Moussab/ORKG-training-evaluation-set huggingface dataset:
Research field: Earth Sciences
Title: Mapping Hydrothermally Altered Rocks at Cuprite, Nevada, Using the Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER), a New Satellite-Imaging System
Abstract: The Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) is a 14-band multispectral instrument on board the Earth Observing System (EOS), TERRA. The three bands between 0.52 and 0.86 μ m and the six bands from 1.60 and 2.43 μ m, which have 15- and 30-m spatial resolution, respectively, were selected primarily for making remote mineralogical determinations. The Cuprite, Nevada, mining district comprises two hydrothermal alteration centers where Tertiary volcanic rocks have been hydrothermally altered mainly to bleached silicified rocks and opalized rocks, with a marginal zone of limonitic argillized rocks. Country rocks are mainly Cambrian phyllitic siltstone and limestone. Evaluation of an ASTER image of the Cuprite district shows that spectral reflectance differences in the nine bands in the 0.52 to 2.43 μ m region provide a basis for identifying and mapping mineralogical components which characterize the main hydrothermal alteration zones: opal is the spectrally dominant mineral in the silicified zone; whereas, alunite and kaolinite are dominant in the opalized zone. In addition, the distribution of unaltered country rocks was mapped because of the presence of spectrally dominant muscovite in the siltstone and calcite in limestone, and the tuffaceous rocks and playa deposits were distinguishable due to their relatively flat spectra and weak absorption features at 2.33 and 2.20 μ m, respectively. An Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) image of the study area was processed using a similar methodology used with the ASTER data. Comparison of the ASTER and AVIRIS results shows that the results are generally similar, but the higher spectral resolution of AVIRIS (224 bands) permits identification of more individual minerals, including certain polymorphs. However, ASTER has recorded images of more than 90 percent of the Earth’s land surface with less than 20 percent cloud cover, and these data are available at nominal or no cost. Landsat TM images have a similar spatial resolution to ASTER images, but TM has fewer bands, which limits its usefulness for making mineral determinations.
Extracted statement — Data used: AVIRIS
Research field: Earth Sciences
Title: Simple mineral mapping algorithm based on multitype spectral diagnostic absorption features: a case study at Cuprite, Nevada
Abstract: Abstract. Hyperspectral remote sensing has been widely used in mineral identification using the particularly useful short-wave infrared (SWIR) wavelengths (1.0 to 2.5 μm). Current mineral mapping methods are easily limited by the sensor’s radiometric sensitivity and atmospheric effects. Therefore, a simple mineral mapping algorithm (SMMA) based on the combined application with multitype diagnostic SWIR absorption features for hyperspectral data is proposed. A total of nine absorption features are calculated, respectively, from the airborne visible/infrared imaging spectrometer data, the Hyperion hyperspectral data, and the ground reference spectra data collected from the United States Geological Survey (USGS) spectral library. Based on spectral analysis and statistics, a mineral mapping decision-tree model for the Cuprite mining district in Nevada, USA, is constructed. Then, the SMMA algorithm is used to perform mineral mapping experiments. The mineral map from the USGS (USGS map) in the Cuprite area is selected for validation purposes. Results showed that the SMMA algorithm is able to identify most minerals with high coincidence with USGS map results. Compared with Hyperion data (overall accuracy=74.54%), AVIRIS data showed overall better mineral mapping results (overall accuracy=94.82%) due to low signal-to-noise ratio and high spatial resolution.
