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  • 11
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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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  • 12
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    Effects of Measuring Devices and Sampling Strategies on the Interpretation of Monitoring Data for Long-Term Trend Analysis (2021)
    In:  EPIC3Frontiers in Marine Science, 8, pp. 1784
    Details
    Publication Date: 2023-06-21
    Description: A thorough and reliable assessment of changes in sea surface water temperatures (SSWTs) is essential for understanding the effects of global warming on long-term trends in marine ecosystems and their communities. The first long-term temperature measurements were established almost a century ago, especially in coastal areas, and some of them are still in operation. However, while in earlier times these measurements were done by hand every day, current environmental long-term observation stations (ELTOS) are often fully automated and integrated in cabled underwater observatories (UWOs). With this new technology, year-round measurements became feasible even in remote or difficult to access areas, such as coastal areas of the Arctic Ocean in winter, where measurements were almost impossible just a decade ago. In this context, there is a question over what extent the sampling frequency and accuracy influence results in long-term monitoring approaches. In this paper, we address this with a combination of lab experiments on sensor accuracy and precision and a simulated sampling program with different sampling frequencies based on a continuous water temperature dataset from Svalbard, Arctic, from 2012 to 2017. Our laboratory experiments showed that temperature measurements with 12 different temperature sensor types at different price ranges all provided measurements accurate enough to resolve temperature changes over years on a level discussed in the literature when addressing climate change effects in coastal waters. However, the experiments also revealed that some sensors are more suitable for measuring absolute temperature changes over time, while others are more suitable for determining relative temperature changes. Our simulated sampling program in Svalbard coastal waters over 5 years revealed that the selection of a proper sampling frequency is most relevant for discriminating significant long-term temperature changes from random daily, seasonal, or interannual fluctuations. While hourly and daily sampling could deliver reliable, stable, and comparable results concerning temperature increases over time, weekly sampling was less able to reliably detect overall significant trends. With even lower sampling frequencies (monthly sampling), no significant temperature trend over time could be detected. Although the results were obtained for a specific site, they are transferable to other aquatic research questions and non-polar regions.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
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  • 13
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    The Holocene lake-evaporation history of the afro-alpine Lake Garba Guracha in the Bale Mountains, Ethiopia, based on δ18O records of sugar biomarkers and diatoms (2021)
    ACADEMIC PRESS INC ELSEVIER SCIENCE
    In:  EPIC3Quaternary Research, ACADEMIC PRESS INC ELSEVIER SCIENCE, pp. 1-14, ISSN: 0033-5894
    Details
    Publication Date: 2024-06-21
    Description: In eastern Africa, there are few long, high-quality records of environmental change at high altitudes, inhibiting a broader understanding of regional climate change. We investigated a Holocene lacustrine sediment archive from Lake Garba Guracha, Bale Mountains, Ethiopia, (3,950 m a.s.l.), and reconstructed high-altitude lake evaporation history using δ18O records derived from the analysis of compound-specific sugar biomarkers and diatoms. The δ18Odiatom and δ18Ofuc records are clearly correlated and reveal similar ranges (7.9‰ and 7.1‰, respectively). The lowest δ18O values occurred between 10 and 7 cal ka BP and were followed by a continuous shift towards more positive δ18O values. Due to the aquatic origin of the sugar biomarker and the similar trends of δ18Odiatom, we suggest that our lacustrine δ18Ofuc record reflects δ18Olake water. Therefore, without completely excluding the influence of the ‘amount-effect’ and the ‘source-effect‘, we interpret our record to reflect primarily the precipitation-to-evaporation ratio (P/E). We conclude that precipitation increased at the beginning of the Holocene, leading to an overflowing lake between ~10 and ~8 cal ka BP, indicated by low δ18Olake water values interpreted as reduced evaporative enrichment. This is followed by a continuous trend towards drier conditions, indicating at least a seasonally closed lake system.
