cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12853074.v1
title: Characterization of Est-SSR markers related to <i>Colletotrichum fructicola</i> infection in strawberry (<i>Fragaria</i> ×<i>ananassa</i> Duchase)

description: <i>Colletotrichum fructicola</i> causes strawberry anthracnose, which results in considerable economic losses in quality and production in Asia. However, the molecular mechanism of strawberry infection with <i>C. fructicola</i> is still poorly understood. Here, we employed RNA-Seq technology to mine the strawberry transcriptome for EST-SSRs (Expressed Sequence Tag–Simple Sequence Repeats) following <i>C. fructicola</i> infection. Fortunately, we detected 3019 potential EST-SSRs from the transcriptomic data of cv. Jiuxiang. The seven commonly occurring repeat motifs were A/T (278), GAA/TTC (263), GAG/CTC (215), AAG/CTT(188), GGA/TCC (163), AGA/TCT (153) and AGG/CCT (153). We identified 31, 84 and 129 differentially expressed EST-SSR-containing sequences corresponding to 24, 72 and 96 Hpi, while 13 DE-EST-SSRs -containing sequences were differentially expressed and common for all the three time points. Furthermore, we identified allele polymorphisms for some DE-EST-SSRs among several resistant and susceptible strawberry varieties and wild species. The EST-SSRs in our research were related to the reported QTL resistance loci in strawberry which are differentially expressed after <i>C. fructicola</i> infection and have allele polymorphisms in different strawberry varieties and wild species. These provide a clue for utilisation of the EST-SSRs in marker-assisted breeding to improve anthracnose-resistant breeding in future.
DOI: 10.6084/m9.figshare.8088485
title: Ozone ultrafine bubble water induces the cellular signaling involved in oxidative stress responses in human periodontal ligament fibroblasts

description: Periodontitis is a chronic inflammatory disease caused by oral microorganisms in the subgingival biofilm. Stable aqueous ozone ultrafine bubble water (OUFBW) has recently begun to be used as an antiseptic in the treatment of periodontitis. The effectiveness of OUFBW is thought to depend on the bactericidal actions of dissolved ozone exerted via its oxidizing effect. On the other hand, the effects of ozone on the periodontal tissues are largely unknown. In this paper we examined the cellular responses after OUFBW treatment. Human primary periodontal ligament fibroblasts (hPDLFs) or Ca9-22 human gingival epithelial cells were treated with OUFBW or UV-inactivated OUFBW. The production of reactive oxygen species (ROS), the activation of mitogen-activated protein kinase (MAPK) and the nuclear factor-kappa B (NF-κB) activation were analyzed. The transcript profiles of hPDLFs after OUFBW treatment were also analyzed by RNA sequencing (RNA-seq). Our results showed that OUFBW induces oxidative stress by generating ROS, which, in turn, activated the MAPK pathway. OUFBW triggered activation of c-Fos, a major component of the transcription factor activator protein 1 (AP-1), and also nuclear factor erythroid 2 (NF-E2)-related factor 2 (Nrf2), which possessed a high sensitivity to oxidative stress. The results of RNA-seq analysis revealed that the numerous genes involved in oxidative stress responses or MAPK signaling pathway were up-regulated after OUFBW treatment. Investigation of the signaling pathways activated by OUFBW highlights another aspect of the biological roles of OUFBW, in addition to its bactericidal activity, in the treatment of periodontitis.
DOI: 10.6084/m9.figshare.8088485.v3
title: Ozone ultrafine bubble water induces the cellular signaling involved in oxidative stress responses in human periodontal ligament fibroblasts

