cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5372851.v1
title: Foliar and soil N and <i>δ</i><sup>15</sup>N as restoration metrics at Pūtaringamotu Riccarton Bush, Christchurch city

description: Delta<sup>15</sup>N values and associated N concentrations may be useful nutrient cycling metrics for assessing restoration progress, and complement biodiversity assessment. We tested this hypothesis at Pūtaringamotu Riccarton Bush (‘Pūtaringamotu’), a low-rainfall urban forest fragment under restoration since 1974. Foliar and soil measurements came from four indigenous forests (Pūtaringamotu; Saltwater, high rainfall, logged until 2002; Ōkārito, high rainfall, never logged; Scotchman’s Creek, high rainfall, burrowing seabirds present). Despite different disturbance histories, Pūtaringamotu, Ōkārito and Saltwater results all fitted global <i>δ</i><sup>15</sup>N regressions between rainfall and foliar N concentration. Enhanced foliar N concentrations accompanying low rainfall at Pūtaringamotu were similar to seabird-affected Scotchman’s Creek. Although Pūtaringamotu foliar <i>δ</i><sup>15</sup>N values showed differences between taxa, they were less pronounced than for Ōkārito; Saltwater showed no effect. Further investigation of nutrient cycling restoration metrics at Pūtaringamotu should therefore emphasise progressive development of differences in foliar <i>δ</i><sup>15</sup>N between plant taxa, pooled values being insufficiently sensitive.
DOI: 10.6084/m9.figshare.5372845
title: Epiphytic diatoms as indicators of ecological condition in New Zealand’s lowland wetlands

description: The condition of New Zealand’s remnant wetlands has been documented by landscape-scale assessments such as the Index of Ecological Integrity and Wetland Condition Index. We explored the potential for microscopic aquatic biota (epiphytic diatoms) to provide complementary information about wetland condition using data from 77 lowland sites (mainly palustrine swamps) with circumneutral pH. In the South Island, correspondence between diatoms and wetland indices or water quality was weak. In the North Island, conductivity and total dissolved nitrogen (TDN) together explained 49% of the variance in assemblage composition and several diatom genera were indicative of high or low conductivity, dissolved phosphorus and TDN. Changes in these water quality variables may trigger changes in wetland condition, which are eventually reflected by the landscape-scale indices. Diatoms respond rapidly to water quality changes suggesting potential for diatom indicator taxa to provide early warning of wetland degradation or to track restoration.
DOI: 10.6084/m9.figshare.5372845.v1
title: Epiphytic diatoms as indicators of ecological condition in New Zealand’s lowland wetlands

description: The condition of New Zealand’s remnant wetlands has been documented by landscape-scale assessments such as the Index of Ecological Integrity and Wetland Condition Index. We explored the potential for microscopic aquatic biota (epiphytic diatoms) to provide complementary information about wetland condition using data from 77 lowland sites (mainly palustrine swamps) with circumneutral pH. In the South Island, correspondence between diatoms and wetland indices or water quality was weak. In the North Island, conductivity and total dissolved nitrogen (TDN) together explained 49% of the variance in assemblage composition and several diatom genera were indicative of high or low conductivity, dissolved phosphorus and TDN. Changes in these water quality variables may trigger changes in wetland condition, which are eventually reflected by the landscape-scale indices. Diatoms respond rapidly to water quality changes suggesting potential for diatom indicator taxa to provide early warning of wetland degradation or to track restoration.
DOI: 10.6084/m9.figshare.5372788
title: Force field parameters for transition state-based ST6Gal I inhibitors

description: This depository contains the force field parameters for transition state-based ST6Gal I inhibitors reported in the following publication.<br><br>Montgomery AP, Skropeta D, Yu H (2017) Transition state-based ST6Gal I inhibitors: Mimicking the phosphodiester linkage with a triazole or carbamate through an enthalpy-entropy compensation. <i>Scientific Reports</i> 7:14428 doi: 10.1038/s41598-017-14560-0<br><br><br>
DOI: 10.6084/m9.figshare.5372782
title: LATEMO-E: A film database to elicit discrete emotions and evaluate emotional dimensions for Latin-Americans (supplementary material)

