cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.17041641.v1
title: Effects of whole grain intake on glycemic traits: A systematic review and meta-analysis of randomized controlled trials

description: Whole grains (WGs) may have various health benefits, including lowering blood glucose and improving insulin sensitivity. To conduct a meta-analysis of the effects of WGs compared with non-WGs on changes in fasting glucose, fasting insulin, glycated hemoglobin (HbA1c), and homeostasis model assessment of insulin resistance (HOMA-IR). A systematic literature search was performed for all published randomized controlled trials on the effects of WG intake on fasting glucose, fasting insulin, HbA1c and HOMA-IR response up to February 2021. Weighted mean differences (WMD) were calculated. Pre-specified subgroup and univariate meta-regression analyses were explored to identify the sources of heterogeneity. Sensitivity analysis and bias analysis were conducted to appraise study quality. Among 12,435 articles screened for eligibility, data were extracted from 48 articles. Meta-analysis of 4,118 participants showed that WG consumption resulted in a significant reduction in fasting glucose by −0.15 mmol/L, fasting insulin by −2.71 pmol/L, HbA1c by −0.44%, and HOMA-IR by −0.28, respectively. Compared with mixed grains, brown rice, and wheat, oats were significantly lower on marker of glycemic. Besides, multiple interventions per day consolidated effectiveness of WGs. WG consumption decreased the levels of fasting glucose, fasting insulin, HbA1c, and HOMA-IR compared with non-WG consumption.
DOI: 10.6084/m9.figshare.7604483
title: MOESM3 of QBMG: quasi-biogenic molecule generator with deep recurrent neural network

description: Additional file 3. Top-200 PCL compounds and their natural product-likeness scores.
DOI: 10.6084/m9.figshare.7604483.v1
title: MOESM3 of QBMG: quasi-biogenic molecule generator with deep recurrent neural network

description: Additional file 3. Top-200 PCL compounds and their natural product-likeness scores.
DOI: 10.6084/m9.figshare.7604486
title: MOESM4 of QBMG: quasi-biogenic molecule generator with deep recurrent neural network

description: Additional file 4. Compounds reproduced by the RNN model from test library.
DOI: 10.6084/m9.figshare.7604486.v1
title: MOESM4 of QBMG: quasi-biogenic molecule generator with deep recurrent neural network

description: Additional file 4. Compounds reproduced by the RNN model from test library.
DOI: 10.6084/m9.figshare.7138595
title: Additional file 11: of Identification, characterization and expression analysis of the VQ motif-containing gene family in tea plant (Camellia sinensis)

description: Table S9. Expression levels of CsVQ genes following the NaCl treatment in tea plants. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.7138595.v1
title: Additional file 11: of Identification, characterization and expression analysis of the VQ motif-containing gene family in tea plant (Camellia sinensis)

description: Table S9. Expression levels of CsVQ genes following the NaCl treatment in tea plants. (XLSX 16 kb)
DOI: 10.17028/rd.lboro.11798829
title: Supplementary Information Files for 'Acetate production from inorganic carbon (HCO3-) in photo-assisted biocathode microbial electrosynthesis systems using WO3/MoO3/g-C3N4 heterojunctions and Serratia marcescens species.'

