cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8107904.v2
title: Evaluation of the published kinase inhibitor set to identify multiple inhibitors of bacterial ATP-dependent mur ligases

description: The Mur ligases form a series of consecutive enzymes that participate in the intracellular steps of bacterial peptidoglycan biosynthesis. They therefore represent interesting targets for antibacterial drug discovery. MurC, D, E and F are all ATP-dependent ligases. Accordingly, with the aim being to find multiple inhibitors of these enzymes, we screened a collection of ATP-competitive kinase inhibitors, on <i>Escherichia coli</i> MurC, D and F, and identified five promising scaffolds that inhibited at least two of these ligases. Compounds <b>1</b>, <b>2</b>, <b>4</b> and <b>5</b> are multiple inhibitors of the whole MurC to MurF cascade that act in the micromolar range (IC<sub>50</sub>, 32–368 µM). NMR-assisted binding studies and steady-state kinetics studies performed on aza-stilbene derivative <b>1</b> showed, surprisingly, that it acts as a competitive inhibitor of MurD activity towards D-glutamic acid, and additionally, that its binding to the D-glutamic acid binding site is independent of the enzyme closure promoted by ATP.
DOI: 10.6084/m9.figshare.8107880
title: OGW_CFRP_Temperature_dam_D24

description: OGW_CFRP_Temperature_dam_D24
DOI: 10.6084/m9.figshare.8107883.v1
title: OGW_CFRP_Temperature_dam_D16

description: OGW_CFRP_Temperature_dam_D16
DOI: 10.6084/m9.figshare.8107886
title: OGW_CFRP_Temperature_dam_D12

description: OGW_CFRP_Temperature_dam_D12
DOI: 10.6084/m9.figshare.8107886.v1
title: OGW_CFRP_Temperature_dam_D12

description: OGW_CFRP_Temperature_dam_D12
DOI: 10.6084/m9.figshare.8107904.v1
title: Evaluation of the published kinase inhibitor set to identify multiple inhibitors of bacterial ATP-dependent mur ligases

description: The Mur ligases form a series of consecutive enzymes that participate in the intracellular steps of bacterial peptidoglycan biosynthesis. They therefore represent interesting targets for antibacterial drug discovery. MurC, D, E and F are all ATP-dependent ligases. Accordingly, with the aim being to find multiple inhibitors of these enzymes, we screened a collection of ATP-competitive kinase inhibitors, on <i>Escherichia coli</i> MurC, D and F, and identified five promising scaffolds that inhibited at least two of these ligases. Compounds <b>1</b>, <b>2</b>, <b>4</b> and <b>5</b> are multiple inhibitors of the whole MurC to MurF cascade that act in the micromolar range (IC<sub>50</sub>, 32–368 µM). NMR-assisted binding studies and steady-state kinetics studies performed on aza-stilbene derivative <b>1</b> showed, surprisingly, that it acts as a competitive inhibitor of MurD activity towards D-glutamic acid, and additionally, that its binding to the D-glutamic acid binding site is independent of the enzyme closure promoted by ATP.
DOI: 10.6084/m9.figshare.8107853
title: Sysmalvac intermediate results II

description: This dataset contains the WGCNA-based enrichment analysis of SysMalVac
DOI: 10.6084/m9.figshare.8107880.v1
title: OGW_CFRP_Temperature_dam_D24

description: OGW_CFRP_Temperature_dam_D24
DOI: 10.6084/m9.figshare.8107826
title: FLORA_2019_173.xlsx

description: Biomass reallocation and increased plasticity might contribute to successful invasion of Chromolaena odorata
DOI: 10.6084/m9.figshare.8107853.v1
title: Sysmalvac intermediate results II

description: This dataset contains the WGCNA-based enrichment analysis of SysMalVac
DOI: 10.6084/m9.figshare.8107811
title: Supplementary Material for: Nrf2 Activation by SK-119 Attenuates Oxidative Stress, UVB, and LPS-Induced Damage

