cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25903/5b874df2ecc9a
title: Monogenean parasites infect ornamental fish imported to Australia

description: <p>The following dataset was collected as part of a PhD thesis candidature.</p><p>Data provides Hamuli armature measurements of Dactylogyrus, Gyrodactylus, Trianchoratus and Urocleidoides parasites collected from imported ornamental fish species.</p><p>More than 1000 parasites were identified from 31 ornamental fish consignments examined for monogenean parasite fauna. One hamulus per pair from each individual monogeanean was measured to facilitate species identification. The full methodology for parasite collection/preparation and measurement is included in the Related Publication, available from the link below.</p><p>Hamuli mounted on glass slides for each species were accessioned to the Australian Helminth Collection (AHC) at the South Australian Museum, Adelaide (SAMA, AHC 36559–36609), and sequenced data was accesioned in the National Center for Biotechnology Information (NCBI) (MF356235-52).</p><p>This dataset is available as a spreadsheet saved in MS Excel (.xlsx) and Open Document format (.ods) and consists of 7 worksheets: </p><ol><li>Metadata</li><li>Prevalence and intensity (data used in Table 1 of the data chapter and publication)</li><li>Hamuli measurement publication (data used in Table 2)</li><li>Parasite count</li><li>Dactylogyrus_Hamuli_measures</li><li>Trianchoratus_urocleioides_measures</li><li>Gyrodactylus_Hamuli_measures</li></ol>
DOI: 10.4225/28/591abebf0e781
title: Acropora bleaching data, Lizard Island 2016
DOI: 10.25903/y12c-xd63
title: Data from: Algal turf productivity on coral reefs: a meta-analysis

description: This dataset contains the data associated with the following publication:

Tebbett SB, Bellwood DR (2021) Algal turf productivity on coral reefs: A meta-analysis. Marine Environmental Research 168: 105311 https://doi.org/10.1016/j.marenvres.2021.105311

In this study we examined the productivity and turnover of algal turfs on coral reefs. To do this we sourced data on algal turf productivity and turnover from the literature. In addition, we sourced data on variables related to where and how these data were collected to examine how these factors shaped algal turf productivity and turnover patterns. To source this data we used a meta-analysis of the literature following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) protocols. As this dataset was based on a literature search it spans a number of coral reef locations including the Great Barrier Reef, Caribbean and Hawaii and over 50 years (1965-2017). 

For full methodological details, please see the published manuscript (referenced above).

Details of the two datasets (productivity and turnover) including units of measure can be found in the 'read me' file.
DOI: 10.25903/8vxk-4w08
title: Glycosyl linkage data from methylation analysis of native and desulfated ulvan polysaccharides

description: <p>See chapter 4 of the thesis for full details. The aims of this study were to compare the glycosyl linkage positions and sulfate ester substitutions of each component monosaccharide from four ulvan samples, two isolated from blade species of Ulva (U. rigida and U. sp. B) and two isolated from filamentous species of Ulva (U. prolifera and U. ralfsii). Data were collected by gas chromatography-mass spectrometry of partially methylated alditol acetate derivatives of desulfated and carboxyl reduced ulvan.</p>
<p>The full methodologies will be available in the author's thesis (Chapter 4) from the Related Publications link below. </p>
DOI: 10.25903/zea2-8159
title: Paddock boundaries

description: <p>This is the GIS dataset for paddock boundaries for the Babinda and surrounding areas produced for the project titled &lsquo;Modelling unseen flow pathways of water and contaminants in the Wet Tropics: the role of alluvial palaeochannels&rsquo;, funded by the Queensland Government Department of Environment and Science, Queensland Water Modelling Network. Paddock boundaries are crucial to understanding the extent of palaeochannels within each paddock unit which was the basis of spatial analysis for the project. The paddock boundaries were based on the drain lines which were often running along the boundaries of paddocks. Boundaries that extended beyond the drain lines were digitised. The spatial analysis was based on 1x1 m LiDAR topographic data, drone imagery and the drain line dataset produced by Lim et al. (2023)</p>
<p>Lim, Han She; Nelson, Paul; Cheesman, Alexander; Bulstrode, Marcus; Rashid, Raf (2023): Russell Mulgrave surface drain lines. James Cook University. <a href="https://doi.org/10.25903/bf6q-1q13">https://doi.org/10.25903/bf6q-1q13</a><br />DOI: 10.25903/bf6q-1q13</p>
<p>Software/equipment used to create/collect the data: ArcGIS (ArcMAP) and ArcGIS Pro</p>
<p>Software/equipment used to manipulate/analyse the data: ArcGIS (ArcMAP) and ArcGIS Pro</p>
DOI: 10.25903/zs2a-p187
title: Metabolic responses of Pacific crown-of-thorns sea stars (Acanthaster sp.) to acute warming
DOI: 10.15468/dl.sjpf67
title: Occurrence Download

description: A dataset containing 339 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ecuador",
 "OccurrenceStatus is Present",
 "TaxonKey is Fuchsia loxensis Kunth"
 ]
}

