cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20016289
title: SAMHD1, positively regulated by KLF4, suppresses the proliferation of gastric cancer cells through MAPK p38 signaling pathway

description: SAMHD1 was reported to be related with the development of tumors, while its function in gastric cancer (GC) has not been elucidated yet. Here, we investigated the role and mechanism of SAMHD1 in regulating the proliferation of GC, as well as the mechanism of its expression regulation. Our results revealed that SAMHD1 was downregulated in GC tissues and cell lines, which was correlated with tumor size, depth of invasion and TNM stage. Overexpression of SAMHD1 inhibited the proliferation, clone formation, DNA synthesis and cell cycle progression, while knockdown of SAMHD1 promoted the proliferation of GC cells in vitro and vivo. Meanwhile, SAMHD1 inhibited the activation of MAPK p38 signaling pathway. Moreover, SB203580, as a MAPK p38 inhibitor, could reverse the proliferation and activation of MAPK p38 signaling pathway caused by knockdown of SAMHD1 in GC cells. Additionally, transcription factor Krüppel-like factor 4 (KLF4) bound to the core promoter of SAMHD1, increasing its transcriptional expression in GC cells. In conclusion, SAMHD1 suppressed the proliferation of GC through negatively regulating the activation of MAPK p38 signaling pathway and was upregulated by KLF4 in GC cells.
DOI: 10.6084/m9.figshare.25188818
title: Bird_ecomorphology.zip from Macroevolutionary drivers of morphological disparity in the avian quadrate

description: In birds, the quadrate connects the mandible and skull, and plays an important role in cranial kinesis. Avian quadrate morphology may therefore be assumed to have been influenced by selective pressures related to feeding ecology, yet large-scale variation in quadrate morphology and its potential relationship with ecology have never been quantitatively investigated. Here, we used geometric morphometrics and phylogenetic comparative methods to quantify morphological variation of the quadrate and its relationship with key ecological features across a wide phylogenetic sample. We found non-significant associations between quadrate shape and feeding ecology across different scales of phylogenetic comparison; indeed, allometry and phylogeny exhibit stronger relationships with quadrate shape than ecological features. We show that similar quadrate shapes are associated with widely varying dietary ecologies (one-to-many mapping), while divergent quadrate shapes are associated with similar dietary ecologies (many-to-one mapping). Moreover, we show that the avian quadrate evolves as an integrated unit and exhibits strong associations with the morphologies of neighbouring bones. Our results collectively illustrate that quadrate shape has evolved jointly with other elements of the avian kinetic system, with the major crown bird lineages exploring alternative quadrate morphologies, highlighting the potential diagnostic value of quadrate morphology in investigations of bird systematics.
DOI: 10.6084/m9.figshare.13725020
title: Additional file 2 of Correlation of mutational landscape and survival outcome of peripheral T-cell lymphomas

description: Additional file 2: Table S2. Somatic mutations detected in patients with PTCL.
DOI: 10.6084/m9.figshare.13725020.v1
title: Additional file 2 of Correlation of mutational landscape and survival outcome of peripheral T-cell lymphomas

description: Additional file 2: Table S2. Somatic mutations detected in patients with PTCL.
DOI: 10.6084/m9.figshare.13725026
title: Additional file 4 of Correlation of mutational landscape and survival outcome of peripheral T-cell lymphomas

description: Additional file 4: Table S3. Patients' characteristics based on gene mutational status.
DOI: 10.6084/m9.figshare.13725029.v1
title: Additional file 5 of Correlation of mutational landscape and survival outcome of peripheral T-cell lymphomas

description: Additional file 5: Table S4. Impact of mutations on the efficacy of CHOP‐like chemotherapy.
DOI: 10.6084/m9.figshare.13725029
title: Additional file 5 of Correlation of mutational landscape and survival outcome of peripheral T-cell lymphomas

