cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.rxnm5t
title: Occurrence Download

description: A dataset containing 20 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Peru",
 "TaxonKey is Capsicum hookerianum (Miers) Kuntze"
 ]
}

 The dataset includes 20 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020063-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7a7jsb
title: Occurrence Download

description: A dataset containing 27 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pristimantis citriogaster (Duellman, 1992)"
 ]
}

 The dataset includes 27 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0295825-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cx9sy6
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Decaschistia ficifolia Mart."
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016650-240314170635999/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qvbk4s
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Human Observation",
 "BasisOfRecord is Specimen"
 ]
 },
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Guibemantis liber (Peracca, 1893)",
 "Year 2017-2020"
 ]
}

 The dataset includes 5 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0062145-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jscxk3
title: Occurrence Download

description: A dataset containing 167 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Huberia espiritosantensis Baumgratz"
 ]
}

 The dataset includes 167 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0299331-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bvygcq
title: Occurrence Download

description: A dataset containing 2268 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Engraulis japonicus Temminck & Schlegel, 1846"
 ]
}

 The dataset includes 2268 records from 63 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0259992-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wfz5g9
title: Occurrence Download

description: A dataset containing 36010 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Wild bees of Chile - The PUCV collection"
 ]
}

 The dataset includes 36010 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003206-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cegmen
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lonicera spinosa Jacquem.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0320330-200613084148143/datasets/export for details.
DOI: 10.15468/dl.tqn1mu
title: Occurrence Download

description: A dataset containing 6304 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Youngia japonica (L.) DC."
 ]
}

 The dataset includes 6304 records from 182 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008438-180131172636756/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.8028872.v4
title: Mapping Tumor-Specific Expression QTLs in Impure Tumor Samples

description: The study of gene expression quantitative trait loci (eQTL) is an effective approach to illuminate the functional roles of genetic variants. Computational methods have been developed for eQTL mapping using gene expression data from microarray or RNA-seq technology. Application of these methods for eQTL mapping in tumor tissues is problematic because tumor tissues are composed of both tumor and infiltrating normal cells (e.g., immune cells) and eQTL effects may vary between tumor and infiltrating normal cells. To address this challenge, we have developed a new method for eQTL mapping using RNA-seq data from tumor samples. Our method separately estimates the eQTL effects in tumor and infiltrating normal cells using both total expression and allele-specific expression (ASE). We demonstrate that our method controls Type I error rate and has higher power than some alternative approaches. We applied our method to study RNA-seq data from The Cancer Genome Atlas and illustrated the similarities and differences of eQTL effects in tumor and normal cells. Supplementary materials for this article, including a standardized description of the materials available for reproducing the work, are available as an online supplement.
DOI: 10.6084/m9.figshare.16417411.v1
title: Additional file 3 of Systematic functional interrogation of human pseudogenes using CRISPRi

description: Additional file 3: Supplementary Table 2. The CRISPRi screen results for individual pseudogenes and parent genes in MCF7 cells, including the positive and negative selection information about pseudogene/parent genes as well as the significant negatively selected sgRNAs that may have putative off-target effect on pseudogene/parent gene hits.
DOI: 10.6084/m9.figshare.16417405.v1
title: Additional file 1 of Systematic functional interrogation of human pseudogenes using CRISPRi

description: Additional file 1: Supplementary Table 1. The sequences of the sgRNAs that were designed to target pseudogenes, parent genes as well as positive and negative control sgRNAs.
DOI: 10.6084/m9.figshare.8028872.v3
title: Mapping Tumor-Specific Expression QTLs in Impure Tumor Samples

description: The study of gene expression quantitative trait loci (eQTL) is an effective approach to illuminate the functional roles of genetic variants. Computational methods have been developed for eQTL mapping using gene expression data from microarray or RNA-seq technology. Application of these methods for eQTL mapping in tumor tissues is problematic because tumor tissues are composed of both tumor and infiltrating normal cells (e.g., immune cells) and eQTL effects may vary between tumor and infiltrating normal cells. To address this challenge, we have developed a new method for eQTL mapping using RNA-seq data from tumor samples. Our method separately estimates the eQTL effects in tumor and infiltrating normal cells using both total expression and allele-specific expression (ASE). We demonstrate that our method controls Type I error rate and has higher power than some alternative approaches. We applied our method to study RNA-seq data from The Cancer Genome Atlas and illustrated the similarities and differences of eQTL effects in tumor and normal cells. Supplementary materials for this article, including a standardized description of the materials available for reproducing the work, are available as an online supplement.
DOI: 10.6084/m9.figshare.5931661
title: Design and Analysis of a Novel Spacecraft for Mitigating Global Warming