description: Supplementary Information Files for 'Acetate production from inorganic carbon (HCO3-) in photo-assisted biocathode microbial electrosynthesis systems using WO3/MoO3/g-C3N4 heterojunctions and Serratia marcescens species.'<br>Abstract:The efficient production of acetate from HCO3− is demonstrated in a photo-assisted microbial electrosynthesis system (MES) incorporating a WO3/MoO3/g-C3N4 heterojunction photo-assisted biocathode supporting Serratia marcescens Q1 electrotroph. The WO3/MoO3/g-C3N4 structured electrode consisting of a layer of g-C3N4 coated on graphite felt decorated with W/Mo oxides nanoparticles exhibited stable photocurrents, 4.8 times higher than the g-C3N4 electrode and acetate production of 3.12 ± 0.20 mM/d with a CEacetate of 73 ± 4 % and current of 2.5 ± 0.3 A/m2. Photo-induced electrons on the conduction bands of WO3/MoO3/g-C3N4 favoured hydrogen evolution, which was metabolized by S. marcescens with HCO3− to acetate, while the holes were refilled by the electrons travelling from the anode. Such mechanism reduced the interfacial resistances creating a supplementary driving force leading to higher acetate production. The biocompatible components of WO3/MoO3/g-C3N4 synergistically couple light-harvesting and further catalyze S. marcescens to acetate from HCO3−, providing a feasible strategy for achieving sustainable high rates of acetate production.<br>
DOI: 10.17028/rd.lboro.11798829.v1
title: Supplementary Information Files for 'Acetate production from inorganic carbon (HCO3-) in photo-assisted biocathode microbial electrosynthesis systems using WO3/MoO3/g-C3N4 heterojunctions and Serratia marcescens species.'

description: Supplementary Information Files for 'Acetate production from inorganic carbon (HCO3-) in photo-assisted biocathode microbial electrosynthesis systems using WO3/MoO3/g-C3N4 heterojunctions and Serratia marcescens species.'<br>Abstract:The efficient production of acetate from HCO3− is demonstrated in a photo-assisted microbial electrosynthesis system (MES) incorporating a WO3/MoO3/g-C3N4 heterojunction photo-assisted biocathode supporting Serratia marcescens Q1 electrotroph. The WO3/MoO3/g-C3N4 structured electrode consisting of a layer of g-C3N4 coated on graphite felt decorated with W/Mo oxides nanoparticles exhibited stable photocurrents, 4.8 times higher than the g-C3N4 electrode and acetate production of 3.12 ± 0.20 mM/d with a CEacetate of 73 ± 4 % and current of 2.5 ± 0.3 A/m2. Photo-induced electrons on the conduction bands of WO3/MoO3/g-C3N4 favoured hydrogen evolution, which was metabolized by S. marcescens with HCO3− to acetate, while the holes were refilled by the electrons travelling from the anode. Such mechanism reduced the interfacial resistances creating a supplementary driving force leading to higher acetate production. The biocompatible components of WO3/MoO3/g-C3N4 synergistically couple light-harvesting and further catalyze S. marcescens to acetate from HCO3−, providing a feasible strategy for achieving sustainable high rates of acetate production.<br>
DOI: 10.6084/m9.figshare.24906041
title: Extraction and <i>in vitro</i> active evaluation of essential oil of <i>Acorus tatarinowii</i> Schott rhizome rich in β-asarone using enzymatic pretreatment and solvent-free microwave-assisted method

description: The essential oil from fresh rhizomes of <i>Acorus tatarinowii</i> Schott was obtained using the EP-SFM method (an enzymatic pretreatment and solvent-free microwave-assisted method) and characterized. The optimal conditions for essential oil extraction have been obtained experimentally through experiments on single-factor and response surface-based optimization. The highest essential oil content (1.48%, w/w) was obtained under the optimal conditions by SEM, TGA, FTIR, GC-MS and acetylcholinesterase inhibition activity analysis <i>in vitro</i> assay. The EP-SFM method was found to be effective in improving the extraction rate of essential oils and reducing extraction time, as indicated by the results. More importantly, this method greatly increased the active component content of β-asarone (65.87%), and the content of β-asarone was increased by 18.06% compared with the conventional steam distillation method (SD). The acetylcholinesterase inhibiting activity of EP-SFM essential oil was evaluated as well, which had the best acetylcholinesterase inhibitory activity and was closest to the positive control group.
DOI: 10.6084/m9.figshare.24906041.v1
title: Extraction and <i>in vitro</i> active evaluation of essential oil of <i>Acorus tatarinowii</i> Schott rhizome rich in β-asarone using enzymatic pretreatment and solvent-free microwave-assisted method