    Repository Name: EPIC Alfred Wegener Institut
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  • 14
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    Statistical upscaling of ecosystem CO 2 fluxes across the terrestrial tundra and boreal domain: Regional patterns and uncertainties (2021)
    In:  EPIC3Global Change Biology, 27(17), pp. 4040-4059, ISSN: 1354-1013
    Details
    Publication Date: 2024-04-22
    Description: The regional variability in tundra and boreal carbon dioxide (CO2) fluxes can be high, complicating efforts to quantify sink-source patterns across the entire region. Statistical models are increasingly used to predict (i.e., upscale) CO2 fluxes across large spatial domains, but the reliability of different modeling techniques, each with different specifications and assumptions, has not been assessed in detail. Here, we compile eddy covariance and chamber measurements of annual and growing season CO2 fluxes of gross primary productivity (GPP), ecosystem respiration (ER), and net ecosystem exchange (NEE) during 1990–2015 from 148 terrestrial high-latitude (i.e., tundra and boreal) sites to analyze the spatial patterns and drivers of CO2 fluxes and test the accuracy and uncertainty of different statistical models. CO2 fluxes were upscaled at relatively high spatial resolution (1 km2) across the high-latitude region using five commonly used statistical models and their ensemble, that is, the median of all five models, using climatic, vegetation, and soil predictors. We found the performance of machine learning and ensemble predictions to outperform traditional regression methods. We also found the predictive performance of NEE-focused models to be low, relative to models predicting GPP and ER. Our data compilation and ensemble predictions showed that CO2 sink strength was larger in the boreal biome (observed and predicted average annual NEE −46 and −29 g C m−2 yr−1, respectively) compared to tundra (average annual NEE +10 and −2 g C m−2 yr−1). This pattern was associated with large spatial variability, reflecting local heterogeneity in soil organic carbon stocks, climate, and vegetation productivity. The terrestrial ecosystem CO2 budget, estimated using the annual NEE ensemble prediction, suggests the high-latitude region was on average an annual CO2 sink during 1990–2015, although uncertainty remains high.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev , info:eu-repo/semantics/article
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  • 15
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    Late Quaternary Climate Reconstruction and Lead-Lag Relationships of Biotic and Sediment-Geochemical Indicators at Lake Bolshoe Toko, Siberia (2021)
    Frontiers
    In:  EPIC3Frontiers in Earth Science, Frontiers, 9, ISSN: 2296-6463
    Details
    Publication Date: 2024-06-22
    Description: Millennial-scale climate change history in eastern Siberia and relationships between diatom diversity, paleoclimate, and sediment-geochemical lake system trajectories are still poorly understood. This study investigates multi-proxy time series reaching back to the Late Pleistocene derived from radiocarbon dated Lake Bolshoe Toko sediment cores, southeastern Yakutia, Russia. We analyzed diatoms, elements (XRF), minerals (XRD), grain-size, organic carbon, and included chironomid analyses and published pollen-data for quantitative paleoclimate reconstruction. Changes in diatom species abundances reveal repeated episodes of thermal stratification indicated by shifts from euplanktonic Aulacoseira to Cyclotella species. Chironomid and pollen-inferred temperature reconstruction reveal that the main shift between these diatom species is related to the onset of Holocene Thermal Maximum (HTM) at 7.1 cal ka BP. Comparison to other paleoclimate records along a north-south transect through Yakutia shows that the HTM was delayed as far south as the Stanovoy mountains. Relationships between sediment-geochemistry, paleoclimate variability and diatom species richness (alpha diversity) was tested in a moving temporal offset approach to detect lead-lag relationships. Sediment-geochemical data, mainly uniform during the Holocene, revealed strongest positive or negative correlations ahead of species richness changes. Mean July air temperature (TJuly) reconstructions correlate with both Hill numbers and relative assemblage changes indicated by sample scores of multidimensional scaling analysis (MDS) over the entire time series. We found that sediment organic carbon revealed distinct positive correlations, i.e., centennial-scale delay to increases in diatom effective richness (Hill numbers N0 and N2). We conclude that a lag of deposited organic carbon concentrations behind changes in diatom alpha diversity reveals that species richness can augment the production and thus sequestration of organic matter in comparable lake systems.