description: We developed two studies to construct LATEMO, an emotion-eliciting film database in Latin Spanish language. In study 1, we identified 70 film clips suggested by film experts and then 147 female and male evaluated them according to capacity to induct seven discrete emotional states: disgust, amusement, anger, fear, neutral, tenderness and sadness. Based on pre-defined cut-off values, in study 2, we select the 28 best films-clips (four film-clips for each emotional category) and then 106 participants evaluated them according to dimensional (valence and arousal) and discreteness (intensity, certainty, and control) indexes of emotion with a post-emotion eliciting questionnaire, generated for this purpose. We obtained an optimal audio-visual tool in Latin Spanish language to study emotions experimentally and to explore cognition-emotion interactions.
DOI: 10.6084/m9.figshare.5372788.v1
title: Force field parameters for transition state-based ST6Gal I inhibitors

description: This depository contains the force field parameters for transition state-based ST6Gal I inhibitors reported in the following publication.<br><br>Montgomery AP, Skropeta D, Yu H (2017) Transition state-based ST6Gal I inhibitors: Mimicking the phosphodiester linkage with a triazole or carbamate through an enthalpy-entropy compensation. <i>Scientific Reports</i> 7:14428 doi: 10.1038/s41598-017-14560-0<br><br><br>
DOI: 10.6084/m9.figshare.5372776
title: Crater stratigraphy and the post-eruptive evolution of Foulden Maar, southern New Zealand

description: Foulden Maar, Waipiata Volcanic Field, New Zealand is a partly eroded maar–diatreme formed by phreatomagmatic eruptions c. 23 Ma. Its post-eruptive evolution is reconstructed by combining outcrop, drillcore and physical core rock properties with pollen data. Facies associations in a 190 m thick composite section of the central crater sediments record four depositional stages: (1) immediate post-eruptive deposition of collapsed crater wall and tephra ring material by subaqueous gravity flows; (2) re-deposition of tephra by hyperconcentrated to turbulent gravity flows in a steep-sided lake; (3) seasonally mediated background sedimentation with recurring gravity flows in a meromictic lake; and (4) diminishing turbidity currents under decreasing relief and biogenic sedimentation over c. 130 ka. Clasts in the basal crater fill represent accidental lithic clasts of primary ejecta and indicate eruption into a mixed hard-soft rock substrate. Foulden Maar represents a ‘classical’ lacustrine maar crater sequence and confirms generally similar post-eruptive processes and sedimentation patterns in enclosed, lacustrine maar basins.
DOI: 10.6084/m9.figshare.5372776.v1
title: Crater stratigraphy and the post-eruptive evolution of Foulden Maar, southern New Zealand

description: Foulden Maar, Waipiata Volcanic Field, New Zealand is a partly eroded maar–diatreme formed by phreatomagmatic eruptions c. 23 Ma. Its post-eruptive evolution is reconstructed by combining outcrop, drillcore and physical core rock properties with pollen data. Facies associations in a 190 m thick composite section of the central crater sediments record four depositional stages: (1) immediate post-eruptive deposition of collapsed crater wall and tephra ring material by subaqueous gravity flows; (2) re-deposition of tephra by hyperconcentrated to turbulent gravity flows in a steep-sided lake; (3) seasonally mediated background sedimentation with recurring gravity flows in a meromictic lake; and (4) diminishing turbidity currents under decreasing relief and biogenic sedimentation over c. 130 ka. Clasts in the basal crater fill represent accidental lithic clasts of primary ejecta and indicate eruption into a mixed hard-soft rock substrate. Foulden Maar represents a ‘classical’ lacustrine maar crater sequence and confirms generally similar post-eruptive processes and sedimentation patterns in enclosed, lacustrine maar basins.
DOI: 10.6084/m9.figshare.5372737
title: Resistance and tolerance: the role of nutrients on pathogen dynamics and infection outcomes in an insect host

description: Tolerance and resistance are the two ways in which hosts can lessen the effects of infection. Tolerance aims to minimise the fitness effects resulting from incumbent pathogen populations, whereas resistance aims to reduce the pathogen population size within the host. While environmental impacts on resistance have been extensively recorded their impacts on variation in tolerance are virtually unexplored. Here we ask how the environment, namely the host diet, influences the capacity of an organism to tolerate and resist infection, using a model host-parasite system, the burying beetle, <i>Nicrophorus vespilloides</i> and the entomopathogenic bacteria, <i>Photorhabdus luminescens. </i>We first considered dose-responses and pathogen dynamics within the host, and compared our findings to responses known from other host species. We then investigated how investment in tolerance and resistance changed under different nutritional regimes. Beetles were maintained on one of five diets that varied in their ratio of protein to fat for 48 hours and then injected with P. luminescens. Survival was monitored and the phenoloxidase (PO) response and bacterial load at 24 hours post infection were ascertained. The dose required to kill 50% of individuals in this species was several magnitudes higher than in other species and the bacteria were shown to display massive decreases in population size, in contrast to patterns of proliferation found in other host species. Diet strongly modified host survival after infection, with those on the high fat/low protein diet showing 30% survival at 8 days, versus almost 0% survival on the low fat/high protein diet. However, this was independent of bacterial load or variation in PO, providing evidence for diet-mediated tolerance mechanisms rather than immune-driven resistance. Evolutionary ecology has long focussed on immune resistance when investigating how organisms avoid succumbing to infection. Tolerance of infection has recently become a much more prominent concept and is suggested to be influential in disease dynamics. This is one of the first studies to find diet-mediated tolerance.<br>
DOI: 10.6084/m9.figshare.5372782.v3
title: LATEMO-E: A film database to elicit discrete emotions and evaluate emotional dimensions for Latin-Americans