description: <b><i>Background/Aims:</i></b> The Nrf2 signaling pathway plays a pivotal role in neutralizing excess reactive oxygen species formation and therefore enhancing the endogenous cellular protection mechanism. Thus, activating this pathway may provide therapeutic options against oxidative stress-related disorders. We have recently applied a computer-aided drug design approach to the design and synthesis of novel Nrf2 enhancers. The current study was aimed at investigating the potential beneficial impact of (E)-5-oxo-1-(4-((2,4,6-trihydroxybenzylidene)amino)phenyl)pyrrolidine-3-carboxylic acid (SK-119) in skin oxidative damage models. <b><i>Methods:</i></b> SK-119, tested initially in PC-12 cells, attenuated oxidative stress-induced cytotoxicity concomitantly with Nrf2 activation. The potential impact of this compound was evaluated in skin-based disease models both in vitro (HaCaT cells) and ex vivo (human skin organ culture). <b><i>Results:</i></b> The data clearly showed the marked anti-inflammatory and photoprotection properties of the compound; SK-119-treated cells or tissues displayed a reduction in cytokine secretion induced by lipopolysaccharides (LPS) in a manner comparable with dexamethasone. In addition, topical application of SK-119 was able to block UVB-induced oxidative stress and attenuated caspase-mediated apoptosis, DNA adduct formation, and the concomitant cellular damage. <b><i>Conclusion:</i></b> These results indicate that SK-119 is an Nrf2 activator that can be used as a prototype molecule for the development of novel treatments of dermatological disorders related to oxidative stress.
DOI: 10.6084/m9.figshare.8107826.v1
title: FLORA_2019_173.xlsx

description: Biomass reallocation and increased plasticity might contribute to successful invasion of Chromolaena odorata
DOI: 10.6084/m9.figshare.8107787
title: Sysmalvac intermediate results

description: Intermediate results SysmalVac, enrichment analysis based on differential gene expression
DOI: 10.6084/m9.figshare.8107766
title: Supplementary Material for: High Sodium Intake Impairs Small Artery Vasoreactivity in vivo in Dahl Salt-Sensitive Rats

description: The effects of high sodium intake on the functionality of resistance arteries have been repeatedly studied in vitro, but no study has focused on salt-sensitive hypertension in vivo. We studied the in vivo reactivity of mesenteric small arteries (MSAs) to vasoactive agents in Dahl salt-sensitive (DS) rats with various sodium diets. Twenty-four male DS rats were randomized into 3 groups: LS (0.3% NaCl diet), NS (0.6% NaCl diet), and HS (8% NaCl diet). After a 12-week intervention, the diameter changes of the MSAs after noradrenaline (NA) and acetylcholine (ACh) exposure were detected by a microscope, and changes in blood perfusion through the MSAs were measured by full-field laser perfusion imaging. HS enhanced the constrictive response of the MSAs to NA and attenuated the relaxing response to ACh. Low sodium intake reduced the response of the MSAs to NA and promoted ACh-induced vasodilatation. HS also aggravated NA-induced blood perfusion reduction and impaired ACh-induced hyperperfusion of the MSAs. Pathologically, HS was associated with arteriolar structural damage and fibrosis of the MSAs. We conclude that sodium intake affects the responsiveness of the MSAs to vasoactive agents in DS rats and might play important roles in modulating blood pressure in hypertensive individuals.
DOI: 10.6084/m9.figshare.8107787.v1
title: Sysmalvac intermediate results

description: Intermediate results SysmalVac, enrichment analysis based on differential gene expression
DOI: 10.6084/m9.figshare.8107682
title: Supplementary Material for: Cardiovascular Risk Factor Control and Lifestyle Factors in Young to Middle-Aged Adults with Newly Diagnosed Obstructive Coronary Artery Disease

