cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3080971
title: Quantitative genome-wide methylation analysis of high-grade non-muscle invasive bladder cancer

description: High-grade non-muscle invasive bladder cancer (HG-NMIBC) is a clinically unpredictable disease with greater risks of recurrence and progression relative to their low-intermediate-grade counterparts. The molecular events, including those affecting the epigenome, that characterize this disease entity in the context of tumor development, recurrence, and progression, are incompletely understood. We therefore interrogated genome-wide DNA methylation using HumanMethylation450 BeadChip arrays in 21 primary HG-NMIBC tumors relative to normal bladder controls. Using strict inclusion-exclusion criteria we identified 1,057 hypermethylated CpGs within gene promoter-associated CpG islands, representing 256 genes. We validated the array data by bisulphite pyrosequencing and examined 25 array-identified candidate genes in an independent cohort of 30 HG-NMIBC and 18 low-intermediate-grade NMIBC. These analyses revealed significantly higher methylation <i>frequencies</i> in high-grade tumors relative to low-intermediate-grade tumors for the <i>ATP5G2, IRX1</i> and <i>VAX2</i> genes (<i>P</i>&lt;0.05), and similarly significant increases in <i>mean levels</i> of methylation in high-grade tumors for the <i>ATP5G2, VAX2, INSRR, PRDM14, VSX1, TFAP2b, PRRX1</i>, and <i>HIST1H4F</i> genes (<i>P</i>&lt;0.05). Although inappropriate promoter methylation was not invariantly associated with reduced transcript expression, a significant association was apparent for the <i>ARHGEF4, PON3, STAT5a</i>, and <i>VAX2</i> gene transcripts (<i>P</i>&lt;0.05). Herein, we present the first genome-wide DNA methylation analysis in a unique HG-NMIBC cohort, showing extensive and discrete methylation changes relative to normal bladder and low-intermediate-grade tumors. The genes we identified hold significant potential as targets for novel therapeutic intervention either alone, or in combination, with more conventional therapeutic options in the treatment of this clinically unpredictable disease.
DOI: 10.6084/m9.figshare.3080980.v2
title: Graphite Nanosheet as Low Shrinkage Additive, Curing Accelerator, and Conducting Filler for Unsaturated Polyester Resin

description: The effect of graphite nanosheets on electrical properties, curing behavior, and polymerization shrinkage of unsaturated polyester resin has been investigated. A solution of polystyrene was used as low profile additive to reduce shrinkage. The results showed that graphite nanosheets have been well dispersed/distributed in the unsaturated polyester matrix where they have high aspect ratio and high surface area. Graphite nanosheet exhibited an accelerating effect on the curing of unsaturated polyester and reduced the polymerization shrinkage as low as 3.6%. Despite large reduction of flexural properties by low profile additive, graphite nanosheet considerably increased the flexural strength and modulus of unsaturated polyester/low profile additive by 47 and 103%, respectively. Therefore, graphite nanosheet can be used as a new low profile additive for unsaturated polyester resins where it is also able to improve mechanical properties and curing rate.
DOI: 10.6084/m9.figshare.3080971.v1
title: Quantitative genome-wide methylation analysis of high-grade non-muscle invasive bladder cancer

description: High-grade non-muscle invasive bladder cancer (HG-NMIBC) is a clinically unpredictable disease with greater risks of recurrence and progression relative to their low-intermediate-grade counterparts. The molecular events, including those affecting the epigenome, that characterize this disease entity in the context of tumor development, recurrence, and progression, are incompletely understood. We therefore interrogated genome-wide DNA methylation using HumanMethylation450 BeadChip arrays in 21 primary HG-NMIBC tumors relative to normal bladder controls. Using strict inclusion-exclusion criteria we identified 1,057 hypermethylated CpGs within gene promoter-associated CpG islands, representing 256 genes. We validated the array data by bisulphite pyrosequencing and examined 25 array-identified candidate genes in an independent cohort of 30 HG-NMIBC and 18 low-intermediate-grade NMIBC. These analyses revealed significantly higher methylation <i>frequencies</i> in high-grade tumors relative to low-intermediate-grade tumors for the <i>ATP5G2, IRX1</i> and <i>VAX2</i> genes (<i>P</i>&lt;0.05), and similarly significant increases in <i>mean levels</i> of methylation in high-grade tumors for the <i>ATP5G2, VAX2, INSRR, PRDM14, VSX1, TFAP2b, PRRX1</i>, and <i>HIST1H4F</i> genes (<i>P</i>&lt;0.05). Although inappropriate promoter methylation was not invariantly associated with reduced transcript expression, a significant association was apparent for the <i>ARHGEF4, PON3, STAT5a</i>, and <i>VAX2</i> gene transcripts (<i>P</i>&lt;0.05). Herein, we present the first genome-wide DNA methylation analysis in a unique HG-NMIBC cohort, showing extensive and discrete methylation changes relative to normal bladder and low-intermediate-grade tumors. The genes we identified hold significant potential as targets for novel therapeutic intervention either alone, or in combination, with more conventional therapeutic options in the treatment of this clinically unpredictable disease.
DOI: 10.6084/m9.figshare.3080974.v2
title: Synthesis, Characterization and Adsorptive Properties of Quaternized 2-Dimethylaminoethyl Methacrylate Based Polymer–Clay Nanocomposites

