cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.17020710
title: Additional file 9 of STOML2 interacts with PHB through activating MAPK signaling pathway to promote colorectal Cancer proliferation

description: Additional file 9.
DOI: 10.6084/m9.figshare.21215048
title: Flavonoids as promising anticancer agents: an <i>in silico</i> investigation of ADMET, binding affinity by molecular docking and molecular dynamics simulations

description: Cancer is one of the most concerning diseases to humankind. Various treatment strategies are being employed for its treatment, out of which use of natural products is an essential one. Flavonoids have proven to be promising anticancer targets since decades. Also, tubulin is a significant biological target for the development of anticancer agents due to its crucial role in mitosis and abundance throughout the body. In the current study, <i>in silico</i> ADMET parameters of 104 flavonoids were examined, followed by molecular docking with the colchicine binding site of Tubulin protein (PDB; Id 4O2B). The best conformation from each flavonoid subcategory with the best docking score (MolDock score) was further subjected to 100 ns of molecular dynamics to investigate the protein-ligand complex’s stability. Different parameters such as RMSD, RMSF, rGy and SASA were calculated for the six flavonoids using molecular dynamic studies. The top most compound from all the six subcategories of flavonoids elicited best behavior in the colchicine binding site of Tubulin protein. This <i>in silico</i> study employing molecular docking and molecular dynamics simulation provides strong evidence for flavonoids to be excellent anti-tubulin agents for the treatment of cancer. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.19642067
title: Additional file 1 of Transcriptome-based biomarker gene screening and evaluation of the extracellular fatty acid-binding protein (Ex-FABP) on immune and angiogenesis-related genes in chicken erythrocytes of tibial dyschondroplasia

description: Additional file 1.
DOI: 10.6084/m9.figshare.19642067.v1
title: Additional file 1 of Transcriptome-based biomarker gene screening and evaluation of the extracellular fatty acid-binding protein (Ex-FABP) on immune and angiogenesis-related genes in chicken erythrocytes of tibial dyschondroplasia

description: Additional file 1.
DOI: 10.6084/m9.figshare.17020710.v1
title: Additional file 9 of STOML2 interacts with PHB through activating MAPK signaling pathway to promote colorectal Cancer proliferation

description: Additional file 9.
DOI: 10.6084/m9.figshare.19642085.v1
title: Additional file 6 of Transcriptome-based biomarker gene screening and evaluation of the extracellular fatty acid-binding protein (Ex-FABP) on immune and angiogenesis-related genes in chicken erythrocytes of tibial dyschondroplasia

description: Additional file 6.
DOI: 10.6084/m9.figshare.19642088
title: Additional file 7 of Transcriptome-based biomarker gene screening and evaluation of the extracellular fatty acid-binding protein (Ex-FABP) on immune and angiogenesis-related genes in chicken erythrocytes of tibial dyschondroplasia

description: Additional file 7.
DOI: 10.6084/m9.figshare.21215048.v1
title: Flavonoids as promising anticancer agents: an <i>in silico</i> investigation of ADMET, binding affinity by molecular docking and molecular dynamics simulations

description: Cancer is one of the most concerning diseases to humankind. Various treatment strategies are being employed for its treatment, out of which use of natural products is an essential one. Flavonoids have proven to be promising anticancer targets since decades. Also, tubulin is a significant biological target for the development of anticancer agents due to its crucial role in mitosis and abundance throughout the body. In the current study, <i>in silico</i> ADMET parameters of 104 flavonoids were examined, followed by molecular docking with the colchicine binding site of Tubulin protein (PDB; Id 4O2B). The best conformation from each flavonoid subcategory with the best docking score (MolDock score) was further subjected to 100 ns of molecular dynamics to investigate the protein-ligand complex’s stability. Different parameters such as RMSD, RMSF, rGy and SASA were calculated for the six flavonoids using molecular dynamic studies. The top most compound from all the six subcategories of flavonoids elicited best behavior in the colchicine binding site of Tubulin protein. This <i>in silico</i> study employing molecular docking and molecular dynamics simulation provides strong evidence for flavonoids to be excellent anti-tubulin agents for the treatment of cancer. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.19642094
title: Additional file 9 of Transcriptome-based biomarker gene screening and evaluation of the extracellular fatty acid-binding protein (Ex-FABP) on immune and angiogenesis-related genes in chicken erythrocytes of tibial dyschondroplasia

