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  • 1
    Online Resource
    Online Resource
    Large expert-curated database for benchmarking document similarity detection in biomedical literature search
    Oxford University Press (OUP) ; 2019
    In:  Database Vol. 2019 ( 2019-01-01)
    Details
    In: Database, Oxford University Press (OUP), Vol. 2019 ( 2019-01-01)
    Abstract: Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency–Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.
    Type of Medium: Online Resource
    ISSN: 1758-0463
    URL: Article
    DOI: 10.1093/database/baz085
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2019
    detail.hit.zdb_id: 2496706-3
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  • 2
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    Continental-scale animal tracking reveals functional movement classes across marine taxa
    Springer Science and Business Media LLC ; 2018
    In:  Scientific Reports Vol. 8, No. 1 ( 2018-02-27)
    Details
    In: Scientific Reports, Springer Science and Business Media LLC, Vol. 8, No. 1 ( 2018-02-27)
    Abstract: Acoustic telemetry is a principle tool for observing aquatic animals, but coverage over large spatial scales remains a challenge. To resolve this, Australia has implemented the Integrated Marine Observing System’s Animal Tracking Facility which comprises a continental-scale hydrophone array and coordinated data repository. This national acoustic network connects localized projects, enabling simultaneous monitoring of multiple species over scales ranging from 100 s of meters to 1000 s of kilometers. There is a need to evaluate the utility of this national network in monitoring animal movement ecology, and to identify the spatial scales that the network effectively operates over. Cluster analyses assessed movements and residency of 2181 individuals from 92 species, and identified four functional movement classes apparent only through aggregating data across the entire national network. These functional movement classes described movement metrics of individuals rather than species, and highlighted the plasticity of movement patterns across and within populations and species. Network analyses assessed the utility and redundancy of each component of the national network, revealing multiple spatial scales of connectivity influenced by the geographic positioning of acoustic receivers. We demonstrate the significance of this nationally coordinated network of receivers to better reveal intra-specific differences in movement profiles and discuss implications for effective management.
    Type of Medium: Online Resource
    ISSN: 2045-2322
    URL: Article
    DOI: 10.1038/s41598-018-21988-5
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2018
    detail.hit.zdb_id: 2615211-3
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  • 3
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    Estimating Fishing Effort and Spatio-Temporal Distribution of Longline Vessels in the Indian Ocean
    Frontiers Media SA ; 2021
    In:  Frontiers in Marine Science Vol. 8 ( 2021-8-26)
    Details
    In: Frontiers in Marine Science, Frontiers Media SA, Vol. 8 ( 2021-8-26)
    Abstract: Protein from fish is essential for feeding the world’s population and is increasingly recognized as critical for food security. To ensure that fisheries resources can be sustainably maintained, fisheries management must be appropriately implemented. When logbook and landing records data are not complete or are incorrect, it is challenging to have an accurate understanding of catch volume. Focusing on Indonesian longline vessels operating in the Indian Ocean from 2012–2019 ( n = 1124 vessels), our aims were to (1) assess compliance through identification of landing sites and potentially illicit behavior inferred by interruptions in VMS transmission, and (2) understand how the fishery operates along with quantifying the spatio-temporal distribution of fishing intensity by applying a Hidden Markov Model, which automatically classified each VMS position as fishing, steaming and anchoring. We found vessel compliance gaps in 90% of vessels in the dataset. Compliance was questionable due both to the widespread occurrence of long intermissions in relaying VMS positions (mean = 17.8 h, n = 973 vessels) and the use of unauthorized landing sites. We also observed substantial changes in fishing effort locations among years. The introduction of regulatory measures during the study period banning transshipment and foreign vessels may be responsible for the spatial shift in fishing activity we observed, from encompassing nearly the whole Indian Ocean to more recent intense efforts off western Sumatra and northern Australia.
