cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3486749
title: Mojave National Preserve 2013 insect diversity data.csv

description: The primary data for this publication: Ruttan, A., Filazzola, A. and Lortie, C. J. (2016) Shrub-annual facilitation complexes mediate insect community structure in arid environments. Journal of Arid Environments 134: 1-9.http://www.sciencedirect.com/science/article/pii/S0140196316301100<br> Insect samples were collected at Kelso dunes over a nine-day period between April 24th and May 2nd, 2013. Insects were sampled daily using pan traps (approximately 18 cm in diameter) set at ground-level along an east-west axis parallel to Kelso Dunes. Thirty pairs of pan traps were set along two parallel 45 m transects (transects were 10 m apart) with alternating blue, yellow, and white traps approximately every 3 m using the NSERC-CANPOLIN protocol (http://www.uoguelph.ca/canpolin). Pan traps were paired so that each replicate had one pan trap under the southern portion of a L. tridentata canopy, halfway between the base of the shrub and the drip-line, and within a patch of annual plants. The other pan traps were deployed 2 m south of each paired shrub in an adjacent open microsite, also with annual plants present (see Appendix A; Fig. A2). Open microsites were located two metres from the drip-line of shrubs because this was on average the maximum distance possible without being within a two metre radius of another shrub (Ruttan pers. obs). Pan traps were half-filled with a solution of soapy water prepared by mixing five drops of unscented dish detergent per litre of water (for protocol, see: http://www.uoguelph.ca/canpolin). Pan traps were set out by 9:00 a.m. and collected at 5:00 p.m. daily targeting typical peak insect activity (http://www.uoguelph.ca/canpolin). All samples were collected on sunny days with no precipitation. Samples were collected from each pan trap replicate and stored in vials of 70% ethanol. Insects were then sorted from samples and identified to the family level for ease of identification using Goulet and Huber (1993) and Borror et al. (1989). <br>
DOI: 10.6084/m9.figshare.3486737
title: Peach SNP database

description: The SNP dataset of Nature Communications paper "Genome-wide association study of 12 agronomic traits in peach"
DOI: 10.17608/k6.auckland.3486728
title: ISSP2015: Work Orientations IV

description: The second International Social Survey Programme (ISSP) survey by COMPASS Research Centre at the University of Auckland, with funding support from its Business School, and also the New Zealand European Union Centres Network, via colleagues at UoA and also Victoria University of Wellington.<br>We were short on resources to run the survey in 2014, so this one included the 2014 ISSP module on Citizenship.A verbose rundown on topics covered follows.Attitudes towards work; importance of different things in a job; balancing work and family life; discrimination; opinions on trade unions; current employment status. Current financial situation plus changes over time; attitudes towards retirement age. Employed: preference for full- or part-time employment; preference for more work (and money) or for reduction in working hours; opinions about own job plus presence of "heavy" tasks; freedom in work hours; use of past experience; job satisfaction and pride; chances of looking for another job in the next 12 months; multiple jobs.Unemployed: ever had a paid job - if so satisfaction in it plus why it ended; desire to have a paid job plus worry about it; willingness to take steps to find a job; advertising oneself; economic support.Demography: sex; age; marital-status; education; current employment status; hours worked weekly; occupation; working for private or public sector or self-employed; if self-employed: number of employees; supervisor function; trade union membership; current employment status; earnings; family income; household size; religious denomination; attendance of religious services; size of community; type of community: urban-rural area; ethnicity.Sampling: We took a random sample of 2,500 from the New Zealand Electoral Rolls, ensuring first that they all had New Zealand mailing addresses. They were all sent a questionnaire, identified by a barcode, and then three weeks later, those that had not responded were sent a reminder postcard - this was why the questionnaires were identified, so as not to annoy more people than necessary. Finally, after another three weeks, those that still had not responded were sent a second copy of the questionnaire. Ultimately we completed a data set of 901 respondents, a basic response rate of 36%.Universe: People on the New Zealand Electoral Rolls, 18 years old or more, and at least a New Zealand Permanent Resident.Weighting: A weighting variable is provided, to make the respondent population representative of the original random sample.<br>
DOI: 10.17608/k6.auckland.3486728.v1
title: ISSP2015: Work Orientations IV