description: Additional file 9.
DOI: 10.6084/m9.figshare.19642094.v1
title: Additional file 9 of Transcriptome-based biomarker gene screening and evaluation of the extracellular fatty acid-binding protein (Ex-FABP) on immune and angiogenesis-related genes in chicken erythrocytes of tibial dyschondroplasia

description: Additional file 9.
DOI: 10.6084/m9.figshare.19642278
title: Noncoding-RNA mediated high expression of zinc finger protein 268 suppresses clear cell renal cell carcinoma progression by promoting apoptosis and regulating immune cell infiltration

description: Clear cell renal cell carcinoma (ccRCC) is one of the most common malignant kidney tumors with a poor prognosis. Accumulating evidence proves that zinc finger protein 268 (ZNF268) is associated with tumor progression, but the detailed regulatory functions of ZNF268 in ccRCC require further exploration. Thus, here we aim to characterize the role of ZNF268 in ccRCC. The clinical significance of ZNF268 was evaluated using The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) databases. Subsequently, tumor-infiltrating immune cells, as well as upstream noncoding RNAs (ncRNAs) related to the tumor-suppressing function of ZNF268, were identified by <i>in silico</i> analyses. The expression of ZNF268 was significantly decreased in ccRCC samples compared with adjacent normal tissues. In addition, ZNF268 expression was negatively correlated with tumor progression and positively correlated with overall and disease-specific survival. TCGA and GTEx databases proved the potential tumor-suppressing function, which was measured both <i>in vitro</i> and <i>in vivo</i> after ZNF268 over-expression. Overexpression of ZNF268 effectively inhibited the proliferation, migration, invasion and promotied apoptosis of the Caki-1. The level of ZNF268 was positively related to the immune cell infiltration in the tumor. Moreover, we determined that the AC093157.1/miR-27a-3p axis can potentially regulate ZNF268 function in ccRCC. Our work describes a novel ncRNA-mediated ZNF268 function in ccRCC. ZNF268 acts as a tumor suppressor, and it is associated with apoptosis and immune cell infiltration in ccRCC.
DOI: 10.6084/m9.figshare.11777904.v4
title: Supplementary figures from “Metabolite Identification, Tissue Distribution, Excretion and Preclinical Pharmacokinetic Studies of ET-26-HCl, a New Analog of Etomidate”

description: ET-26-HCl, a novel anaesthetic agent with promising pharmacological properties, lacks extensive studies on pharmacokinetics and disposition <i>in vitro</i> and <i>in vivo</i>. In this study, we investigated the metabolic stability, metabolite production and plasma protein binding (PPB) of ET-26-HCl along with its tissue distribution, excretion and pharmacokinetics in animals after intravenous administration. Ultra-high performance liquid chromatography–tandem quadrupole time-of-flight mass spectrometry identified a total of eight new metabolites after ET-26-HCl biotransformation in liver microsomes from different species. A hypothetical cytochrome P450-metabolic pathway including dehydrogenation, hydroxylation and demethylation was proposed. The PPB rate was highest in mouse and lowest in human. After intravenous administration, ET-26-HCl distributed rapidly to all tissues in rats and beagle dogs, with the highest concentrations in fat and liver. High concentrations of ET-26-acid, a major hydroxylation metabolite of ET-26-HCl, were found in liver, plasma and kidney. Almost complete clearance of ET-26-HCl from plasma occurred within 4 h after administration. Only a small fraction of the parent compound and its acid form were excreted via the urine and faeces. Taken together, the results added to a better understanding of the metabolic and pharmacokinetic properties of ET-26-HCl, which may contribute to the further development of this drug.
DOI: 10.6084/m9.figshare.19642085
title: Additional file 6 of Transcriptome-based biomarker gene screening and evaluation of the extracellular fatty acid-binding protein (Ex-FABP) on immune and angiogenesis-related genes in chicken erythrocytes of tibial dyschondroplasia

description: Additional file 6.
DOI: 10.6084/m9.figshare.19642088.v1
title: Additional file 7 of Transcriptome-based biomarker gene screening and evaluation of the extracellular fatty acid-binding protein (Ex-FABP) on immune and angiogenesis-related genes in chicken erythrocytes of tibial dyschondroplasia

description: Additional file 7.
DOI: 10.6084/m9.figshare.7059359
title: RNASeq results

description: These files include (1) the updated gene models with alternative splicing transcripts using RNASeq data (in GFF3 and FASTA format), (2) as well as their expression levels in TSV format.
DOI: 10.6084/m9.figshare.7059359.v1
title: RNASeq results