description: ABSTRACT: A device called Huge Space Shield (HSS) has been put forward for mitigating global warming. This is a space tethers system, which use cables to connect a shielding surface and a mechanism control. In this study, orbital analysis was carried out to choose the best orbit for getting the best effect. Simulation studies were employed to understand the HSS at the beginning of entering the orbit, which were based on completely and semi-simplified model. Therefore, the force analysis gives rise to the system would not fail in the period of running on the orbit. All the results show that the HSS is stable at launch and operation, which can help ease global warming.
DOI: 10.6084/m9.figshare.16417411
title: Additional file 3 of Systematic functional interrogation of human pseudogenes using CRISPRi

description: Additional file 3: Supplementary Table 2. The CRISPRi screen results for individual pseudogenes and parent genes in MCF7 cells, including the positive and negative selection information about pseudogene/parent genes as well as the significant negatively selected sgRNAs that may have putative off-target effect on pseudogene/parent gene hits.
DOI: 10.6084/m9.figshare.16417432
title: Additional file 2 of Sequencing of methylase-accessible regions in integral circular extrachromosomal DNA reveals differences in chromatin structure

description: Additional file 2: Table S1. The profiles of the ecDNAs.
DOI: 10.6084/m9.figshare.16417405
title: Additional file 1 of Systematic functional interrogation of human pseudogenes using CRISPRi

description: Additional file 1: Supplementary Table 1. The sequences of the sgRNAs that were designed to target pseudogenes, parent genes as well as positive and negative control sgRNAs.
DOI: 10.6084/m9.figshare.16417414
title: Additional file 4 of Systematic functional interrogation of human pseudogenes using CRISPRi

description: Additional file 4: Supplementary Table 3. The sequences of the sgRNAs, siRNAs, shRNAs and PCR primers and the information about antibodies.
DOI: 10.6084/m9.figshare.16417420.v1
title: Additional file 5 of Systematic functional interrogation of human pseudogenes using CRISPRi

description: Additional file 5: Supplementary Table 4. The list of differentially expressed protein-coding genes between MCF7-dCas9 cells transduced with non-targeting sgRNA control and MGAT4EP-targeting sgRNA.
DOI: 10.6084/m9.figshare.16417423
title: Additional file 6 of Systematic functional interrogation of human pseudogenes using CRISPRi

description: Additional file 6: Supplementary Table 5. The results of differential expression analysis between tumors and the corresponding normal tissues and multivariate Cox proportional hazards regression analysis of association between gene expression and clinical outcomes including patient OS and RFS for all unitary pseudogenes annotated in GENCODE V22, across different cancer types.
DOI: 10.6084/m9.figshare.16417414.v1
title: Additional file 4 of Systematic functional interrogation of human pseudogenes using CRISPRi

description: Additional file 4: Supplementary Table 3. The sequences of the sgRNAs, siRNAs, shRNAs and PCR primers and the information about antibodies.
DOI: 10.6084/m9.figshare.23751796
title: Additional file 4 of The determination of peanut (Arachis hypogaea L.) pod-sizes during the rapid-growth stage by phytohormones

description: Additional file 4: Table S2. Logistic growth function.
DOI: 10.6084/m9.figshare.23751799
title: Additional file 5 of The determination of peanut (Arachis hypogaea L.) pod-sizes during the rapid-growth stage by phytohormones

description: Additional file 5: Table S3. GO enrichment analysis.
DOI: 10.6084/m9.figshare.16417588
title: Additional file 5 of Comparative phylogenetic analysis of CBL reveals the gene family evolution and functional divergence in Saccharum spontaneum

description: Additional file 5.
DOI: 10.6084/m9.figshare.16417579.v1
title: Additional file 2 of Comparative phylogenetic analysis of CBL reveals the gene family evolution and functional divergence in Saccharum spontaneum

description: Additional file 2.
DOI: 10.6084/m9.figshare.16417588.v1
title: Additional file 5 of Comparative phylogenetic analysis of CBL reveals the gene family evolution and functional divergence in Saccharum spontaneum

description: Additional file 5.
DOI: 10.6084/m9.figshare.16417591
title: Additional file 6 of Comparative phylogenetic analysis of CBL reveals the gene family evolution and functional divergence in Saccharum spontaneum

description: Additional file 6.
DOI: 10.6084/m9.figshare.14320414
title: Overexpression of klotho suppresses growth and pulmonary metastasis of osteosarcoma in vivo