Extracted statement — Data used: AVIRIS
Research field: Earth Sciences
Title: Mapping hydrothermal alteration minerals using high-resolution AVIRIS-NG hyperspectral data in the Hutti-Maski gold deposit area, India
Abstract: ABSTRACT The present study exploits high-resolution hyperspectral imagery acquired by the Airborne Visible/Infrared Imaging Spectrometer-Next Generation (AVIRIS-NG) sensor from the Hutti-Maski gold deposit area, India, to map hydrothermal alteration minerals. The study area is a volcanic-dominated late Archean greenstone belt that hosts major gold mineralization in the Eastern Dharwar Craton of southern India. The study encompasses pre-processing, spectral and spatial image reduction using Minimum Noise Fraction (MNF) and Fast Pixel Purity Index (FPPI), followed by endmember extraction using n-dimensional visualizer and the United States Geological Survey (USGS) mineral spectral library. Image derived endmembers such as goethite, chlorite, chlorite at the mine site (chlorite mixed with mined materials), kaolinite, and muscovite were subsequently used in spectral mapping methods such as Spectral Angle Mapper (SAM), Spectral Information Divergence (SID) and its hybrid, i.e. SIDSAMtan. Spectral similarity matrix of the target and non-target-based method has been proposed to find the possible optimum threshold needed to obtain mineral map using spectral mapping methods. Relative Spectral Discrimination Power (RSDPW) and Confusion Matrix (CM) have been used to evaluate the performance of SAM, SID, and SIDSAMtan. The RSDPW and CM illustrate that the SIDSAMtan benefits from the unique characteristics of SAM and SID to achieve better discrimination capability. The Overall Accuracy (OA) and kappa coefficient (ҡ) of SAM, SID, and SIDSAMtan were computed using 900 random validation points and obtained 90% (OA) and 0.88 (ҡ), 91.4% and 0.90, and 94.4% and 0.93, respectively. Obtained mineral map demonstrates that the northern portion of the area mainly consists of muscovite whereas the southern part is marked by chlorite, goethite, muscovite and kaolinite, indicating the propylitic alteration. Most of these minerals are associated with altered metavolcanic rocks and migmatite.
Extracted statement — yields: SIDSAM
Research field: Earth Sciences
Title: Classification of Iowa wetlands using an airborne hyperspectral image: a comparison of the spectral angle mapper classifier and an object-oriented approach
Abstract: Wetlands mapping using multispectral imagery from Landsat multispectral scanner (MSS) and thematic mapper (TM) and Système pour l'observation de la Terre (SPOT) does not in general provide high classification accuracies because of poor spectral and spatial resolutions. This study tests the feasibility of using high-resolution hyperspectral imagery to map wetlands in Iowa with two nontraditional classification techniques: the spectral angle mapper (SAM) method and a new nonparametric object-oriented (OO) classification. The software programs used were ENVI and eCognition. Accuracies of these classified images were assessed by using the information collected through a field survey with a global positioning system and high-resolution color infrared images. Wetlands were identified more accurately with the OO method (overall accuracy 92.3%) than with SAM (63.53%). This paper also discusses the limitations of these classification techniques for wetlands, as well as discussing future directions for study.
Extracted statement — Softwares:  eCognition
Research field: Earth Sciences
Title: Spectral angle mapper and object-based classification combined with hyperspectral remote sensing imagery for obtaining land use/cover mapping in a Mediterranean region
Abstract: In this study, we test the potential of two different classification algorithms, namely the spectral angle mapper (SAM) and object-based classifier for mapping the land use/cover characteristics using a Hyperion imagery. We chose a study region that represents a typical Mediterranean setting in terms of landscape structure, composition and heterogeneous land cover classes. Accuracy assessment of the land cover classes was performed based on the error matrix statistics. Validation points were derived from visual interpretation of multispectral high resolution QuickBird-2 satellite imagery. Results from both the classifiers yielded more than 70% classification accuracy. However, the object-based classification clearly outperformed the SAM by 7.91% overall accuracy (OA) and a relatively high kappa coefficient. Similar results were observed in the classification of the individual classes. Our results highlight the potential of hyperspectral remote sensing data as well as object-based classification approach for mapping heterogeneous land use/cover in a typical Mediterranean setting.