    Repository Name: EPIC Alfred Wegener Institut
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  • 16
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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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  • 17
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    Mollusc species response to drivers in space and time: Rise and demise of the unique Pontocaspian fauna (2020)
    Details
    Publication Date: 2024-01-12
    Description: The evolution of the Pontocaspian lakes and seas (Caspian Sea, Black Sea, Aral Sea) is characterised by major changes in water levels, which developed into a pulsating system of connected and isolated basins. During the late Quaternary (Late Pleistocene and Holocene), these basins have hosted a unique endemic biodiversity that experienced species turnover events. There are indications that the Pontocaspian species diversity is now in demise because of anthropogenic modifications of the ecosystem, such as habitat alteration, poaching, pollution and invasive species. Little data is available on faunal changes and resilience of Pontocaspian species to help discerning the effect of natural drivers and anthropogenic drivers on the endemic fauna, which is of direct relevance for conservation strategies. \nThis thesis aims to characterize species richness and abundance of fossil faunas to establish a baseline for comparison with the changing biodiversity of today. Mollusc species are used as the study group as they easily fossilize and are abundant in the geological record. They inform us about the composition of communities and how they change, and enable us to reconstruct environments (\xe2\x80\x98habitats\xe2\x80\x99). This is necessary in order to compare biodiversity through different time intervals and establish whether comparable habitats existed as those of today. A baseline of Pontocaspian mollusc faunas was achieved by analysing snapshots from the Caspian Sea basin and the Black Sea basin. Caspian mollusc assemblages are analysed from late Pleistocene (corresponding to the late Khazarian, Hyrcanian, early Khvalynian and late Khvalynian regional stages) and pre-20th century Holocene (Novocaspian) assemblages. Black Sea assemblages from the late Neoeuxinian and late Holocene are described. They are both compared with modern day assemblages. \nThis study shows clear indications of a Pontocaspian mollusc diversity crisis. Overall, in the 20th\xe2\x80\x9321st century, Pontocaspian molluscs have experienced a severe decline in species richness and abundance: a strong turnover towards invasive species in the Caspian basin, a strong habitat decline in parts of the Black Sea basin and a total obliteration in the Aral basin. The late Quaternary mollusc fauna snapshots demonstrate that endemic species dominated the Caspian communities with minor contributions of native species until the late Holocene. The Pontocaspian mollusc species richness in the Caspian Sea basin is higher than in the Pontocaspian habitats of the Black Sea basin, or the Aral Sea basin. Throughout the Late Quaternary, the strong natural fluctuations of Caspian Sea level affected shallow water bivalve species of the genus Didacna, but barely changed the overall composition of the mollusc faunas. Late Quaternary mollusc fauna snapshots of the Black Sea basin show very little change in the Pontocaspian species community since humans impacted the habitats. However, the Black Sea Pontocaspian mollusc communities are currently under severe threat of habitat deterioration and destruction. \nThis research indicates that the Caspian Sea could act as a source for Pontocaspian biota, hence conservation efforts are imperative there. The deeper parts (〉50 m water depth) possibly present a (partial) refuge, and urgent research is required to assess these habitats and their faunas. Future research should focus on improving the taxonomic framework to elucidate the identity of some Pontocaspian cryptic and sister species. We need more distribution and ecological data of current Pontocaspian species and more detailed biodiversity time series coupled with detailed environmental proxies to assess the nature of the Pontocaspian biodiversity crisis more comprehensively and plan conservation actions accordingly.
