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  • Journals
  • Articles  (10)
  • MDPI  (6)
  • Pensoft Publishers  (4)
  • 2020-2024  (10)
  • 1
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    Towards a scientific workflow featuring Natural Language Processing for the digitisation of natural history collections (2020)
    Pensoft Publishers
    In:  Research Ideas and Outcomes vol. 6 no. e58030
    Details
    Publication Date: 2024-01-12
    Description: We describe an effective approach to automated text digitisation with respect to natural history specimen labels. These labels contain much useful data about the specimen including its collector, country of origin, and collection date. Our approach to automatically extracting these data takes the form of a pipeline. Recommendations are made for the pipeline\'s component parts based on state-of-the-art technologies. \n \nOptical Character Recognition (OCR) can be used to digitise text on images of specimens. However, recognising text quickly and accurately from these images can be a challenge for OCR. We show that OCR performance can be improved by prior segmentation of specimen images into their component parts. This ensures that only text-bearing labels are submitted for OCR processing as opposed to whole specimen images, which inevitably contain non-textual information that may lead to false positive readings. In our testing Tesseract OCR version 4.0.0 offers promising text recognition accuracy with segmented images. \n \nNot all the text on specimen labels is printed. Handwritten text varies much more and does not conform to standard shapes and sizes of individual characters, which poses an additional challenge for OCR. Recently, deep learning has allowed for significant advances in this area. Google\'s Cloud Vision, which is based on deep learning, is trained on large-scale datasets, and is shown to be quite adept at this task. This may take us some way towards negating the need for humans to routinely transcribe handwritten text. \n \nDetermining the countries and collectors of specimens has been the goal of previous automated text digitisation research activities. Our approach also focuses on these two pieces of information. An area of Natural Language Processing (NLP) known as Named Entity Recognition (NER) has matured enough to semi-automate this task. Our experiments demonstrated that existing approaches can accurately recognise location and person names within the text extracted from segmented images via Tesseract version 4.0.0. \n \nWe have highlighted the main recommendations for potential pipeline components. The paper also provides guidance on selecting appropriate software solutions. These include automatic language identification, terminology extraction, and integrating all pipeline components into a scientific workflow to automate the overall digitisation process.
    Keywords: automated text digitisation ; natural language processing ; named entity recognition ; optical character recognition ; handwritten text recognition ; language identification ; terminology extraction ; scientific workflows ; natural history specimens ; label data
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 2
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    Navigating taxonomic complexity: a use-case report on FAIR scientific name-matching service usage in ENVRI Research infrastructures (2024)
    Pensoft Publishers
    In:  Research Ideas and Outcomes vol. 10 no. e121871
    Details
    Publication Date: 2024-04-12
    Description: This paper presents a use-case conducted within the ENVRI FAIR project, examining challenges and opportunities in deploying FAIR-aligned (ensuring Findability, Accessibility, Interoperability and Reusability) scientific name-matching services across Environmental Research Infrastructures (RIs). Six services were tested using various name variations, revealing inconsistencies in match types, status reporting and handling of canonical forms and typos. These diversities pose challenges for RI data pipelines and interoperability. The paper underscores the importance of standardised tools, enhanced communication, training, collaboration and shared resources. Addressing these needs can facilitate more effective FAIR implementation within the ENVRI community and biodiversity research. This, in turn, will empower RIs to seamlessly integrate and leverage scientific names, unlocking the full potential of their data for research and policy implementation.