 The dataset includes 339 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0075344-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.4225/28/5902a9c436aa4
title: Neurobiology of pair bonding in Chaetodon lunulatus (f. Chaetodontidae), with respect to isotocin, arginine vasotocin V1a, dopamine D1 and D2, and mu-opioid receptor systems
DOI: 10.4225/28/5a713fd9b1f94
title: Data from: Lonnstedt OM, McCormick MI (2013) Ultimate predators: lionfish have evolved to circumvent prey risk assessment abilities. PLoS ONE 8:e75781
DOI: 10.25903/jf55-1755
title: Data from: Drug-resistant tuberculosis in the Torres Strait / Papua New Guinea border Region [Chapter 4 PhD Thesis]

description: <p><strong>Background: </strong>Drug-resistant tuberculosis (DR-TB) is an ongoing challenge in the Torres Strait Islands (TSI) / Papua New Guinea (PNG) border region. Treatment success rates have historically been poor for patients diagnosed with DR-TB, leading to increased transmission. Further, delays between self-reported symptom onset and commencement of effective treatment contribute to ongoing tuberculosis (TB) transmission, is a particular concern in patients with drug-resistant (DR)-TB. This study identified variables associated with unfavourable outcome in patients diagnosed with DR-TB to inform programmatic improvements and assessed improvements in time to commencement of effective treatment in patients diagnosed with DR-TB in the Torres Strait&ndash;Papua New Guinea cross-border region.</p>
<p>Study population: All residents of the Torres Strait Islands and Papua New Guinea nationals who presented to health facilities in the Torres Strait and were diagnosed with drug-resistant-TB between 2000 and 2020</p>
<p>This record consists of:</p>
<ul>
<li>1 SPSS (.sav) file containing the spatiotemporal mapping of drug-resistant TB</li>
<li>1 SPSS (.sav) file containing data on the time to commencement of effective treatment in patients with drug-resistant tuberculosis</li>
<li>1 SPSS (.sav) file which contains a Multiple Imputation Dataset for Predictors of unfavourable outcome in patients diagnosed with drug-resistant tuberculosis</li>
<li>1 SPSS (.sav) file with the full dataset of the 133 patients</li>
<li>1 README (.txt) file which contains dataset definitions and variables</li>
</ul>
<p>Data files are also saved in csv. format <p>
<p>Software/equipment used to store/analyse the data: SPSS and Microsoft Excel</p>
<p>The full metholodgy is available in the Open Access publications in the Related publications link below.</p>
<p>Once access to the data has been obtained via negotiation with the Data Manager, use of the dataset is governed by the CC BY-NC-SA 4.0 licence.</p>
<p><strong>Note: The Data Manager may release age-related data in 5-year intervals to researchers, contingent upon consultation to establish research specifications and obtaining ethics approval.</strong></p>
DOI: 10.25903/sx6c-re28
title: Do Pandemics Trigger Death Thoughts Study 1

description: <p><strong>Background:</strong></p>
<p>These studies aim to investigate the effects of pandemics of varying severity on death thought accessibility in two studies while controlling for health anxiety. Study 1 (n = 203) examined the effect of standard MS, severe pandemic, mild pandemic, and dental conditions on death thought accessibility as assessed by the death word fragment task (DWFT).  Study 2 (n = 163) was conducted with more sensitive death thought accessibility measures such as the lexical decision task and dot probe task.</p>
<p>Study 1 hypothesized that severe pandemic condition and standard MS condition will yield significantly higher levels of death cognitions than the mild pandemic and dental conditions after a time delay, and continued to do so when we control for health anxiety.</p>
<p>Information pertaining to Study 2 is located at: <a href="https://doi.org/10.25903/cn68-9963">https://doi.org/10.25903/cn68-9963</a> </p>
<p><strong>This data record contains:</strong></p>
<p>1 x SPSS (.sav) file containing input data and calculation of number of death words completed used in analysis. File is also available in Open Document (.ods) format.</p>
<p>--//--</p>
<p>Software/equipment used to collect the data: Qualtrics</p>
<p>Software/equipment used to analyse the data: SPSS</p>
DOI: 10.25903/5f45d97cc5081
title: Richness of primary producers and consumer abundance mediate epiphyte loads in a tropical seagrass system

