kb)
DOI: 10.6084/m9.figshare.7968260.v1
title: Additional file 6: of Development of a core SNP arrays based on the KASP method for molecular breeding of rice

description: Table S6. Subset 4 of SNPs. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.21382949
title: Additional file 11 of Profiling ATM regulated genes in Drosophila at physiological condition and after ionizing radiation

description: Additional file 11: Table S8. lncRNA counts.
DOI: 10.6084/m9.figshare.21382949.v1
title: Additional file 11 of Profiling ATM regulated genes in Drosophila at physiological condition and after ionizing radiation

description: Additional file 11: Table S8. lncRNA counts.
DOI: 10.6084/m9.figshare.7968233.v1
title: Additional file 3: of GTSE1 is involved in breast cancer progression in p53 mutation-dependent manner

description: The GTSE1 protein expression level with clinical and pathological characteristics in 64 non-TNBC patients. (XLSX 14 kb)
DOI: 10.25549/usctheses-c3-601291
title: etd-GaddisMala-3657~72
DOI: 10.6084/m9.figshare.12687133
title: Additional file 2 of Identification of resistance loci in Chinese and Canadian canola/rapeseed varieties against Leptosphaeria maculans based on genome-wide association studies

description: Additional file 2.
DOI: 10.25549/usctheses-c3-589673
title: etd-ChiuCathle-3452~005
DOI: 10.6084/m9.figshare.12687139.v1
title: Additional file 3 of Identification of resistance loci in Chinese and Canadian canola/rapeseed varieties against Leptosphaeria maculans based on genome-wide association studies

description: Additional file 3.
DOI: 10.6084/m9.figshare.12687148.v1
title: Additional file 6 of Identification of resistance loci in Chinese and Canadian canola/rapeseed varieties against Leptosphaeria maculans based on genome-wide association studies

description: Additional file 6.
DOI: 10.6084/m9.figshare.6395336.v1
title: Additional file 2: of Comparative mitogenomics supports synonymy of the genera Ligula and Digramma (Cestoda: Diphyllobothriidae)

description: Table S2. The list of cestode species and outgroups used for comparative mitogenomic and phylogenetic analyses, and accession number, A+T content and skewness of different elements of each mitogenome. (XLSX 19 kb)
DOI: 10.6084/m9.figshare.6395357
title: Additional file 3: of Comparative mitogenomics supports synonymy of the genera Ligula and Digramma (Cestoda: Diphyllobothriidae)

description: Table S3. General statistics (length and codons) for mitochondrial protein-coding genes and rRNAs of 38 cestodes. Abbreviations of species name are the initials of genus and species name combined. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.7968275.v1
title: Additional file 9: of Development of a core SNP arrays based on the KASP method for molecular breeding of rice

description: Table S9. Subset 7 of SNPs. (XLSX 12 kb)
DOI: 10.25549/usctheses-c3-589719
title: etd-ChiuCathle-3452~051
DOI: 10.6084/m9.figshare.12687142
title: Additional file 4 of Identification of resistance loci in Chinese and Canadian canola/rapeseed varieties against Leptosphaeria maculans based on genome-wide association studies

description: Additional file 4.
DOI: 10.6084/m9.figshare.21382982
title: Additional file 8 of Profiling ATM regulated genes in Drosophila at physiological condition and after ionizing radiation

description: Additional file 8: Table S5. miRNA counts.
DOI: 10.6084/m9.figshare.6395315
title: Additional file 4: of Integrative analysis of DNA methylation and gene expression reveals hepatocellular carcinoma-specific diagnostic biomarkers

description: Primers of CpGs or genes in BSP and gene expression experiments. BSP and qPCR data of fresh frozen tissues from ten HCC patients. (XLSX 14Â kb)
DOI: 10.6084/m9.figshare.7968188
title: Additional file 1: of Novel parent-of-origin-specific differentially methylated loci on chromosome 16

description: Table S1. Overview of available genomic information for upd(16). Table S2. Differentially methylated regions identified in blood-based analysis (n = 1579), sorted by number of differentially methylated sites. Table S3. Differentially methylated regions identified in lung-based analysis (n = 8), sorted by number of differentially methylated sites contained. (XLSX 589 kb)
DOI: 10.6084/m9.figshare.6395357.v1
title: Additional file 3: of Comparative mitogenomics supports synonymy of the genera Ligula and Digramma (Cestoda: Diphyllobothriidae)