description: [2-(Methacryloyloxy)ethyl]dimethylhexadecylammonium bromide (QDMA) was synthesized by means of quaternization of 2-dimethylaminoethyl methacrylate. Poly(QDMA) and poly(QDMA)-bentonite nanocomposites containing different amount of bentonite were prepared by in situ suspension polymerization and characterized. Adsorption behaviors of these materials towards acid orange 8 and <i>p</i>-nitrophenol were investigated with respect to solution pH. For both adsorbate, adsorption capacities of some nanocomposites were found to be higher than those of bentonite and poly(QDMA). Effects of various parameters such as contact time, initial adsorbate concentration, and temperature on the adsorption of acid orange 8 and <i>p</i>-nitrophenol onto NC3 from aqueous solutions were also evaluated.
DOI: 10.6084/m9.figshare.3080980.v1
title: Graphite Nanosheet as Low Shrinkage Additive, Curing Accelerator and Conducting Filler for Unsaturated Polyester Resin

description: The effect of graphite nanosheets (GNSs) on electrical properties, curing behavior and polymerization shrinkage of unsaturated polyester (UP) resin has been investigated. A solution of polystyrene was used as low profile additive (LPA) to reduce shrinkage. The results showed that GNSs have been well dispersed/distributed in the UP matrix where they have high aspect ratio and high surface area. GNS exhibited an accelerating effect on the curing of UP and reduced the polymerization shrinkage as low as 3.6%. Despite large reduction of flexural properties by LPA, GNS considerably increased the flexural strength and modulus of UP/LPA by 47% and 103%, respectively. Therefore GNS can be used as a new LPA for UP resins where it is also able to improve mechanical properties and curing rate.
DOI: 10.6084/m9.figshare.3080974.v1
title: Synthesis, Characterization and Adsorptive Properties of Quaternized 2-Dimethylaminoethyl Methacrylate Based Polymer-Clay Nanocomposites

description: [2-(methacryloyloxy)ethyl]dimethylhexadecylammonium bromide (QDMA) was synthesized by means of quaternization of 2-dimethylaminoethyl methacrylate. Poly(QDMA) and poly(QDMA)-bentonite nanocomposites containing different amount of bentonite were prepared by in situ suspension polymerization and characterized. Adsorption behaviors of these materials towards Acid Orange 8 (AO8) and <i>p</i>-nitrophenol (pNP) were investigated with respect to solution pH. For both adsorbate, adsorption capacities of some nanocomposites were found to be higher than those of bentonite and poly(QDMA). Effects of various parameters such as contact time, initial adsorbate concentration, and temperature on the adsorption of AO8 and pNP onto NC3 from aqueous solutions were also evaluated.
DOI: 10.6084/m9.figshare.3080917
title: A combination of ellagic acid and tetracycline inhibits biofilm formation and the associated virulence of <i>Propionibacterium acnes in vitro</i> and <i>in vivo</i>

description: <i>Propionibacterium acnes</i> is an opportunistic pathogen which has become notorious owing to its ability to form a recalcitrant biofilm and to develop drug resistance. The current study aimed to develop anti-biofilm treatments against clinical isolates of <i>P. acnes</i> under <i>in vitro</i> and <i>in vivo</i> conditions. A combination of ellagic acid and tetracycline (ETC; 250 μg ml<sup>−1</sup> + 0.312 μg ml<sup>−1</sup>) was determined to effectively inhibit biofilm formation by <i>P. acnes</i> (80–91%) without affecting its growth, therefore potentially limiting the possibility of the bacterium attaining resistance. In addition, ETC reduced the production of extracellular polymeric substances (EPS) (20–26%), thereby making <i>P. acnes</i> more susceptible to the human immune system and antibiotics. The anti-biofilm potential of ETC was further substantiated under <i>in vivo</i> conditions using <i>Caenorhabditis elegans</i>. This study reports a novel anti-biofilm combination that could be developed as an ideal therapeutic agent with broad cosmeceutical and pharmaceutical applicability in the era of antibiotic resistance.
DOI: 10.6084/m9.figshare.3080917.v1
title: A combination of ellagic acid and tetracycline inhibits biofilm formation and the associated virulence of <i>Propionibacterium acnes in vitro</i> and <i>in vivo</i>