    Keywords: Pontocaspian ; Biodiversity ; Quaternary ; Mollusca ; Marie Sk\xc5\x82odowska-Curie Actions ; Action: H2020-MSCA-ITN-2014 ; PRIDE ; Grant agreement no: 642973
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/doctoralThesis
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  • 18
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    Diversity and regional distribution of harmful algal events along the Atlantic margin of Europe (2021)
    Elsevier
    In:  EPIC3Harmful Algae, Elsevier, ISSN: 15689883
    Details
    Publication Date: 2023-03-13
    Description: The IOC-ICES-PICES Harmful Algal Event Database (HAEDAT) was used to describe the diversity and spatiotemporal distribution of harmful algal events along the Atlantic margin of Europe from 1987 - 2018. The majority of events recorded are caused by Diarrhetic Shellfish Toxins (DSTs). These events are recorded annually over a wide geographic area from southern Spain to northern Scotland and Iceland, and are responsible for annual closures of many shellfish harvesting areas. The dominant causative dinoflagellates, members of the morphospecies ‘Dinophysis acuminata complex’ and D. acuta, are common in the waters of the majority of countries affected. There are regional differences in the causative species associated with PST events; the coasts of Spain and Portugal with the dinoflagellates Alexandrium minutum and Gymnodinium catenatum, north west France/south west England/south Ireland with A. minutum, and Scotland/Faroe Islands/Iceland with A. catenella. This can influence the duration and spatial scale of PST events as well as the toxicity of shellfish. The diatom Pseudo-nitzschia australis is the most widespread Domoic Acid (DA) producer, with records coming from Spain, Portugal, France, Ireland and the UK. Amnesic Shellfish Toxins (ASTs) have caused prolonged closures for the scallop fishing industry due to the slow depuration rate of DA. Amendments to EU shellfish hygiene regulations introduced between 2002 and 2005 facilitated end-product testing and sale of adductor muscle. This reduced the impact of ASTs on the scallop fishing industry and thus the number of recorded HAEDAT events. Azaspiracids (AZAs) are the most recent toxin group responsible for events to be characterised in the ICES area. Events associated with AZAs have a discrete distribution with the majority recorded along the west coast of Ireland. Ciguatera Poisoning (CP) has been an emerging issue in the Canary Islands and Madeira since 2004. The majority of aquaculture and wild fish mortality events are associated with blooms of the dinoflagellate Karenia mikimotoi and raphidophyte Heterosigma akashiwo. Such fish killing events occur infrequently yet can cause significant mortalities. Interannual variability was observed in the annual number of HAEDAT areas with events associated with individual shellfish toxin groups. HABs represent a continued risk for the aquaculture industry along the Atlantic margin of Europe and along the Atlantic margin of Europe and should be accounted for when considering expansion of the industry or operational shifts to offshore areas.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev , info:eu-repo/semantics/article
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  • 19
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    Thermokarst Lagoons: A Core-Based Assessment of Depositional Characteristics and an Estimate of Carbon Pools on the Bykovsky Peninsula (2021)
    Frontiers Research Foundation
    In:  EPIC3Frontiers in Earth Science, Frontiers Research Foundation, 9, ISSN: 2296-6463
    Details
    Publication Date: 2024-01-31
    Description: Permafrost region subsurface organic carbon (OC) pools are a major component of the terrestrial carbon cycle and vulnerable to a warming climate. Thermokarst lagoons are an important transition stage with complex depositional histories during which permafrost and lacustrine carbon pools are transformed along eroding Arctic coasts. The effects of temperature and salinity changes during thermokarst lake to lagoon transitions on thaw history and lagoon deposits are understudied. We analyzed two 30-m-long sediment cores from two thermokarst lagoons on the Bykovsky Peninsula, Northeast Siberia, using sedimentological, geochronological, hydrochemical, and biogeochemical techniques. Using remote sensing we distinguished between a semi-closed and a nearly closed lagoon. We (1) characterized