description: These files include (1) the updated gene models with alternative splicing transcripts using RNASeq data (in GFF3 and FASTA format), (2) as well as their expression levels in TSV format.
DOI: 10.6084/m9.figshare.7059362
title: OrthoMCL gene families

description: The ortholog groups (gene families) file is presented as original outputs by the OrthoMCL. Prefix of each sequence ID is the abbreviation of species name to make the ID unique and to distinguish the source easily.
DOI: 10.6084/m9.figshare.19642275
title: Family with sequence similarity 46 member a confers chemo-resistance to ovarian carcinoma via TGF-β/Smad2 signaling

description: Ovarian cancer is the most lethal malignancy with depressive 5-year survival rate, mainly due to patients with advanced stages experience tumor recurrence and resistance to the current chemotherapeutic agents. Thus, exploring the underlying molecular mechanisms involved in chemo-resistance is crucial for management of treatment to improve therapeutic outcomes. In the current study, we found overexpression of FAM46A in ovarian cancer patients demonstrated an aggressive phenotype and poor outcome. Furthermore, FAM46A overexpression in ovarian cancer cells induces higher CDDP resistance. However, inhibition of FAM46A sensitized ovarian cancer cell lines to CDDP cytotoxicity both in vitro and in vivo. Mechanically, upregulation of FAM46A activated transforming growth factor-β (TGF-β)/Smad signaling and upregulated the levels of nuclear Smad2. Taken together, our results highlight the important oncogenic role of FAM46A in ovarian cancer progression and might provide a potential clinical target for patients with chemo resistant ovarian cancer.
DOI: 10.6084/m9.figshare.19642275.v1
title: Family with sequence similarity 46 member a confers chemo-resistance to ovarian carcinoma via TGF-β/Smad2 signaling

description: Ovarian cancer is the most lethal malignancy with depressive 5-year survival rate, mainly due to patients with advanced stages experience tumor recurrence and resistance to the current chemotherapeutic agents. Thus, exploring the underlying molecular mechanisms involved in chemo-resistance is crucial for management of treatment to improve therapeutic outcomes. In the current study, we found overexpression of FAM46A in ovarian cancer patients demonstrated an aggressive phenotype and poor outcome. Furthermore, FAM46A overexpression in ovarian cancer cells induces higher CDDP resistance. However, inhibition of FAM46A sensitized ovarian cancer cell lines to CDDP cytotoxicity both in vitro and in vivo. Mechanically, upregulation of FAM46A activated transforming growth factor-β (TGF-β)/Smad signaling and upregulated the levels of nuclear Smad2. Taken together, our results highlight the important oncogenic role of FAM46A in ovarian cancer progression and might provide a potential clinical target for patients with chemo resistant ovarian cancer.
DOI: 10.6084/m9.figshare.7059362.v1
title: OrthoMCL gene families

description: The ortholog groups (gene families) file is presented as original outputs by the OrthoMCL. Prefix of each sequence ID is the abbreviation of species name to make the ID unique and to distinguish the source easily.
DOI: 10.6084/m9.figshare.19642278.v1
title: Noncoding-RNA mediated high expression of zinc finger protein 268 suppresses clear cell renal cell carcinoma progression by promoting apoptosis and regulating immune cell infiltration

description: Clear cell renal cell carcinoma (ccRCC) is one of the most common malignant kidney tumors with a poor prognosis. Accumulating evidence proves that zinc finger protein 268 (ZNF268) is associated with tumor progression, but the detailed regulatory functions of ZNF268 in ccRCC require further exploration. Thus, here we aim to characterize the role of ZNF268 in ccRCC. The clinical significance of ZNF268 was evaluated using The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) databases. Subsequently, tumor-infiltrating immune cells, as well as upstream noncoding RNAs (ncRNAs) related to the tumor-suppressing function of ZNF268, were identified by <i>in silico</i> analyses. The expression of ZNF268 was significantly decreased in ccRCC samples compared with adjacent normal tissues. In addition, ZNF268 expression was negatively correlated with tumor progression and positively correlated with overall and disease-specific survival. TCGA and GTEx databases proved the potential tumor-suppressing function, which was measured both <i>in vitro</i> and <i>in vivo</i> after ZNF268 over-expression. Overexpression of ZNF268 effectively inhibited the proliferation, migration, invasion and promotied apoptosis of the Caki-1. The level of ZNF268 was positively related to the immune cell infiltration in the tumor. Moreover, we determined that the AC093157.1/miR-27a-3p axis can potentially regulate ZNF268 function in ccRCC. Our work describes a novel ncRNA-mediated ZNF268 function in ccRCC. ZNF268 acts as a tumor suppressor, and it is associated with apoptosis and immune cell infiltration in ccRCC.
DOI: 10.6084/m9.figshare.7059350.v1
title: MCScanX results