description: We developed two studies to construct LATEMO, an emotion-eliciting film database in Latin Spanish language. In study 1, we identified 70 film clips suggested by film experts and then 147 female and male evaluated them according to capacity to induct seven discrete emotional states: disgust, amusement, anger, fear, neutral, tenderness and sadness. Based on pre-defined cut-off values, in study 2, we select the 28 best films-clips (four film-clips for each emotional category) and then 106 participants evaluated them according to dimensional (valence and arousal) and discreteness (intensity, certainty, and control) indexes of emotion with a post-emotion eliciting questionnaire, generated for this purpose. We obtained an optimal audio-visual tool in Latin Spanish language to study emotions experimentally and to explore cognition-emotion interactions.
DOI: 10.6084/m9.figshare.5372728
title: OXT PicMod minimal data 20170829.sav

description: This minimal dataset was for the maniscript "Does trait anxiety influence effects of oxytocin on eye-blink startle reactivity? A<br>randomized, double-blind, placebo-controlled crossover study".<br>
DOI: 10.6084/m9.figshare.5372737.v1
title: Resistance and tolerance: the role of nutrients on pathogen dynamics and infection outcomes in an insect host

description: Tolerance and resistance are the two ways in which hosts can lessen the effects of infection. Tolerance aims to minimise the fitness effects resulting from incumbent pathogen populations, whereas resistance aims to reduce the pathogen population size within the host. While environmental impacts on resistance have been extensively recorded their impacts on variation in tolerance are virtually unexplored. Here we ask how the environment, namely the host diet, influences the capacity of an organism to tolerate and resist infection, using a model host-parasite system, the burying beetle, <i>Nicrophorus vespilloides</i> and the entomopathogenic bacteria, <i>Photorhabdus luminescens. </i>We first considered dose-responses and pathogen dynamics within the host, and compared our findings to responses known from other host species. We then investigated how investment in tolerance and resistance changed under different nutritional regimes. Beetles were maintained on one of five diets that varied in their ratio of protein to fat for 48 hours and then injected with P. luminescens. Survival was monitored and the phenoloxidase (PO) response and bacterial load at 24 hours post infection were ascertained. The dose required to kill 50% of individuals in this species was several magnitudes higher than in other species and the bacteria were shown to display massive decreases in population size, in contrast to patterns of proliferation found in other host species. Diet strongly modified host survival after infection, with those on the high fat/low protein diet showing 30% survival at 8 days, versus almost 0% survival on the low fat/high protein diet. However, this was independent of bacterial load or variation in PO, providing evidence for diet-mediated tolerance mechanisms rather than immune-driven resistance. Evolutionary ecology has long focussed on immune resistance when investigating how organisms avoid succumbing to infection. Tolerance of infection has recently become a much more prominent concept and is suggested to be influential in disease dynamics. This is one of the first studies to find diet-mediated tolerance.<br>
DOI: 10.6084/m9.figshare.5372722
title: Supporting information 4

description: BayesTraits MultiState ML and MCMC ancestral state reconstruction output for colour character 1 on ML phylogram and ultrametric trees. The grey panel lists internal node IDs and subtending terminal taxa. The blue panel are results from ML ancestral state reconstruction. The yellow panel are results from MCMC ancestral state reconstruction. Abbreviations: Ultra 0, ultrametric tree generated with penalty = 0; Ultra 10, ultrametric tree generated with penalty = 10; Ultra 10000, ultrametric tree generated with penalty = 10000.
DOI: 10.6084/m9.figshare.5372728.v1
title: OXT PicMod minimal data 20170829.sav