description: <b><i>Background:</i></b> While progress in the prevention of cardiovascular disease (CVD) has been noted over the past several decades, there are still those who develop CVD earlier in life than others. <b><i>Objective:</i></b> We investigated traditional and lifestyle CVD risk factors in young to middle-aged patients compared to older ones with obstructive coronary artery disease (CAD). <b><i>Methods:</i></b> A retrospective analysis of patients with a new diagnosis of obstructive CAD undergoing coronary intervention was performed. Young to middle-aged patients were defined as those in the youngest quartile (<i>n</i> = 281, mean age 50 ± 6 years, 81% male) compared to the other three older quartiles combined (<i>n</i> = 799, mean age 69 ± 7.5 years, 71% male). Obstructive CAD was determined by angiography. <b><i>Results:</i></b> Young to middle-aged patients compared to older ones were more likely to be male (<i>p</i> &lt; 0.01), smokers (21 vs. 9%, <i>p</i> &lt; 0.001), and have a higher body mass index (31 ± 6 vs. 29 ± 6 kg/m<sup>2</sup>, <i>p</i> &lt; 0.001). Younger patients were less likely to eat fruits, vegetables, and fish and had fewer controlled CVD risk factors (2.7 ± 1.2 vs. 3.0 ± 1.0, <i>p</i> &lt; 0.001). Compared to older patients, higher levels of psychological stress (aOR 1.6, 95% CI 1.1–2.4), financial stress (aOR 1.8, 95% CI 1.3–2.5), and low functional capacity (aOR 3.3, 95% CI 2.4–4.5) were noted in the young to middle-aged population as well. <b><i>Conclusion:</i></b> Lifestyle in addition to traditional CVD risk factors should be taken into account when evaluating risk for development of CVD in a younger population.
DOI: 10.6084/m9.figshare.8107655
title: figures for erythrocyte traits and platelets.pdf

description: <b>Erythrocyte traits results</b> The GWAS results is shown in Table1. And the results are also visualrized by Manhattan plots and corresponding quantile-quantile plots(QQ-plots), which are shown in Figure1 and Figure2. We performed a genome-wide association study for six traits of erythrocyte traits: red blood cell(RBC),mean corpuscular haemoglobin(MCH),mean corpuscular haemoglobin concentration(MCHC),mean corpuscular volume(MCV),haematocrit(HCT),and haemoglobin(HGB). After analysed by Farm-CPU, there are in total twenty three significant SNPs associated with erythrocyte traits: six for RBC, two for MCH, seven for MCHC, two for MCV, four for HCT and two for HGB.Three of these twenty-three SNPs fall into the regions that related with hepatoma (liver cancer), carcinoma of the rectum (colorectal cancer) and cancer, which are harboured within regions of known genes. Other two SNPs fall into regions that have been reported to harbour QTL for Alzheimer’s disease and regulating and controlling of hemameba (WBC) and phagocyte, which fall into regions of known genes. Others are located 11157 to 89626bp away from the nearest known genes. All SNPs are not assigned to any chromosome but all significant SNPs reached genome-wide level. We find KCNJ2 as an candidate gene meanwhile the SNP (BOVINEHD1900016940) on Bos taurus chromosome (BTA)19 was located in the known gene(KCNJ2), and 13Mbp away nearby the gene, which was highly associated with RBC(p= 1.93E-07). <b>Platelet traits results</b> The GWAS study for platelet contain five traits: platelet count(PLT),platelet distribution width(PDW),mean platelet volume(MPV),large platelet count ratio(LPCR),platelet distribution wide ratio(PDWR).Twenty-seven significant SNPs were detected to be associated with five platelet traits: none for PLT, five for PDW, eleven for MPV, five for LPCR, five for PDWR. The association of these 27 highly significant SNP loci with immunity, cancer occurrence, cancer suppression and health-related traits has not been clearly verified. Moreover, among these 27 significant SNPs, 10SNPs are harboured within regions of nearest known genes, these SNPs are located from 2709 to 621763 bp away from the nearest genes. But none is assigned to any chromosome. And the GWAS results are shown in Table2. Results are also visualrized via Manhattan plots and corresponding quantile-quantile plots(QQ-plots), which are shown in Figure3 and Figure4.
DOI: 10.6084/m9.figshare.8107655.v1
title: figures for erythrocyte traits and platelets.pdf