description: Periodontitis is a chronic inflammatory disease caused by oral microorganisms in the subgingival biofilm. Stable aqueous ozone ultrafine bubble water (OUFBW) has recently begun to be used as an antiseptic in the treatment of periodontitis. The effectiveness of OUFBW is thought to depend on the bactericidal actions of dissolved ozone exerted via its oxidizing effect. On the other hand, the effects of ozone on the periodontal tissues are largely unknown. In this paper we examined the cellular responses after OUFBW treatment. Human primary periodontal ligament fibroblasts (hPDLFs) or Ca9-22 human gingival epithelial cells were treated with OUFBW or UV-inactivated OUFBW. The production of reactive oxygen species (ROS), the activation of mitogen-activated protein kinase (MAPK) and the nuclear factor-kappa B (NF-κB) activation were analyzed. The transcript profiles of hPDLFs after OUFBW treatment were also analyzed by RNA sequencing (RNA-seq). Our results showed that OUFBW induces oxidative stress by generating ROS, which, in turn, activated the MAPK pathway. OUFBW triggered activation of c-Fos, a major component of the transcription factor activator protein 1 (AP-1), and also nuclear factor erythroid 2 (NF-E2)-related factor 2 (Nrf2), which possessed a high sensitivity to oxidative stress. The results of RNA-seq analysis revealed that the numerous genes involved in oxidative stress responses or MAPK signaling pathway were up-regulated after OUFBW treatment. Investigation of the signaling pathways activated by OUFBW highlights another aspect of the biological roles of OUFBW, in addition to its bactericidal activity, in the treatment of periodontitis.
DOI: 10.6084/m9.figshare.8282327
title: Comb-structured triboelectric nanogenerators for multi-directional energy scavenging from human movements

description: A triboelectric nanogenerator (TENG) is an emerging energy harvesting technology utilizing multi-directional, wasted mechanical energies stemming from vibrations, winds, waves, body movements, etc. In this study, we report a comb-structured TENG (CTENG) capable of effectively scavenging multi-directional motions from human movements, which include walking, jumping, and running. By attaching CTENG to a person’s calf, we obtain a root-mean-square (RMS) power value of 5.28 μW (i.e. 13.12 V and 0.4 μA) for 1 s during mild running action (~5 m/s), which is sufficient for powering 10 light emitting diodes (LEDs). We integrate a CTENG with a simple hand-held pendulum (HHP) system with a natural frequency of 5.5 Hz. The natural frequency and input energy of our HHP system can be easily controlled by changing the holder mass and initial bending displacement, thus producing different output behaviors for the CTENG. Under the optimal HHP-based CTENG system design, the maximum output reaches 116 V at 6.5 μA under 0.1 kg mass and 4 cm bending displacement conditions. The corresponding output energy is 52.7 μJ for an operation time of 10.8 s. Our HHP-CTENG system can sufficiently power 45 LEDs and shows different output performances by varying the driving velocity of a vehicle, thus demonstrating the possibility for a self-powered velocity monitoring system.
DOI: 10.6084/m9.figshare.8282327.v2
title: Comb-structured triboelectric nanogenerators for multi-directional energy scavenging from human movements

description: A triboelectric nanogenerator (TENG) is an emerging energy harvesting technology utilizing multi-directional, wasted mechanical energies stemming from vibrations, winds, waves, body movements, etc. In this study, we report a comb-structured TENG (CTENG) capable of effectively scavenging multi-directional motions from human movements, which include walking, jumping, and running. By attaching CTENG to a person’s calf, we obtain a root-mean-square (RMS) power value of 5.28 μW (i.e. 13.12 V and 0.4 μA) for 1 s during mild running action (~5 m/s), which is sufficient for powering 10 light emitting diodes (LEDs). We integrate a CTENG with a simple hand-held pendulum (HHP) system with a natural frequency of 5.5 Hz. The natural frequency and input energy of our HHP system can be easily controlled by changing the holder mass and initial bending displacement, thus producing different output behaviors for the CTENG. Under the optimal HHP-based CTENG system design, the maximum output reaches 116 V at 6.5 μA under 0.1 kg mass and 4 cm bending displacement conditions. The corresponding output energy is 52.7 μJ for an operation time of 10.8 s. Our HHP-CTENG system can sufficiently power 45 LEDs and shows different output performances by varying the driving velocity of a vehicle, thus demonstrating the possibility for a self-powered velocity monitoring system.
DOI: 10.6084/m9.figshare.8088485.v2
title: Ozone ultrafine bubble water induces the cellular signaling involved in oxidative stress responses in human periodontal ligament fibroblasts