description: Abstract Klotho is originally discovered as an anti-aging gene and knock-out of klotho accelerates aging in mice. Subsequent studies support the anti-carcinogenesis role of klotho in a variety of human malignancies. The present study investigated the role of klotho on growth and metastasis of osteosarcoma cells. The osteosarcoma cells were transduced with lentivirus particles encoding klotho or scramble control. The reconstructed osteosarcoma cells were injected into the femoral medullary cavity of nude mice to establish a xenograft animal model. The anti-tumor properties of klotho were evaluated in terms of tumor growth, apoptosis, glycogen production, and pulmonary metastasis. Lentivirus-mediated overexpression of klotho significantly decreased tumor volume and weight in osteosarcoma mice. Determination of PCNA and Ki67 expression revealed that overexpression of klotho inhibited cell proliferation in tumor tissues obtained from osteosarcoma xenografts. PAS staining also showed that overexpression of klotho significantly decreased the production of glycogen in osteosarcoma. Moreover, TUNEL positive cells were significantly increased after lentivirus-mediated overexpression of klotho. Furthermore, lentivirus-mediated upregulation of klotho reduced the number of pulmonary metastatic lesions in mice compared to control mice. These findings demonstrated that elevated klotho could inhibit osteosarcoma cell growth and pulmonary metastasis in vivo, suggesting that klotho may be a valuable therapeutic target for osteosarcoma.
DOI: 10.6084/m9.figshare.16417594
title: Additional file 7 of Comparative phylogenetic analysis of CBL reveals the gene family evolution and functional divergence in Saccharum spontaneum

description: Additional file 7.
DOI: 10.6084/m9.figshare.16417594.v1
title: Additional file 7 of Comparative phylogenetic analysis of CBL reveals the gene family evolution and functional divergence in Saccharum spontaneum

description: Additional file 7.
DOI: 10.6084/m9.figshare.8028872.v1
title: Mapping Tumor-Specific Expression QTLs in Impure Tumor Samples

description: The study of gene expression quantitative trait loci (eQTL) is an effective approach to illuminate the functional roles of genetic variants. Computational methods have been developed for eQTL mapping using gene expression data from microarray or RNA-seq technology. Application of these methods for eQTL mapping in tumor tissues is problematic because tumor tissues are composed of both tumor and infiltrating normal cells (e.g. immune cells) and eQTL effects may vary between tumor and infiltrating normal cells. To address this challenge, we have developed a new method for eQTL mapping using RNA-seq data from tumor samples. Our method separately estimates the eQTL effects in tumor and infiltrating normal cells using both total expression and allele-specific expression (ASE). We demonstrate that our method controls type I error rate and has higher power than some alternative approaches. We applied our method to study RNA-seq data from The Cancer Genome Atlas and illustrated the similarities and differences of eQTL effects in tumor and normal cells.
DOI: 10.6084/m9.figshare.8028872.v2
title: Mapping Tumor-Specific Expression QTLs in Impure Tumor Samples

description: The study of gene expression quantitative trait loci (eQTL) is an effective approach to illuminate the functional roles of genetic variants. Computational methods have been developed for eQTL mapping using gene expression data from microarray or RNA-seq technology. Application of these methods for eQTL mapping in tumor tissues is problematic because tumor tissues are composed of both tumor and infiltrating normal cells (e.g., immune cells) and eQTL effects may vary between tumor and infiltrating normal cells. To address this challenge, we have developed a new method for eQTL mapping using RNA-seq data from tumor samples. Our method separately estimates the eQTL effects in tumor and infiltrating normal cells using both total expression and allele-specific expression (ASE). We demonstrate that our method controls Type I error rate and has higher power than some alternative approaches. We applied our method to study RNA-seq data from The Cancer Genome Atlas and illustrated the similarities and differences of eQTL effects in tumor and normal cells. Supplementary materials for this article, including a standardized description of the materials available for reproducing the work, are available as an online supplement.
DOI: 10.6084/m9.figshare.14320471.v1
title: Isosorbide mononitrate promotes angiogenesis in embryonic development of zebrafish

description: Abstract Coronary heart disease (CHD) is a leading cause of death worldwide, and angiogenesis plays important roles in CHD. Thus, in the present study, the angiogenic efficacy of four common cardiovascular medicines (aspirin, pravastatin, metoprolol and isosorbide mononitrate (ISMN)) was determined by the number and length of zebrafish intersegmental vessels (ISVs) after immersing zebrafish embryos in different medicines. Results showed that ISMN significantly increased the length and number of ISVs. ISMN is a long-acting nitrate ester drug. It has been used as a vasodilator to dilate arteries and veins to reduce the cardiac preload and postload. However, the effect of ISMN on angiogenesis remains unclear. Thus, by in vitro experiments, the angiogenic mechanism of ISMN was evaluated through detecting the viability and proliferation of human umbilical vein endothelial cells (HUVECs) and the expression of angiogenesis-related genes and miRNAs. Results indicated that ISMN could increase the viability and proliferation of HUVECs by decreasing apoptosis, and elevated the expressions of vedf, kdrl, pdgfr in zebrafish embryos. Furthermore, the expressions of miR-126, miR-130a and miR-210 were also regulated in ISMN-treated HUVECs. In conclusion, ISMN could promote angiogenesis in zebrafish embryos and HUVECs, implying ISMN may be a potential therapeutic in treating angiogenesis-related diseases.
DOI: 10.6084/m9.figshare.14320414.v1
title: Overexpression of klotho suppresses growth and pulmonary metastasis of osteosarcoma in vivo