description: The second ISSP survey administered by COMPASS Research Centre at the University of Auckland, with funding support from its Business School, and also the New Zealand European Union Centres Network, via colleagues at UoA and also Victoria University of Wellington.We were short on resources to run the survey in 2014, so this one included the 2014 ISSP module on Citizenship.A verbose rundown on topics covered follows.Work Orientations<br>Attitudes towards work; importance of different things in a job; balancing work and family life; discrimination; opinions on trade unions; current employment status.Current financial situation plus changes over time; attitudes towards retirement age.Employed<br>Preference for full- or part-time employment; preference for more work (and money) or for reduction in working hours; opinions about own job plus presence of "heavy" tasks; freedom in work hours; use of past experience; job satisfaction and pride; chances of looking for another job in the next 12 months; multiple jobs.Unemployed<br>Ever had a paid job - if so satisfaction in it plus why it ended; desire to have a paid job plus worry about it; willingness to take steps to find a job; advertising oneself; economic support.Demography<br>Sex; age; marital-status; education; current employment status; hours worked weekly; occupation; working for private or public sector or self-employed; if self-employed: number of employees; supervisor function; trade union membership; current employment status; earnings; family income; household size; religious denomination; attendance of religious services; size of community; type of community: urban-rural area; ethnicity.<br>
DOI: 10.17608/k6.auckland.3486728.v2
title: ISSP2015: Work Orientations IV

description: The second ISSP survey administered by COMPASS Research Centre at the University of Auckland, with funding support from its Business School, and also the New Zealand European Union Centres Network, via colleagues at UoA and also Victoria University of Wellington.We were short on resources to run the survey in 2014, so this one included the 2014 ISSP module on Citizenship.A verbose rundown on topics covered follows.Work Orientations<br>Attitudes towards work; importance of different things in a job; balancing work and family life; discrimination; opinions on trade unions; current employment status.Current financial situation plus changes over time; attitudes towards retirement age.Employed<br>Preference for full- or part-time employment; preference for more work (and money) or for reduction in working hours; opinions about own job plus presence of "heavy" tasks; freedom in work hours; use of past experience; job satisfaction and pride; chances of looking for another job in the next 12 months; multiple jobs.Unemployed<br>Ever had a paid job - if so satisfaction in it plus why it ended; desire to have a paid job plus worry about it; willingness to take steps to find a job; advertising oneself; economic support.Demography<br>Sex; age; marital-status; education; current employment status; hours worked weekly; occupation; working for private or public sector or self-employed; if self-employed: number of employees; supervisor function; trade union membership; current employment status; earnings; family income; household size; religious denomination; attendance of religious services; size of community; type of community: urban-rural area; ethnicity.<br>
DOI: 10.17608/k6.auckland.3486728.v3
title: ISSP2015: Work Orientations IV

description: The second International Social Survey Programme (ISSP) survey by COMPASS Research Centre at the University of Auckland, with funding support from its Business School, and also the New Zealand European Union Centres Network, via colleagues at UoA and also Victoria University of Wellington.We were short on resources to run the survey in 2014, so this one included the 2014 ISSP module on Citizenship.A verbose rundown on topics covered follows.Work Orientations<br>Attitudes towards work; importance of different things in a job; balancing work and family life; discrimination; opinions on trade unions; current employment status.Current financial situation plus changes over time; attitudes towards retirement age.Employed<br>Preference for full- or part-time employment; preference for more work (and money) or for reduction in working hours; opinions about own job plus presence of "heavy" tasks; freedom in work hours; use of past experience; job satisfaction and pride; chances of looking for another job in the next 12 months; multiple jobs.Unemployed<br>Ever had a paid job - if so satisfaction in it plus why it ended; desire to have a paid job plus worry about it; willingness to take steps to find a job; advertising oneself; economic support.Demography<br>Sex; age; marital-status; education; current employment status; hours worked weekly; occupation; working for private or public sector or self-employed; if self-employed: number of employees; supervisor function; trade union membership; current employment status; earnings; family income; household size; religious denomination; attendance of religious services; size of community; type of community: urban-rural area; ethnicity.<br>
DOI: 10.17608/k6.auckland.3486728.v5
title: ISSP2015: Work Orientations IV