description: The essential oil from fresh rhizomes of <i>Acorus tatarinowii</i> Schott was obtained using the EP-SFM method (an enzymatic pretreatment and solvent-free microwave-assisted method) and characterized. The optimal conditions for essential oil extraction have been obtained experimentally through experiments on single-factor and response surface-based optimization. The highest essential oil content (1.48%, w/w) was obtained under the optimal conditions by SEM, TGA, FTIR, GC-MS and acetylcholinesterase inhibition activity analysis <i>in vitro</i> assay. The EP-SFM method was found to be effective in improving the extraction rate of essential oils and reducing extraction time, as indicated by the results. More importantly, this method greatly increased the active component content of β-asarone (65.87%), and the content of β-asarone was increased by 18.06% compared with the conventional steam distillation method (SD). The acetylcholinesterase inhibiting activity of EP-SFM essential oil was evaluated as well, which had the best acetylcholinesterase inhibitory activity and was closest to the positive control group.
DOI: 10.6084/m9.figshare.8128928
title: Additional file 4: of Comparative transcriptome analyses of genes involved in sulforaphane metabolism at different treatment in Chinese kale using full-length transcriptome sequencing

description: Table S1. Significant GO classifications associated with dfifferentially expressed genes (DEGs) induced by different treatments. (XLSX 754 kb)
DOI: 10.6084/m9.figshare.8128928.v1
title: Additional file 4: of Comparative transcriptome analyses of genes involved in sulforaphane metabolism at different treatment in Chinese kale using full-length transcriptome sequencing

description: Table S1. Significant GO classifications associated with dfifferentially expressed genes (DEGs) induced by different treatments. (XLSX 754 kb)
DOI: 10.6084/m9.figshare.8128934
title: Additional file 5: of Comparative transcriptome analyses of genes involved in sulforaphane metabolism at different treatment in Chinese kale using full-length transcriptome sequencing

description: Table S2. Significant KEGG pathways associated with dfifferentially expressed genes (DEGs) induced by different treatments. (XLSX 72 kb)
DOI: 10.6084/m9.figshare.8128934.v1
title: Additional file 5: of Comparative transcriptome analyses of genes involved in sulforaphane metabolism at different treatment in Chinese kale using full-length transcriptome sequencing

description: Table S2. Significant KEGG pathways associated with dfifferentially expressed genes (DEGs) induced by different treatments. (XLSX 72 kb)
DOI: 10.6084/m9.figshare.7604708
title: Deciphering foot-and-mouth disease (FMD) virus–host tropism

description: The pattern of interactions between foot and mouth disease (FMD) viral protein 1 (VP1) with susceptible and resistant host integrins were deciphered. The putative effect of site-directed mutation on alteration of interaction is illustrated using predicted and validated 3D structures of VP1, mutated VP1 and integrins of <i>Bos taurus</i>, <i>Gallus</i> and <i>Canis</i>. Strong interactions were observed between FMDV-VP1 protein motifs at conserved tripeptide, Arg-Gly-Asp <sup>143</sup>RGD<sup>145</sup> and at domain <sup>676</sup>SIPLQ<sup>680</sup> in alpha-integrin of <i>B. taurus.</i> Notably, <i>in-silico</i> site-directed mutation in FMDV-VP1 protein led to complete loss of interaction between FMD-VP1 protein and <i>B. taurus</i> integrin, which confirmed the active role of arginine-glycine-aspartic acid (RGD) domain. Interestingly, <i>in-vitro</i> analysis demonstrates the persistence of the putative tropism site ‘SIPLQ’ in different cattle breeds undertaken. Thus, the attempt to decipher the tropism of FMDV at host receptor level interaction might be useful for future FMD control strategies through development of mimetic marker vaccines and/or host receptor manipulations. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.7604708.v3
title: Deciphering foot-and-mouth disease (FMD) virus–host tropism

