cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4515851.v1
title: Nicotine affects protein complex rearrangement in <i>Caenorhabditis elegans</i> cells

description: Nicotine may affect cell function by rearranging protein complexes. We aimed to determine nicotine-induced alterations of protein complexes in <i>Caenorhabditis elegans</i> (<i>C. elegans</i>) cells, thereby revealing links between nicotine exposure and protein complex modulation. We compared the proteomic alterations induced by low and high nicotine concentrations (0.01 mM and 1 mM) with the control (no nicotine) <i>in vivo</i> by using mass spectrometry (MS)-based techniques, specifically the cetyltrimethylammonium bromide (CTAB) discontinuous gel electrophoresis coupled with liquid chromatography (LC)–MS/MS and spectral counting. As a result, we identified dozens of <i>C. elegans</i> proteins that are present exclusively or in higher abundance in either nicotine-treated or untreated worms. Based on these results, we report a possible network that captures the key protein components of nicotine-induced protein complexes and speculate how the different protein modules relate to their distinct physiological roles. Using functional annotation of detected proteins, we hypothesize that the identified complexes can modulate the energy metabolism and level of oxidative stress. These proteins can also be involved in modulation of gene expression and may be crucial in Alzheimer’s disease. The findings reported in our study reveal putative intracellular interactions of many proteins with the cytoskeleton and may contribute to the understanding of the mechanisms of nicotinic acetylcholine receptor (nAChR) signaling and trafficking in cells.
DOI: 10.6084/m9.figshare.4515845.v1
title: Temporal expansion of annual crop classification layers for the CONUS using the C5 decision tree classifier

description: Crop cover maps have become widely used in a range of research applications. Multiple crop cover maps have been developed to suite particular research interests. The National Agricultural Statistics Service (NASS) Cropland Data Layers (CDL) are a series of commonly used crop cover maps for the conterminous United States (CONUS) that span from 2008 to 2013. In this investigation, we sought to contribute to the availability of consistent CONUS crop cover maps by extending temporal coverage of the NASS CDL archive back eight additional years to 2000 by creating annual NASS CDL-like crop cover maps derived from a classification tree model algorithm. We used over 11 million records to train a classification tree algorithm and develop a crop classification model (CCM). The model was used to create crop cover maps for the CONUS for years 2000–2013 at 250 m spatial resolution. The CCM and the maps for years 2008–2013 were assessed for accuracy relative to resampled NASS CDLs. The CCM performed well against a withheld test data set with a model prediction accuracy of over 90%. The assessment of the crop cover maps indicated that the model performed well spatially, placing crop cover pixels within their known domains; however, the model did show a bias towards the ‘Other’ crop cover class, which caused frequent misclassifications of pixels around the periphery of large crop cover patch clusters and of pixels that form small, sparsely dispersed crop cover patches.
DOI: 10.6084/m9.figshare.4515842.v1
title: SEBT & FPI EFA, normative data & relationship

description: Relationship between the Star Excursion Balance Test and Foot Posture Index.
DOI: 10.6084/m9.figshare.4515761
title: Dataset for: Incorporation of the time-aspect into the liability-threshold model for case-control-family data

description: Familial aggregation and the role of genetic and environmental factors can be investigated through family studies analysed using the liability-threshold model. The liability-threshold model ignores the timing of events including age of disease onset and right-censoring, which can lead to estimates that are difficult to interpret and potentially biased. We incorporate the time-aspect into the liability-threshold model for case-control-family data following the same approach that has been applied in twin setting. Thus, the data are considered as arising from a competing risks setting and inverse probability of censoring weights (IPCWs) are used to adjust for right-censoring. In the case-control-family setting, recognising the existence of competing events is highly relevant to the sampling of control probands. Due to the presence of multiple family members who may be censored at different ages, estimation of IPCWs is not as straightforward as in the twin setting but requires consideration. We propose to employ a composite likelihood conditioning on proband status that markedly simplifies adjustment for right-censoring. We assess the proposed approach using simulation studies and apply it in analysis of two Danish register-based case-control-family studies: one on cancer diagnosed in childhood and adolescence, and one on early onset breast cancer.
DOI: 10.6084/m9.figshare.4515728
title: 2016 - Research Crowdfunding v3.xlsx