description: Additional file 5: Table S4. Impact of mutations on the efficacy of CHOP‐like chemotherapy.
DOI: 10.25549/usctheses-ouc11257981
title: 00001.tif
DOI: 10.6084/m9.figshare.16870652.v1
title: Long non-coding RNA TRPM2-AS regulates microRNA miR-138-5p and PLAU (Plasminogen Activator, Urokinase) to promote the progression of gastric adenocarcinoma

description: Gastric adenocarcinoma (GAC) is a common malignant tumor, accounting for 95% of gastric cancers. However, the effects and regulatory mechanisms of long non-coding RNA TRPM2-AS (TRPM2-AS) in GAC have not been fully explored. Our study investigates the action mechanism of TRPM2-AS in GAC. After performing quantitative Real-Time polymerase chain reaction or western blotting, we found that the levels of TRPM2-AS and Plasminogen Activator, Urokinase (PLAU) were upregulated in GAC, whereas the level of miR-138-5p was downregulated. Cell function experiments proved that silencing TRPM2-AS suppressed proliferation and migration and induced apoptosis in GAC cells. Bioinformatic analysis and luciferase assay identified the interaction between TRPM2-AS, miR-138-5p, and PLAU. In addition, the inhibitory effect of silencing TRPM2-AS on GAC cells could be partially relieved by PLAU overexpression. In conclusion, our study revealed that TRPM2-AS sponging miR-138-5p to upregulate PLAU could contribute to GAC progression, which might be useful for identifying biomarkers for GAC therapy. <b>Abbreviation</b> Gastric adenocarcinoma (GAC); Long non-coding RNA (lncRNA); lncRNA TRPM2 antisense RNA (TRPM2-AS); Plasminogen Activator, Urokinase (PLAU); Wild-type (WT); mutant (MUT).
DOI: 10.6084/m9.figshare.13724942.v1
title: Additional file 6 of Targeted enrichment of novel chloroplast-based probes reveals a large-scale phylogeny of 412 bamboos

description: Additional file 6: Supplementary File F1. Pan-genome file. The file can be opened as txt file.
DOI: 10.25549/usctheses-ouc11257992
title: 00001.tif
DOI: 10.25549/usctheses-ouc11258410
title: Microsoft Word - Youn Jung Choi Dissertation 2017 March (final).docx
DOI: 10.25549/usctheses-ouc11258411
title: Microsoft Word - TaylorDissertationFinal.docx
DOI: 10.6084/m9.figshare.13725017
title: Additional file 1 of Correlation of mutational landscape and survival outcome of peripheral T-cell lymphomas

description: Additional file 1: Table S1. Gene list.
DOI: 10.6084/m9.figshare.7961378
title: Additional file 1: of A positive feed-forward loop between LncRNA-URRCC and EGFL7/P-AKT/FOXO3 signaling promotes proliferation and metastasis of clear cell renal cell carcinoma

description: Table S1. Primers used for real-time PCR, vector construction, and ChIP. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7961417.v1
title: Additional file 6: of A positive feed-forward loop between LncRNA-URRCC and EGFL7/P-AKT/FOXO3 signaling promotes proliferation and metastasis of clear cell renal cell carcinoma

description: Table S5. Univariate and Multivariate Cox Regression Analyses of URRCC. (XLSX 11 kb)
DOI: 10.5281/zenodo.10635800
title: Macrorhamphosodes_platycheilus_EPLATE_53_H03_decontaminated_FSCR.fasta.gz 27%

description: .
DOI: 10.5281/zenodo.10635801
title: Macrorhamphosodes_platycheilus_EPLATE_53_H03_decontaminated_FSCR.fasta.gz 27%

description: .
DOI: 10.6084/m9.figshare.13725048
title: Additional file 1 of Broad range detection of viral and bacterial pathogens in bronchoalveolar lavage fluid of children to identify the cause of lower respiratory tract infections

description: Additional file 1 Table S1. Pathogens detected by CD or PCR.
DOI: 10.6084/m9.figshare.13725048.v1
title: Additional file 1 of Broad range detection of viral and bacterial pathogens in bronchoalveolar lavage fluid of children to identify the cause of lower respiratory tract infections