description: <b>Erythrocyte traits results</b> The GWAS results is shown in Table1. And the results are also visualrized by Manhattan plots and corresponding quantile-quantile plots(QQ-plots), which are shown in Figure1 and Figure2. We performed a genome-wide association study for six traits of erythrocyte traits: red blood cell(RBC),mean corpuscular haemoglobin(MCH),mean corpuscular haemoglobin concentration(MCHC),mean corpuscular volume(MCV),haematocrit(HCT),and haemoglobin(HGB). After analysed by Farm-CPU, there are in total twenty three significant SNPs associated with erythrocyte traits: six for RBC, two for MCH, seven for MCHC, two for MCV, four for HCT and two for HGB.Three of these twenty-three SNPs fall into the regions that related with hepatoma (liver cancer), carcinoma of the rectum (colorectal cancer) and cancer, which are harboured within regions of known genes. Other two SNPs fall into regions that have been reported to harbour QTL for Alzheimer’s disease and regulating and controlling of hemameba (WBC) and phagocyte, which fall into regions of known genes. Others are located 11157 to 89626bp away from the nearest known genes. All SNPs are not assigned to any chromosome but all significant SNPs reached genome-wide level. We find KCNJ2 as an candidate gene meanwhile the SNP (BOVINEHD1900016940) on Bos taurus chromosome (BTA)19 was located in the known gene(KCNJ2), and 13Mbp away nearby the gene, which was highly associated with RBC(p= 1.93E-07). <b>Platelet traits results</b> The GWAS study for platelet contain five traits: platelet count(PLT),platelet distribution width(PDW),mean platelet volume(MPV),large platelet count ratio(LPCR),platelet distribution wide ratio(PDWR).Twenty-seven significant SNPs were detected to be associated with five platelet traits: none for PLT, five for PDW, eleven for MPV, five for LPCR, five for PDWR. The association of these 27 highly significant SNP loci with immunity, cancer occurrence, cancer suppression and health-related traits has not been clearly verified. Moreover, among these 27 significant SNPs, 10SNPs are harboured within regions of nearest known genes, these SNPs are located from 2709 to 621763 bp away from the nearest genes. But none is assigned to any chromosome. And the GWAS results are shown in Table2. Results are also visualrized via Manhattan plots and corresponding quantile-quantile plots(QQ-plots), which are shown in Figure3 and Figure4.
DOI: 10.6084/m9.figshare.8107682.v1
title: Supplementary Material for: Cardiovascular Risk Factor Control and Lifestyle Factors in Young to Middle-Aged Adults with Newly Diagnosed Obstructive Coronary Artery Disease

description: <b><i>Background:</i></b> While progress in the prevention of cardiovascular disease (CVD) has been noted over the past several decades, there are still those who develop CVD earlier in life than others. <b><i>Objective:</i></b> We investigated traditional and lifestyle CVD risk factors in young to middle-aged patients compared to older ones with obstructive coronary artery disease (CAD). <b><i>Methods:</i></b> A retrospective analysis of patients with a new diagnosis of obstructive CAD undergoing coronary intervention was performed. Young to middle-aged patients were defined as those in the youngest quartile (<i>n</i> = 281, mean age 50 ± 6 years, 81% male) compared to the other three older quartiles combined (<i>n</i> = 799, mean age 69 ± 7.5 years, 71% male). Obstructive CAD was determined by angiography. <b><i>Results:</i></b> Young to middle-aged patients compared to older ones were more likely to be male (<i>p</i> &lt; 0.01), smokers (21 vs. 9%, <i>p</i> &lt; 0.001), and have a higher body mass index (31 ± 6 vs. 29 ± 6 kg/m<sup>2</sup>, <i>p</i> &lt; 0.001). Younger patients were less likely to eat fruits, vegetables, and fish and had fewer controlled CVD risk factors (2.7 ± 1.2 vs. 3.0 ± 1.0, <i>p</i> &lt; 0.001). Compared to older patients, higher levels of psychological stress (aOR 1.6, 95% CI 1.1–2.4), financial stress (aOR 1.8, 95% CI 1.3–2.5), and low functional capacity (aOR 3.3, 95% CI 2.4–4.5) were noted in the young to middle-aged population as well. <b><i>Conclusion:</i></b> Lifestyle in addition to traditional CVD risk factors should be taken into account when evaluating risk for development of CVD in a younger population.
DOI: 10.6084/m9.figshare.8107640
title: Genome-wide association study for erythrocyte traits and platelet in Chinese Holstein cattle

