cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14702670
title: Additional file 8 of The whole profiling and competing endogenous RNA network analyses of noncoding RNAs in adipose-derived stem cells from diabetic, old, and young patients

description: Additional file 8: Data S6. Differentially expressed mRNAs between D-ASCs and O-ASCs.
DOI: 10.6084/m9.figshare.14702670.v1
title: Additional file 8 of The whole profiling and competing endogenous RNA network analyses of noncoding RNAs in adipose-derived stem cells from diabetic, old, and young patients

description: Additional file 8: Data S6. Differentially expressed mRNAs between D-ASCs and O-ASCs.
DOI: 10.6084/m9.figshare.14702673
title: Additional file 9 of The whole profiling and competing endogenous RNA network analyses of noncoding RNAs in adipose-derived stem cells from diabetic, old, and young patients

description: Additional file 9: Data S7. Differentially expressed lncRNAs between D-ASCs and O-ASCs.
DOI: 10.6084/m9.figshare.14702673.v1
title: Additional file 9 of The whole profiling and competing endogenous RNA network analyses of noncoding RNAs in adipose-derived stem cells from diabetic, old, and young patients

description: Additional file 9: Data S7. Differentially expressed lncRNAs between D-ASCs and O-ASCs.
DOI: 10.6084/m9.figshare.16799824
title: A novel circular RNA circ_HN1/miR-628-5p/Ecto-5’-nucleotidase competing endogenous RNA network regulates gastric cancer development

description: The competing endogenous RNA (ceRNA) activity of circular RNAs (circRNAs) has been implicated in the development of gastric cancer. Here, we sought to explore the ceRNA function of circRNA Jupiter microtubule associated homolog 1 (circ_HN1) in gastric tumorigenesis. Circ_HN1, microRNA (miR)-628-5p, and NT5E expression levels were quantified by qRT-PCR and western blot. Dual-luciferase reporter assays were used to assess the direct relationship between miR-628-5p and circ_HN1 or NT5E. Our data showed that circ_HN1 expression was enhanced in human gastric cancer. Depletion of circ_HN1 impeded cell proliferation, spheroid formation, invasion, and migration and promoted apoptosis <i>in vitro</i>, as well as diminished tumor growth <i>in vivo</i>. NT5E was a downstream effector of circ_HN1 function. NT5E was targeted and inhibited by miR-628-5p through the perfect complementary site in NT5E 3ʹUTR, and circ_HN1 affected NT5E expression through miR-628-5p competition. Moreover, depletion of miR-628-5p reversed the effects of circ_HN1 silencing on regulating cell functional behaviors. Our findings identify a novel ceRNA network, the circ_HN1/miR-628-5p/NT5E axis, for the oncogenic activity of circ_HN1 in gastric cancer, highlighting circ_HN1 inhibition as a promising targeted treatment against gastric cancer.
DOI: 10.6084/m9.figshare.16799824.v1
title: A novel circular RNA circ_HN1/miR-628-5p/Ecto-5’-nucleotidase competing endogenous RNA network regulates gastric cancer development

description: The competing endogenous RNA (ceRNA) activity of circular RNAs (circRNAs) has been implicated in the development of gastric cancer. Here, we sought to explore the ceRNA function of circRNA Jupiter microtubule associated homolog 1 (circ_HN1) in gastric tumorigenesis. Circ_HN1, microRNA (miR)-628-5p, and NT5E expression levels were quantified by qRT-PCR and western blot. Dual-luciferase reporter assays were used to assess the direct relationship between miR-628-5p and circ_HN1 or NT5E. Our data showed that circ_HN1 expression was enhanced in human gastric cancer. Depletion of circ_HN1 impeded cell proliferation, spheroid formation, invasion, and migration and promoted apoptosis <i>in vitro</i>, as well as diminished tumor growth <i>in vivo</i>. NT5E was a downstream effector of circ_HN1 function. NT5E was targeted and inhibited by miR-628-5p through the perfect complementary site in NT5E 3ʹUTR, and circ_HN1 affected NT5E expression through miR-628-5p competition. Moreover, depletion of miR-628-5p reversed the effects of circ_HN1 silencing on regulating cell functional behaviors. Our findings identify a novel ceRNA network, the circ_HN1/miR-628-5p/NT5E axis, for the oncogenic activity of circ_HN1 in gastric cancer, highlighting circ_HN1 inhibition as a promising targeted treatment against gastric cancer.
DOI: 10.6084/m9.figshare.7362641
title: MOESM1 of Deficiency in interleukin-18 promotes differentiation of brown adipose tissue resulting in fat accumulation despite dyslipidemia

description: Additional file 1. Primer sequences used for qRT-PCR.
DOI: 10.6084/m9.figshare.7362641.v1
title: MOESM1 of Deficiency in interleukin-18 promotes differentiation of brown adipose tissue resulting in fat accumulation despite dyslipidemia

description: Additional file 1. Primer sequences used for qRT-PCR.
DOI: 10.6084/m9.figshare.14178434
title: Supplementary Material to NEM 3450

description: <b>Supplementary Table S1.</b> Primers used in this study.