description: The spreadsheet 'Crowdfunding research...' provides information on crowdfunding projects involving Australian university staff. Information is drawn from Pozible, Kickstarter, Indiegogo and Rockethub. Information covers the time period October 2011 to 21 August 2015.The spreadsheet '2016 - Research Crowdfunding v2' provides an update with information drawn from Chuffed, FundScience, GetFunding, Indiegogo, Kickstarter, Pozible, Rockethub, and Thinkable.The spreadsheet '2016 - Research Crowdfunding v3' tidies up some of the data, adds a key to explain each column heading in each sheet of the spreadsheet. It also includes Australian and New Zealand Field of Research (FoR) codes for each crowdfunding campaign.<br>
DOI: 10.6084/m9.figshare.4515752
title: Nanopore sequencing fasta files

description: Sequencing data in FASTA format using Oxford Nanopore MinION
DOI: 10.6084/m9.figshare.4515761.v1
title: Dataset for: Incorporation of the time-aspect into the liability-threshold model for case-control-family data

description: Familial aggregation and the role of genetic and environmental factors can be investigated through family studies analysed using the liability-threshold model. The liability-threshold model ignores the timing of events including age of disease onset and right-censoring, which can lead to estimates that are difficult to interpret and potentially biased. We incorporate the time-aspect into the liability-threshold model for case-control-family data following the same approach that has been applied in twin setting. Thus, the data are considered as arising from a competing risks setting and inverse probability of censoring weights (IPCWs) are used to adjust for right-censoring. In the case-control-family setting, recognising the existence of competing events is highly relevant to the sampling of control probands. Due to the presence of multiple family members who may be censored at different ages, estimation of IPCWs is not as straightforward as in the twin setting but requires consideration. We propose to employ a composite likelihood conditioning on proband status that markedly simplifies adjustment for right-censoring. We assess the proposed approach using simulation studies and apply it in analysis of two Danish register-based case-control-family studies: one on cancer diagnosed in childhood and adolescence, and one on early onset breast cancer.
DOI: 10.6084/m9.figshare.4515752.v1
title: New draft item

description: Sequencing data in FASTA format using Oxford Nanopore MinION
DOI: 10.6084/m9.figshare.4512668
title: Prokaryote metabolism activity

description: I wrote this activity to emphasize that prokaryotic organisms can carry out 6 different types of metabolisms (as presented in Freeman’s Biological Science textbook) and this contrasts to eukaryotes, which can only use 2 metabolism pathways (photoautotroph and heterotroph). For in class materials I remove the red box (upper right corner) and print slides 3-10, place them back-to-back and laminate them. The students get a key (slide 2) and a two-sided organism sheet. They are instructed to answer the questions based on the info provided. After class the slides (with the red box restored) are provided on-line as a pdf so they can use to prepare for the exam. Exam questions are taken from sheets: for example, the students may be given the picture and notes about Thaumarchaeota and asked “This organism would be considered a…. (a) prokaryote (b) eukaryote (c) fungi (d) chordate” If you have questions or improvements to this activity please email me Lori Biederman Iowa State University lbied@iastate.edu
DOI: 10.6084/m9.figshare.4515752.v2
title: Nanopore sequencing fasta files

description: Sequencing data in FASTA format using Oxford Nanopore MinION
DOI: 10.6084/m9.figshare.4509815
title: Population consequences of individual heterogeneity in life histories: Overcompensation in response to harvesting of alternative reproductive tactics

description: Data and analyses of the experiments, as well as the simulation code of the population experiment, conducted in:<br><br>Smallegange, I.M., Fernandes, R.E., and Croll, C.C. 2017. Data from: Population consequences of individual heterogeneity in life histories: overcompensation in response to harvesting of alternative reproductive tactics. <i>Oikos</i>. doi: 10.1111/oik.04130
DOI: 10.6084/m9.figshare.4509785
title: Peculiar reaction behavior of 1,3-oxathiolan-5-one toward various reagents: Molecular modeling studies and in vitro antioxidant and cytotoxicity evaluation

description: Chemical reactivity of 2-methyl-2-phenyl-1,3-oxathiolan-5-one (<b>1</b>) toward various reagents such as hydroxyaldehyde, ketone, α,β unsaturated carbonyl compounds, heterocyclic amine, hydrazine, and hydrazide to give unpredicative opened and fused heterocyclic systems was investigated. Moreover, treatment of compound <b>1</b> with bromoester to afford the respective fused system, 2-methyl-2-phenylfuro[3,2-d][1,3]oxathiol-5(6<i>H</i>)-one (<b>6</b>) was implemented. Besides, <sup>1</sup>H–<sup>1</sup>H nuclear overhauser effect spectroscopy was used for full confirmation of the compound <b>19</b>. In addition, the density functional theory modeling study outcomes were discussed and all of the new synthesized compounds were evaluated as antioxidants and cytotoxicity assay against hepatocellular carcinoma cell line.
DOI: 10.6084/m9.figshare.4509815.v1
title: Population consequences of individual heterogeneity in life histories: Overcompensation in response to harvesting of alternative reproductive tactics