description: <p class="MDPI18keywords"><span lang="EN-US">Consumer communities play an important role in maintaining ecosystem structure and function. In seagrass systems, algal regulation by mesograzers provides a critical maintenance function which promotes seagrass productivity. Consumer communities also represent a key link in trophic energy transfer and buffer negative effects to seagrasses associated with eutrophication. Such interactions have now been well documented in literature from temperate systems, however, it is not clear if the same relationships hold in tropical systems. This study aimed to identify if the invertebrate communities within a tropical, multispecies seagrass meadow moderated epiphyte abundance under natural conditions. This was done by comparing algal abundance across two sites at Green Island, Australia. At each site, paired plots were established where the invertebrate assemblages were perturbed via insecticide manipulation, and compared to un-manipulated plots. An 89% increase in epiphyte abundance was seen after six weeks of experimental invertebrate reductions within the system. Using generalized linear mixed effects models and path analysis we found that the abundance of invertebrates was negatively correlated with epiphyte load on seagrass leaves. Habitat species richness was seen to be positively correlated with invertebrate abundance. These findings mirror those of temperate systems, suggesting this mechanism operates similarly across latitudinal gradients.</span></p><p class="MDPI18keywords"><span lang="EN-US">The full methodology will be made available in the Open Access publication listed in the Related Publications link below.</span></p><p class="MDPI18keywords"> </p>
DOI: 10.25903/5d0ada7f84903
title: Data from: A 3D perspective on sediment accumulation in algal turfs: implications of coral reef flattening

description: <p>This dataset consists of one MS Excel (.xlsx) file. This file contains site information (3 sites at Lizard Island on the Great Barrier Reef, Australia), coral reef complexity metrics (elevation above lowest point in each site, and angle of sampled surface) and metrics associated with algal turf condition (algal turf length, particulate depth, particulate mass, inorganic sediment mass, organic particulate mass, proportion of particulates composed of organic particulates by mass, and grain size distribution of inorganic sediment by mass). Complexity metrics were calculated using digitial elevation models based on 3D photogrammetry of 36 m^2 areas of reef (following Streit et al. 2019). Algal turf metrics were collected using veneir callipers following Goatley and Bellwood 2013, and an underwater vacuum sampler (modified after Purcell 1996). Collected sediments were processed following Tebbett et al. 2018. </p><p>Literature cited:</p><p>Goatley, C. H. R., & Bellwood, D. R. (2013). Ecological consequences of sediment on high-energy coral reefs. PLoS ONE, 8, e77737. doi:10.1371/journal.pone.0077737</p><p>Purcell, S. W. (1996). A direct method for assessing sediment load in epilithic algal communities. Coral Reefs, 15, 211–213. doi:10.1007/BF01787453</p><p>Streit, R.P., Cumming, G., & Bellwood, D.R. (2019) Patchy delivery of functions undermines functional redundancy in a high diversity system. Functional Ecology, doi: 0.1111/1365-2435.13322</p><p>Tebbett, S. B., Goatley, C. H. R., & Bellwood, D. R. (2018). Algal turf sediments across the Great Barrier Reef: Putting coastal reefs in perspective. Marine Pollution Bulletin, 137, 518-525. 10.1016/j.marpolbul.2018.10.056</p>
DOI: 10.4225/28/55ac49f6647bd
title: Hafnium isotope data for the Simuku Igneous Complex, New Britain, Papua New Guinea
DOI: 10.25903/g9am-9w70
title: Data from: Parrotfish corallivory on stress-tolerant corals in the Anthropocene

description: This entry refers to Huertas et al."Parrotfish corallivory on stress-tolerant corals in the Anthropocene, PLoS one. It encompasses R scripts and data tables used to reproduce the analyses of the paper.

Includes data collected in 2008 and in 2018.

Software/equipment used to create/collect the data: Still images to document benthic composition changes were extracted from 20 meter long video transects recorded with a GoPro 6. 
Photographs of massive Porites colonies were taken with a Nikon Coolpix W300.