<b>Supplementary Table S2. </b>Summary statistics of RNA-seq
data.
DOI: 10.6084/m9.figshare.14178434.v1
title: Supplementary Material to NEM 3450

description: <b>Supplementary Table S1.</b> Primers used in this study.

<b>Supplementary Table S2. </b>Summary statistics of RNA-seq
data.
DOI: 10.6084/m9.figshare.7362701
title: MOESM4 of Deficiency in interleukin-18 promotes differentiation of brown adipose tissue resulting in fat accumulation despite dyslipidemia

description: Additional file 4. Core analysis of molecules isolated at 6 weeks of age by microarray. Core analyses using IPA.
DOI: 10.6084/m9.figshare.7362701.v1
title: MOESM4 of Deficiency in interleukin-18 promotes differentiation of brown adipose tissue resulting in fat accumulation despite dyslipidemia

description: Additional file 4. Core analysis of molecules isolated at 6 weeks of age by microarray. Core analyses using IPA.
DOI: 10.6084/m9.figshare.7362716
title: MOESM5 of Deficiency in interleukin-18 promotes differentiation of brown adipose tissue resulting in fat accumulation despite dyslipidemia

description: Additional file 5. Core analysis of molecules isolated at 12 weeks of age by microarray. Core analyses using IPA.
DOI: 10.6084/m9.figshare.7362716.v1
title: MOESM5 of Deficiency in interleukin-18 promotes differentiation of brown adipose tissue resulting in fat accumulation despite dyslipidemia

description: Additional file 5. Core analysis of molecules isolated at 12 weeks of age by microarray. Core analyses using IPA.
DOI: 10.6084/m9.figshare.14178488
title: The prohibitins (PHB) gene family in tomato: Bioinformatic identification and expression analysis under abiotic and phytohormone stresses

description: The prohibitins (PHB) are SPFH domain-containing proteins found in the prokaryotes to eukaryotes. The plant PHBs are associated with a wide range of biological processes, including senescence, development, and responses to biotic and abiotic stresses. The PHB proteins are identified and characterized in the number of plant species, such as <i>Arabidopsis</i>, rice, maize, and soybean. However, no systematic identification of PHB proteins was performed in <i>Solanum lycopersicum</i>. In this study, we identified 16 PHB proteins in the tomato genome. The analysis of conserved motifs and gene structure validated the phylogenetic classification of tomato PHB proteins. It was observed that various members of tomato PHB proteins undergo purifying selection based on the Ka/Ks ratio and are targeted by four families of miRNAs. Moreover, SlPHB proteins displayed a very unique expression pattern in different plant parts including fruits at various development stages. It was found that SlPHBs processed various development-related and phytohormone responsive <i>cis</i>-regulatory elements in their promoter regions. Furthermore, the exogenous phytohormones treatments (Abscisic acid, indole-3-acetic acid, gibberellic acid, methyl jasmonate) salt and drought stresses induce the expression of SlPHB. Moreover, the subcellular localization assay revealed that SlPHB5 and SlPHB10 were located in the mitochondria. This study systematically summarized the general characterization of SlPHBs in the tomato genome and provides a foundation for the functional characterization of PHB genes in tomato and other plant species.
DOI: 10.6084/m9.figshare.14178488.v1
title: The prohibitins (PHB) gene family in tomato: Bioinformatic identification and expression analysis under abiotic and phytohormone stresses