description: Table S3. General statistics (length and codons) for mitochondrial protein-coding genes and rRNAs of 38 cestodes. Abbreviations of species name are the initials of genus and species name combined. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.7968224
title: Additional file 2: of GTSE1 is involved in breast cancer progression in p53 mutation-dependent manner

description: The GTSE1 protein expression level with clinical and pathological characteristics in 90 TNBC patients. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.20551410
title: MicroRNA-124a Protects the Myocardium Against Ischemia Reperfusion Injury Through Regulation of the Notch Signaling Pathway

description: Abstract Introduction: This study’s objective is to investigate the effect of downregulation of micro ribonucleic acid (miR)-124a on myocardial injury after ischemia reperfusion (I/R) in rats. Methods: Sprague Dawley (SD) rats (n=20) were divided into four groups - sham, I/R, I/R+miR-124a antagomir (I/R+ant-miR-124a), and I/R+ant-normal control (NC). The pathomorphological and infarct size variance of injured myocardial tissues with IR were conducted with hematoxylin (HE) and triphenyltetrazolium chloride (TTC) staining. The expression levels of miR-124a, BAX, nuclear factor kappa B (NF-KB), Notch1, and Hes1 were examined by quantitative real-time polymerase chain reaction or Western blot in myocardium. The inflammatory cytokines interleukin (IL)-6, IL-1β, and tumor necrosis factor alpha (TNF-α) were detected by the enzyme-linked immunosorbent assay, as well as the activity of lactate dehydrogenase (LDH) and creatine kinase (CK) in serum by colorimetry. Results: The expression of miR-124a was increased in the I/R group. Compared with I/R and I/R+ant-NC groups, after downregulating miR-124a, the expression of IL-6, IL-1β, TNF-α, BAX, NF-KB, LDH, and CK were decreased, but the expression of Notch1 and Hes1 were increased. In HE staining, myocardial tissue edema, red blood cell exudation, and myocardial fiber arrangement disorder were accompanied by inflammatory cell infiltration and local necrosis in the I/R group. However, the pathological injury of myocardial tissue was alleviated after downregulating miR-124a. Additionally, TTC results showed that the myocardial infarction area was decreased in the I/R+ant-miR-124a group. Conclusion: Downregulation of miR-124a expression through Notch pathway can significantly reduce myocardial damage after 24 hours of I/R in SD rats. Therefore, miR-124a may become a potential therapeutic target for I/R injury.
DOI: 10.6084/m9.figshare.21382979
title: Additional file 7 of Profiling ATM regulated genes in Drosophila at physiological condition and after ionizing radiation

description: Additional file 7: Table S4. Differentially expressed protein-coding genes in atm mutated flies after X-ray irradiation.
DOI: 10.6084/m9.figshare.7968233
title: Additional file 3: of GTSE1 is involved in breast cancer progression in p53 mutation-dependent manner

description: The GTSE1 protein expression level with clinical and pathological characteristics in 64 non-TNBC patients. (XLSX 14 kb)
DOI: 10.25549/usctheses-c3-589749
title: etd-ChiuCathle-3452~081
DOI: 10.6084/m9.figshare.21382982.v1
title: Additional file 8 of Profiling ATM regulated genes in Drosophila at physiological condition and after ionizing radiation

description: Additional file 8: Table S5. miRNA counts.
DOI: 10.6084/m9.figshare.19503047.v1
title: Enhancing integrated denitrifying anaerobic methane oxidation and Anammox processes for nitrogen and methane removal: A review

description: The integration of denitrifying anaerobic methane oxidation (DAMO) and anaerobic ammonium oxidation (Anammox) simultaneously converts ammonium, methane, and oxidized nitrogen species (nitrite and nitrate) to harmless N<sub>2</sub> and CO<sub>2</sub>. This integrated and complementary process achieves the nitrogen and carbon cycles in wastewater with the potential to be applied widely at full scale to realize energy-positive wastewater treatment plants (WWTPs). In this review, we summarize the collaborative and competitive interactions of DAMO–Anammox microorganisms and systematically evaluate the challenges for the full-scale application of integrated DAMO–Anammox for wastewater treatment, including their extremely slow growth rate, low metabolic activity, and limited nitrogen and methene removal rate. We examine comprehensively the critical role of bioreactor design (attached, suspended, and granular sludge systems) for biomass retention and substrate transfer. The paper also discussed strategies involving trace elements (Cu(II) and Fe(II)), Zero Valent Iron (ZVI), and External Electrostatic Fields (EEFs) to enhance the DAMO–Anammox microbial activities. Further review is provided on the addition of Humics, quinone-compound anthraquinone-2,6-disulfonate (AQDs), Fe(III), Mn(IV) as electron acceptors through extracellular electron transfer (EET) and couple with autotrophic denitrification (AuDen) (H<sub>2</sub>S and Fe(II)) to accelerate nitrogen and methane removal. Finally, a conceptual design of innovative WWTPs based on the integrated DAMO–Anammox was proposed.
DOI: 10.6084/m9.figshare.14260192
title: Identification of differential DNA methylation alterations of ovarian cancer in peripheral whole blood based on within-sample relative methylation orderings