    Type of Medium: Online Resource
    ISSN: 2296-7745
    URL: Article
    DOI: 10.3389/fmars.2021.671036
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2021
    detail.hit.zdb_id: 2757748-X
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  • 4
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    A continuous-time state-space model for rapid quality control of argos locations from animal-borne tags
    Springer Science and Business Media LLC ; 2020
    In:  Movement Ecology Vol. 8, No. 1 ( 2020-12)
    Details
    In: Movement Ecology, Springer Science and Business Media LLC, Vol. 8, No. 1 ( 2020-12)
    Abstract: State-space models are important tools for quality control and analysis of error-prone animal movement data. The near real-time (within 24 h) capability of the Argos satellite system can aid dynamic ocean management of human activities by informing when animals enter wind farms, shipping lanes, and other intensive use zones. This capability also facilitates the use of ocean observations from animal-borne sensors in operational ocean forecasting models. Such near real-time data provision requires rapid, reliable quality control to deal with error-prone Argos locations. Methods We formulate a continuous-time state-space model to filter the three types of Argos location data (Least-Squares, Kalman filter, and Kalman smoother), accounting for irregular timing of observations. Our model is deliberately simple to ensure speed and reliability for automated, near real-time quality control of Argos location data. We validate the model by fitting to Argos locations collected from 61 individuals across 7 marine vertebrates and compare model-estimated locations to contemporaneous GPS locations. We then test assumptions that Argos Kalman filter/smoother error ellipses are unbiased, and that Argos Kalman smoother location accuracy cannot be improved by subsequent state-space modelling. Results Estimation accuracy varied among species with Root Mean Squared Errors usually 〈 5 km and these decreased with increasing data sampling rate and precision of Argos locations. Including a model parameter to inflate Argos error ellipse sizes in the north - south direction resulted in more accurate location estimates. Finally, in some cases the model appreciably improved the accuracy of the Argos Kalman smoother locations, which should not be possible if the smoother is using all available information. Conclusions Our model provides quality-controlled locations from Argos Least-Squares or Kalman filter data with accuracy similar to or marginally better than Argos Kalman smoother data that are only available via fee-based reprocessing. Simplicity and ease of use make the model suitable both for automated quality control of near real-time Argos data and for manual use by researchers working with historical Argos data.
    Type of Medium: Online Resource
    ISSN: 2051-3933
    URL: Article
    DOI: 10.1186/s40462-020-00217-7
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2020
    detail.hit.zdb_id: 2724975-X
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  • 5
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    Nesting ecology of hawksbill turtles at a rookery of international significance in Australia’s Northern Territory
    CSIRO Publishing ; 2016
    In:  Wildlife Research Vol. 43, No. 6 ( 2016), p. 461-
    Details
    In: Wildlife Research, CSIRO Publishing, Vol. 43, No. 6 ( 2016), p. 461-
    Abstract: Context Following centuries of intense human exploitation, the global stocks of hawksbill turtle have decreased precipitously and the species is currently considered Critically Endangered by the IUCN. Australia supports the largest breeding aggregations worldwide; however, there are no accurate estimates of population abundance and seasonality for hawksbill turtles at important nesting grounds in eastern Arnhem Land. Aims This study was designed to fill in this lack of ecological information and assist with the conservation and management of hawksbill turtles. More specifically, our overarching goals were to assess nesting seasonality, habitat preferences and provide the first estimate of annual nesting population size at a Northern Territory rookery. Methods In 2009 and 2010 we collected beach monitoring, satellite telemetry and sand temperature data over two nesting seasons at a group of three islands located 30 km off Groote Eylandt in the Gulf of Carpentaria, northern Australia. We subsequently analysed these data to unravel hawksbill nesting behaviour and reproductive outputs, and examined the vulnerability of this rookery to climate change. Key results Hawksbill turtle nesting seasonality consistently started in mid-May, peaked in mid-August and ended in late November. Annual nesting abundance showed a near 3-fold increase between 2009 and 2010, with an average of 220 and 580 hawksbill females nesting on this island group respectively. Sand temperature at 50 cm reached more than 30°C at all monitored sites during most of the peak of the incubation period. Conclusions This remote and untouched group of islands constitutes a major hawksbill turtle rookery both nationally and globally. While anthropogenic impacts and predation are low year round, climate change threatens to skew hatchling sex ratios, eventually leading to an increase in hatchling mortality. Implications Additional ground-based surveys are required to refine the accuracy of population estimates presented in this study. Given the paucity of data in the region, we recommend this island group off Groote Eylandt be used as a population-monitoring index site for the eastern Arnhem Land hawksbill turtle breeding aggregation.