description: The prohibitins (PHB) are SPFH domain-containing proteins found in the prokaryotes to eukaryotes. The plant PHBs are associated with a wide range of biological processes, including senescence, development, and responses to biotic and abiotic stresses. The PHB proteins are identified and characterized in the number of plant species, such as <i>Arabidopsis</i>, rice, maize, and soybean. However, no systematic identification of PHB proteins was performed in <i>Solanum lycopersicum</i>. In this study, we identified 16 PHB proteins in the tomato genome. The analysis of conserved motifs and gene structure validated the phylogenetic classification of tomato PHB proteins. It was observed that various members of tomato PHB proteins undergo purifying selection based on the Ka/Ks ratio and are targeted by four families of miRNAs. Moreover, SlPHB proteins displayed a very unique expression pattern in different plant parts including fruits at various development stages. It was found that SlPHBs processed various development-related and phytohormone responsive <i>cis</i>-regulatory elements in their promoter regions. Furthermore, the exogenous phytohormones treatments (Abscisic acid, indole-3-acetic acid, gibberellic acid, methyl jasmonate) salt and drought stresses induce the expression of SlPHB. Moreover, the subcellular localization assay revealed that SlPHB5 and SlPHB10 were located in the mitochondria. This study systematically summarized the general characterization of SlPHBs in the tomato genome and provides a foundation for the functional characterization of PHB genes in tomato and other plant species.
DOI: 10.6084/m9.figshare.14178516
title: miRNA and mRNA expression profiling reveals potential biomarkers for metastatic cutaneous melanoma

description: <b>Purpose</b>: This study aims to uncover potential biomarkers associated with cutaneous melanoma (CM) metastasis. <b>Methods</b>: The mRNA and microRNA (miRNA) expression data from the metastatic CM and non-metastatic CM population were obtained from The Cancer Genome Atlas database. Functional analysis, protein–protein interaction (PPI), and survival analysis were performed for differentially expressed mRNAs (DEmRNAs) and miRNAs (DEmiRNAs). The interaction between DEmRNAs and DEmiRNAs was analyzed. The expression of several key DEmRNAs and DEmiRNAs was validated by Gene Expression Omnibus datasets. <b>Results</b>: Overall, 1172 DEmRNAs and 26 DEmiRNAs were identified from metastatic and non-metastatic CM. Cytokine–cytokine receptor interaction and chemokine signaling pathway were key pathways. <i>CXCR1, CXCR2, CXCR4, CCR1, CCR2</i>, and <i>CCR5</i> were hub genes in the PPI network. Among these, miR-29 c-3p, miR-100-5p, miR-150-5p, and miR-150-3p were not only diagnostic biomarkers but also related to survival time. miR-203a-3p interacted with <i>CCR5</i> and <i>LIFR</i>, while miR-224-5p was strongly associated with <i>CXCR4. LIFR, CXCR1, CXCR2, CXCR4, CCR1, CCR2</i>, and <i>CCR5</i> were enriched in the cytokine–cytokine receptor interaction pathway. The levels of seven DEmRNAs (<i>CXCR1, CXCR2, CXCR4, CCR1, CCR2, CCR5</i>, and <i>LIFR</i>) and two DEmiRNAs (miR-203a-3p and miR-224-5p) were validated using the GSE65568 and GSE109244 datasets, respectively. <b>Conclusion</b>: Our findings may provide novel biomarkers for CM metastasis.
DOI: 10.6084/m9.figshare.14178516.v1
title: miRNA and mRNA expression profiling reveals potential biomarkers for metastatic cutaneous melanoma

description: <b>Purpose</b>: This study aims to uncover potential biomarkers associated with cutaneous melanoma (CM) metastasis. <b>Methods</b>: The mRNA and microRNA (miRNA) expression data from the metastatic CM and non-metastatic CM population were obtained from The Cancer Genome Atlas database. Functional analysis, protein–protein interaction (PPI), and survival analysis were performed for differentially expressed mRNAs (DEmRNAs) and miRNAs (DEmiRNAs). The interaction between DEmRNAs and DEmiRNAs was analyzed. The expression of several key DEmRNAs and DEmiRNAs was validated by Gene Expression Omnibus datasets. <b>Results</b>: Overall, 1172 DEmRNAs and 26 DEmiRNAs were identified from metastatic and non-metastatic CM. Cytokine–cytokine receptor interaction and chemokine signaling pathway were key pathways. <i>CXCR1, CXCR2, CXCR4, CCR1, CCR2</i>, and <i>CCR5</i> were hub genes in the PPI network. Among these, miR-29 c-3p, miR-100-5p, miR-150-5p, and miR-150-3p were not only diagnostic biomarkers but also related to survival time. miR-203a-3p interacted with <i>CCR5</i> and <i>LIFR</i>, while miR-224-5p was strongly associated with <i>CXCR4. LIFR, CXCR1, CXCR2, CXCR4, CCR1, CCR2</i>, and <i>CCR5</i> were enriched in the cytokine–cytokine receptor interaction pathway. The levels of seven DEmRNAs (<i>CXCR1, CXCR2, CXCR4, CCR1, CCR2, CCR5</i>, and <i>LIFR</i>) and two DEmiRNAs (miR-203a-3p and miR-224-5p) were validated using the GSE65568 and GSE109244 datasets, respectively. <b>Conclusion</b>: Our findings may provide novel biomarkers for CM metastasis.
DOI: 10.6084/m9.figshare.14178522
title: Table S1-S3 from Ecological dynamics of terrestrial and freshwater ecosystems across three mid-Phanerozoic mass extinctions from northwest China