description: The second International Social Survey Programme (ISSP) survey by COMPASS Research Centre at the University of Auckland, with funding support from its Business School, and also the New Zealand European Union Centres Network, via colleagues at UoA and also Victoria University of Wellington.<br>We were short on resources to run the survey in 2014, so this one included the 2014 ISSP module on Citizenship.A verbose rundown on topics covered follows.Attitudes towards work; importance of different things in a job; balancing work and family life; discrimination; opinions on trade unions; current employment status. Current financial situation plus changes over time; attitudes towards retirement age. Employed: preference for full- or part-time employment; preference for more work (and money) or for reduction in working hours; opinions about own job plus presence of "heavy" tasks; freedom in work hours; use of past experience; job satisfaction and pride; chances of looking for another job in the next 12 months; multiple jobs.Unemployed: ever had a paid job - if so satisfaction in it plus why it ended; desire to have a paid job plus worry about it; willingness to take steps to find a job; advertising oneself; economic support.Demography: sex; age; marital-status; education; current employment status; hours worked weekly; occupation; working for private or public sector or self-employed; if self-employed: number of employees; supervisor function; trade union membership; current employment status; earnings; family income; household size; religious denomination; attendance of religious services; size of community; type of community: urban-rural area; ethnicity.Sampling: We took a random sample of 2,500 from the New Zealand Electoral Rolls, ensuring first that they all had New Zealand mailing addresses. They were all sent a questionnaire, identified by a barcode, and then three weeks later, those that had not responded were sent a reminder postcard - this was why the questionnaires were identified, so as not to annoy more people than necessary. Finally, after another three weeks, those that still had not responded were sent a second copy of the questionnaire. Ultimately we completed a data set of 901 respondents, a basic response rate of 36%.Universe: People on the New Zealand Electoral Rolls, 18 years old or more, and at least a New Zealand Permanent Resident.Weighting: A weighting variable is provided, to make the respondent population representative of the original random sample.<br>
DOI: 10.17608/k6.auckland.3486728.v4
title: ISSP2015: Work Orientations IV

description: The second International Social Survey Programme (ISSP) survey by COMPASS Research Centre at the University of Auckland, with funding support from its Business School, and also the New Zealand European Union Centres Network, via colleagues at UoA and also Victoria University of Wellington.<br>The ISSP is a continuing annual programme of cross-national collaboration on surveys covering topics important for social science research. It brings together pre-existing social science projects and coordinates research goals, thereby adding a cross-national, cross-cultural perspective to the individual national studies. ISSP researchers especially concentrate on developing questions that are meaningful and relevant to all countries, and can be expressed in an equivalent manner in all relevant languages.<br><br>We were short on resources to run the survey in 2014, so this one included the 2014 ISSP module on Citizenship.A verbose rundown on topics covered follows.<br>Work Orientations<br>Attitudes towards work; importance of different things in a job; balancing work and family life; discrimination; opinions on trade unions; current employment status. Current financial situation plus changes over time; attitudes towards retirement age. Employed: preference for full- or part-time employment; preference for more work (and money) or for reduction in working hours; opinions about own job plus presence of "heavy" tasks; freedom in work hours; use of past experience; job satisfaction and pride; chances of looking for another job in the next 12 months; multiple jobs.Unemployed: ever had a paid job - if so satisfaction in it plus why it ended; desire to have a paid job plus worry about it; willingness to take steps to find a job; advertising oneself; economic support.<br>Demography: sex; age; marital-status; education; current employment status; hours worked weekly; occupation; working for private or public sector or self-employed; if self-employed: number of employees; supervisor function; trade union membership; current employment status; earnings; family income; household size; religious denomination; attendance of religious services; size of community; type of community: urban-rural area; ethnicity.<br>Sampling: We took a random sample of 2,500 from the New Zealand Electoral Rolls, ensuring first that they all had New Zealand mailing addresses. They were all sent a questionnaire, identified by a barcode, and then three weeks later, those that had not responded were sent a reminder postcard - this was why the questionnaires were identified, so as not to annoy more people than necessary. Finally, after another three weeks, those that still had not responded were sent a second copy of the questionnaire. Ultimately we completed a data set of 901 respondents, a basic response rate of 36%.<br>Universe: People on the New Zealand Electoral Rolls, 18 years old or more, and at least a New Zealand Permanent Resident.<br>Weighting:A weighting variable is provided, to make the respondent population representative of the original random sample.<br>
DOI: 10.6084/m9.figshare.3486581
title: Exploring an animal model of amodiaquine-induced liver injury in rats and mice