description: The pattern of interactions between foot and mouth disease (FMD) viral protein 1 (VP1) with susceptible and resistant host integrins were deciphered. The putative effect of site-directed mutation on alteration of interaction is illustrated using predicted and validated 3D structures of VP1, mutated VP1 and integrins of <i>Bos taurus</i>, <i>Gallus</i> and <i>Canis</i>. Strong interactions were observed between FMDV-VP1 protein motifs at conserved tripeptide, Arg-Gly-Asp <sup>143</sup>RGD<sup>145</sup> and at domain <sup>676</sup>SIPLQ<sup>680</sup> in alpha-integrin of <i>B. taurus.</i> Notably, <i>in-silico</i> site-directed mutation in FMDV-VP1 protein led to complete loss of interaction between FMD-VP1 protein and <i>B. taurus</i> integrin, which confirmed the active role of arginine-glycine-aspartic acid (RGD) domain. Interestingly, <i>in-vitro</i> analysis demonstrates the persistence of the putative tropism site ‘SIPLQ’ in different cattle breeds undertaken. Thus, the attempt to decipher the tropism of FMDV at host receptor level interaction might be useful for future FMD control strategies through development of mimetic marker vaccines and/or host receptor manipulations. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.7604708.v2
title: Deciphering foot-and-mouth disease (FMD) virus–host tropism

description: The pattern of interactions between foot and mouth disease (FMD) viral protein 1 (VP1) with susceptible and resistant host integrins were deciphered. The putative effect of site-directed mutation on alteration of interaction is illustrated using predicted and validated 3D structures of VP1, mutated VP1 and integrins of <i>Bos taurus</i>, <i>Gallus</i> and <i>Canis</i>. Strong interactions were observed between FMDV-VP1 protein motifs at conserved tripeptide, Arg-Gly-Asp <sup>143</sup>RGD<sup>145</sup> and at domain <sup>676</sup>SIPLQ<sup>680</sup> in alpha-integrin of <i>B. taurus.</i> Notably, <i>in-silico</i> site-directed mutation in FMDV-VP1 protein led to complete loss of interaction between FMD-VP1 protein and <i>B. taurus</i> integrin, which confirmed the active role of arginine-glycine-aspartic acid (RGD) domain. Interestingly, <i>in-vitro</i> analysis demonstrates the persistence of the putative tropism site ‘SIPLQ’ in different cattle breeds undertaken. Thus, the attempt to decipher the tropism of FMDV at host receptor level interaction might be useful for future FMD control strategies through development of mimetic marker vaccines and/or host receptor manipulations. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.12323312
title: A novel energy sequence optimization algorithm for efficient spot-scanning proton arc (SPArc) treatment delivery

description: Spot-scanning proton arc therapy (SPArc) has been proposed to improve dosimetric outcome and to simplify treatment workflow. To efficiently deliver a SPArc plan, it’s crucial to minimize the number of energy layer switches (ELS) a sending because of the magnetic hysteresis effect. In this study, we introduced a new SPArc energy sequence optimization algorithm (SPArc_seq) to reduce ascended ELS and to investigate its impact on the beam delivery time (BDT). An iterative energy layer sorting and re-distribution mechanism following the direction of the gantry rotation was implemented in the original SPArc algorithm (SPArc_orig). Five disease sites, including prostate, lung, brain, head neck cancer (HNC) and breast cancer were selected to evaluate this new algorithm. Dose-volume histogram (DVH) and plan robustness were used to assess the plan quality for both SPArc_seq and SPArc_orig plans. The BDT evaluations were analyzed through two methods: 1. fixed gantry angle delivery (BDT<sub>fixed</sub>) and 2. An in-house dynamic arc scanning controller simulation which considered of gantry rotation speed, acceleration and deceleration (BDT<sub>arc</sub>). With a similar total number of energy layers, SPArc_seq plans provided a similar nominal plan quality and plan robustness compared to SPArc_orig plans. SPArc_seq significantly reduced the number of ascended ELS by 83% (19 <i>vs.</i>115), 70% (16 <i>vs.</i> 64), 82% (19 <i>vs.</i> 104), 80% (19 <i>vs.</i> 94) and 70% (9 <i>vs.</i> 30), which effectively shortened the BDT<sub>fixed</sub> by 65% (386 <i>vs.</i> 1091 s), 61% (235 <i>vs.</i> 609 s), 64% (336 <i>vs.</i> 928 s), 48% (787 <i>vs.</i>1521 s) and 25% (384 <i>vs.</i> 511 s) and shortened BDT<sub>arc</sub> by 54% (522 <i>vs.</i>1128 s), 52% (310 <i>vs.</i>645 s), 53% (443 <i>vs.</i> 951 s), 49% (803 <i>vs.</i>1583 s) and 26% (398 <i>vs.</i> 534 s) in prostate, lung, brain, HNC and breast cancer, respectively. The SPArc_seq optimization algorithm could effectively reduce the BDT compared to the original SPArc algorithm. The improved efficiency of the SPArc_seq algorithm has the potential to increase patient throughput, thereby reducing the operation cost of proton therapy.
DOI: 10.6084/m9.figshare.12323312.v1
title: A novel energy sequence optimization algorithm for efficient spot-scanning proton arc (SPArc) treatment delivery