    Keywords: scientific names ; taxonomy ; biodiversity ; FAIR ; ENVRI
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 3
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    Numerous new records of tropical non-indigenous species in the Eastern Mediterranean highlight the challenges of their recognition and identification (2021)
    Pensoft Publishers
    In:  ZooKeys vol. 1010, pp. 1-95
    Details
    Publication Date: 2024-01-12
    Description: New data on 52 non-indigenous mollusks in the Eastern Mediterranean Sea is reported. Fossarus sp. (aff. aptus sensu Blatterer 2019), Coriophora lessepsiana Albano, Bakker & Sabelli, sp. nov., Cerithiopsis sp. aff. pulvis, Joculator problematicus Albano & Steger, sp. nov., Cerithiopsis sp., Elachisina sp., Iravadia aff. elongata, Vitrinella aff. Vitrinella sp. 1 (sensu Blatterer 2019), Melanella orientalis, Parvioris aff. dilecta, Odostomia cf. dalli, Oscilla virginiae, Parthenina cossmanni, Parthenina typica, Pyrgulina craticulata, Turbonilla funiculata, Cylichna collyra, Musculus coenobitus, Musculus aff. viridulus, Chavania erythraea, Scintilla cf. violescens, Iacra seychellarum and Corbula erythraeensis are new records for the Mediterranean. An unidentified gastropod, Skeneidae indet., Triphora sp., Hypermastus sp., Sticteulima sp., Vitreolina cf. philippi, Odostomia (s.l.) sp. 1, Henrya (?) sp., and Semelidae sp. are further potential new non-indigenous species although their status should be confirmed upon final taxonomic assessment. Additionally, the status of Dikoleps micalii, Hemiliostraca clandestina comb. nov. and H. athenamariae comb. nov. is changed to non-indigenous, range extensions for nine species and the occurrence of living individuals for species previously recorded from empty shells only are reported. Opimaphora blattereri Albano, Bakker & Sabelli, sp. nov. is described from the Red Sea for comparison with the morphologically similar C. lessepsiana Albano, Bakker & Sabelli, sp. nov. The taxonomic part is followed by a discussion on how intensive fieldwork and cooperation among institutions and individuals enabled such a massive report, and how the poor taxonomic knowledge of the Indo-Pacific fauna hampers non-indigenous species detection and identification. Finally, the hypothesis that the simultaneous analysis of quantitative benthic death assemblages can support the assignment of non-indigenous status to taxonomically undetermined species is discussed.
    Keywords: Animal Science and Zoology ; Ecology ; Evolution ; Behavior and Systematics ; Cerithiopsidae ; invasion biology ; Lessepsian invasion ; Mollusca ; new species ; Red Sea ; taxonomy ; Triphoridae
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 4
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    Dynamics and Economics of Shallow Lakes: A Survey (2021)
    MDPI
    In:  EPIC3Sustainability, MDPI, 13(24), pp. 13763-13763, ISSN: 2071-1050
    Details
    Publication Date: 2023-10-23
    Description: We provide an overview of the results devoted to the analysis of the dynamics and economics of shallow lakes, spanning the period from 1999 until now. A shallow lake serves as a typical representative of an ecological system subject to (possibly irreversible) regime shifts. The dynamics of a shallow lake are described by a non-linear model with multiple steady states and multiple domains of attraction and is thus suitable to model the evolution of an ecosystem featuring both resilience within a domain of stability and an abrupt regime shift outside of it. Beyond this, the shallow lake model can also be viewed as a metaphor for many other ecological problems. Due to the broad applicability of this model, there is substantial interest in the management of shallow lakes and both their optimal regulation and competitive usage.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , peerRev
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  • 5
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    The Response of Beech (Fagus sylvatica L.) Populations to Climate in the Easternmost Sites of Its European Distribution (2022)
    MDPI
    In:  EPIC3Plants, MDPI, 11(23), pp. 3310-3310, ISSN: 2223-7747
    Details
    Publication Date: 2024-04-22
    Description: In the context of forecasted climate change scenarios, the growth of forest tree species at their distribution margin is crucial to adapt current forest management strategies. Analyses of beech (Fagus sylvatica L.) growth have shown high plasticity, but easternmost beech populations have been rarely studied. To describe the response of the marginal beech population to the climate in the far east sites of its distribution, we first compiled new tree ring width chronologies. Then we analyzed climate–growth relationships for three marginal beech populations in the Republic of Moldova. We observed a relatively high growth rate in the marginal populations compared to core distribution sites. Our analyses further revealed a distinct and significant response of beech growth to all climatic variables, assessing for the first time the relationship between growth and vapor pressure deficit (VPD) which described how plant growth responds to drought. These results highlight that accumulated water deficit is an essential limiting factor of beech growth in this region. In conclusion, beech growth in the easternmost marginal population is drought-limited, and the sensitivity to VPD will need to be considered in future studies to update the forest management of other economic and ecologically important species.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