description: <b>3.1 Erythrocyte traits results</b> The GWAS results is shown in Table1. And the results are also visualrized by Manhattan plots and corresponding quantile-quantile plots(QQ-plots), which are shown in Figure1 and Figure2. We performed a genome-wide association study for six traits of erythrocyte traits: red blood cell(RBC),mean corpuscular haemoglobin(MCH),mean corpuscular haemoglobin concentration(MCHC),mean corpuscular volume(MCV),haematocrit(HCT),and haemoglobin(HGB). After analysed by Farm-CPU, there are in total twenty three significant SNPs associated with erythrocyte traits: six for RBC, two for MCH, seven for MCHC, two for MCV, four for HCT and two for HGB.Three of these twenty-three SNPs fall into the regions that related with hepatoma (liver cancer), carcinoma of the rectum (colorectal cancer) and cancer, which are harboured within regions of known genes. Other two SNPs fall into regions that have been reported to harbour QTL for Alzheimer’s disease and regulating and controlling of hemameba (WBC) and phagocyte, which fall into regions of known genes. Others are located 11157 to 89626bp away from the nearest known genes. All SNPs are not assigned to any chromosome but all significant SNPs reached genome-wide level. We find KCNJ2 as an candidate gene meanwhile the SNP (BOVINEHD1900016940) on Bos taurus chromosome (BTA)19 was located in the known gene(KCNJ2), and 13Mbp away nearby the gene, which was highly associated with RBC(p= 1.93E-07). <b>3.2 Platelet traits results</b> The GWAS study for platelet contain five traits: platelet count(PLT),platelet distribution width(PDW),mean platelet volume(MPV),large platelet count ratio(LPCR),platelet distribution wide ratio(PDWR).Twenty-seven significant SNPs were detected to be associated with five platelet traits: none for PLT, five for PDW, eleven for MPV, five for LPCR, five for PDWR. The association of these 27 highly significant SNP loci with immunity, cancer occurrence, cancer suppression and health-related traits has not been clearly verified. Moreover, among these 27 significant SNPs, 10SNPs are harboured within regions of nearest known genes, these SNPs are located from 2709 to 621763 bp away from the nearest genes. But none is assigned to any chromosome. And the GWAS results are shown in Table2. Results are also visualrized via Manhattan plots and corresponding quantile-quantile plots(QQ-plots), which are shown in Figure3 and Figure4.
DOI: 10.6084/m9.figshare.8107646
title: Data used to apply the three-step strategy for predicting algae growth inhibition toxicity [1].