Extracted statement — Datasets: Quickbird-2
Research field: Earth Sciences
Title: Development and utilization of urban spectral library for remote sensing of urban environment
Abstract: Hyperspectral technology is useful for urban studies due to its capability in examining detailed spectral characteristics of urban materials. This study aims to develop a spectral library of urban materials and demonstrate its application in remote sensing analysis of an urban environment. Field measurements were conducted by using ASD FieldSpec 3 Spectroradiometer with wavelength range from 350 to 2500 nm. The spectral reflectance curves of urban materials were interpreted and analyzed. A collection of 22 spectral data was compiled into a spectral library. The spectral library was put to practical use by utilizing the reference spectra for WorldView-2 satellite image classification which demonstrates the usability of such infrastructure to facilitate further progress of remote sensing applications in Malaysia.
Extracted statement — Sensors: WorldView-2
Research field: Earth Sciences
Title: Development and evaluation of an Earth-System model – HadGEM2
Abstract: Abstract. We describe here the development and evaluation of an Earth system model suitable for centennial-scale climate prediction. The principal new components added to the physical climate model are the terrestrial and ocean ecosystems and gas-phase tropospheric chemistry, along with their coupled interactions. The individual Earth system components are described briefly and the relevant interactions between the components are explained. Because the multiple interactions could lead to unstable feedbacks, we go through a careful process of model spin up to ensure that all components are stable and the interactions balanced. This spun-up configuration is evaluated against observed data for the Earth system components and is generally found to perform very satisfactorily. The reason for the evaluation phase is that the model is to be used for the core climate simulations carried out by the Met Office Hadley Centre for the Coupled Model Intercomparison Project (CMIP5), so it is essential that addition of the extra complexity does not detract substantially from its climate performance. Localised changes in some specific meteorological variables can be identified, but the impacts on the overall simulation of present day climate are slight. This model is proving valuable both for climate predictions, and for investigating the strengths of biogeochemical feedbacks.
Extracted statement — has research problem: CMIP5
Research field: Ecology and Biodiversity of Animals and Ecosystems, Organismic Interactions
Title: Characterization and comparison of poorly known moth communities through DNA barcoding in two Afrotropical environments in Gabon
Abstract: Biodiversity research in tropical ecosystems-popularized as the most biodiverse habitats on Earth-often neglects invertebrates, yet invertebrates represent the bulk of local species richness. Insect communities in particular remain strongly impeded by both Linnaean and Wallacean shortfalls, and identifying species often remains a formidable challenge inhibiting the use of these organisms as indicators for ecological and conservation studies. Here we use DNA barcoding as an alternative to the traditional taxonomic approach for characterizing and comparing the diversity of moth communities in two different ecosystems in Gabon. Though sampling remains very incomplete, as evidenced by the high proportion (59%) of species represented by singletons, our results reveal an outstanding diversity. With about 3500 specimens sequenced and representing 1385 BINs (Barcode Index Numbers, used as a proxy to species) in 23 families, the diversity of moths in the two sites sampled is higher than the current number of species listed for the entire country, highlighting the huge gap in biodiversity knowledge for this country. Both seasonal and spatial turnovers are strikingly high (18.3% of BINs shared between seasons, and 13.3% between sites) and draw attention to the need to account for these when running regional surveys. Our results also highlight the richness and singularity of savannah environments and emphasize the status of Central African ecosystems as hotspots of biodiversity.
Extracted statement — higher number estimated species (Method): BINs
Research field: Ecology and Biodiversity of Animals and Ecosystems, Organismic Interactions
Title: Probing planetary biodiversity with DNA barcodes: The Noctuoidea of North America
Abstract: This study reports the assembly of a DNA barcode reference library for species in the lepidopteran superfamily Noctuoidea from Canada and the USA. Based on the analysis of 69,378 specimens, the library provides coverage for 97.3% of the noctuoid fauna (3565 of 3664 species). In addition to verifying the strong performance of DNA barcodes in the discrimination of these species, the results indicate close congruence between the number of species analyzed (3565) and the number of sequence clusters (3816) recognized by the Barcode Index Number (BIN) system. Distributional patterns across 12 North American ecoregions are examined for the 3251 species that have GPS data while BIN analysis is used to quantify overlap between the noctuoid faunas of North America and other zoogeographic regions. This analysis reveals that 90% of North American noctuoids are endemic and that just 7.5% and 1.8% of BINs are shared with the Neotropics and with the Palearctic, respectively. One third (29) of the latter species are recent introductions and, as expected, they possess low intraspecific divergences.