description: Spot-scanning proton arc therapy (SPArc) has been proposed to improve dosimetric outcome and to simplify treatment workflow. To efficiently deliver a SPArc plan, it’s crucial to minimize the number of energy layer switches (ELS) a sending because of the magnetic hysteresis effect. In this study, we introduced a new SPArc energy sequence optimization algorithm (SPArc_seq) to reduce ascended ELS and to investigate its impact on the beam delivery time (BDT). An iterative energy layer sorting and re-distribution mechanism following the direction of the gantry rotation was implemented in the original SPArc algorithm (SPArc_orig). Five disease sites, including prostate, lung, brain, head neck cancer (HNC) and breast cancer were selected to evaluate this new algorithm. Dose-volume histogram (DVH) and plan robustness were used to assess the plan quality for both SPArc_seq and SPArc_orig plans. The BDT evaluations were analyzed through two methods: 1. fixed gantry angle delivery (BDT<sub>fixed</sub>) and 2. An in-house dynamic arc scanning controller simulation which considered of gantry rotation speed, acceleration and deceleration (BDT<sub>arc</sub>). With a similar total number of energy layers, SPArc_seq plans provided a similar nominal plan quality and plan robustness compared to SPArc_orig plans. SPArc_seq significantly reduced the number of ascended ELS by 83% (19 <i>vs.</i>115), 70% (16 <i>vs.</i> 64), 82% (19 <i>vs.</i> 104), 80% (19 <i>vs.</i> 94) and 70% (9 <i>vs.</i> 30), which effectively shortened the BDT<sub>fixed</sub> by 65% (386 <i>vs.</i> 1091 s), 61% (235 <i>vs.</i> 609 s), 64% (336 <i>vs.</i> 928 s), 48% (787 <i>vs.</i>1521 s) and 25% (384 <i>vs.</i> 511 s) and shortened BDT<sub>arc</sub> by 54% (522 <i>vs.</i>1128 s), 52% (310 <i>vs.</i>645 s), 53% (443 <i>vs.</i> 951 s), 49% (803 <i>vs.</i>1583 s) and 26% (398 <i>vs.</i> 534 s) in prostate, lung, brain, HNC and breast cancer, respectively. The SPArc_seq optimization algorithm could effectively reduce the BDT compared to the original SPArc algorithm. The improved efficiency of the SPArc_seq algorithm has the potential to increase patient throughput, thereby reducing the operation cost of proton therapy.
DOI: 10.6084/m9.figshare.11799108
title: Cholesterol derivatives induce dephosphorylation of the histone deacetylases Rpd3/HDAC1 to upregulate autophagy