description: The intra- and inter-species collinear blocks are in text format and html format generated by MCScanX.
DOI: 10.6084/m9.figshare.7059356.v1
title: Predicted coding genes

description: The protein-coding gene annotation results contain (1) the coordinates of genes, transcripts, exon and coding sequenes (CDS) in GFF3 format, (2) CDS of transcripts and their corresponding protein sequences (FASTA format).
DOI: 10.6084/m9.figshare.17020872.v1
title: Additional file 1 of Comprehensive analysis of expression, prognosis and immune infiltration for TIMPs in glioblastoma

description: Additional file 1.
DOI: 10.6084/m9.figshare.17020931.v1
title: Additional file 2 of Identification of candidate genes and enriched biological functions for feed efficiency traits by integrating plasma metabolites and imputed whole genome sequence variants in beef cattle

description: Additional file 2. This file contains a summary of SNPs significantly associated with the 11 metabolites.
DOI: 10.6084/m9.figshare.7583753
title: Table S2 from Distinct effects of short-term reconstructed topsoil on soya bean and corn rhizosphere bacterial abundance and communities in Chinese Mollisol.

description: The correlations between soil biogeochemical characteristics and significantly affected genus by topsoil depths
DOI: 10.6084/m9.figshare.7583753.v2
title: Table S2 from Distinct effects of short-term reconstructed topsoil on soya bean and corn rhizosphere bacterial abundance and communities in Chinese Mollisol.

description: The correlations between soil biogeochemical characteristics and significantly affected genus by topsoil depths
DOI: 10.6084/m9.figshare.7583756
title: Table S1 from Distinct effects of short-term reconstructed topsoil on soya bean and corn rhizosphere bacterial abundance and communities in Chinese Mollisol.

description: The correlation of OTU numbers, a-diversity, bacterial abundance and soil respiration with soil properties
DOI: 10.6084/m9.figshare.17020928
title: Additional file 1 of Identification of candidate genes and enriched biological functions for feed efficiency traits by integrating plasma metabolites and imputed whole genome sequence variants in beef cattle

description: Additional file 1: Table S1. Additive genetic variances and heritability estimates for 11 metabolites based on the imputed whole genome sequence (WGS) variants in a beef cattle multibreed population; Table S2. Uniquely common candidate genes for feed efficiency traits in a beef cattle multibreed population; Table S3. Enriched biological functions significantly associated with RFI in a beef cattle multibreed population; Table S4. Enriched biological functions significantly associated with DMI in a beef cattle multibreed population; Table S5. Enriched biological functions significantly associated with ADG in a beef cattle multibreed population; Table S6. Enriched biological functions significantly associated with MWT in a beef cattle multibreed population; Table S7. Uniquely common biological functions for feed efficiency traits in a beef cattle multibreed population; Table S8. The comparison of candidate genes between the current study and Zhang et al; Table S9. Genomic breed composition for animals; Table S10. Descriptive statistics of phenotypic data on feed efficiency traits and metabolites.
DOI: 10.6084/m9.figshare.19106230.v1
title: Additional file 3 of Diagnostic Evidence GAuge of Single cells (DEGAS): a flexible deep transfer learning framework for prioritizing cells in relation to disease

description: Additional file 3. HAM markers derived from Srinivasan et. al. [64]
DOI: 10.6084/m9.figshare.17020928.v1
title: Additional file 1 of Identification of candidate genes and enriched biological functions for feed efficiency traits by integrating plasma metabolites and imputed whole genome sequence variants in beef cattle

