cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.23911422.v1
title: CircEpha5 regulates the synthesis and secretion of androgen in mouse preantral follicles by targeting miR-758-5p

description: Circular RNAs are involved in the pathogenesis of various diseases, although its expression pattern and role in polycystic ovary syndrome (PCOS), characterised by hyperandrogenism, are not very clear. This article assessed the circRNAs expression profile in the ovaries of PCOS mice by circRNAs high-throughput sequencing and explored the role of circEpha5 in hyperandrogenism. The results showed that the overexpression of circEpha5 in mouse preantral follicles could increase the expression of <i>Cyp17a1</i>, an androgen synthesis-related gene, which resulted in a higher serum level of testosterone. Dual-luciferase reporter gene studies identified miR-758-5p as a direct target of circEpha5. Consequently, miR-758-5p expression was downregulated upon circEpha5 overexpression. Ectopically expressed miR-758-5p reversed the stimulation effects of circEpha5 on steroidogenesis-related gene expression and testosterone release. Therefore, circEpha5 could sponge miR-758-5p to regulate the expression of <i>Cyp17a1</i>, thereby promoting the synthesis and secretion of androgen in the preantral follicles. This work is contributed to the understanding of the pathogenesis of hyperandrogenemia and lays the foundation for the development of therapeutic targets of PCOS hyperandrogenism. <b>What is already known on this subject?</b> PCOS is a complex endocrine and metabolic disorders with hyperandrogenism as the main clinical manifestation. There are a variety of abnormal expression circRNAs in PCOS, however, the relationship between circEpha5 and hyperandrogenism has yet to be fully elucidated. <b>What do the results of this study add?</b> We first found that expression levels of serum circEpha5 were significantly higher in PCOS than in a normal group. Using mouse preantral follicle culture model and the letrozole-induced PCOS mouse model, the mechanism of CircEpha5 regulating androgen secretion was studied. <b>What the implications are of these findings for clinical practice and/or further research?</b> It was revealed that CircEpha5 can absorb miR-758-5p in the sponge to regulate the expression of <i>Cyp17a1</i>, thereby promoting the synthesis and secretion of androgen in preantral follicles, which may become a key target for the screening and treatment of PCOS hyperandrogenism.
DOI: 10.6084/m9.figshare.12377102
title: Two novel coordination polymers: protective activity on acute lung injury via inhibiting the release of inflammatory cytokines in alveolar macrophages

description: By using a mixed-ligand approach, two new coordination polymers with the chemical formula of {[Co<sub>2.5</sub>(nbta)(trz)<sub>2</sub>(H<sub>2</sub>O)]·3H<sub>2</sub>O}<sub>n</sub> (<b>1</b>, H<sub>3</sub>nbta = 5-nitros,2,3-benzenetricarboxylic acid and Htrz = 1<i>H</i>-1,2,4-triazole) and [Cu<sub>3</sub>(tib)<sub>2</sub>(TATB)<sub>2</sub>]·DMF·2H<sub>2</sub>O (<b>2</b>, tib = 1,3,5-tris(1-imidazolyl)benzene and H<sub>3</sub>TATB = 4,4′,4″-s-triazine-2,4,6-triyltribenzoic acid) were constructed using a solvothermal method by reaction of metal salts with the corresponding carboxylate and the N-donor co-ligands. After that, they were used for the treatment of acute lung injury animal model. The content of the IL-18 and TNF-α released by the alveolar macrophages was evaluated with enzyme-linked immunosorbent assay (ELISA) detection assay. The activation level of the NF-κB was measured with real-time RT-PCR.
DOI: 10.6084/m9.figshare.12377102.v1
title: Two novel coordination polymers: protective activity on acute lung injury via inhibiting the release of inflammatory cytokines in alveolar macrophages

description: By using a mixed-ligand approach, two new coordination polymers with the chemical formula of {[Co<sub>2.5</sub>(nbta)(trz)<sub>2</sub>(H<sub>2</sub>O)]·3H<sub>2</sub>O}<sub>n</sub> (<b>1</b>, H<sub>3</sub>nbta = 5-nitros,2,3-benzenetricarboxylic acid and Htrz = 1<i>H</i>-1,2,4-triazole) and [Cu<sub>3</sub>(tib)<sub>2</sub>(TATB)<sub>2</sub>]·DMF·2H<sub>2</sub>O (<b>2</b>, tib = 1,3,5-tris(1-imidazolyl)benzene and H<sub>3</sub>TATB = 4,4′,4″-s-triazine-2,4,6-triyltribenzoic acid) were constructed using a solvothermal method by reaction of metal salts with the corresponding carboxylate and the N-donor co-ligands. After that, they were used for the treatment of acute lung injury animal model. The content of the IL-18 and TNF-α released by the alveolar macrophages was evaluated with enzyme-linked immunosorbent assay (ELISA) detection assay. The activation level of the NF-κB was measured with real-time RT-PCR.
DOI: 10.6084/m9.figshare.10279958
title: MOESM5 of Functional exploration of co-expression networks identifies a nexus for modulating protein and citric acid titres in Aspergillus niger submerged culture