description: <i>Propionibacterium acnes</i> is an opportunistic pathogen which has become notorious owing to its ability to form a recalcitrant biofilm and to develop drug resistance. The current study aimed to develop anti-biofilm treatments against clinical isolates of <i>P. acnes</i> under <i>in vitro</i> and <i>in vivo</i> conditions. A combination of ellagic acid and tetracycline (ETC; 250 μg ml<sup>−1</sup> + 0.312 μg ml<sup>−1</sup>) was determined to effectively inhibit biofilm formation by <i>P. acnes</i> (80–91%) without affecting its growth, therefore potentially limiting the possibility of the bacterium attaining resistance. In addition, ETC reduced the production of extracellular polymeric substances (EPS) (20–26%), thereby making <i>P. acnes</i> more susceptible to the human immune system and antibiotics. The anti-biofilm potential of ETC was further substantiated under <i>in vivo</i> conditions using <i>Caenorhabditis elegans</i>. This study reports a novel anti-biofilm combination that could be developed as an ideal therapeutic agent with broad cosmeceutical and pharmaceutical applicability in the era of antibiotic resistance.
DOI: 10.6084/m9.figshare.3080911
title: Exploiting the antivirulence efficacy of an ajoene-ciprofloxacin combination against <i>Pseudomonas aeruginosa</i> biofilm associated murine acute pyelonephritis

description: The study investigated the <i>in vitro</i>, <i>ex vivo</i> and <i>in vivo</i> efficacy of ajoene and ciprofloxacin (CIP) alone and in combination against <i>Pseudomonas aeruginosa</i> biofilms and biofilm-associated murine acute pyelonephritis. The ajoene–CIP combination exhibited significant greater (<i>p</i> &lt; 0.05) antimotility and biofilm inhibitory effects than those obtained when they were applied individually. The combined action of the agents resulted in a significant increase in serum sensitivity and phagocytic uptake and killing of <i>P. aeruginosa</i> (<i>p</i> &lt; 0.001) compared to the untreated control. Mice groups treated with an ajoene (25 mg kg<sup>−1</sup>) and CIP (30 mg kg<sup>−1</sup> or 15 mg kg<sup>−1</sup>) combination showed a significantly (<i>p</i> &lt; 0.001) reduced bacterial load in the kidney and bladder as compared to that of infected controls and mice treated with solo agents on the fifth day post-infection. The decreased levels of biomarkers and photomicrographs of the kidney tissue of the treated mice showed a reduced severity of damage. Hence, the study highlights the antivirulent and therapeutic efficacy of the ajoene-CIP combination at the minimal dosage of CIP.
DOI: 10.6084/m9.figshare.3080911.v1
title: Exploiting the antivirulence efficacy of an ajoene-ciprofloxacin combination against <i>Pseudomonas aeruginosa</i> biofilm associated murine acute pyelonephritis

description: The study investigated the <i>in vitro</i>, <i>ex vivo</i> and <i>in vivo</i> efficacy of ajoene and ciprofloxacin (CIP) alone and in combination against <i>Pseudomonas aeruginosa</i> biofilms and biofilm-associated murine acute pyelonephritis. The ajoene–CIP combination exhibited significant greater (<i>p</i> &lt; 0.05) antimotility and biofilm inhibitory effects than those obtained when they were applied individually. The combined action of the agents resulted in a significant increase in serum sensitivity and phagocytic uptake and killing of <i>P. aeruginosa</i> (<i>p</i> &lt; 0.001) compared to the untreated control. Mice groups treated with an ajoene (25 mg kg<sup>−1</sup>) and CIP (30 mg kg<sup>−1</sup> or 15 mg kg<sup>−1</sup>) combination showed a significantly (<i>p</i> &lt; 0.001) reduced bacterial load in the kidney and bladder as compared to that of infected controls and mice treated with solo agents on the fifth day post-infection. The decreased levels of biomarkers and photomicrographs of the kidney tissue of the treated mice showed a reduced severity of damage. Hence, the study highlights the antivirulent and therapeutic efficacy of the ajoene-CIP combination at the minimal dosage of CIP.
DOI: 10.6084/m9.figshare.3080893
title: A “bag-of-arguments” mechanism for initial verb predictions