description: Table I lists the names of the 309 chemicals selected from the data set of 425 chemicals in Kusk et al. [2], along with the SMILES strings used to calculate their physicochemical properties (log <i>P</i>, log <i>D</i> at pH10, log <i>S</i><sub>0</sub>, and log <i>S</i><sub>w</sub>) by means of ACD/Labs [3]. Tables II, III, and IV list log (1/48h-algal EC<sub>50</sub> [mM]) values, physicochemical properties, and values used for Steps 1–3 of the three-step strategy [1]; values are from the algal toxicity data set of Kusk et al. [2].<br>Log <i>P</i>: log of octanol–water partition coefficient, calculated with ACD/Labs using Consensus LogP values. <br>Log <i>D</i> at pH 10: log of octanol–water distribution coefficient at pH 10 (log <i>D</i><sub>pH10</sub> in Tables II, III, and IV), calculated with ACD/Labs using the Consensus LogP and GALAS pKa modules.<br>Log <i>S</i><sub>0</sub>: log of intrinsic solubility (i.e., solubility of the neutral form [mol L<sup>−1</sup>]) in water at 25 °C, calculated with the GALAS algorithm in ACD/Labs.<br>Log <i>S</i><sub>w</sub>: log of solubility in pure water along with pH of the resulting solution (mol L<sup>−1</sup> with a defined pH), calculated with the GALAS algorithm in ACD/Labs.<br>Values of log (1/48h-algal EC<sub>50</sub> [mM]) were calculated by converting EC<sub>50</sub> values in milligrams per liter to the corresponding millimolar values by using the molecular weights listed in the supplemental data of ref. [2]. <br><br>[1] Furuhama A, Hasunuma K, Hayashi TI, Tatarazako N (2016) Predicting algal growth inhibition toxicity: three-step strategy using structural and physicochem-ical properties. SAR QSAR Environ Res 27:343–362.<br>[2] Kusk KO, Christensen AM, Nyholm N (2018) Algal growth inhibition test re-sults of 425 organic chemical substances. Chemosphere 204:405–412.<br>[3] ACD/Labs, version 2018 (2018). Advanced Chemistry Development, Inc., To-ronto, ON, Canada.<br><br>
DOI: 10.6084/m9.figshare.8107640.v1
title: Genome-wide association study for erythrocyte traits and platelet in Chinese Holstein cattle

description: <b>3.1 Erythrocyte traits results</b> The GWAS results is shown in Table1. And the results are also visualrized by Manhattan plots and corresponding quantile-quantile plots(QQ-plots), which are shown in Figure1 and Figure2. We performed a genome-wide association study for six traits of erythrocyte traits: red blood cell(RBC),mean corpuscular haemoglobin(MCH),mean corpuscular haemoglobin concentration(MCHC),mean corpuscular volume(MCV),haematocrit(HCT),and haemoglobin(HGB). After analysed by Farm-CPU, there are in total twenty three significant SNPs associated with erythrocyte traits: six for RBC, two for MCH, seven for MCHC, two for MCV, four for HCT and two for HGB.Three of these twenty-three SNPs fall into the regions that related with hepatoma (liver cancer), carcinoma of the rectum (colorectal cancer) and cancer, which are harboured within regions of known genes. Other two SNPs fall into regions that have been reported to harbour QTL for Alzheimer’s disease and regulating and controlling of hemameba (WBC) and phagocyte, which fall into regions of known genes. Others are located 11157 to 89626bp away from the nearest known genes. All SNPs are not assigned to any chromosome but all significant SNPs reached genome-wide level. We find KCNJ2 as an candidate gene meanwhile the SNP (BOVINEHD1900016940) on Bos taurus chromosome (BTA)19 was located in the known gene(KCNJ2), and 13Mbp away nearby the gene, which was highly associated with RBC(p= 1.93E-07). <b>3.2 Platelet traits results</b> The GWAS study for platelet contain five traits: platelet count(PLT),platelet distribution width(PDW),mean platelet volume(MPV),large platelet count ratio(LPCR),platelet distribution wide ratio(PDWR).Twenty-seven significant SNPs were detected to be associated with five platelet traits: none for PLT, five for PDW, eleven for MPV, five for LPCR, five for PDWR. The association of these 27 highly significant SNP loci with immunity, cancer occurrence, cancer suppression and health-related traits has not been clearly verified. Moreover, among these 27 significant SNPs, 10SNPs are harboured within regions of nearest known genes, these SNPs are located from 2709 to 621763 bp away from the nearest genes. But none is assigned to any chromosome. And the GWAS results are shown in Table2. Results are also visualrized via Manhattan plots and corresponding quantile-quantile plots(QQ-plots), which are shown in Figure3 and Figure4.