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  • 6
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    DiSSCo Transition Abridged Grant Proposal (2024)
    Pensoft Publishers
    In:  Research Ideas and Outcomes vol. 10 no. e118241
    Details
    Publication Date: 2024-02-01
    Description: The Distributed System of Scientific Collections (DiSSCo) is a pan-European Research \nInfrastructure (RI) initiative. DiSSCo aims to bring together natural science collections from \n175 museums, botanical gardens, universities and research institutes across 23 countries \nin a distributed infrastructure that makes these collections physically and digitally open and \naccessible for all forms of research and innovation. DiSSCo RI entered the ESFRI \nroadmap in 2018 and successfully concluded its Preparatory Phase in early 2023. The RI \nis now transitioning towards the constitution of its legal entity (an ERIC) and the start of its \nscaled-up construction (implementation) programme. This publication is an abridged \nversion of the successful grant proposal for the DiSSCo Transition Project which has the \ngoal of ensuring the seamless transition of the DiSSCo RI from its Preparatory Phase to \nthe Construction Phase (expected to start in 2025). In this transition period, the Project will \naddress five objectives building on the outcomes of the Preparatory Phase project: \n1) Advance the DiSSCo ERIC process and complete its policy framework, ensuring the \nsmooth early-phase Implementation of DISSCo; \n2) Engage & support DiSSCo National Nodes to strengthen national commitments; \n3) Advance the development of core e-services to avoid the accumulation of technical debt \nbefore the start of the Implementation Phase; \n4) Continue international collaboration on standards & best practices needed for the \nDiSSCo service provision; and \n5) Continue supporting DiSSCo RI interim governance bodies and transition them to the \nDiSSCo ERIC formal governance. \nThe Project\xe2\x80\x99s impact will be measured against the increase in the RI\'s overall \nImplementation Readiness Level (IRL). More specifically, we will monitor its impact towards \nreaching the required level of maturity in four of the five dimensions of the IRL that can \nbenefit from further developments. These include the organisational, financial, \ntechnological and data readiness levels.
    Keywords: natural science collections ; natural history collections ; research infrastructure ; global ; natural science ; digitisation ; data standards ; Distributed System of Scientific Collections ; DiSSCo ; Digital Specimen Architecture ; FAIR Data Ecosystem ; FAIR digital objects
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 7
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    The Impact of Sea Ice Cover on Microbial Communities in Antarctic Shelf Sediments (2023)
    MDPI
    In:  EPIC3Microorganisms, MDPI, 11(6), pp. 1572-1572, ISSN: 2076-2607
    Details
    Publication Date: 2023-08-03
    Description: The area around the Antarctic Peninsula (AP) is facing rapid climatic and environmental changes, with so far unknown impacts on the benthic microbial communities of the continental shelves. In this study, we investigated the impact of contrasting sea ice cover on microbial community compositions in surface sediments from five stations along the eastern shelf of the AP using 16S ribosomal RNA (rRNA) gene sequencing. Redox conditions in sediments with long ice-free periods are characterized by a prevailing ferruginous zone, whereas a comparatively broad upper oxic zone is present at the heavily ice-covered station. Low ice cover stations were highly dominated by microbial communities of Desulfobacterota (mostly Sva1033, Desulfobacteria, and Desulfobulbia), Myxococcota, and Sva0485, whereas Gammaproteobacteria, Alphaproteobacteria, Bacteroidota, and NB1-j prevail at the heavy ice cover station. In the ferruginous zone, Sva1033 was the dominant member of Desulfuromonadales for all stations and, along with eleven other taxa, showed significant positive correlations with dissolved Fe concentrations, suggesting a significant role in iron reduction or an ecological relationship with iron reducers. Our results indicate that sea ice cover and its effect on organic carbon fluxes are the major drivers for changes in benthic microbial communities, favoring potential iron reducers at stations with increased organic matter fluxes.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
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  • 8
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    An Overview of Extreme Years in Quercus sp. Tree Ring Records from the Northern Moldavian Plateau (2023)
    MDPI
    In:  EPIC3Forests, MDPI, 14(5), pp. 894-894, ISSN: 1999-4907
    Details
    Publication Date: 2024-04-22