description: Table S1. Taxa and guilds assigned to the 14 paleocommunities ranging from middle Permian to Lower Jurassic in northern Xinjiang, NW China; Table S2. List of guilds and guild richnesses of each paleocommunity; Table S3. Guild interactions binary matrix.
DOI: 10.6084/m9.figshare.14178522.v1
title: Table S1-S3 from Ecological dynamics of terrestrial and freshwater ecosystems across three mid-Phanerozoic mass extinctions from northwest China

description: Table S1. Taxa and guilds assigned to the 14 paleocommunities ranging from middle Permian to Lower Jurassic in northern Xinjiang, NW China; Table S2. List of guilds and guild richnesses of each paleocommunity; Table S3. Guild interactions binary matrix.
DOI: 10.6084/m9.figshare.3168481
title: Synthesis, cytotoxicity, and long-term single dose anti-cancer pharmacological evaluation of dimethyltin(IV) complex of <i>N</i>(4)-methylthiosemicarbazone (having ONS donor ligand)

description: Background and Objective: Toxicity of the chemotherapeutic compounds is widely investigated. An organotin (IV) derivative was designed to modulate the toxicity and long-term anticancer efficacy of the single dose. Materials and Methods: The reaction of dimethyltin(IV) dichloride with <i>N</i>(4)-methylthiosemicarbazone derived by condensation of 4-methylthiosemicarbazone with 5-bromo-2-hydroxybenzaldehyde was prepared in 1:1 M ratio in absolute methanol. The newly synthesized complex was characterized by elemental analysis, FT-IR, electronic, and <sup>1</sup>H, <sup>13</sup>C and <sup>119</sup>Sn NMR spectroscopy. In vitro cytotoxicity (MTT, (3-(4,5-Dimethylthiazol-2-yl)-2,5-Diphenyltetrazolium Bromide)), anticancer (migration, clonogenic, 3D tumor aggregation, nucleus condensation and mitochondrial membrane potential) activity, and in silico QSAR and molecular docking studies were performed. Results: The title compound was observed to be potent and selective toxic against MCF-7, HCT-116, and A549 human cancer cell lines. Moreover, this derivative was found to be less-cytotoxic and higher cytostatic at the single dose than other organotin (IV) complexes due to modulation of chelation of ligand with Sn(IV) ion. The anticancer activities against A549 cancer cells, however, were only moderate. The reason for this could be due to inhibition of enzymatic reaction in the cells for glucose uptake, DNA and protein synthesis. Discussion and Conclusion: The resonance impact of aromatic rings, hydrogen bonding, and ROS reduction, NO generation, caspase induction showed potential impact to the cancer cell apoptosis, antimigration, and inhibition of tumor aggregation of this compound.
DOI: 10.6084/m9.figshare.7887080
title: Effect of impact factor and discipline on journal data sharing policies

description: Data sharing is crucial to the advancement of science because it facilitates collaboration, transparency, reproducibility, criticism, and re-analysis. Publishers are well-positioned to promote sharing of research data by implementing data sharing policies. While there is an increasing trend toward requiring data sharing, not all journals mandate that data be shared at the time of publication. In this study, we extended previous work to analyze the data sharing policies of 447 journals across several scientific disciplines, including biology, clinical sciences, mathematics, physics, and social sciences. Our results showed that only a small percentage of journals require data sharing as a condition of publication, and that this varies across disciplines and Impact Factors. Both Impact Factors and discipline are associated with the presence of a data sharing policy. Our results suggest that journals with higher Impact Factors are more likely to have data sharing policies; use shared data in peer review; require deposit of specific data types into publicly available data banks; and refer to reproducibility as a rationale for sharing data. Biological science journals are more likely than social science and mathematics journals to require data sharing.
DOI: 10.6084/m9.figshare.7887080.v2
title: Effect of impact factor and discipline on journal data sharing policies