description: Periodontitis is a chronic inflammatory disease caused by oral microorganisms in the subgingival biofilm. Stable aqueous ozone ultrafine bubble water (OUFBW) has recently begun to be used as an antiseptic in the treatment of periodontitis. The effectiveness of OUFBW is thought to depend on the bactericidal actions of dissolved ozone exerted via its oxidizing effect. On the other hand, the effects of ozone on the periodontal tissues are largely unknown. In this paper we examined the cellular responses after OUFBW treatment. Human primary periodontal ligament fibroblasts (hPDLFs) or Ca9-22 human gingival epithelial cells were treated with OUFBW or UV-inactivated OUFBW. The production of reactive oxygen species (ROS), the activation of mitogen-activated protein kinase (MAPK) and the nuclear factor-kappa B (NF-κB) activation were analyzed. The transcript profiles of hPDLFs after OUFBW treatment were also analyzed by RNA sequencing (RNA-seq). Our results showed that OUFBW induces oxidative stress by generating ROS, which, in turn, activated the MAPK pathway. OUFBW triggered activation of c-Fos, a major component of the transcription factor activator protein 1 (AP-1), and also nuclear factor erythroid 2 (NF-E2)-related factor 2 (Nrf2), which possessed a high sensitivity to oxidative stress. The results of RNA-seq analysis revealed that the numerous genes involved in oxidative stress responses or MAPK signaling pathway were up-regulated after OUFBW treatment. Investigation of the signaling pathways activated by OUFBW highlights another aspect of the biological roles of OUFBW, in addition to its bactericidal activity, in the treatment of periodontitis.
DOI: 10.6084/m9.figshare.8282327.v1
title: Comb-structured triboelectric nanogenerators for multi-directional energy scavenging from human movements

description: A triboelectric nanogenerator (TENG) is an emerging energy harvesting technology utilizing multi-directional, wasted mechanical energies stemming from vibrations, winds, waves, body movements, etc. In this study, we report a comb-structured TENG (CTENG) capable of effectively scavenging multi-directional motions from human movements, which include walking, jumping, and running. By attaching CTENG to a person’s calf, we obtain a root-mean-square (RMS) power value of 5.28 μW (i.e. 13.12 V and 0.4 μA) for 1 s during mild running action (~5 m/s), which is sufficient for powering 10 light emitting diodes (LEDs). We integrate a CTENG with a simple hand-held pendulum (HHP) system with a natural frequency of 5.5 Hz. The natural frequency and input energy of our HHP system can be easily controlled by changing the holder mass and initial bending displacement, thus producing different output behaviors for the CTENG. Under the optimal HHP-based CTENG system design, the maximum output reaches 116 V at 6.5 μA under 0.1 kg mass and 4 cm bending displacement conditions. The corresponding output energy is 52.7 μJ for an operation time of 10.8 s. Our HHP-CTENG system can sufficiently power 45 LEDs and shows different output performances by varying the driving velocity of a vehicle, thus demonstrating the possibility for a self-powered velocity monitoring system.
DOI: 10.6084/m9.figshare.7667999
title: Tunable nonenzymatic degradability of <i>N</i>-substituted polyaspartamide main chain by amine protonation and alkyl spacer length in side chains for enhanced messenger RNA transfection efficiency

description: Degradability of polycations under physiological conditions is an attractive feature for their use in biomedical applications, such as the delivery of nucleic acids. This study aims to design polycations with tunable nonenzymatic degradability. A series of cationic <i>N</i>-substituted polyaspartamides were prepared to possess primary amine via various lengths of alkyl spacers in side chains. The degradation rate of each polyaspartamide derivative was determined by size exclusion chromatography under different pH conditions. The <i>N</i>-substituted polyaspartamide containing a 2-aminoethyl moiety in the side chain (PAsp(AE)) showed considerable degradability under physiological conditions (pH 7.4, 37 °C). In contrast, the <i>N</i>-substituted polyaspartamides bearing a longer alkyl spacer in the side chain, i.e. the 3-aminopropyl (PAsp(AP)) and 4-aminobutyl moieties (PAsp(AB)), more strongly suppressed degradation. Further, a positive correlation was observed between the degradation rate of <i>N</i>-substituted polyaspartamides and a deprotonation degree of primary amines in their side chains. Therefore, we conclude that the deprotonated primary amine in the side chain of <i>N</i>-substituted polyaspartamides can induce the degradation of the main chain through the activation of amide nitrogen in the side chain. When <i>N</i>-substituted polyaspartamides were utilized as a messenger RNA (mRNA) delivery vehicle via formation of polyion complexes (PICs), degradable PAsp(AE) elicited significantly higher mRNA expression efficiency in cultured cells compared to PAsp(AP) and PAsp(AB). The higher efficiency of PAsp(AE) might be due to the facilitated destabilization of PICs within the cells, directed toward mRNA release. Additionally, degradation of PAsp(AE) considerably reduced its cytotoxicity. Thus, our study highlights a useful design of well-defined cationic poly(amino acid)s with tunable nonenzymatic degradability.
DOI: 10.6084/m9.figshare.7667999.v2
title: Tunable nonenzymatic degradability of <i>N</i>-substituted polyaspartamide main chain by amine protonation and alkyl spacer length in side chains for enhanced messenger RNA transfection efficiency