description: Abstract Klotho is originally discovered as an anti-aging gene and knock-out of klotho accelerates aging in mice. Subsequent studies support the anti-carcinogenesis role of klotho in a variety of human malignancies. The present study investigated the role of klotho on growth and metastasis of osteosarcoma cells. The osteosarcoma cells were transduced with lentivirus particles encoding klotho or scramble control. The reconstructed osteosarcoma cells were injected into the femoral medullary cavity of nude mice to establish a xenograft animal model. The anti-tumor properties of klotho were evaluated in terms of tumor growth, apoptosis, glycogen production, and pulmonary metastasis. Lentivirus-mediated overexpression of klotho significantly decreased tumor volume and weight in osteosarcoma mice. Determination of PCNA and Ki67 expression revealed that overexpression of klotho inhibited cell proliferation in tumor tissues obtained from osteosarcoma xenografts. PAS staining also showed that overexpression of klotho significantly decreased the production of glycogen in osteosarcoma. Moreover, TUNEL positive cells were significantly increased after lentivirus-mediated overexpression of klotho. Furthermore, lentivirus-mediated upregulation of klotho reduced the number of pulmonary metastatic lesions in mice compared to control mice. These findings demonstrated that elevated klotho could inhibit osteosarcoma cell growth and pulmonary metastasis in vivo, suggesting that klotho may be a valuable therapeutic target for osteosarcoma.
DOI: 10.6084/m9.figshare.16417579
title: Additional file 2 of Comparative phylogenetic analysis of CBL reveals the gene family evolution and functional divergence in Saccharum spontaneum

description: Additional file 2.
DOI: 10.6084/m9.figshare.14320477
title: Comprehensive analysis of gene expression and DNA methylation data identifies potential biomarkers and functional epigenetic modules for lung adenocarcinoma

description: Abstract Lung cancer has one of the highest mortality rates of malignant neoplasms. Lung adenocarcinoma (LUAD) is one of the most common types of lung cancer. DNA methylation is more stable than gene expression and could be used as a biomarker for early tumor diagnosis. This study is aimed to screen potential DNA methylation signatures to facilitate the diagnosis and prognosis of LUAD and integrate gene expression and DNA methylation data of LUAD to identify functional epigenetic modules. We systematically integrated gene expression and DNA methylation data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO), bioinformatic models and algorithms were implemented to identify signatures and functional modules for LUAD. Three promising diagnostic and five potential prognostic signatures for LUAD were screened by rigorous filtration, and our tumor-normal classifier and prognostic model were validated in two separate data sets. Additionally, we identified functional epigenetic modules in the TCGA LUAD dataset and GEO independent validation data set. Interestingly, the MUC1 module was identified in both datasets. The potential biomarkers for the diagnosis and prognosis of LUAD are expected to be further verified in clinical practice to aid in the diagnosis and treatment of LUAD.
DOI: 10.6084/m9.figshare.14320477.v1
title: Comprehensive analysis of gene expression and DNA methylation data identifies potential biomarkers and functional epigenetic modules for lung adenocarcinoma

description: Abstract Lung cancer has one of the highest mortality rates of malignant neoplasms. Lung adenocarcinoma (LUAD) is one of the most common types of lung cancer. DNA methylation is more stable than gene expression and could be used as a biomarker for early tumor diagnosis. This study is aimed to screen potential DNA methylation signatures to facilitate the diagnosis and prognosis of LUAD and integrate gene expression and DNA methylation data of LUAD to identify functional epigenetic modules. We systematically integrated gene expression and DNA methylation data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO), bioinformatic models and algorithms were implemented to identify signatures and functional modules for LUAD. Three promising diagnostic and five potential prognostic signatures for LUAD were screened by rigorous filtration, and our tumor-normal classifier and prognostic model were validated in two separate data sets. Additionally, we identified functional epigenetic modules in the TCGA LUAD dataset and GEO independent validation data set. Interestingly, the MUC1 module was identified in both datasets. The potential biomarkers for the diagnosis and prognosis of LUAD are expected to be further verified in clinical practice to aid in the diagnosis and treatment of LUAD.
DOI: 10.6084/m9.figshare.16417582
title: Additional file 3 of Comparative phylogenetic analysis of CBL reveals the gene family evolution and functional divergence in Saccharum spontaneum

description: Additional file 3.
DOI: 10.6084/m9.figshare.16417585
title: Additional file 4 of Comparative phylogenetic analysis of CBL reveals the gene family evolution and functional divergence in Saccharum spontaneum

description: Additional file 4.