description: Additional file 1: Table S1. Additive genetic variances and heritability estimates for 11 metabolites based on the imputed whole genome sequence (WGS) variants in a beef cattle multibreed population; Table S2. Uniquely common candidate genes for feed efficiency traits in a beef cattle multibreed population; Table S3. Enriched biological functions significantly associated with RFI in a beef cattle multibreed population; Table S4. Enriched biological functions significantly associated with DMI in a beef cattle multibreed population; Table S5. Enriched biological functions significantly associated with ADG in a beef cattle multibreed population; Table S6. Enriched biological functions significantly associated with MWT in a beef cattle multibreed population; Table S7. Uniquely common biological functions for feed efficiency traits in a beef cattle multibreed population; Table S8. The comparison of candidate genes between the current study and Zhang et al; Table S9. Genomic breed composition for animals; Table S10. Descriptive statistics of phenotypic data on feed efficiency traits and metabolites.
DOI: 10.6084/m9.figshare.19106227.v1
title: Additional file 2 of Diagnostic Evidence GAuge of Single cells (DEGAS): a flexible deep transfer learning framework for prioritizing cells in relation to disease

description: Additional file 2. DAA markers derived from Habib et al. [63]
DOI: 10.6084/m9.figshare.19106233
title: Additional file 4 of Diagnostic Evidence GAuge of Single cells (DEGAS): a flexible deep transfer learning framework for prioritizing cells in relation to disease

description: Additional file 4. DAM markers were derived from Keren-Shaul et al. [65]
DOI: 10.6084/m9.figshare.19106236.v1
title: Additional file 5 of Diagnostic Evidence GAuge of Single cells (DEGAS): a flexible deep transfer learning framework for prioritizing cells in relation to disease

description: Additional file 5. Differential gene expression for Subtype 1 cells
DOI: 10.6084/m9.figshare.19106236
title: Additional file 5 of Diagnostic Evidence GAuge of Single cells (DEGAS): a flexible deep transfer learning framework for prioritizing cells in relation to disease

description: Additional file 5. Differential gene expression for Subtype 1 cells
DOI: 10.6084/m9.figshare.21203361
title: Additional file 1 of Longitudinal multi-omics analysis identifies early blood-based predictors of anti-TNF therapy response in inflammatory bowel disease

description: Additional file 1: Table S1. Sampling scheme and samples used for the study.
DOI: 10.6084/m9.figshare.19642069
title: Additional file 2 of Central nervous system infection with Seoul Orthohantavirus in a child after hematopoietic stem cell transplantation: a case report

description: Additional file 2. Supplementary Table S1. The SEOV unique reads detected by four times of mNGS in CSF and blood samples.
DOI: 10.6084/m9.figshare.7583762.v1
title: Supplementary Table 2 from Large-scale gene analysis using a rabbit atherosclerosis model to discover new biomarkers for human coronary artery disease

description: The genes for each of the enriched GO analysis in Figure 5
DOI: 10.6084/m9.figshare.7583774
title: Data used in this study from Egg retrieval versus egg rejection in cuckoo hosts

description: Before complex nests evolved, birds laid eggs on the ground, and egg retrieval evolved as an adaptation against accidental displacement of eggs outside the nest. Therefore, egg retrieval is an ancient, and likely ancestral, widespread behaviour in birds. However, it has received little attention in studies of avian brood parasitism, perhaps because most parasitism occurs in species with complex nests, a context in which egg retrieval seems irrelevant. However, for cavity-nesting hosts of avian brood parasites, egg retrieval may still play an important role in the coevolutionary interactions between obligate brood parasites and hosts, because egg retrieval can be considered to be antagonistic to egg rejection behaviour in hosts, yet both may involve cognition to recognize eggs. We hypothesized that (1) cavity-nesting hosts should retrieve misplaced eggs from outside the nest cup, (2) brood parasitism has modulated egg retrieval behaviour in cavity-nesting hosts and (3) hosts use the same visual cues for decision-making during egg recognition in both egg retrieval and egg rejection actions. To test these hypotheses, we performed a series of experiments in a cavity-nesting host, the green-backed tit (<i>Parus monticolus</i>). Foreign eggs with different levels of mimicry were placed within or outside nest cups of hosts to test their responses. We found that host decisions about whether to retrieve or reject an egg both depended on the degree of mimicry. However, hosts sometimes first retrieved poorly mimetic foreign eggs and then rejected them. Alternatively, hosts sometimes failed to retrieve highly mimetic conspecific eggs. We suggest that egg retrieval in hosts is likely to be a result of the interaction between ancient retrieval behaviour and subsequent adaptation against brood parasitism.This article is part of the theme issue ‘The co-evolutionary biology of brood parasitism: from mechanism to pattern’.
DOI: 10.6084/m9.figshare.21203361.v1
title: Additional file 1 of Longitudinal multi-omics analysis identifies early blood-based predictors of anti-TNF therapy response in inflammatory bowel disease

description: Additional file 1: Table S1. Sampling scheme and samples used for the study.