    Description: In this study, we made use of a regional oak tree-ring network from six stands that cover the northern Moldavian Plateau (eastern Europe) to analyze how different tree ring parameters (i.e., early wood tree-ring width, late wood tree-ring width, and total tree-ring width) of Quercus sp. are influenced by the occurrence of extreme climatic events (e.g., long-lasting drought events). In order to explore the influence of extreme hydroclimatic events on tree ring width, we have selected each of the six most extreme positive and negative years of tree growth and addressed the seasonal cycle of tree growth in comparison with the main climatic parameters, then evaluated both the current and lagged consequences of extreme hydroclimatic events on tree ring width and the capacity of trees to recover. Our results indicate that the variability of oak tree ring width from the Moldavian Plateau is mainly influenced by the availability of water resources, and that an important limiting growth factor for Quercus sp. is the occurrence of long-lasting drought events, e.g., at least two years in a row with severe drought conditions.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
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  • 9
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    Defining a Precipitation Stable Isotope Framework in the Wider Carpathian Region (2022)
    MDPI
    In:  EPIC3Water, MDPI, 14(16), pp. 2547-2547, ISSN: 2073-4441
    Details
    Publication Date: 2024-04-22
    Description: The eastern part of Europe is very poorly represented in the Global Network for Isotopes in Precipitation (GNIP) database, mainly because the monitoring of the stable isotopes in precipitation started only recently compared with other regions. In this respect, the main objective of this article is to fill the gap in the GNIP database over the eastern part of Europe and show the temporal variability and potential drivers of an extended network of δ18O values in precipitation collected from 27 locations in Romania and the Republic of Moldova. We also present the first high-resolution map of the spatio-temporal distribution of δ18O values in precipitation in Romania and the Republic of Moldova, according to an observational dataset. According to our results, the stations from western and northern Romania tend to have LMWLS with higher values than those from southwestern Romania. The monthly variation of the δ18O and δ2H showed a clearly interannual variation, with distinct seasonal differences, following the seasonal temperatures. The analysis of the spatial distribution of stable isotopes in precipitation water was made on the basis of both observational data and modeled data. This allowed us to study the origin of the air moisture and the interaction with regional and local patterns and to analyze the link between the spatial δ18O variations and the large-scale circulation patterns on a seasonal scale.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
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  • 10
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    Investigating High-Resolution Spatial Wave Patterns on the Canadian Beaufort Shelf Using Synthetic Aperture Radar Imagery at Herschel Island, Qikiqtaruk, Yukon, Canada (2023)
    MDPI
    In:  EPIC3Remote Sensing, MDPI, 15(19), pp. 4753-4753, ISSN: 2072-4292
    Details
    Publication Date: 2024-05-07
    Description: The Arctic is experiencing the greatest increase in air temperature on Earth. This significant climatic change is leading to a significant positive trend of increasing wave heights and greater coastal erosion. This in turn effects local economies and ecosystems. Increasing wave energy is one of the main drivers of this alarming trend. However, the data on spatial and temporal patterns of wave heights in the Arctic are either coarse, interpolated or limited to point measurements. The aim of this study is to overcome this shortcoming by using remote sensing data. In this study, the Synthetic Aperture Radar (SAR) satellite TerraSAR-X (TS-X) and TanDEM-X (TD-X) imagery are used to obtain sea state information with a high spatial resolution in Arctic nearshore waters in the Canadian Beaufort Sea. From the entire archive of the TS-X/TD-X StripMap mode with coverage around 30 km × 50 km acquired between 2009 and 2020 around Herschel Island, Qikiqtaruk (HIQ), all the ice-free scenes were processed. The resulting dataset of 175 collocated scenes was used to map the significant wave height ((Formula presented.)) and to link spatial and temporal patterns to local coastal processes. Sea state parameters are estimated in raster format with a 600 m step using the empirical algorithm CWAVE_EX. The statistics of the (Formula presented.) were aggregated according to spatial variability, seasonality and wind conditions. The results show that the spatial wave climate is clearly related to the dominant wind regime and seasonality. For instance, the aggregation of all the scenes recorded in July between 2009 and 2020 results in an average of 0.82 m (Formula presented.), while in October the average (Formula presented.) is almost 0.40 m higher. The analysis by wind direction shows that fetch length and wind speed are likely the most important variables influencing the spatial variability. A larger fetch under NW conditions results in a mean wave height of 0.92 m, while waves generated under ESE conditions are lower at 0.81 m on average.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
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