description: Additional file 1 Table S1. Pathogens detected by CD or PCR.
DOI: 10.6084/m9.figshare.13725054
title: Additional file 1 of Prognostic role of preoperative D-dimer, fibrinogen and platelet levels in patients with oral squamous cell carcinoma

description: Additional file 1.
DOI: 10.25549/usctheses-ouc11258415
title: Microsoft Word - Devang Dasani, Thesis (as uploaded).docx
DOI: 10.25549/usctheses-ouc11258424
title: Microsoft Word - THE SLOPPY DEVELOPMENT OF DIVERSITY.docx
DOI: 10.25549/usctheses-ouc11363282
title: An Occupational Analysis Procedure for Developing Curricula in Vocational Education
DOI: 10.5281/zenodo.10635788
title: Macroramphosus_scolopax_USNMAD9NG79_decontaminated_FSCR.fasta.gz

description: .
DOI: 10.5281/zenodo.10635789
title: Macroramphosus_scolopax_USNMAD9NG79_decontaminated_FSCR.fasta.gz

description: .
DOI: 10.5281/zenodo.10635780
title: Determining Factors of Physical Activity and Sedentary Behaviour in University Students During the COVID-19 Pandemic: A Longitudinal Study
DOI: 10.5281/zenodo.10635781
title: Determining Factors of Physical Activity and Sedentary Behaviour in University Students During the COVID-19 Pandemic: A Longitudinal Study
DOI: 10.6084/m9.figshare.13724948
title: Additional file 8 of Targeted enrichment of novel chloroplast-based probes reveals a large-scale phylogeny of 412 bamboos

description: Additional file 8: Table X. The genes used in species tree construction.
DOI: 10.6084/m9.figshare.21065163.v1
title: <i>Arabidopsis</i> sucrose transporter 4 (AtSUC4) is involved in high sucrose-mediated inhibition of root elongation

description: Sucrose transporters (SUCs/SUTs) play crucial roles in apoplast transport and long-distance distribution of sucrose throughout the whole plant. However, whether and how the <i>Arabidopsis</i> AtSUC4 modulates sucrose import from apoplast to cytosol remains unclear. In the present study, we found that AtSUC4 protein was localized to the plasma membrane in the root. Expression of <i>AtSUC4</i> in roots was gradually induced with the increasing sucrose concentrations (0%, 2%, 4% and 6%). When feeding high concentrations (4% and 6%) of sucrose, the primary root growth of seedling was inhibited. Interestingly, <i>atsuc4</i> mutants exhibited longer primary root than the wild type under these conditions, indicating that <i>atsuc4</i> mutants were less sensitive to excess sucrose. Moreover, the root of <i>atsuc4</i> mutants accumulated less sucrose and abscisic acid (ABA) and more indole-3-acetic acid (IAA) on 4% and 6% sucrose supplementation. Transcriptomic analysis revealed that numerous genes associated with sugar transport and metabolism, as well as ABA signalling were down-regulated, whereas many IAA signaling-related genes were up-regulated in mutant plants relative to the wild type under 6% sucrose treatment. Collectively, our finding demonstrated that the deficiency of <i>AtSUC4</i> reduced the inhibition of primary root growth under high sucrose condition, probably through reducing the sucrose transportation and metabolism, and subsequent alteration in IAA and ABA signalling.
DOI: 10.6084/m9.figshare.13725017.v1
title: Additional file 1 of Correlation of mutational landscape and survival outcome of peripheral T-cell lymphomas

description: Additional file 1: Table S1. Gene list.
DOI: 10.6084/m9.figshare.21065162.v1
title: Transcriptome analysis identifies key genes involved in anthocyanin biosynthesis in black and purple fruits (<i>Lycium ruthenicum</i> Murr. L)