description: Degradability of polycations under physiological conditions is an attractive feature for their use in biomedical applications, such as the delivery of nucleic acids. This study aims to design polycations with tunable nonenzymatic degradability. A series of cationic <i>N</i>-substituted polyaspartamides were prepared to possess primary amine via various lengths of alkyl spacers in side chains. The degradation rate of each polyaspartamide derivative was determined by size exclusion chromatography under different pH conditions. The <i>N</i>-substituted polyaspartamide containing a 2-aminoethyl moiety in the side chain (PAsp(AE)) showed considerable degradability under physiological conditions (pH 7.4, 37 °C). In contrast, the <i>N</i>-substituted polyaspartamides bearing a longer alkyl spacer in the side chain, i.e. the 3-aminopropyl (PAsp(AP)) and 4-aminobutyl moieties (PAsp(AB)), more strongly suppressed degradation. Further, a positive correlation was observed between the degradation rate of <i>N</i>-substituted polyaspartamides and a deprotonation degree of primary amines in their side chains. Therefore, we conclude that the deprotonated primary amine in the side chain of <i>N</i>-substituted polyaspartamides can induce the degradation of the main chain through the activation of amide nitrogen in the side chain. When <i>N</i>-substituted polyaspartamides were utilized as a messenger RNA (mRNA) delivery vehicle via formation of polyion complexes (PICs), degradable PAsp(AE) elicited significantly higher mRNA expression efficiency in cultured cells compared to PAsp(AP) and PAsp(AB). The higher efficiency of PAsp(AE) might be due to the facilitated destabilization of PICs within the cells, directed toward mRNA release. Additionally, degradation of PAsp(AE) considerably reduced its cytotoxicity. Thus, our study highlights a useful design of well-defined cationic poly(amino acid)s with tunable nonenzymatic degradability.
DOI: 10.6084/m9.figshare.12844876
title: Computational modeling of transforming growth factor β and activin a receptor complex formation in the context of promiscuous signaling regulation

description: The Transforming growth factor-beta (TGFβ) superfamily is a group of multipotent growth factors that control proliferation, quiescence and differentiation. Aberrant signal transduction and downstream target activation contribute to tumorigenesis and targeted therapy has therefore been considered a promising avenue. Using various modeling pipelines, we analyzed the structure-function relationship between ligand and receptor molecules of the TGFβ family. We further simulated the molecular docking of Galunisertib, a small molecule inhibitor targeting TGFβ signaling in cancer, which is currently undergoing FDA-approved clinical trials. We found that proprotein dimers of Activin isoforms differ at intrachain disulfide bonds, which support prior evidence of varying pro-domain stability and isoform preference. Further, mature proteins possess flexibility around conserved cystine knots to functionally interact with receptors or regulatory molecules in similar but distinct ways to TGFβ. We show that all Activin isoforms are capable of assuming a closed- or open-dimer state, revealing structural promiscuity of their open forms for receptor binding. We propose the first structural landscape for Activin receptor complexes containing a type I receptor (ACVR1B), which shares a pre-helix extension with TGFβ type I receptor (TGFβR1). Here, we artificially demonstrate that Activin can bind TGFβR1 in a TGFβ-like manner and that TGFβ1 can form signaling complexes with ACVR1B. Interestingly, Galunisertib was found to form stable inhibitory structures within the homologous kinase domains of both TGFβR1 and ACVR1B, thus halting receptor-promiscuous signaling. Overall, these observations highlight the challenges of specific TGFβ cascade targeting in the context of cancer therapies. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.12844906
title: Identification of luteolin -7-glucoside and epicatechin gallate from <i>Vernonia</i> <i>cinerea</i>, as novel EGFR L858R kinase inhibitors against lung cancer: Docking and simulation-based study