description: This minimal dataset was for the maniscript "Does trait anxiety influence effects of oxytocin on eye-blink startle reactivity? A<br>randomized, double-blind, placebo-controlled crossover study".<br>
DOI: 10.6084/m9.figshare.5372731
title: Supporting information 6

description: BayesTraits MultiState ML ancestral state reconstruction of colour character 2 on the ML phylogram (tree converted to cladogram for visual). Terminal taxa coded as cryptic or uniform metallic (black) or aposematic or aposematic and metallic (blue). Pie charts at select nodes show probability values from the ML reconstruc- tions; branches are coloured to reflect the highest probability of a colour state at that branch.
DOI: 10.6084/m9.figshare.5372716
title: Supporting information 2

description: Character matrix for colour characters and male body length in nexus format for ASRs.
DOI: 10.6084/m9.figshare.5372731.v2
title: Supporting information 6

description: BayesTraits MultiState ML ancestral state reconstruction of colour character 2 on the ML phylogram (tree converted to cladogram for visual). Terminal taxa coded as cryptic or uniform metallic (black) or aposematic or aposematic and metallic (blue). Pie charts at select nodes show probability values from the ML reconstruc- tions; branches are coloured to reflect the highest probability of a colour state at that branch.
DOI: 10.6084/m9.figshare.5372722.v2
title: Supporting information 4

description: BayesTraits MultiState ML and MCMC ancestral state reconstruction output for colour character 1 on ML phylogram and ultrametric trees. The grey panel lists internal node IDs and subtending terminal taxa. The blue panel are results from ML ancestral state reconstruction. The yellow panel are results from MCMC ancestral state reconstruction. Abbreviations: Ultra 0, ultrametric tree generated with penalty = 0; Ultra 10, ultrametric tree generated with penalty = 10; Ultra 10000, ultrametric tree generated with penalty = 10000.
DOI: 10.6084/m9.figshare.5372722.v1
title: Supplementary material 4

description: BayesTraits MultiState ML and MCMC ancestral state reconstruction output for colour character 1 on ML phylogram and ultrametric trees. The grey panel lists internal node IDs and subtending terminal taxa. The blue panel are results from ML ancestral state reconstruction. The yellow panel are results from MCMC ancestral state reconstruction. Abbreviations: Ultra 0, ultrametric tree generated with penalty = 0; Ultra 10, ultrametric tree generated with penalty = 10; Ultra 10000, ultrametric tree generated with penalty = 10000.
DOI: 10.6084/m9.figshare.5372716.v2
title: Supporting information 2

description: Character matrix for colour characters and male body length in nexus format for ASRs.
DOI: 10.6084/m9.figshare.5372716.v1
title: Supplementary material 2

description: Character matrix for colour characters and male body length in nexus format for ASRs.
DOI: 10.6084/m9.figshare.5372653
title: Log2 Ratios

description: Log2 Ratio estimates for each sample<br>
DOI: 10.6084/m9.figshare.5372665
title: Personalized computer simulations of a NeoAva non-responder patient: comparison of standard and alternative schedules

description: The videos show personalized computer simulation of a breast tumor portion under the combined effect of chemotherapy and anti-angiogenic treatment. The simulations corresponds to 12 weeks of therapy in a luminal non-responder patient of the NeoAva clinical trial using standard and alternative schedules. Cancer, stroma cells and oxygen tension are shown. To produce the simulations we use a multiscale pharmacokinetic and pharmacodynamic model informed by individual, multisource clinical data, including histological, molecular and magnetic resonance imaging data. See reference below.
DOI: 10.6084/m9.figshare.5372665.v1
title: Personalized computer simulations of a NeoAva non-responder patient: comparison of standard and alternative schedules

description: The videos show personalized computer simulation of a breast tumor portion under the combined effect of chemotherapy and anti-angiogenic treatment. The simulations corresponds to 12 weeks of therapy in a luminal non-responder patient of the NeoAva clinical trial using standard and alternative schedules. Cancer, stroma cells and oxygen tension are shown. To produce the simulations we use a multiscale pharmacokinetic and pharmacodynamic model informed by individual, multisource clinical data, including histological, molecular and magnetic resonance imaging data. See reference below.
DOI: 10.6084/m9.figshare.5371633
title: TetraDENSITY: Population Density dataset

description: Population density estimates in terrestrial vertebrates
DOI: 10.6084/m9.figshare.5372653.v1
title: Log2 Ratios

description: Log2 Ratio estimates for each sample<br>
DOI: 10.6084/m9.figshare.5371627
title: Research crowdfunding interview with UWA - Lindy Fitzgerald