description: Data and analyses of the experiments, as well as the simulation code of the population experiment, conducted in:<br><br>Smallegange, I.M., Fernandes, R.E., and Croll, C.C. 2017. Data from: Population consequences of individual heterogeneity in life histories: overcompensation in response to harvesting of alternative reproductive tactics. <i>Oikos</i>. doi: 10.1111/oik.04130
DOI: 10.6084/m9.figshare.4512668.v2
title: Prokaryote metabolism activity

description: I wrote this activity to emphasize that prokaryotic organisms can carry out 6 different types of metabolisms (as presented in Freeman’s Biological Science textbook) and this contrasts to eukaryotes, which can only use 2 metabolism pathways (photoautotroph and heterotroph). For in class materials I remove the red box (upper right corner) and print slides 3-10, place them back-to-back and laminate them. The students get a key (slide 2) and a two-sided organism sheet. They are instructed to answer the questions based on the info provided. After class the slides (with the red box restored) are provided on-line as a pdf so they can use to prepare for the exam. Exam questions are taken from sheets: for example, the students may be given the picture and notes about Thaumarchaeota and asked “This organism would be considered a…. (a) prokaryote (b) eukaryote (c) fungi (d) chordate” If you have questions or improvements to this activity please email me Lori Biederman Iowa State University lbied@iastate.edu
DOI: 10.6084/m9.figshare.4509785.v2
title: Peculiar reaction behavior of 1,3-oxathiolan-5-one toward various reagents: Molecular modeling studies and in vitro antioxidant and cytotoxicity evaluation

description: Chemical reactivity of 2-methyl-2-phenyl-1,3-oxathiolan-5-one (<b>1</b>) toward various reagents such as hydroxyaldehyde, ketone, α,β unsaturated carbonyl compounds, heterocyclic amine, hydrazine, and hydrazide to give unpredicative opened and fused heterocyclic systems was investigated. Moreover, treatment of compound <b>1</b> with bromoester to afford the respective fused system, 2-methyl-2-phenylfuro[3,2-d][1,3]oxathiol-5(6<i>H</i>)-one (<b>6</b>) was implemented. Besides, <sup>1</sup>H–<sup>1</sup>H nuclear overhauser effect spectroscopy was used for full confirmation of the compound <b>19</b>. In addition, the density functional theory modeling study outcomes were discussed and all of the new synthesized compounds were evaluated as antioxidants and cytotoxicity assay against hepatocellular carcinoma cell line.
DOI: 10.6084/m9.figshare.4509755
title: Simulated data emulating real mQTL data

description: Simulated data emulating real metabolite quantitative trait locus data. SNPs are generated under Hardy–Weinberg equilibrium (binomial distribution) using the sample minor allele frequencies and spatial correlation structure of more than 200k real SNPs. 250 metabolic outcomes are simulated with block-wise dependence from Gaussian distributions. A small proportion of SNPs is associated to the metabolic outcomes; some outcomes are under pleiotropic control.
DOI: 10.6084/m9.figshare.4509785.v1
title: Peculiar Reaction Chemical Reactivity Behavior of 1,3-Oxathiolane-5-one Towards Various Reagents: Assisted by Molecular Modeling Studies and in Vitro Antioxidant and Cytotoxicity Evaluation

description: Chemical reactivity of 2-methyl-2-phenyl-1,3-oxathiolan-5-one (<b>1</b>) towards various reagents such as hydroxyaldehyde, ketone, α-β unsaturated carbonyl compounds, heterocyclic amine, hydrazine and hydrazide to give unpredicative opened and fused heterocyclic systems were investigated. Moreover, treatment of compound <b>1</b> with bromoester <b>8</b> to afford the respective fused system, 2-methyl-2-phenylfuro[3,2-d][1,3]oxathiol-5(6<i>H</i>)-one (<b>9</b>) was implemented. Besides, <sup>1</sup>H-<sup>1</sup>H nuclear overhauser effect spectroscopy (NOESY) was used for full confirmation of compound <b>25</b>. In addition, the density functional theory (DFT) modeling studies outcomes were discussed and all of the new synthesized compounds were evaluated as antioxidant and cytotoxicity assay against Hepatocellular carcinoma (HePG-2) the cell line.
DOI: 10.6084/m9.figshare.4509752
title: Do Fish Drive Recreational Fishing License Sales?