description: Amodiaquine (AQ) is associated with a relatively high incidence of idiosyncratic drug-induced liver injury (IDILI) and agranulocytosis. A previous study reported that a combination of high dose AQ and glutathione (GSH) depletion led to liver injury. However, the characteristics of this toxicity were very different from AQ-induced liver injury in humans. We developed a model of AQ-induced liver injury with characteristics similar to the injury in humans by treating mice with lower doses of AQ for several weeks. In this study we found that not only did GSH depletion not increase AQ covalent binding to hepatic proteins at this lower dose, but also it paradoxically prevented the liver injury. We extended the model to rats and found AQ treatment led to a mild delayed onset liver injury that resolved despite continued treatment with AQ. Immunohistochemistry indicated the presence of Kupffer cell activation, apoptosis and hepatocyte proliferation in the liver. There was also an increase in serum IL-2, IL-5, IL-9, IL-12, MCP-1 and TGFβ, but a decrease in leptin. Coincident with the elevated serum ALT, the number of liver CD4<sup>+</sup> T-cells, IL-17 secreting cells and T<sub>H</sub>17/T<sub>reg</sub> cells increased at Week 3 and decreased during continued treatment. Increases in NK1.1+ cells and activated M2 macrophages were also observed during liver injury. These results suggest that the outcome of the liver injury was determined by the balance between effector and regulatory cells. Co-treatment with cyclosporin prevented AQ-induced liver injury, which supports an immune mechanism. Retinoic acid (RA), which has been reported to enhance natural killer (NK) cell activity, exacerbated AQ-induced liver injury. These results suggest that AQ-induced IDILI is immune mediated and the subsequent adaptation appears to represent immune tolerance.
DOI: 10.6084/m9.figshare.3486581.v1
title: Exploring an animal model of amodiaquine-induced liver injury in rats and mice

description: Amodiaquine (AQ) is associated with a relatively high incidence of idiosyncratic drug-induced liver injury (IDILI) and agranulocytosis. A previous study reported that a combination of high dose AQ and glutathione (GSH) depletion led to liver injury. However, the characteristics of this toxicity were very different from AQ-induced liver injury in humans. We developed a model of AQ-induced liver injury with characteristics similar to the injury in humans by treating mice with lower doses of AQ for several weeks. In this study we found that not only did GSH depletion not increase AQ covalent binding to hepatic proteins at this lower dose, but also it paradoxically prevented the liver injury. We extended the model to rats and found AQ treatment led to a mild delayed onset liver injury that resolved despite continued treatment with AQ. Immunohistochemistry indicated the presence of Kupffer cell activation, apoptosis and hepatocyte proliferation in the liver. There was also an increase in serum IL-2, IL-5, IL-9, IL-12, MCP-1 and TGFβ, but a decrease in leptin. Coincident with the elevated serum ALT, the number of liver CD4<sup>+</sup> T-cells, IL-17 secreting cells and T<sub>H</sub>17/T<sub>reg</sub> cells increased at Week 3 and decreased during continued treatment. Increases in NK1.1+ cells and activated M2 macrophages were also observed during liver injury. These results suggest that the outcome of the liver injury was determined by the balance between effector and regulatory cells. Co-treatment with cyclosporin prevented AQ-induced liver injury, which supports an immune mechanism. Retinoic acid (RA), which has been reported to enhance natural killer (NK) cell activity, exacerbated AQ-induced liver injury. These results suggest that AQ-induced IDILI is immune mediated and the subsequent adaptation appears to represent immune tolerance.
DOI: 10.6084/m9.figshare.3486551
title: Testing consumer pressure and water addition on plant interactions