Software/equipment used to manipulate/analyse the data: All statistical analyses were conducted in the software R v.3.6.1 using the packages 'ggplot2', 'glmmTMB', 'MASS', 'MuMIn', and 'emmeans'.
DOI: 10.25903/v7pp-7e51
title: Marine habitats of the Madang Lagoon, Papua New Guina

description: <p><strong>Background [Modified extract from related publications] </strong>The overall goal of the study was to simulate the design of hypothetical reserves that would protect marine habitat types within the Riwo waters (a coastal community in the Madang Lagoon), while minimizing loss of access by the community to important ecosystem services and benefits. Therefore, spatial data on habitat types present in the region were necessary, as well as maps of the benefits provided by the Madang Lagoon as perceived by the community. This dataset corresponds to habitat maps covering the Madang Lagoon, Papua New Guinea.</p>
<p><strong>Methods [Modified extract]</strong> We created a habitat map of the Madang Lagoon from a high spatial resolution (2 m) Worldview satellite image captured on 12/06/2010. The map was created following the steps in the &ldquo;user approach&rdquo; described in Andrefouet, 2008: a priori manual delineation of habitats, ground truthing data collected separately in 2012 from this project during the Coral-Triangle cruise on board R/V ALIS (Andr&eacute;fou&euml;t 2012), contextual editing, classification and merging of habitat segments. The resulting hierarchical habitat typology for the Madang Lagoon describes 4 levels of geomorphic habitats, and 2 levels of benthic habitats (current at the time of the benthic survey, 2012).</p>
<p><strong>Data sources acknowledgement:</strong></p>
<ol>
<li>Andr&eacute;fou&euml;t S. Coral reef habitat mapping using remote sensing: A user vs producer perspective. Implications for research, management and capacity building. Journal of Spatial Science. 2008;53(1):113-29. doi: 10.1080/14498596.2008.9635140. PubMed PMID: WOS:000258303000011.</li>
<li>Andr&eacute;fou&euml;t S. CORAL-TRIANGLE cruise, RV Alis. 2012.</li>
</ol>
<p>This dataset consists of 1 .zip archive containing an ESRI Shapefile (one set of 8 related files in total) with habitat polygons, covering the Madang Lagoon, Papua New Guinea. The attribute table for this shapefile contains code labels and descriptions (attributes) for each marine habitat type, at 6 different levels of detail.</p>
DOI: 10.25903/0app-1r90
title: 1823 Kotzebue expedition

description: <p>This dataset describes the 1823-1826 voyage of the Predpriatie under Captain Kotzebue<p>
<p>Software/equipment used to create/collect the data: Excel, JCU Libraries<p>
<p>Software/equipment used to manipulate/analyse the data: TLCMap<p>
DOI: 10.25903/5def4406fe7b7
title: Similar thermal breadth of temperate and tropical coral species

description: <p>Temperate organisms are generally exposed to a more variable and cooler climate than tropical organisms, and are therefore expected to have a broader thermal tolerance and higher capacity for acclimation. This study investigated this hypothesis by comparing the thermal performance of two common tropical coral species found in the Great Barrier Reef with two temperate coral species from the Mediterranean Sea. Photosynthesis rates, respiration rates, maximum PSII quantum yield (F<sub>v</sub>/F<sub>m</sub>) and electron transport rates (rETR<sub>m</sub>) were measured on coral fragments exposed to an acute temperature increase and decrease above and below the average environmental seawater temperature. </p>
DOI: 10.25903/5c89bb8aba60f
title: Elevated CO2 affects reproduction and embryonic development in the pygmy squid, Idiosepius pygmaeus

description: <p>This is a study on the effects parental exposure of elevated CO<sub>2</sub> on the reproduction and embryonic development of the two-toned pygmy squid (<em>Idiosepius pygmaeus</em>). Adult squid were exposed to either control or elevated CO<sub>2</sub> conditions for 14 days prior to being paired together to breed. After eggs were spawned, they were counted and photographed under microscope. The development of the embryos was then recorded with photographs (every 24 hours) until all embryos had hatched. From the photographs and count data, variables of development and reproduction were collected including number of eggs per clutch, percent of eggs that were fertile, percent of embryos that were deformed, number of embryos to hatch, time it took them to hatch from spawning, as well as size of the egg cases and embryos during distinct stages of embryonic development. These variables were compared to determine if there was an effect of elevated CO<sub>2.</sub></p><p>Abstract [Related Publication]: The oceans continue to absorb atmospheric carbon dioxide (CO<sub>2</sub>) and projected future CO<sub>2</sub> levels could have negative implications for many marine organisms, especially during early life stages. Cephalopods are ecologically important in marine ecosystems, yet the potential effects of elevated CO<sub>2</sub> on cephalopod reproduction and embryonic development are little studied. We allowed adult two-toned pygmy squid (<em>Idiosepius pygmaeus</em>) to breed in ambient control (~445 µatm) or elevated CO<sub>2</sub> conditions (~940 µatm) and compared reproductive traits in adults and developmental characteristics of their eggs between treatments. Breeding pairs at elevated CO<sub>2</sub> produced clutches with 40% fewer eggs, embryos that were 14% smaller directly after spawning and 5% smaller upon hatching, and an 8% increase in late-stage egg swelling compared with pairs at control conditions. Elevated CO<sub>2</sub> did not affect fertility, time to hatch, or hatching success. Eggs were laid 40% closer together in elevated CO<sub>2</sub> compared with control conditions, indicating a possible effect of elevated CO<sub>2</sub> on reproductive behaviour. These results show that elevated CO<sub>2</sub> can adversely affect reproduction and embryonic development of the two-toned pygmy squid. As the potential for adaptation is influenced by reproductive success, testing the capacity for squid to adapt to future ocean conditions should be a priority for future research. </p><p> </p>
DOI: 10.25903/5c89c4ebba610
title: Data from 'Pelagic subsidies underpin fish productivity on a degraded coral reef'