the depositional history, (2) studied the impact of marine inundation on ice-bearing permafrost and taliks, and (3) quantified the OC pools for different stages of thermokarst lagoons. Fluvial and former Yedoma deposits were found at depth between 30 and 8.5 m, while lake and lagoon deposits formed the upper layers. The electrical conductivity of the pore water indicated hypersaline conditions for the semi-closed lagoon (max: 108 mS/cm), while fresh to brackish conditions were observed beneath a 5 m-thick surface saline layer at the nearly closed lagoon. The deposits had a mean OC content of 15 ± 2 kg/m3, with higher values in the semi-closed lagoon. Based on the cores we estimated a total OC pool of 5.7 Mt-C for the first 30 m of sediment below five mapped lagoons on the Bykovsky Peninsula. Our results suggest that paleo river branches shaped the middle Pleistocene landscape followed by late Pleistocene Yedoma permafrost accumulation and early Holocene lake development. Afterward, lake drainage, marine flooding, and bedfast ice formation caused the saline enrichment of pore water, which led to cryotic talik development. We find that the OC-pool of Arctic lagoons may comprise a substantial inventory of partially thawed and partially refrozen OC, which is available for microbial degradation processes at the Arctic terrestrial-marine interface. Climate change in the Arctic leading to sea level rise, permafrost thaw, coastal erosion, and sea ice loss may increase the rate of thermokarst lagoon formation and thus increase the importance of lagoons as biogeochemical processors of former permafrost OC.
    Repository Name: EPIC Alfred Wegener Institut
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  • 20
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    Vibrio and Bacterial Communities Across a Pollution Gradient in the Bay of Bengal: Unraveling Their Biogeochemical Drivers (2020)
    Frontiers Media SA
    In:  EPIC3Frontiers in Microbiology, Frontiers Media SA, 11, pp. 594-, ISSN: 1664-302X
    Details
    Publication Date: 2024-04-09
    Description: The highly populated coasts of the Bay of Bengal are particularly vulnerable to water-borne diseases, pollution and climatic extremes. The environmental factors behind bacterial community composition and Vibrio distribution were investigated in an estuarine system of a cholera-endemic region in the coastline of Bangladesh. Higher temperatures and sewage pollution were important drivers of the abundance of toxigenic Vibrio cholerae. A closer relation between non-culturable Vibrio and particulate organic matter (POM) was inferred during the post-monsoon. The distribution of operational taxonomic units (OTUs) of Vibrio genus was likely driven by salinity and temperature. The resuspension of sediments increased Vibrio abundance and organic nutrient concentrations. The δ13C dynamic in POM followed an increasing gradient from freshwater to marine stations; nevertheless, it was not a marker of sewage pollution. Bacteroidales and culturable coliforms were reliable indicators of untreated wastewater during pre and post-monsoon seasons. The presumptive incorporation of depleted-ammonium derived from ammonification processes under the hypoxic conditions, by some microorganisms such as Cloacibacterium and particularly by Arcobacter nearby the sewage discharge, contributed to the drastic 15N depletion in the POM. The likely capacity of extracellular polymeric substances production of these taxa may facilitate the colonization of POM from anthropogenic origin and may signify important properties for wastewater bioremediation. Genera of potential pathogens other than Vibrio associated with sewage pollution were Acinetobacter, Aeromonas, Arcobacter, and Bergeyella. The changing environmental conditions of the estuary favored the abundance of early colonizers and the island biogeography theory explained the distribution of some bacterial groups. This multidisciplinary study evidenced clearly the eutrophic conditions of the Karnaphuli estuary and assessed comprehensively its current bacterial baseline and potential risks. The prevailing conditions together with human overpopulation and frequent natural disasters, transform the region in one of the most vulnerable to climate change. Adaptive management strategies are urgently needed to enhance ecosystem health.
    Repository Name: EPIC Alfred Wegener Institut
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