description: Histone deacetylases (HDACs) are important for global gene expression and contribute to numerous physiological events. Deacetylase Rpd3 in yeast and its conserved homolog HDAC1 in mammals oppositely regulate autophagy; however, how Rpd3/HDAC1 is regulated to mediate autophagy remains unclear. Here, we showed autophagy occurrence in silkworm (<i>Bombyx mori</i>) required BmRpd3, wherein steroid hormone 20-hydroxyecdysone (20E) signaling regulated its protein level and nuclear localization negatively. Inhibition of MTOR led to dephosphorylation and nucleo-cytoplasmic translocation of BmRpd3/HsHDAC1. Besides, cholesterol, 20E, and 27-hydroxycholesterol could all induce massive dephosphorylation and cytoplasmic localization of BmRpd3/HsHDAC1, and thus autophagy by affecting MTORC1 activity. In addition, three phosphorylation sites (Ser392, Ser421, and Ser423) identified in BmRpd3 were conserved in HsHDAC1. Single or triple phosphorylation-site mutation attenuated the phosphorylation levels of BmRpd3/HsHDAC1, leading to their cytoplasmic localization and autophagy activation. In general, cholesterol derivatives, especially hydroxylated cholesterol, caused dephosphorylation and nucleo-cytoplasmic shuttling of BmRpd3/HsHDAC1 through inhibition of MTOR signaling to facilitate autophagy in <i>B. mori</i> and mammals. These findings improve our understandings of BmRpd3/HsHDAC1-mediated autophagy induced by cholesterol derivatives and shed light on their potential as a therapeutic target for neurodegenerative diseases and autophagy-related studies. <b>Abbreviations:</b> 20E: 20-hydroxyecdysone; 27-OH: 27-hydroxycholesterol; ACTB: actin beta; AMPK: AMP-activated protein kinase; Atg: autophagy-related; BmSqstm1: <i>Bombyx</i> sequestosome 1; CQ: chloroquine; HDAC: histone deacetylase; LMNB: Lamin B1; MTOR: mechanistic target of rapamycin kinase; PE: phosphatidylethanolamine; SQSTM1/p62: sequestosome 1; TUBA1A: tubulin alpha 1a.
DOI: 10.6084/m9.figshare.11799108.v2
title: Cholesterol derivatives induce dephosphorylation of the histone deacetylases Rpd3/HDAC1 to upregulate autophagy

description: Histone deacetylases (HDACs) are important for global gene expression and contribute to numerous physiological events. Deacetylase Rpd3 in yeast and its conserved homolog HDAC1 in mammals oppositely regulate autophagy; however, how Rpd3/HDAC1 is regulated to mediate autophagy remains unclear. Here, we showed autophagy occurrence in silkworm (<i>Bombyx mori</i>) required BmRpd3, wherein steroid hormone 20-hydroxyecdysone (20E) signaling regulated its protein level and nuclear localization negatively. Inhibition of MTOR led to dephosphorylation and nucleo-cytoplasmic translocation of BmRpd3/HsHDAC1. Besides, cholesterol, 20E, and 27-hydroxycholesterol could all induce massive dephosphorylation and cytoplasmic localization of BmRpd3/HsHDAC1, and thus autophagy by affecting MTORC1 activity. In addition, three phosphorylation sites (Ser392, Ser421, and Ser423) identified in BmRpd3 were conserved in HsHDAC1. Single or triple phosphorylation-site mutation attenuated the phosphorylation levels of BmRpd3/HsHDAC1, leading to their cytoplasmic localization and autophagy activation. In general, cholesterol derivatives, especially hydroxylated cholesterol, caused dephosphorylation and nucleo-cytoplasmic shuttling of BmRpd3/HsHDAC1 through inhibition of MTOR signaling to facilitate autophagy in <i>B. mori</i> and mammals. These findings improve our understandings of BmRpd3/HsHDAC1-mediated autophagy induced by cholesterol derivatives and shed light on their potential as a therapeutic target for neurodegenerative diseases and autophagy-related studies. <b>Abbreviations:</b> 20E: 20-hydroxyecdysone; 27-OH: 27-hydroxycholesterol; ACTB: actin beta; AMPK: AMP-activated protein kinase; Atg: autophagy-related; BmSqstm1: <i>Bombyx</i> sequestosome 1; CQ: chloroquine; HDAC: histone deacetylase; LMNB: Lamin B1; MTOR: mechanistic target of rapamycin kinase; PE: phosphatidylethanolamine; SQSTM1/p62: sequestosome 1; TUBA1A: tubulin alpha 1a.