    Type of Medium: Online Resource
    ISSN: 1035-3712
    URL: Article
    DOI: 10.1071/WR16047
    Language: English
    Publisher: CSIRO Publishing
    Publication Date: 2016
    SSG: 12
    SSG: 23
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  • 6
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    A standardisation framework for bio‐logging data to advance ecological research and conservation
    Wiley ; 2021
    In:  Methods in Ecology and Evolution Vol. 12, No. 6 ( 2021-06), p. 996-1007
    Details
    In: Methods in Ecology and Evolution, Wiley, Vol. 12, No. 6 ( 2021-06), p. 996-1007
    Abstract: Bio‐logging data obtained by tagging animals are key to addressing global conservation challenges. However, the many thousands of existing bio‐logging datasets are not easily discoverable, universally comparable, nor readily accessible through existing repositories and across platforms, slowing down ecological research and effective management. A set of universal standards is needed to ensure discoverability, interoperability and effective translation of bio‐logging data into research and management recommendations. We propose a standardisation framework adhering to existing data principles (FAIR: Findable, Accessible, Interoperable and Reusable; and TRUST: Transparency, Responsibility, User focus, Sustainability and Technology) and involving the use of simple templates to create a data flow from manufacturers and researchers to compliant repositories, where automated procedures should be in place to prepare data availability into four standardised levels: (a) decoded raw data, (b) curated data, (c) interpolated data and (d) gridded data. Our framework allows for integration of simple tabular arrays (e.g. csv files) and creation of sharable and interoperable network Common Data Form (netCDF) files containing all the needed information for accuracy‐of‐use, rightful attribution (ensuring data providers keep ownership through the entire process) and data preservation security. We show the standardisation benefits for all stakeholders involved, and illustrate the application of our framework by focusing on marine animals and by providing examples of the workflow across all data levels, including filled templates and code to process data between levels, as well as templates to prepare netCDF files ready for sharing. Adoption of our framework will facilitate collection of Essential Ocean Variables (EOVs) in support of the Global Ocean Observing System (GOOS) and inter‐governmental assessments (e.g. the World Ocean Assessment), and will provide a starting point for broader efforts to establish interoperable bio‐logging data formats across all fields in animal ecology.
    Type of Medium: Online Resource
    ISSN: 2041-210X , 2041-210X
    URL: Issue
    URL: Article
    DOI: 10.1111/mee3.v12.6
    DOI: 10.1111/2041-210X.13593
    Language: English
    Publisher: Wiley
    Publication Date: 2021
    detail.hit.zdb_id: 2528492-7
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  • 7
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    Optimising the design of large-scale acoustic telemetry curtains
    CSIRO Publishing ; 2017
    In:  Marine and Freshwater Research Vol. 68, No. 8 ( 2017), p. 1403-
    Details
    In: Marine and Freshwater Research, CSIRO Publishing, Vol. 68, No. 8 ( 2017), p. 1403-
    Abstract: Broad-scale acoustic telemetry networks are being established worldwide. The 10-year anniversary of the Integrated Marine Observing System’s Animal Tracking Facility provided the opportunity to assess the efficiency of one of the first national-scale acoustic telemetry networks. Acoustic networks are comprised of acoustic receiver arrays that detect high-frequency transmitters attached to animals that pass within detection range. Herein we assessed the efficiency of eight curtains to detect passing animals by calculating the standardised mean number of detections and transmitters detected at each station. The aim was to determine how many receivers could be decommissioned from each curtain while maintaining its integrity (i.e. detection of all species passing the array). Pivotal locations were defined as the furthest station at which all species would still be detected and where at least 75% of the detections and transmitters would still be detected. By applying these criteria, we were able to improve the cost-effectiveness of our network significantly, reducing the number of stations from 132 to 85 (64% of the original network), yet still retaining 84% of total detections, 86% of transmitters and 100% of detected species. The present study provides a useful framework for refining acoustic telemetry networks.