description: On 19 August 2016, I conducted an interview with Lindy Fitzgerald of University of Western Australia. Lindy had run an interesting crowdfunding campaign, to raise funds to attend Homeward Bound, a women in science leadership program. <br>This data set contains the interview (MP3), a transcript of the interview (PDF) and two consent forms (JPG) for the interview and for the public release of the information.<br>I would like to take this opportunity to thank Lindy for her interview, and for agreeing to make it public.
DOI: 10.6084/m9.figshare.5371627.v1
title: Research crowdfunding interview with UWA - Lindy Fitzgerald

description: On 19 August 2016, I conducted an interview with Lindy Fitzgerald of University of Western Australia. Lindy had run an interesting crowdfunding campaign, to raise funds to attend Homeward Bound, a women in science leadership program. <br>This data set contains the interview (MP3), a transcript of the interview (PDF) and two consent forms (JPG) for the interview and for the public release of the information.<br>I would like to take this opportunity to thank Lindy for her interview, and for agreeing to make it public.
DOI: 10.6084/m9.figshare.5371633.v2
title: TetraDENSITY: Population Density dataset

description: Population density estimates in terrestrial vertebrates
DOI: 10.6084/m9.figshare.5371519
title: Work-related fatal injuries in Chile, supplementary material

description: Data set in Excel spreadsheet.<br>
DOI: 10.6084/m9.figshare.5371519.v1
title: Medwave-fatales-consolidada-2014-2015.xlsx

description: Data set in Excel spreadsheet.<br>
DOI: 10.6084/m9.figshare.5371489
title: Course of subject participation

description: Definition of subject's participation within the Phys-Stroke Trial. Subjects are categorized in Screening failures, per Protocol subjects, withdrawal from Treatment and Lost-to-follow-up.
DOI: 10.6084/m9.figshare.5371477
title: Datasets and R codes: An empirical test of the relative and combined effects of land-cover and climate change on local colonization and extinction

description: This fileset includes the R code and associated data used in Yalcin & Leroux (2018).<br><br>Yalcin, S. and Leroux, S. J. (2018), An empirical test of the relative and combined effects of land‐cover and climate change on local colonization and extinction. Glob Change Biol. doi:10.1111/gcb.14169<br><br> Thanks to all data providers:Ontario Breeding Bird Atlas (Bird Studies Canada, Canadian Wildlife Service, Federation of Ontario Naturalists, Ontario Field Ornithologists, and Ontario Ministry of Natural Resources) for supplying Atlas data, and to the thousands of volunteer participants who gathered data for the project, and Cadman <i>et al. </i>(1987; 2007);Natural Resource Canada and McKenney <i>et al</i>. (2011) for supplying climate data;Global Forest Watch Canada and Lee (2007) for publicly sharing datasets of anthropogenic changes;Food and Agriculture Organization of the United Nations and Bai <i>et al</i>. (2008) for publicly sharing data of net primary productivity changes. <br>The raw datasets can be found: <b>Ontario Breeding Bird Atlas</b>:Website: http://www.birdsontario.org/atlas/index.jspCadman M. D., Eagles, P. F. J., Helleiner, F. M. (Eds.) (1987) <i>Atlas of Breeding Birds of Ontario 1980-1985</i>. Waterloo, Canada: University of Waterloo Press.Cadman M. D., Sutherland, D. A., Beck G. G., Lepage D., Couturier, A. R. (Eds.) (2007) <i>Atlas of Breeding Birds of Ontario 2001-2005. </i>Toronto, Canada: Bird Studies Canada, Environment Canada, Ontario Field Ornithologists, Ontario Ministry of Natural Resources, Ontario Nature.<b>Climate data:</b><br>McKenney, D. W., Hutchinson, M. F., Papadopol, P. <i>et al</i>., (2011) Customized spatial climate models for North America. <i>Bulletin of the American Meteorological Society</i>, <b>92</b>, 1611-1622.<br><b>Global Forest Watch Canada:</b>Website: http://www.globalforestwatch.ca/data/20101210ALee P. (2007)<i> Recent Anthropogenic Changes within the Boreal Forests of Ontario and Their Potential Impacts on Woodland Caribou (A Global Forest Watch Canada Report)</i>. Edmonton, Canada: Global Forest Watch Canada.<b>Changes in net primary productivity:</b>Bai Z., Dent D., Olsson L., Schaepman M. (2008) Proxy global assessment of land degradation. <i>Soil Use and Management</i>, <b>24</b>, 223–234.