Extracted statement — higher number estimated species (Method): BINs
Research field: Ecology and Biodiversity of Animals and Ecosystems, Organismic Interactions
Title: A DNA barcode library for 5,200 German flies and midges (Insecta: Diptera) and its implications for metabarcoding‐based biomonitoring
Abstract: This study summarizes results of a DNA barcoding campaign on German Diptera, involving analysis of 45,040 specimens. The resultant DNA barcode library includes records for 2,453 named species comprising a total of 5,200 barcode index numbers (BINs), including 2,700 COI haplotype clusters without species‐level assignment, so called “dark taxa.” Overall, 88 out of 117 families (75%) recorded from Germany were covered, representing more than 50% of the 9,544 known species of German Diptera. Until now, most of these families, especially the most diverse, have been taxonomically inaccessible. By contrast, within a few years this study provided an intermediate taxonomic system for half of the German Dipteran fauna, which will provide a useful foundation for subsequent detailed, integrative taxonomic studies. Using DNA extracts derived from bulk collections made by Malaise traps, we further demonstrate that species delineation using BINs and operational taxonomic units (OTUs) constitutes an effective method for biodiversity studies using DNA metabarcoding. As the reference libraries continue to grow, and gaps in the species catalogue are filled, BIN lists assembled by metabarcoding will provide greater taxonomic resolution. The present study has three main goals: (a) to provide a DNA barcode library for 5,200 BINs of Diptera; (b) to demonstrate, based on the example of bulk extractions from a Malaise trap experiment, that DNA barcode clusters, labelled with globally unique identifiers (such as OTUs and/or BINs), provide a pragmatic, accurate solution to the “taxonomic impediment”; and (c) to demonstrate that interim names based on BINs and OTUs obtained through metabarcoding provide an effective method for studies on species‐rich groups that are usually neglected in biodiversity research projects because of their unresolved taxonomy.
Extracted statement — higher number estimated species (Method): BINs
Research field: Ecology and Biodiversity of Animals and Ecosystems, Organismic Interactions
Title: DNA barcode library for European Gelechiidae (Lepidoptera) suggests greatly underestimated species diversity
Abstract: For the first time, a nearly complete barcode library for European Gelechiidae is provided. DNA barcode sequences (COI gene - cytochrome c oxidase 1) from 751 out of 865 nominal species, belonging to 105 genera, were successfully recovered. A total of 741 species represented by specimens with sequences ≥ 500bp and an additional ten species represented by specimens with shorter sequences were used to produce 53 NJ trees. Intraspecific barcode divergence averaged only 0.54% whereas distance to the Nearest-Neighbour species averaged 5.58%. Of these, 710 species possessed unique DNA barcodes, but 31 species could not be reliably discriminated because of barcode sharing or partial barcode overlap. Species discrimination based on the Barcode Index System (BIN) was successful for 668 out of 723 species which clustered from minimum one to maximum 22 unique BINs. Fifty-five species shared a BIN with up to four species and identification from DNA barcode data is uncertain. Finally, 65 clusters with a unique BIN remained unidentified to species level. These putative taxa, as well as 114 nominal species with more than one BIN, suggest the presence of considerable cryptic diversity, cases which should be examined in future revisionary studies.