    Type of Medium: Online Resource
    ISSN: 1323-1650
    URL: Article
    DOI: 10.1071/MF16126
    Language: English
    Publisher: CSIRO Publishing
    Publication Date: 2017
    detail.hit.zdb_id: 1283028-8
    SSG: 12
    SSG: 21,3
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  • 8
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    Animal Borne Ocean Sensors – AniBOS – An Essential Component of the Global Ocean Observing System
    Frontiers Media SA ; 2021
    In:  Frontiers in Marine Science Vol. 8 ( 2021-11-5)
    Details
    In: Frontiers in Marine Science, Frontiers Media SA, Vol. 8 ( 2021-11-5)
    Abstract: Marine animals equipped with biological and physical electronic sensors have produced long-term data streams on key marine environmental variables, hydrography, animal behavior and ecology. These data are an essential component of the Global Ocean Observing System (GOOS). The Animal Borne Ocean Sensors (AniBOS) network aims to coordinate the long-term collection and delivery of marine data streams, providing a complementary capability to other GOOS networks that monitor Essential Ocean Variables (EOVs), essential climate variables (ECVs) and essential biodiversity variables (EBVs). AniBOS augments observations of temperature and salinity within the upper ocean, in areas that are under-sampled, providing information that is urgently needed for an improved understanding of climate and ocean variability and for forecasting. Additionally, measurements of chlorophyll fluorescence and dissolved oxygen concentrations are emerging. The observations AniBOS provides are used widely across the research, modeling and operational oceanographic communities. High latitude, shallow coastal shelves and tropical seas have historically been sampled poorly with traditional observing platforms for many reasons including sea ice presence, limited satellite coverage and logistical costs. Animal-borne sensors are helping to fill that gap by collecting and transmitting in near real time an average of 500 temperature-salinity-depth profiles per animal annually and, when instruments are recovered (∼30% of instruments deployed annually, n = 103 ± 34), up to 1,000 profiles per month in these regions. Increased observations from under-sampled regions greatly improve the accuracy and confidence in estimates of ocean state and improve studies of climate variability by delivering data that refine climate prediction estimates at regional and global scales. The GOOS Observations Coordination Group (OCG) reviews, advises on and coordinates activities across the global ocean observing networks to strengthen the effective implementation of the system. AniBOS was formally recognized in 2020 as a GOOS network. This improves our ability to observe the ocean’s structure and animals that live in them more comprehensively, concomitantly improving our understanding of global ocean and climate processes for societal benefit consistent with the UN Sustainability Goals 13 and 14: Climate and Life below Water. Working within the GOOS OCG framework ensures that AniBOS is an essential component of an integrated Global Ocean Observing System.
    Type of Medium: Online Resource
    ISSN: 2296-7745
    URL: Article
    DOI: 10.3389/fmars.2021.751840
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2021
    detail.hit.zdb_id: 2757748-X
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  • 9
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    Australia’s continental-scale acoustic tracking database and its automated quality control process
    Springer Science and Business Media LLC ; 2018
    In:  Scientific Data Vol. 5, No. 1 ( 2018-01-30)
    Details
    In: Scientific Data, Springer Science and Business Media LLC, Vol. 5, No. 1 ( 2018-01-30)
    Abstract: Our ability to predict species responses to environmental changes relies on accurate records of animal movement patterns. Continental-scale acoustic telemetry networks are increasingly being established worldwide, producing large volumes of information-rich geospatial data. During the last decade, the Integrated Marine Observing System’s Animal Tracking Facility (IMOS ATF) established a permanent array of acoustic receivers around Australia. Simultaneously, IMOS developed a centralised national database to foster collaborative research across the user community and quantify individual behaviour across a broad range of taxa. Here we present the database and quality control procedures developed to collate 49.6 million valid detections from 1891 receiving stations. This dataset consists of detections for 3,777 tags deployed on 117 marine species, with distances travelled ranging from a few to thousands of kilometres. Connectivity between regions was only made possible by the joint contribution of IMOS infrastructure and researcher-funded receivers. This dataset constitutes a valuable resource facilitating meta-analysis of animal movement, distributions, and habitat use, and is important for relating species distribution shifts with environmental covariates.
    Type of Medium: Online Resource
    ISSN: 2052-4463
    URL: Article
    DOI: 10.1038/sdata.2017.206
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2018
    detail.hit.zdb_id: 2775191-0
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  • 10
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    Phylogeography, Genetic Diversity, and Management Units of Hawksbill Turtles in the Indo-Pacific
    Oxford University Press (OUP) ; 2016
    In:  Journal of Heredity Vol. 107, No. 3 ( 2016-05), p. 199-213
    Details
    In: Journal of Heredity, Oxford University Press (OUP), Vol. 107, No. 3 ( 2016-05), p. 199-213
    Type of Medium: Online Resource
    ISSN: 0022-1503 , 1465-7333
    URL: Article
    DOI: 10.1093/jhered/esv091
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2016
    detail.hit.zdb_id: 1466720-4
    detail.hit.zdb_id: 2518163-4
    SSG: 12
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