description: Management agencies need to understand the factors that influence fishing license purchases. While traits such as gender can influence the decisions of recreational fishers, a gap remains in understanding the influence of catch-related fishing quality on these decisions. We evaluated the use of fish biomass density as a proxy for catch-related fishing quality along with non-catch-related factors (population density, gender, and ethnicity) to explain variation in 2014 resident fishing license rates across 510 origins in Ontario. License rates were higher in areas with lower population density (i.e., rural areas), in areas with higher fish biomass density, and among populations with stronger representation by ethnic majorities. From simulated scenarios, we predicted that resident license sales could increase between 14% and 25% if fish biomass density increased by 30% and 54% in northeastern and southern Ontario, respectively. However, license sales could decrease between 5% and 10% with a 30% redistribution of rural residents to a major urban area. The relationship between license rates and non-catch-related factors confirms the role of urbanization on recreational fishing participation, while catch-related factors provide support for a functional response by fishers to fish. Received April 28, 2016; accepted October 3, 2016Published online January 3, 2017
DOI: 10.6084/m9.figshare.4509755.v1
title: Simulated data emulating real mQTL data

description: Simulated data emulating real metabolite quantitative trait locus data. SNPs are generated under Hardy–Weinberg equilibrium (binomial distribution) using the sample minor allele frequencies and spatial correlation structure of more than 200k real SNPs. 250 metabolic outcomes are simulated with block-wise dependence from Gaussian distributions. A small proportion of SNPs is associated to the metabolic outcomes; some outcomes are under pleiotropic control.
DOI: 10.6084/m9.figshare.4509752.v1
title: Do Fish Drive Recreational Fishing License Sales?

description: Management agencies need to understand the factors that influence fishing license purchases. While traits such as gender can influence the decisions of recreational fishers, a gap remains in understanding the influence of catch-related fishing quality on these decisions. We evaluated the use of fish biomass density as a proxy for catch-related fishing quality along with non-catch-related factors (population density, gender, and ethnicity) to explain variation in 2014 resident fishing license rates across 510 origins in Ontario. License rates were higher in areas with lower population density (i.e., rural areas), in areas with higher fish biomass density, and among populations with stronger representation by ethnic majorities. From simulated scenarios, we predicted that resident license sales could increase between 14% and 25% if fish biomass density increased by 30% and 54% in northeastern and southern Ontario, respectively. However, license sales could decrease between 5% and 10% with a 30% redistribution of rural residents to a major urban area. The relationship between license rates and non-catch-related factors confirms the role of urbanization on recreational fishing participation, while catch-related factors provide support for a functional response by fishers to fish. Received April 28, 2016; accepted October 3, 2016Published online January 3, 2017
DOI: 10.6084/m9.figshare.4509716
title: International cooperation on biodiversity conservation when spatial structures matter

description: International cooperation on biodiversity conservation when spatial structures matter. <i>Spatial Economic Analysis</i>. This paper considers the stability of international environmental agreements (IEAs) for biodiversity conservation with an explicit spatial structure. It studies the impact of distance between countries on coalition stability. It analyses a circular spatial structure with different spatial patterns. Robust results are obtained for a wide range of cost-and-benefit parameters: stable coalitions have a maximum size of two members. The best global payoff is obtained when coalitions are composed of neighbouring countries with the smallest possible distance. A ‘remoteness effect’ is observed, i.e., some coalitions of two members are unstable when one of the signatory countries is far away from the other coalition member and from the singletons.
DOI: 10.6084/m9.figshare.4509716.v1
title: International cooperation on biodiversity conservation when spatial structures matter