description: Previous studies have shown that comprehenders use rich contextual information to anticipate upcoming input on the fly, but less is known about how comprehenders integrate different sources of information to generate predictions in real time. The current study examines the time course with which the lexical meaning and structural roles of preverbal arguments impact comprehenders’ lexical semantic predictions about an upcoming verb in two event-related potential (ERP) experiments that use the N400 amplitude as a measure of online predictability. Experiment 1 showed that the N400 was sensitive to predictability when the verb's cloze probability was reduced by substituting one of the arguments (e.g. “The superintendent overheard which tenant/realtor the landlord had evicted … ”), but not when the verb's cloze probability was reduced by simply swapping the roles of the arguments (e.g. “The restaurant owner forgot which customer/waitress the waitress/customer had served … ”). Experiment 2 showed that argument substitution elicited an N400 effect even when the substituted argument appeared elsewhere in the sentence, indicating that verb predictions are specifically driven by the arguments in the same clause as the verb, rather than by a simple “bag-of-words” mechanism. We propose that verb predictions initially rely on a “bag-of-arguments” mechanism, which specifically relies on the lexical meaning, but not the structural roles, of the arguments in a clause.
DOI: 10.6084/m9.figshare.3080893.v1
title: A “bag-of-arguments” mechanism for initial verb predictions

description: Previous studies have shown that comprehenders use rich contextual information to anticipate upcoming input on the fly, but less is known about how comprehenders integrate different sources of information to generate predictions in real time. The current study examines the time course with which the lexical meaning and structural roles of preverbal arguments impact comprehenders’ lexical semantic predictions about an upcoming verb in two event-related potential (ERP) experiments that use the N400 amplitude as a measure of online predictability. Experiment 1 showed that the N400 was sensitive to predictability when the verb's cloze probability was reduced by substituting one of the arguments (e.g. “The superintendent overheard which tenant/realtor the landlord had evicted … ”), but not when the verb's cloze probability was reduced by simply swapping the roles of the arguments (e.g. “The restaurant owner forgot which customer/waitress the waitress/customer had served … ”). Experiment 2 showed that argument substitution elicited an N400 effect even when the substituted argument appeared elsewhere in the sentence, indicating that verb predictions are specifically driven by the arguments in the same clause as the verb, rather than by a simple “bag-of-words” mechanism. We propose that verb predictions initially rely on a “bag-of-arguments” mechanism, which specifically relies on the lexical meaning, but not the structural roles, of the arguments in a clause.
DOI: 10.6084/m9.figshare.3080725
title: SuppFile1.tar.gz

description: This tar.gz contains the scripts and .xyz point clouds from Schultz et al. In Press. The genetic basis of baculum size and shape variation in mice. G3: Genes, Genomes, Genetics.
DOI: 10.6084/m9.figshare.3080725.v1
title: SuppFile1.tar.gz

description: This tar.gz contains the scripts and .xyz point clouds from Schultz et al. In Press. The genetic basis of baculum size and shape variation in mice. G3: Genes, Genomes, Genetics.
DOI: 10.6084/m9.figshare.3080608
title: Raw data for Kalathur et al., 2015 ‘The unfolded protein response and its potential role in Huntington ́s disease elucidated by a systems biology approach’

description: Data file 1. Legend: Lists of upregulated genes in 6 murine and 1 human (first sheet), and in at least 4 murine and 1 human HD model (second sheet).Data file 2. Lists of downregulated genes in 5 datasets (first sheet) and in at least 4 datasets (second sheet).Data file 3. Lists of upregulated UPR genes with stress response elements in the promoter regions (-1000bp to +500bp). Results for highly stringent gene list (UPR genes uprgulated in 6 murine and 1 human HD model) are show on sheet 1; results for less stringent gene list (upregulated in at least 4 murine and 1 human HD model) are displayed on sheet 2.Data file 4. List of all the biological processes that are enriched amongin differentially regulated UPR genes. Results for UPR gene list of high stringency are show on sheet 1; results for gene list of lower stringency are displayed on sheet 2.Data file 5. List of all the pathways that are enriched among upregulated UPR genes. Results for UPR gene list of high stringency are show on sheet 1; results for gene list of lower stringency are displayed on sheet 2.Data file 6. List of components of UPR interactome shown in Figure 6Data file 7. List of genes common between UPR and ApoptosisData file 8. List of proteins that interact with HTT directly or indirectly.Data file 9. List of 53 proteins that were found in the intersection of HTT interactors, HDTT and differentially regulated UPR genes (of lower stringeny). It includes the 13 proteins from table 3 that were identified using the high stringency list of differentially regulated UPR genes. Spearman correlation coefficients and the corresponding estimated fdr for correlation or anti correlation, respectively, describe the observed correlation of gene expression and the length of polyglutamine tract in HD mice.
DOI: 10.6084/m9.figshare.3080608.v1
title: Raw data for Kalathur et al., 2015 ‘The unfolded protein response and its potential role in Huntington ́s disease elucidated by a systems biology approach’