description: <i>Lycium ruthenicum</i> is a characteristic plant resource in Northwest China. The fruit with high anthocyanin content is the main reason for its high nutritional value and economic value, while the regulation of key genes regulating anthocyanin biosynthesis in black fruit is not clear. In this study, high-throughput sequencing technology was used to compare the expression differences of all genes in black and purple fruits. The purple samples obtained 45.13 and 51.49 M Raw reads, while the black fruit samples measured 53.85 and 47.38 M Raw Reads. After splicing and assembly, 162,842 transcripts were obtained after removing redundant and duplicated results. Homology comparison of all predicted proteins found that 36,978 (22.43%) genes in <i>Lycium ruthenicum</i> were homologous to <i>Solanum tuberosum</i>, followed by 24,459 (14.84%) genes were homologous to <i>Capsicum annuum</i>. Overall, 3685 genes were up-regulated in purple fruit, 2837 genes were down-regulated in purple fruit, and the remaining 156320 genes were not differentially expressed in black and purple fruit. Through homology comparison of anthocyanin biosynthesis and metabolism structure genes in <i>Lycium ruthenicum</i>, 63 homologous genes, 4 MYB transcription factors and 5 bHLH transcription factors were screened. <i>LrAN2p</i> (909 bp) in purple fruit was 136 bp more upstream of ‘ATG’ than <i>LrAN2</i> (774 bp) in black fruit. Three highly expressed copies of bHLH transcription factors <i>AN1b</i> with different lengths were screened in black fruit, but they were almost not expressed in purple fruit. This study possibly identified the major <i>LrAN1b</i> genes regulating the black fruit trait.
DOI: 10.6084/m9.figshare.21065163
title: <i>Arabidopsis</i> sucrose transporter 4 (AtSUC4) is involved in high sucrose-mediated inhibition of root elongation

description: Sucrose transporters (SUCs/SUTs) play crucial roles in apoplast transport and long-distance distribution of sucrose throughout the whole plant. However, whether and how the <i>Arabidopsis</i> AtSUC4 modulates sucrose import from apoplast to cytosol remains unclear. In the present study, we found that AtSUC4 protein was localized to the plasma membrane in the root. Expression of <i>AtSUC4</i> in roots was gradually induced with the increasing sucrose concentrations (0%, 2%, 4% and 6%). When feeding high concentrations (4% and 6%) of sucrose, the primary root growth of seedling was inhibited. Interestingly, <i>atsuc4</i> mutants exhibited longer primary root than the wild type under these conditions, indicating that <i>atsuc4</i> mutants were less sensitive to excess sucrose. Moreover, the root of <i>atsuc4</i> mutants accumulated less sucrose and abscisic acid (ABA) and more indole-3-acetic acid (IAA) on 4% and 6% sucrose supplementation. Transcriptomic analysis revealed that numerous genes associated with sugar transport and metabolism, as well as ABA signalling were down-regulated, whereas many IAA signaling-related genes were up-regulated in mutant plants relative to the wild type under 6% sucrose treatment. Collectively, our finding demonstrated that the deficiency of <i>AtSUC4</i> reduced the inhibition of primary root growth under high sucrose condition, probably through reducing the sucrose transportation and metabolism, and subsequent alteration in IAA and ABA signalling.
DOI: 10.6084/m9.figshare.13725026.v1
title: Additional file 4 of Correlation of mutational landscape and survival outcome of peripheral T-cell lymphomas

description: Additional file 4: Table S3. Patients' characteristics based on gene mutational status.
DOI: 10.6084/m9.figshare.13725054.v1
title: Additional file 1 of Prognostic role of preoperative D-dimer, fibrinogen and platelet levels in patients with oral squamous cell carcinoma

description: Additional file 1.
DOI: 10.6084/m9.figshare.21065162
title: Transcriptome analysis identifies key genes involved in anthocyanin biosynthesis in black and purple fruits (<i>Lycium ruthenicum</i> Murr. L)