description: International cooperation on biodiversity conservation when spatial structures matter. <i>Spatial Economic Analysis</i>. This paper considers the stability of international environmental agreements (IEAs) for biodiversity conservation with an explicit spatial structure. It studies the impact of distance between countries on coalition stability. It analyses a circular spatial structure with different spatial patterns. Robust results are obtained for a wide range of cost-and-benefit parameters: stable coalitions have a maximum size of two members. The best global payoff is obtained when coalitions are composed of neighbouring countries with the smallest possible distance. A ‘remoteness effect’ is observed, i.e., some coalitions of two members are unstable when one of the signatory countries is far away from the other coalition member and from the singletons.
DOI: 10.6084/m9.figshare.4509674
title: Degradation and Metabolite Profiling of Benz (a) Anthracene, Dibenz (a, h) Anthracene and Indeno [1, 2, 3-cd] Pyrene by <i>Aspergillus terricola</i>

description: Mycoremediation of low molecular weight polycyclic aromatic hydrocarbons (PAH) is well studied. This study highlights the degradation of high molecular weight PAH (HMW-PAHs): Benz (a) anthracene (BAA), Dibenz (a, h) anthracene (DBA), and Indeno pyrene (IND) by <i>Aspergillus terricola var americanus.</i> The metabolism of the HMW-PAHs by this fungus was investigated in liquid submerged culture added with 60 mg/L of each compound. Depletion of BAA, DBA, and IND was 94.80, 90.16, and 93.80%, respectively, after 10 days of culture. Fungal broth solvent extracts were analyzed for the presence of metabolites by gas chromatography mass spectrometry and the extracellular enzymes produced were also assayed. The coexistence of two metabolic pathways, cytochrome P450 monooxygenase and ligninolytic pathway were identified. A high laccase activity was observed in BAA cultures on day 4 when compared to other PAH's studied. In conclusion, <i>A. terricola</i> might be a promising fungus for bioremediation of HMW-PAH mixtures co-metabolically.
DOI: 10.6084/m9.figshare.4509629
title: Dataset for: Electron Spin Resonance Studies on Deuterated Nitroxyl Spin Probes Used in Overhauser-enhanced Magnetic Resonance Imaging

description: The Electron Spin Resonance studies were carried out for 2 mM concentration of 14N and 15N -labeled 3-carbamoyl-2,2,5,5-tetramethyl-pyrrolidine-1-oxyl, 3-carboxy-2,2,5,5-tetramethyl-pyrrolidine-1-oxyl, 3-methoxycarbonyl-2,2,5,5-tetramethyl-pyrrolidine-1-oxyl and their deuterated nitroxyl radicals using X-band Electron Spin Resonance spectrometer. The ESR Line shape analysis was carried out. The Electron Spin Resonance parameters such as, linewidth, Lorentzian component, signal intensity ratio, rotational correlation time, hyperfine coupling constant and g-factor were estimated. The deuterated nitroxyl radicals have narrow linewidth and an increase in Lorentzian component, compared with undeuterated nitroxyl radicals. The dynamic nuclear polarization (DNP) factor was observed for all nitroxyl radicals. Upon 2H labeling, about 70% and 40% increase in dynamic nuclear polarization factor were observed for 14N and 15N-labeled nitroxyl radicals respectively. The signal intensity ratio and g value indicate that the isotropic nature of the nitroxyl radicals in pure water. Therefore, the deuterated nitroxyl radicals are suitable spin probes for in vivo/in vitro electron spin resonance and Overhauser-enhanced magnetic resonance imaging modalities.
DOI: 10.6084/m9.figshare.4509674.v1
title: Degradation and Metabolite Profiling of Benz (a) Anthracene, Dibenz (a, h) Anthracene and Indeno [1, 2, 3-cd] Pyrene by <i>Aspergillus terricola</i>

description: Mycoremediation of low molecular weight polycyclic aromatic hydrocarbons (PAH) is well studied. This study highlights the degradation of high molecular weight PAH (HMW-PAHs): Benz (a) anthracene (BAA), Dibenz (a, h) anthracene (DBA), and Indeno pyrene (IND) by <i>Aspergillus terricola var americanus.</i> The metabolism of the HMW-PAHs by this fungus was investigated in liquid submerged culture added with 60 mg/L of each compound. Depletion of BAA, DBA, and IND was 94.80, 90.16, and 93.80%, respectively, after 10 days of culture. Fungal broth solvent extracts were analyzed for the presence of metabolites by gas chromatography mass spectrometry and the extracellular enzymes produced were also assayed. The coexistence of two metabolic pathways, cytochrome P450 monooxygenase and ligninolytic pathway were identified. A high laccase activity was observed in BAA cultures on day 4 when compared to other PAH's studied. In conclusion, <i>A. terricola</i> might be a promising fungus for bioremediation of HMW-PAH mixtures co-metabolically.