description: Additional file 5. DNA primers used in this study.
DOI: 10.6084/m9.figshare.10279958.v1
title: MOESM5 of Functional exploration of co-expression networks identifies a nexus for modulating protein and citric acid titres in Aspergillus niger submerged culture

description: Additional file 5. DNA primers used in this study.
DOI: 10.6084/m9.figshare.10279982
title: MOESM6 of Molecular and transcriptional characterization of phosphatidyl ethanolamine-binding proteins in wild peanuts Arachis duranensis and Arachis ipaensis

description: Additional file 6. Functions of the cis-acting elements found in the promoter regions of wild peanut PEBP genes.
DOI: 10.6084/m9.figshare.10279982.v1
title: MOESM6 of Molecular and transcriptional characterization of phosphatidyl ethanolamine-binding proteins in wild peanuts Arachis duranensis and Arachis ipaensis

description: Additional file 6. Functions of the cis-acting elements found in the promoter regions of wild peanut PEBP genes.
DOI: 10.6084/m9.figshare.10279994
title: MOESM8 of Molecular and transcriptional characterization of phosphatidyl ethanolamine-binding proteins in wild peanuts Arachis duranensis and Arachis ipaensis

description: Additional file 8. Wild and cultivated peanut orthologous genes.
DOI: 10.6084/m9.figshare.10279994.v1
title: MOESM8 of Molecular and transcriptional characterization of phosphatidyl ethanolamine-binding proteins in wild peanuts Arachis duranensis and Arachis ipaensis

description: Additional file 8. Wild and cultivated peanut orthologous genes.
DOI: 10.6084/m9.figshare.24960118
title: Hemoglobin wonders: a fascinating gas transporter dive into molluscs

description: Hemoglobin (Hb) has been identified in at least 14 molluscan taxa so far. Research spanning over 130 years on molluscan Hbs focuses on their genes, protein structures, functions, and evolution. Molluscan Hbs are categorized into single-, two-, and multiple-domain chains, including red blood cell, gill, and extracellular Hbs, based on the number of globin domains and their respective locations. These Hbs exhibit variation in assembly, ranging from monomeric and dimeric to higher-order multimeric forms. Typically, molluscan Hbs display moderately high oxygen affinity, weak cooperativity, and varying pH sensitivity. Hb’s potential role in antimicrobial pathways could augment the immune defense of bivalves, which may be a complement to their lack of adaptive immunity. The role of Hb as a respiratory protein in bivalves likely originated from the substitution of hemocyanin. Molluscan Hbs demonstrate adaptive evolution in response to environmental changes via various strategies (e.g. increasing Hb types, multimerization, and amino acid residue substitutions at key sites), enhancing or altering functional properties for habitat adaptation. Concurrently, an increase in Hb assembly diversity, coupled with a downward trend in oxygen affinity, is observed during molluscan differentiation and evolution. Hb in Protobranchia, Heteroconchia, and Pteriomorphia bivalves originated from separate ancestors, with Protobranchia inheriting a relative ancient molluscan Hb gene. In bivalves, extracellular Hbs share a common origin, while gill Hbs likely emerged from convergent evolution. In summary, research on molluscan Hbs offers valuable insights into the origins, biological variations, and adaptive evolution of animal Hbs.
DOI: 10.6084/m9.figshare.24960118.v1
title: Hemoglobin wonders: a fascinating gas transporter dive into molluscs