description: <i>Lycium ruthenicum</i> is a characteristic plant resource in Northwest China. The fruit with high anthocyanin content is the main reason for its high nutritional value and economic value, while the regulation of key genes regulating anthocyanin biosynthesis in black fruit is not clear. In this study, high-throughput sequencing technology was used to compare the expression differences of all genes in black and purple fruits. The purple samples obtained 45.13 and 51.49 M Raw reads, while the black fruit samples measured 53.85 and 47.38 M Raw Reads. After splicing and assembly, 162,842 transcripts were obtained after removing redundant and duplicated results. Homology comparison of all predicted proteins found that 36,978 (22.43%) genes in <i>Lycium ruthenicum</i> were homologous to <i>Solanum tuberosum</i>, followed by 24,459 (14.84%) genes were homologous to <i>Capsicum annuum</i>. Overall, 3685 genes were up-regulated in purple fruit, 2837 genes were down-regulated in purple fruit, and the remaining 156320 genes were not differentially expressed in black and purple fruit. Through homology comparison of anthocyanin biosynthesis and metabolism structure genes in <i>Lycium ruthenicum</i>, 63 homologous genes, 4 MYB transcription factors and 5 bHLH transcription factors were screened. <i>LrAN2p</i> (909 bp) in purple fruit was 136 bp more upstream of ‘ATG’ than <i>LrAN2</i> (774 bp) in black fruit. Three highly expressed copies of bHLH transcription factors <i>AN1b</i> with different lengths were screened in black fruit, but they were almost not expressed in purple fruit. This study possibly identified the major <i>LrAN1b</i> genes regulating the black fruit trait.
DOI: 10.6084/m9.figshare.21582233
title: Additional file 1 of Two-stage treatment for severe spinal kyphotic deformity secondary to tuberculosis: halo-pelvic traction followed by a posterior-only approach correction

description: Additional file 1.
DOI: 10.5281/zenodo.10252289
title: TrickyBugs

description: This is TrickyBugs, a dataset of corner-case bugs in plausible programs. TrickyBugs contains 3,051 human-written buggy programs from 324 real-world competition coding tasks. Please read the README.md before using the dataset.
DOI: 10.5281/zenodo.7977255
title: TrickyBugs

description: This is TrickyBugs, a dataset of corner-case bugs in plausible programs. TrickyBugs contains 3,051 human-written buggy programs from 324 real-world competition coding tasks. Please read the README.md before using the dataset.
DOI: 10.5281/zenodo.7977256
title: TrickyBugs

description: This is TrickyBugs, the dataset of the ISSTA'23 paper entitled "Who Judges the Judge: An Empirical Study on Online Judge Tests". This dataset contains the detected false positive solutions (bugs) and the corresponding generated hack test inputs and hack test outputs in our paper. Read our paper for detailed information.
DOI: 10.6084/m9.figshare.14253227
title: Subduction initiation of the Neo-Tethys oceanic lithosphere by collision‐induced subduction transference

description: This dataset include zircon U–Pb ages, whole-rock geochemical compositions, and Sr–Nd–Hf isotope data for the Permian-Early Jurassic magmatic rocks from the Lhasa Terrane, Tibet
DOI: 10.6084/m9.figshare.10058927
title: Additional file 2: of Tumor vasculature remolding by thalidomide increases delivery and efficacy of cisplatin

description: Table S1. List of differentially expressed proteins between control tumors and Thal-treated tumors. (XLS 46 kb)
DOI: 10.6084/m9.figshare.10058927.v1
title: Additional file 2: of Tumor vasculature remolding by thalidomide increases delivery and efficacy of cisplatin

description: Table S1. List of differentially expressed proteins between control tumors and Thal-treated tumors. (XLS 46 kb)
DOI: 10.6084/m9.figshare.22117556
title: Establishment of a differential diagnosis method and a online prediction platform for AOSD and sepsis based on machine learning

description:  Raw data and codes for the development of predictive models for the differential diagnosis of AOSD and sepsis
DOI: 10.6084/m9.figshare.10059092
title: EBT-GWAS.zip

description: The raw data could support our manuscript of "The genetic architecture of early body temperature and its correlation with Salmonella Pullorum resistance in three chicken breeds". Any qualified researcher could use the data after our agreement.
DOI: 10.25549/usctheses-ouc11363452
title: The mailed questionnaire as a survey instrument to identify the educational views of California voters
DOI: 10.6084/m9.figshare.21069309
title: SPRY4 promotes adipogenic differentiation of human mesenchymal stem cells through the MEK–ERK1/2 signaling pathway