description: Data file 1. Legend: Lists of upregulated genes in 6 murine and 1 human (first sheet), and in at least 4 murine and 1 human HD model (second sheet).Data file 2. Lists of downregulated genes in 5 datasets (first sheet) and in at least 4 datasets (second sheet).Data file 3. Lists of upregulated UPR genes with stress response elements in the promoter regions (-1000bp to +500bp). Results for highly stringent gene list (UPR genes uprgulated in 6 murine and 1 human HD model) are show on sheet 1; results for less stringent gene list (upregulated in at least 4 murine and 1 human HD model) are displayed on sheet 2.Data file 4. List of all the biological processes that are enriched amongin differentially regulated UPR genes. Results for UPR gene list of high stringency are show on sheet 1; results for gene list of lower stringency are displayed on sheet 2.Data file 5. List of all the pathways that are enriched among upregulated UPR genes. Results for UPR gene list of high stringency are show on sheet 1; results for gene list of lower stringency are displayed on sheet 2.Data file 6. List of components of UPR interactome shown in Figure 6Data file 7. List of genes common between UPR and ApoptosisData file 8. List of proteins that interact with HTT directly or indirectly.Data file 9. List of 53 proteins that were found in the intersection of HTT interactors, HDTT and differentially regulated UPR genes (of lower stringeny). It includes the 13 proteins from table 3 that were identified using the high stringency list of differentially regulated UPR genes. Spearman correlation coefficients and the corresponding estimated fdr for correlation or anti correlation, respectively, describe the observed correlation of gene expression and the length of polyglutamine tract in HD mice.
DOI: 10.6084/m9.figshare.3080602
title: minimal anonymized dataset for the study findings.rar

description: We uploaded the echo data, the survival rate data and the data of relationship between temperature and circumferential strain for PONE-D-15-49846R1
DOI: 10.6084/m9.figshare.3080602.v1
title: minimal anonymized dataset for the study findings.rar

description: We uploaded the echo data, the survival rate data and the data of relationship between temperature and circumferential strain for PONE-D-15-49846R1
DOI: 10.6084/m9.figshare.3079966
title: DFT study of the oxidation of primary alcohols by TEMPO+ cation in presence of NaCO3- buffer: deprotonation/cyclic intermediate pathway

description: Data to support article: Hydrodynamic Rocking Disc Electrode Study of EC’-Type TEMPO-Mediated Primary Alcohol Oxidations <br> DOI: 10.6084/m9.figshare.3079966 Journal: Electroanalysis<br> Authors: Sunyhik D. Ahn <sup>a</sup>, Adrian C. Fisher <sup>b</sup>, Antoine Buchard <sup>a</sup>, <br> Steven D. Bull <sup>a</sup>, Alan M. Bond <sup>c</sup>, and Frank Marken*<sup>a</sup><sup><br></sup> <sup> </sup><i><sup>a</sup> Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK</i> <i><sup>b</sup> Department of Chemical Engineering, University of Cambridge, New Museums Site, Pembroke Street, Cambridge, CB2 3RA, UK</i> <i><sup>c</sup> Monash University, School of Chemistry, Clayton, Vic 3800, Australia</i> DFT study: - The DFT optimised geometries and computed free enthalpies of various primary alcohols and aldehydes was used to calculate the thermodynamics of the oxidation reaction of various primary alcohols in presence of TEMPO+ cation and NaCO3- anion.- The thermodynamics of formation of a cyclic intermediate formed by attack of an alkoxide on the nitrogen of the TEMPO<sup>+</sup> cation was also calculated. - Transition states for the deprotonation step as well as the hydride transfer from the cyclic intermediate were also calculated and used to calculate the related activation barriers for each alcohols.<br> Protocol: rB3LYP/6-311+G(d,p)/cpcm=water/T=298.15K Content: - Gaussian09 rev A.02 output files <br>
DOI: 10.6084/m9.figshare.3079975
title: Contribution Ontology sub graph

description: Credit Subgraph derived from https://github.com/openrif/contribution-ontology. Purpose: a cutdown set of triples to assist with credit data entry scenarios. Additional metadata is provided for illustration purposes