description: During an extreme drought year (2014) and an El Niño year (2016) in the arid central valley of California, USA, we artificially manipulated a soil moisture gradient and erected animal exclosures to examine the interactions between dominant shrubs and the subordinate annual community. Loggers were placed to record the differences in temperature and relative humidity in shrub and open microsites. Loggers used were HOBO ProV2 by Onset burried underground with the sensor raised 2 cm above the ground surface. Six pairs of loggers were used in 2014, and three pairs of loggers were used in 2016.
DOI: 10.6084/m9.figshare.3486551.v1
title: Testing consumer pressure and water addition on plant interactions

description: During an extreme drought year (2014) and an El Niño year (2016) in the arid central valley of California, USA, we artificially manipulated a soil moisture gradient and erected animal exclosures to examine the interactions between dominant shrubs and the subordinate annual community. Loggers were placed to record the differences in temperature and relative humidity in shrub and open microsites. Loggers used were HOBO ProV2 by Onset burried underground with the sensor raised 2 cm above the ground surface. Six pairs of loggers were used in 2014, and three pairs of loggers were used in 2016.
DOI: 10.6084/m9.figshare.3486542
title: Experiment #7

description: Culture #7
DOI: 10.6084/m9.figshare.3486542.v1
title: New draft item

description: Culture #7
DOI: 10.6084/m9.figshare.3486521
title: DNA methylome changes by estradiol benzoate and bisphenol A links early-life environmental exposures to prostate cancer risk

description: Developmental exposure to endocrine-disrupting chemicals (EDCs), 17β-estradiol-3-benzoate (EB) and bisphenol A (BPA), increases susceptibility to prostate cancer (PCa) in rodent models. Here, we used the methylated-CpG island recovery assay (MIRA)-assisted genomic tiling and CpG island arrays to identify treatment-associated methylome changes in the postnatal day (PND)90 dorsal prostate tissues of Sprague-Dawley rats neonatally (PND1, 3, and 5) treated with 25 µg/pup or 2,500 µg EB/kg body weight (BW) or 0.1 µg BPA/pup or 10 µg BPA/kg BW. We identified 111 EB-associated and 86 BPA-associated genes, with 20 in common, that have significant differentially methylated regions. Pathway analysis revealed cancer as the top common disease pathway. Bisulfite sequencing validated the differential methylation patterns observed by array analysis in 15 identified candidate genes. The methylation status of 7 (<i>Pitx3, Wnt10b, Paqr4, Sox2, Chst14, Tpd52, Creb3l4</i>) of these 15 genes exhibited an inverse correlation with gene expression in tissue samples. Cell-based assays, using 5-aza-cytidine-treated normal (NbE-1) and cancerous (AIT) rat prostate cells, added evidence of DNA methylation-mediated gene expression of 6 genes (exception: <i>Paqr4</i>). Functional connectivity of these genes was linked to embryonic stem cell pluripotency. Furthermore, clustering analyses using the dataset from The Cancer Genome Atlas revealed that expression of this set of 7 genes was associated with recurrence-free survival of PCa patients. In conclusion, our study reveals that gene-specific promoter methylation changes, resulting from early-life EDC exposure in the rat, may serve as predictive epigenetic biomarkers of PCa recurrence, and raises the possibility that such exposure may impact human disease.
DOI: 10.6084/m9.figshare.3486509
title: Experiment #8

description: Culture #8
DOI: 10.6084/m9.figshare.3486509.v1
title: New draft item

description: Culture #8
DOI: 10.6084/m9.figshare.3486503
title: Functional and non-functional classes of peptides produced by long non-coding RNAs

description: Supplementary data for the article by Ruiz-Orera et al. (Functional and non-functional classes of peptides produced by long non-coding RNAs). It contains transcript assemblies for human (hsa) and mouse (mmu) - hsa_transcripts.gtf, mmu_transcripts.gtf - as well as mouse ORF sequences and genomic coordinates - total_orfs.fa, total_orfs.gtf. It also contains the C program to compute the expected number of synonymous and non-synonymous polymorphisms under neutrality in mouse sequences, computePNPS.c.<br><br>