description: <p>This entry refers to Morais and Bellwood 'Pelagic subsidies underpin fish productivity on a degraded coral reef' in the journal Current Biology. It encompasses R scripts (compressed in one file) and multiple data tables (compressed in another file) used to reproduce the analyses of the paper.</p>
DOI: 10.15468/dl.jzmpxu
title: Occurrence Download

description: A dataset containing 74 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "MULTIPOLYGON (((144.410158 -36.84511, 144.410158 -36.851848, 144.412404 -36.851848, 144.412404 -36.847356, 144.419141 -36.847356, 144.419141 -36.84511, 144.416896 -36.84511, 144.416896 -36.842865, 144.412404 -36.842865, 144.412404 -36.84511, 144.410158 -36.84511)), ((144.410158 -36.84511, 144.410158 -36.838373, 144.405667 -36.838373, 144.405667 -36.84511, 144.410158 -36.84511)), ((144.419141 -36.847356, 144.419141 -36.851848, 144.434862 -36.851848, 144.434862 -36.84511, 144.439354 -36.84511, 144.439354 -36.842865, 144.434862 -36.842865, 144.434862 -36.838373, 144.441599 -36.838373, 144.441599 -36.831636, 144.432616 -36.831636, 144.432616 -36.838373, 144.423633 -36.838373, 144.423633 -36.831636, 144.419141 -36.831636, 144.419141 -36.836127, 144.416896 -36.836127, 144.416896 -36.842865, 144.419141 -36.842865, 144.419141 -36.84511, 144.423633 -36.84511, 144.423633 -36.847356, 144.419141 -36.847356)))"
 ]
}

 The dataset includes 74 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0075345-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25903/qdmh-4r06
title: Crustacean protein database

description: A database of all crustacean proteins collated to identify novel allergens in king crab and edible crab extracts.
Protein sequences for all IDs under the taxonomy ID 6657 for including all crustacean proteins were collected in a Fasta format from Uniprot, as of November 2019. This database was used in Msile2 (Bio21) and Maxquant for identifying crab allergens.
DOI: 10.25903/pdze-bw08
title: Nonlethally assessing elasmobranch ontogenetic shifts in energetics

description: <p>This study measured body condition of epaulette sharks (Hemiscyllium ocellatum) across ontogeny to assess best-practice metrics for non-lethal assessment of energetic status. </p>
<p>Software/equipment used to manipulate/analyse the data: All statistical analyses were conducted in R (version 4.2.2, R Core Development Team, 2022).</p>
DOI: 10.4225/28/56a1bd8a2258d
title: Nitrate-ammonium utilisation for the green alga species Desmodesmus armatus reared in laboratory batch culture conditions.
DOI: 10.25903/9vj6-1e13
title: Trace element of cassiterite from the Herberton Mineral Field

description: <p>This dataset comprises trace element analyses of cassiterite samples collected from twelve deposits in the Herberton Mineral Field, North Queensland, Australia. Cassiterite samples were collected from greisen, vein and polymetallic vein deposits, including the Big Ben, Black King, Brads Mine, Cobby, Elaine Mary, Great North Freeman, Hope Mine, Levianthan, North Hope Mine, Old Bradlaugh, Baal Gammon, Isabel, and Jumna Granite. The analyses were conducted using laser ablation-inductively coupled plasma-mass spectrometry at the Advanced Analytical Centre of James Cook University.</p>