description: Data sharing is crucial to the advancement of science because it facilitates collaboration, transparency, reproducibility, criticism, and re-analysis. Publishers are well-positioned to promote sharing of research data by implementing data sharing policies. While there is an increasing trend toward requiring data sharing, not all journals mandate that data be shared at the time of publication. In this study, we extended previous work to analyze the data sharing policies of 447 journals across several scientific disciplines, including biology, clinical sciences, mathematics, physics, and social sciences. Our results showed that only a small percentage of journals require data sharing as a condition of publication, and that this varies across disciplines and Impact Factors. Both Impact Factors and discipline are associated with the presence of a data sharing policy. Our results suggest that journals with higher Impact Factors are more likely to have data sharing policies; use shared data in peer review; require deposit of specific data types into publicly available data banks; and refer to reproducibility as a rationale for sharing data. Biological science journals are more likely than social science and mathematics journals to require data sharing.
DOI: 10.34740/kaggle/dsv/7569100
title: Egypt Gold Prices | Daily Updated
DOI: 10.6084/m9.figshare.7887080.v1
title: Effect of impact factor and discipline on journal data sharing policies

description: Data sharing is crucial to the advancement of science because it facilitates collaboration, transparency, reproducibility, criticism, and re-analysis. Publishers are well-positioned to promote sharing of research data by implementing data sharing policies. While there is an increasing trend toward requiring data sharing, not all journals mandate that data be shared at the time of publication. In this study, we extended previous work to analyze the data sharing policies of 447 journals across several scientific disciplines, including biology, clinical sciences, mathematics, physics, and social sciences. Our results showed that only a small percentage of journals require data sharing as a condition of publication, and that this varies across disciplines and Impact Factors. Both Impact Factors and discipline are associated with the presence of a data sharing policy. Our results suggest that journals with higher Impact Factors are more likely to have data sharing policies; use shared data in peer review; require deposit of specific data types into publicly available data banks; and refer to reproducibility as a rationale for sharing data. Biological science journals are more likely than social science and mathematics journals to require data sharing.
DOI: 10.6084/m9.figshare.14178543
title: TP53/miR-129/MDM2/4/TP53 feedback loop modulates cell proliferation and apoptosis in retinoblastoma

description: Retinoblastoma (RB) is commonly-seen cancer in children. The p53 pathway dysfunction, which can lead to elevated MDM2 or MDM4 (p53 antagonists) protein expression, is frequently observed in almost all human cancers, including RB. The present study attempted to investigate the underlying mechanism from the perspective of non-coding RNA regulation. Here, we demonstrated that p53 and miR-129 were positively correlated with each other in RB. miR-129 directly targeted MDM2/4 to inhibit expression, therefore counteracting MDM2/4-mediated p53 signaling suppression and modulating RB cell proliferation and apoptosis. Moreover, p53 could activate the transcription of miR-129 via binding to the miR-129 promoter region, therefore forming a regulatory loop with MDM2/4 to affect RB progression. Altogether, the p53/miR-129/MDM2/4/p53 regulatory loop can modulate RB cell growth. We provide a solid experimental basis for developing novel therapies for RB.
DOI: 10.6084/m9.figshare.14178543.v1
title: TP53/miR-129/MDM2/4/TP53 feedback loop modulates cell proliferation and apoptosis in retinoblastoma

description: Retinoblastoma (RB) is commonly-seen cancer in children. The p53 pathway dysfunction, which can lead to elevated MDM2 or MDM4 (p53 antagonists) protein expression, is frequently observed in almost all human cancers, including RB. The present study attempted to investigate the underlying mechanism from the perspective of non-coding RNA regulation. Here, we demonstrated that p53 and miR-129 were positively correlated with each other in RB. miR-129 directly targeted MDM2/4 to inhibit expression, therefore counteracting MDM2/4-mediated p53 signaling suppression and modulating RB cell proliferation and apoptosis. Moreover, p53 could activate the transcription of miR-129 via binding to the miR-129 promoter region, therefore forming a regulatory loop with MDM2/4 to affect RB progression. Altogether, the p53/miR-129/MDM2/4/p53 regulatory loop can modulate RB cell growth. We provide a solid experimental basis for developing novel therapies for RB.
DOI: 10.6084/m9.figshare.7362809
title: Additional file 2: of Genomic analyses based on pulmonary adenocarcinoma in situ reveal early lung cancer signature

description: Table S1. List of the 107 AIS-specific genes. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.7362809.v1
title: Additional file 2: of Genomic analyses based on pulmonary adenocarcinoma in situ reveal early lung cancer signature

description: Table S1. List of the 107 AIS-specific genes. (XLSX 14 kb)