description: Hemoglobin (Hb) has been identified in at least 14 molluscan taxa so far. Research spanning over 130 years on molluscan Hbs focuses on their genes, protein structures, functions, and evolution. Molluscan Hbs are categorized into single-, two-, and multiple-domain chains, including red blood cell, gill, and extracellular Hbs, based on the number of globin domains and their respective locations. These Hbs exhibit variation in assembly, ranging from monomeric and dimeric to higher-order multimeric forms. Typically, molluscan Hbs display moderately high oxygen affinity, weak cooperativity, and varying pH sensitivity. Hb’s potential role in antimicrobial pathways could augment the immune defense of bivalves, which may be a complement to their lack of adaptive immunity. The role of Hb as a respiratory protein in bivalves likely originated from the substitution of hemocyanin. Molluscan Hbs demonstrate adaptive evolution in response to environmental changes via various strategies (e.g. increasing Hb types, multimerization, and amino acid residue substitutions at key sites), enhancing or altering functional properties for habitat adaptation. Concurrently, an increase in Hb assembly diversity, coupled with a downward trend in oxygen affinity, is observed during molluscan differentiation and evolution. Hb in Protobranchia, Heteroconchia, and Pteriomorphia bivalves originated from separate ancestors, with Protobranchia inheriting a relative ancient molluscan Hb gene. In bivalves, extracellular Hbs share a common origin, while gill Hbs likely emerged from convergent evolution. In summary, research on molluscan Hbs offers valuable insights into the origins, biological variations, and adaptive evolution of animal Hbs.
DOI: 10.6084/m9.figshare.24960118.v3
title: Hemoglobin wonders: a fascinating gas transporter dive into molluscs

description: Hemoglobin (Hb) has been identified in at least 14 molluscan taxa so far. Research spanning over 130 years on molluscan Hbs focuses on their genes, protein structures, functions, and evolution. Molluscan Hbs are categorized into single-, two-, and multiple-domain chains, including red blood cell, gill, and extracellular Hbs, based on the number of globin domains and their respective locations. These Hbs exhibit variation in assembly, ranging from monomeric and dimeric to higher-order multimeric forms. Typically, molluscan Hbs display moderately high oxygen affinity, weak cooperativity, and varying pH sensitivity. Hb’s potential role in antimicrobial pathways could augment the immune defense of bivalves, which may be a complement to their lack of adaptive immunity. The role of Hb as a respiratory protein in bivalves likely originated from the substitution of hemocyanin. Molluscan Hbs demonstrate adaptive evolution in response to environmental changes via various strategies (e.g. increasing Hb types, multimerization, and amino acid residue substitutions at key sites), enhancing or altering functional properties for habitat adaptation. Concurrently, an increase in Hb assembly diversity, coupled with a downward trend in oxygen affinity, is observed during molluscan differentiation and evolution. Hb in Protobranchia, Heteroconchia, and Pteriomorphia bivalves originated from separate ancestors, with Protobranchia inheriting a relative ancient molluscan Hb gene. In bivalves, extracellular Hbs share a common origin, while gill Hbs likely emerged from convergent evolution. In summary, research on molluscan Hbs offers valuable insights into the origins, biological variations, and adaptive evolution of animal Hbs.
DOI: 10.6084/m9.figshare.24960118.v2
title: Hemoglobin wonders: a fascinating gas transporter diving into molluscs

description: Hemoglobin (Hb) has been identified in at least 14 molluscan taxa so far. Research spanning over 130 years on molluscan Hbs focuses on their genes, protein structures, functions, and evolution. Molluscan Hbs are categorized into single-, two-, and multiple-domain chains, including red blood cell, gill, and extracellular Hbs, based on the number of globin domains and their respective locations. These Hbs exhibit variation in assembly, ranging from monomeric and dimeric to higher-order multimeric forms. Typically, molluscan Hbs display moderately high oxygen affinity, weak cooperativity, and varying pH sensitivity. Hb’s potential role in antimicrobial pathways could augment the immune defense of bivalves, which may be a complement to their lack of adaptive immunity. The role of Hb as a respiratory protein in bivalves likely originated from the substitution of hemocyanin. Molluscan Hbs demonstrate adaptive evolution in response to environmental changes via various strategies (e.g. increasing Hb types, multimerization, and amino acid residue substitutions at key sites), enhancing or altering functional properties for habitat adaptation. Concurrently, an increase in Hb assembly diversity, coupled with a downward trend in oxygen affinity, is observed during molluscan differentiation and evolution. Hb in Protobranchia, Heteroconchia, and Pteriomorphia bivalves originated from separate ancestors, with Protobranchia inheriting a relative ancient molluscan Hb gene. In bivalves, extracellular Hbs share a common origin, while gill Hbs likely emerged from convergent evolution. In summary, research on molluscan Hbs offers valuable insights into the origins, biological variations, and adaptive evolution of animal Hbs.
DOI: 10.6084/m9.figshare.25234084
title: Dataset of sintering study of viscoelastic particles: contact rheology DEM model during laser sintering

description: This directory contains the data generated by MercuryDPM software and experiments to analyse the contact rheology of viscoelastic particles sintered by a laser beam. Python scripts are included to open the files.
DOI: 10.6084/m9.figshare.25234084.v1
title: Dataset of sintering study of viscoelastic particles: contact rheology DEM model during laser sintering