description: Lung cancer ranks number one among the all cancer types in the world, out of which 85% are non-small cell lung cancer (NSCLC). In case of NSCLC, a substitution mutation of Leu 858 Arg (L858R) in the gene of Epidermal Growth Factor Receptor (EGFR) has been reported. Hence, targeting EGFR containing L858R mutation using inhibitors is well reported strategy to discover potential drugs against NSCLC. The present work aims to identify the potent inhibitors against EGFR L858R from <i>Vernonia cinerea</i> plant. A library of 45 phytochemicals was subjected to virtual screening using rigid and flexible docking. 12 potential phytochemicals were screened by molecular docking with high binding energy (between -8.0 and -9.7 kcal mol<sup>−1</sup>). Two compounds viz., luteolin -7-glucoside and epicatechin gallate showed interaction with Met793 of EGFR-L858R which was similar to the reference inhibitor PD168393. To analyze the stability of the luteolin -7-glucoside and epicatechin gallate with EGFR L858R, molecular dynamics simulations were conducted in explicit water conditions using 60 nanosecond. The results of hydrogen bonding patterns, radius of gyration, deviations in conformational elements, fluctuations in the residual components, and solvent accessible surface area revealed better stability of luteolin -7-glucoside and epicatechin gallate with EGFR-L858R as compared to PD168393. Therefore, we conclude that luteolin -7-glucoside and epicatechin gallate have excellent inhibition properties thus they can be used further to develop effective drugs against lung cancer having EGFR-L858R mutation. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.12844906.v1
title: Identification of luteolin -7-glucoside and epicatechin gallate from <i>Vernonia</i> <i>cinerea</i>, as novel EGFR L858R kinase inhibitors against lung cancer: Docking and simulation-based study

description: Lung cancer ranks number one among the all cancer types in the world, out of which 85% are non-small cell lung cancer (NSCLC). In case of NSCLC, a substitution mutation of Leu 858 Arg (L858R) in the gene of Epidermal Growth Factor Receptor (EGFR) has been reported. Hence, targeting EGFR containing L858R mutation using inhibitors is well reported strategy to discover potential drugs against NSCLC. The present work aims to identify the potent inhibitors against EGFR L858R from <i>Vernonia cinerea</i> plant. A library of 45 phytochemicals was subjected to virtual screening using rigid and flexible docking. 12 potential phytochemicals were screened by molecular docking with high binding energy (between -8.0 and -9.7 kcal mol<sup>−1</sup>). Two compounds viz., luteolin -7-glucoside and epicatechin gallate showed interaction with Met793 of EGFR-L858R which was similar to the reference inhibitor PD168393. To analyze the stability of the luteolin -7-glucoside and epicatechin gallate with EGFR L858R, molecular dynamics simulations were conducted in explicit water conditions using 60 nanosecond. The results of hydrogen bonding patterns, radius of gyration, deviations in conformational elements, fluctuations in the residual components, and solvent accessible surface area revealed better stability of luteolin -7-glucoside and epicatechin gallate with EGFR-L858R as compared to PD168393. Therefore, we conclude that luteolin -7-glucoside and epicatechin gallate have excellent inhibition properties thus they can be used further to develop effective drugs against lung cancer having EGFR-L858R mutation. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.12844876.v1
title: Computational modeling of transforming growth factor β and activin a receptor complex formation in the context of promiscuous signaling regulation

description: The Transforming growth factor-beta (TGFβ) superfamily is a group of multipotent growth factors that control proliferation, quiescence and differentiation. Aberrant signal transduction and downstream target activation contribute to tumorigenesis and targeted therapy has therefore been considered a promising avenue. Using various modeling pipelines, we analyzed the structure-function relationship between ligand and receptor molecules of the TGFβ family. We further simulated the molecular docking of Galunisertib, a small molecule inhibitor targeting TGFβ signaling in cancer, which is currently undergoing FDA-approved clinical trials. We found that proprotein dimers of Activin isoforms differ at intrachain disulfide bonds, which support prior evidence of varying pro-domain stability and isoform preference. Further, mature proteins possess flexibility around conserved cystine knots to functionally interact with receptors or regulatory molecules in similar but distinct ways to TGFβ. We show that all Activin isoforms are capable of assuming a closed- or open-dimer state, revealing structural promiscuity of their open forms for receptor binding. We propose the first structural landscape for Activin receptor complexes containing a type I receptor (ACVR1B), which shares a pre-helix extension with TGFβ type I receptor (TGFβR1). Here, we artificially demonstrate that Activin can bind TGFβR1 in a TGFβ-like manner and that TGFβ1 can form signaling complexes with ACVR1B. Interestingly, Galunisertib was found to form stable inhibitory structures within the homologous kinase domains of both TGFβR1 and ACVR1B, thus halting receptor-promiscuous signaling. Overall, these observations highlight the challenges of specific TGFβ cascade targeting in the context of cancer therapies. Communicated by Ramaswamy H. Sarma