description: Obesity is a chronic metabolic disorder characterized by the accumulation of excess fat in the body. Preventing and controlling obesity by inhibiting the adipogenic differentiation of mesenchymal stem cells (MSCs) and thereby avoiding the increase of white adipose tissue is safe and effective. Recent studies have demonstrated that Sprouty proteins (SPRYs) are involved in cell differentiation and related diseases. However, the role and mechanism of SPRY4 in MSC adipogenic differentiation remain to be explored. Here, we found that SPRY4 positively correlates with the adipogenic differentiation of human adipose-derived MSCs (hAMSCs). Via gain- and loss-of-function experiments, we demonstrated that SPRY4 promotes hAMSC adipogenesis both in vitro and in vivo. Mechanistically, SPRY4 functioned by activating the MEK–ERK1/2 pathway. Our findings provide new insights into a critical role for SPRY4 as a regulator of adipogenic differentiation, which may illuminate the underlying mechanisms of obesity and suggest the potential of SPRY4 as a novel treatment option.
DOI: 10.6084/m9.figshare.21069309.v1
title: SPRY4 promotes adipogenic differentiation of human mesenchymal stem cells through the MEK–ERK1/2 signaling pathway

description: Obesity is a chronic metabolic disorder characterized by the accumulation of excess fat in the body. Preventing and controlling obesity by inhibiting the adipogenic differentiation of mesenchymal stem cells (MSCs) and thereby avoiding the increase of white adipose tissue is safe and effective. Recent studies have demonstrated that Sprouty proteins (SPRYs) are involved in cell differentiation and related diseases. However, the role and mechanism of SPRY4 in MSC adipogenic differentiation remain to be explored. Here, we found that SPRY4 positively correlates with the adipogenic differentiation of human adipose-derived MSCs (hAMSCs). Via gain- and loss-of-function experiments, we demonstrated that SPRY4 promotes hAMSC adipogenesis both in vitro and in vivo. Mechanistically, SPRY4 functioned by activating the MEK–ERK1/2 pathway. Our findings provide new insights into a critical role for SPRY4 as a regulator of adipogenic differentiation, which may illuminate the underlying mechanisms of obesity and suggest the potential of SPRY4 as a novel treatment option.
DOI: 10.25549/usctheses-ouc11258433
title: Microsoft Word - Suber_PostDefenseDraftManuscript2.docx
DOI: 10.25549/usctheses-ouc11258439
title: Microsoft Word - Xia_Dissertation_v4.docx
DOI: 10.25549/usctheses-ouc11258353
title: Microsoft Word - Master Thesis.docx
DOI: 10.7910/dvn/fx6zyr
title: Replication Data for: The Roach to Reelection is Paved with Good Intentions: Experiments on the Role of Outcomes and Intentions in Voting Behavior

description: Incumbents regularly take actions that they believe will produce good outcomes for voters, but given that incumbents do not have perfect control over policy outcomes, sometimes good intentions lead to unintended bad outcomes. An important question for democratic accountability is whether voters take intentions into consideration or if they are solely focused on outcomes. We propose an outcome-intention hypothesis in which voters reward an incumbent for both good outcomes and good intentions. To investigate this hypothesis, we use a series of incentivized experiments where participants took the role of voters who experienced a better or worse policy outcome. Voters were randomly assigned to additionally receive information about an incumbent’s intended policy outcome. We find that voters reward incumbents for good outcomes and good intentions. However, when we introduce group competition, voters only reward the good intentions of in-group incumbents.
DOI: 10.6084/m9.figshare.22638031.v1
title: Additional file 2 of Prognostic predictors of radical resection of stage I-IIIB non-small cell lung cancer: the role of preoperative CT texture features, conventional imaging features, and clinical features in a retrospectively analyzed

description: Additional file 2.
DOI: 10.25549/usctheses-ouc11258370
title: Microsoft Word - Wise Dissertation FINAL 2017.docx