description: This directory contains the data generated by MercuryDPM software and experiments to analyse the contact rheology of viscoelastic particles sintered by a laser beam. Python scripts are included to open the files.
DOI: 10.6084/m9.figshare.9755813
title: Dissecting dynamic expression of autophagy-related genes during human fetal digestive tract development via single-cell RNA sequencing

description: Macroautophagy/autophagy has been demonstrated to play an essential role in embryonic development. However, the role of autophagy during human fetal digestive tract development has not been investigated. Here, by using over 5,000 human embryonic digestive tract cells ranging from 6 weeks to 25 weeks, we explored the dynamic expression of autophagy-related genes at single-cell resolution, and found that the transcriptional activity of autophagy-related genes boosted remarkably and specifically in the early (between 6 and 9 weeks) stages. Interestingly, the small intestine cells at 9 weeks showed the most significant enrichment of autophagy-related genes than any other stages. In summary, our results for the first time revealed that autophagy may play an essential role in the development of the digestive tract, especially for the small intestine, in early human embryos. <b>Abbreviations:</b> GI: gastrointestinal; S-Intes: small intestine; t-SNE: t-distributed stochastic neighbor embedding
DOI: 10.6084/m9.figshare.9755813.v1
title: Dissecting dynamic expression of autophagy-related genes during human fetal digestive tract development via single-cell RNA sequencing

description: Macroautophagy/autophagy has been demonstrated to play an essential role in embryonic development. However, the role of autophagy during human fetal digestive tract development has not been investigated. Here, by using over 5,000 human embryonic digestive tract cells ranging from 6 weeks to 25 weeks, we explored the dynamic expression of autophagy-related genes at single-cell resolution, and found that the transcriptional activity of autophagy-related genes boosted remarkably and specifically in the early (between 6 and 9 weeks) stages. Interestingly, the small intestine cells at 9 weeks showed the most significant enrichment of autophagy-related genes than any other stages. In summary, our results for the first time revealed that autophagy may play an essential role in the development of the digestive tract, especially for the small intestine, in early human embryos. <b>Abbreviations:</b> GI: gastrointestinal; S-Intes: small intestine; t-SNE: t-distributed stochastic neighbor embedding
DOI: 10.6084/m9.figshare.10280198
title: MOESM1 of Necroptosis regulates tumor repopulation after radiotherapy via RIP1/RIP3/MLKL/JNK/IL8 pathway

description: Additional file 1: Figure S1. Western blot analysis of necroptotic factor in colorectal cancer cells. (a) The endogenous levels of RIP1, RIP3 and MLKL expression in HT29, SW480 and HCT116 cells were evaluated by Western blot. (b) Western bolt showed pMLKL (T357/S358) level in HT29 cells pre-treated with or without Nec-1 and irradiated or non-irradiated by 10 Gy X-ray. (c) Western blot showed the protein level of phosphorylated RIP1 (S166), phosphorylated RIP3 (S227), phosphorylated MLKL (T357/S358) in SW480 cells after 10 Gy irradiation. Figure S2. Clonogenic survival assays of irradiated HT29 and SW480 cells. (a) The picture of survived colonies of HT29 and SW480 cells irradiated by different dose of X-ray and seeded in different numbers. Figure S3. The cell death manners of HT29 and SW480 cells treated by inhibitors and radiation. (a) Representative graphs and statistical results of flow cytometry analyses after Annexin V/PI double staining. HT29 and SW480 cells were analyzed 3 days later after irradiation and inhibitor treatment as shown in Fig. Necroptosis was counted by the percentage of decreased PI positive cells by Nec-1. Apoptosis was counted by the percentage of decreased Annexin V positive cells by Z-vad-fmk. Ferroptosis was counted by the percentage of decreased of Annexin V negative/PI negative cells by Liproxstatin-1. One-way ANOVA, n = 3. ** p &lt; 0.005, *** p &lt; 0.001. Figure S4. Radiation-induced necroptosis depended on the RIP1/RIP3/MLKL signaling pathway. (a) The efficiency of knockdown of RIP1, RIP3 and MLKL by shRNA in HT29 cells were confirmed by western blot. (b) The knockdown of RIP1 by shRNA and its effect on LDH release in HCT116 cells after irradiation was quantified, one-way ANOVA, n = 3. (c) The necroptosis was further confirmed in irradiated or non-irradiated HT29 cells by using MLKL inhibitor (NSA) or shRNAs, one-way ANOVA, n = 3. n.s = not significant. Figure S5. Correlation between Luc activity and Luc gene labeled cell numbers. The measured luciferase activity (HT29 Fluc, SW480 Fluc and HCT116 Fluc) showed linearity with the plated cell numbers. Figure S6. Proliferation-promoting effect of irradiated HT29 and HCT116 cells on HCT116 Fluc in vitro. HCT116 Fluc cells showed differential growth on irradiated HT29 and HCT116 cells, one-way ANOVA, n = 3. * p &lt; 0.05, *** p &lt; 0.001. Table S1. Expression of IL-8 and clinic-pathologic features in colorectal cancer patients.
DOI: 10.6084/m9.figshare.10280198.v1
title: MOESM1 of Necroptosis regulates tumor repopulation after radiotherapy via RIP1/RIP3/MLKL/JNK/IL8 pathway