description: Leukocyte cell proportion changes affect the detection of cancer-associated aberrant DNA methylation alterations in peripheral blood samples. We aimed to detect cellular DNA methylation changes in ovarian cancer (OVC) blood samples avoiding the above-mentioned cell-composition effects. Based on the within-sample relative methylation orderings (RMOs) of CpG loci in leukocyte subtypes, we developed the Ref-RMO method to detect aberrant methylation alterations from OVC blood samples. Stable CpG pairs with consistent RMOs in different leukocyte subtypes were determined, more than 99% of which retained their RMO patterns in peripheral whole blood (PWB) in independent datasets. Based on the stable CpG pairs, significantly reversed CpG pairs were detected from OVC PWB samples, which were relative to clinical information such as age, subtype, grade, stage, or CA125 level. Results showed 439 CpG loci were determined to be significant differential DNA methylations between OVC and healthy blood samples. They were mainly enriched in KEGG pathways, such as cytokine-cytokine receptor interaction, apoptosis, proteoglycans in cancer, and immune-associated Gene Ontology terms. STRING analysis showed that they tended to have functional interactions with cancer-associated genes recorded in the COSMIC database. Leukocyte cellular differential DNA methylations could be identified by the proposed RMO-based method from OVC PWB samples, which were cancer-associated aberrant signals against cell-composition effects.
DOI: 10.6084/m9.figshare.20551635.v1
title: Cornuside ameliorated experimental autoimmune encephalomyelitis by limiting the recruitment of CD4+ T lymphocytes in the spinal cord

description: Abstract We conducted this study to determine whether cornuside could improve the neurological deficit symptoms of experimental autoimmune encephalomyelitis (EAE) rats, as well as determine the potential involvement of CD4+ T lymphocytes, vascular cell adhesion molecule-1 (VCAM-1), intercellular adhesion molecule-1 (ICAM-1), and tumor necrosis factor-α (TNF-α). Altogether, 32 Lewis rats were randomly divided into control, EAE, EAE/prednisolone, and EAE/cornuside, wherein their neurological function was assessed every day. CD4+ T lymphocyte recruitment into the spinal cord (SC) was evaluated using immunohistochemistry. The VCAM-1, ICAM-1 and TNF-α mRNA expressions in the SC were determined by real-time quantitative PCR, and the VCAM-1 and ICAM-1 proteins were determined by western blotting. Compared to the control group, the EAE group rats with neurological deficits had enhanced CD4+ T lymphocyte infiltration and higher expression levels of VCAM-1, ICAM-1, and TNF-α in the SC. Meanwhile, compared with the EAE group, the EAE/cornuside and EAE/prednisolone groups had lower neurological scores, less CD4+ T lymphocyte infiltrations, and lower expression levels of VCAM-1, ICAM-1, and TNF-α in the SC. Thus, cornuside ameliorated EAE, which could be owed to the inhibition of CD4+ T lymphocyte recruitment and VCAM-1, ICAM-1, and TNF-α expressions in the SC.
DOI: 10.6084/m9.figshare.7968266
title: Additional file 7: of Development of a core SNP arrays based on the KASP method for molecular breeding of rice

description: Table S7. Subset 5 of SNPs. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.19501240.v1
title: Additional file 5 of Genome-wide survey of the GATA gene family in camptothecin-producing plant Ophiorrhiza pumila

description: Additional file 5.
DOI: 10.6084/m9.figshare.19501243.v1
title: Additional file 6 of Genome-wide survey of the GATA gene family in camptothecin-producing plant Ophiorrhiza pumila

description: Additional file 6.