description: Additional file 1: Figure S1. Western blot analysis of necroptotic factor in colorectal cancer cells. (a) The endogenous levels of RIP1, RIP3 and MLKL expression in HT29, SW480 and HCT116 cells were evaluated by Western blot. (b) Western bolt showed pMLKL (T357/S358) level in HT29 cells pre-treated with or without Nec-1 and irradiated or non-irradiated by 10 Gy X-ray. (c) Western blot showed the protein level of phosphorylated RIP1 (S166), phosphorylated RIP3 (S227), phosphorylated MLKL (T357/S358) in SW480 cells after 10 Gy irradiation. Figure S2. Clonogenic survival assays of irradiated HT29 and SW480 cells. (a) The picture of survived colonies of HT29 and SW480 cells irradiated by different dose of X-ray and seeded in different numbers. Figure S3. The cell death manners of HT29 and SW480 cells treated by inhibitors and radiation. (a) Representative graphs and statistical results of flow cytometry analyses after Annexin V/PI double staining. HT29 and SW480 cells were analyzed 3 days later after irradiation and inhibitor treatment as shown in Fig. Necroptosis was counted by the percentage of decreased PI positive cells by Nec-1. Apoptosis was counted by the percentage of decreased Annexin V positive cells by Z-vad-fmk. Ferroptosis was counted by the percentage of decreased of Annexin V negative/PI negative cells by Liproxstatin-1. One-way ANOVA, n = 3. ** p &lt; 0.005, *** p &lt; 0.001. Figure S4. Radiation-induced necroptosis depended on the RIP1/RIP3/MLKL signaling pathway. (a) The efficiency of knockdown of RIP1, RIP3 and MLKL by shRNA in HT29 cells were confirmed by western blot. (b) The knockdown of RIP1 by shRNA and its effect on LDH release in HCT116 cells after irradiation was quantified, one-way ANOVA, n = 3. (c) The necroptosis was further confirmed in irradiated or non-irradiated HT29 cells by using MLKL inhibitor (NSA) or shRNAs, one-way ANOVA, n = 3. n.s = not significant. Figure S5. Correlation between Luc activity and Luc gene labeled cell numbers. The measured luciferase activity (HT29 Fluc, SW480 Fluc and HCT116 Fluc) showed linearity with the plated cell numbers. Figure S6. Proliferation-promoting effect of irradiated HT29 and HCT116 cells on HCT116 Fluc in vitro. HCT116 Fluc cells showed differential growth on irradiated HT29 and HCT116 cells, one-way ANOVA, n = 3. * p &lt; 0.05, *** p &lt; 0.001. Table S1. Expression of IL-8 and clinic-pathologic features in colorectal cancer patients.
DOI: 10.6084/m9.figshare.7658768
title: Impact of delivery mode on the levels of essential trace elements in breast milk

description: <b>Aim:</b> This study investigated whether the parturition mode (vaginal or cesarean [C-] section) affects breast milk concentrations of four essential trace elements (iron, copper, zinc, and manganese). <b>Methods:</b> Women giving birth at seven hospitals in seven different regions of China were enrolled in the study. Each participant provided breast milk, collected on postpartum day 3–5, for determination of iron, copper, zinc, and manganese concentrations. Breast milk concentrations of the subject trace elements were compared between women giving birth vaginally or via C-section. <b>Results:</b> Of the 1243 women enrolled in the study, 617 (49.6%) gave birth via the vaginal route and 626 (50.4%) delivered via C-section. The mean milk concentrations of iron, copper, zinc, and manganese in the milk of women delivering via the vaginal route were higher than those in the milk of women delivering via C-section; only the copper concentration differences were statistically significant, after adjusting for confounding factors (<i>p</i> = .023). <b>Conclusion:</b> Delivery mode impacts breast milk concentrations of essential trace elements, with vaginal delivery being associated with higher essential trace element concentrations than C-sections.