Extracted statement — higher number estimated species (Method): BINs
Research field: Ecology and Biodiversity of Animals and Ecosystems, Organismic Interactions
Title: A DNA Barcode Library for North American Pyraustinae (Lepidoptera: Pyraloidea: Crambidae)
Abstract: Although members of the crambid subfamily Pyraustinae are frequently important crop pests, their identification is often difficult because many species lack conspicuous diagnostic morphological characters. DNA barcoding employs sequence diversity in a short standardized gene region to facilitate specimen identifications and species discovery. This study provides a DNA barcode reference library for North American pyraustines based upon the analysis of 1589 sequences recovered from 137 nominal species, 87% of the fauna. Data from 125 species were barcode compliant (>500bp, <1% n), and 99 of these taxa formed a distinct cluster that was assigned to a single BIN. The other 26 species were assigned to 56 BINs, reflecting frequent cases of deep intraspecific sequence divergence and a few instances of barcode sharing, creating a total of 155 BINs. Two systems for OTU designation, ABGD and BIN, were examined to check the correspondence between current taxonomy and sequence clusters. The BIN system performed better than ABGD in delimiting closely related species, while OTU counts with ABGD were influenced by the value employed for relative gap width. Different species with low or no interspecific divergence may represent cases of unrecognized synonymy, whereas those with high intraspecific divergence require further taxonomic scrutiny as they may involve cryptic diversity. The barcode library developed in this study will also help to advance understanding of relationships among species of Pyraustinae.
Extracted statement — higher number estimated species (Method): BINs
Research field: Ecology and Biodiversity of Animals and Ecosystems, Organismic Interactions
Title: Close congruence between Barcode Index Numbers (bins) and species boundaries in the Erebidae (Lepidoptera: Noctuoidea) of the Iberian Peninsula
Abstract: Abstract The DNA barcode reference library for Lepidoptera holds much promise as a tool for taxonomic research and for providing the reliable identifications needed for conservation assessment programs. We gathered sequences for the barcode region of the mitochondrial cytochrome c oxidase subunit I gene from 160 of the 176 nominal species of Erebidae moths (Insecta: Lepidoptera) known from the Iberian Peninsula. These results arise from a research project which constructing a DNA barcode library for the insect species of Spain. New records for 271 specimens (122 species) are coupled with preexisting data for 38 species from the Iberian fauna. Mean interspecific distance was 12.1%, while the mean nearest neighbour divergence was 6.4%. All 160 species possessed diagnostic barcode sequences, but one pair of congeneric taxa (Eublemma rosea and Eublemma rietzi) were assigned to the same BIN. As well, intraspecific sequence divergences higher than 1.5% were detected in four species which likely represent species complexes. This study reinforces the effectiveness of DNA barcoding as a tool for monitoring biodiversity in particular geographical areas and the strong correspondence between sequence clusters delineated by BINs and species recognized through detailed taxonomic analysis.
Extracted statement — lower number estimated species (Method): BINs
Research field: Ecology and Biodiversity of Animals and Ecosystems, Organismic Interactions
Title: A Transcontinental Challenge — A Test of DNA Barcode Performance for 1,541 Species of Canadian Noctuoidea (Lepidoptera)
Abstract: This study provides a first, comprehensive, diagnostic use of DNA barcodes for the Canadian fauna of noctuoids or “owlet” moths (Lepidoptera: Noctuoidea) based on vouchered records for 1,541 species (99.1% species coverage), and more than 30,000 sequences. When viewed from a Canada-wide perspective, DNA barcodes unambiguously discriminate 90% of the noctuoid species recognized through prior taxonomic study, and resolution reaches 95.6% when considered at a provincial scale. Barcode sharing is concentrated in certain lineages with 54% of the cases involving 1.8% of the genera. Deep intraspecific divergence exists in 7.7% of the species, but further studies are required to clarify whether these cases reflect an overlooked species complex or phylogeographic variation in a single species. Non-native species possess higher Nearest-Neighbour (NN) distances than native taxa, whereas generalist feeders have lower NN distances than those with more specialized feeding habits. We found high concordance between taxonomic names and sequence clusters delineated by the Barcode Index Number (BIN) system with 1,082 species (70%) assigned to a unique BIN. The cases of discordance involve both BIN mergers and BIN splits with 38 species falling into both categories, most likely reflecting bidirectional introgression. One fifth of the species are involved in a BIN merger reflecting the presence of 158 species sharing their barcode sequence with at least one other taxon, and 189 species with low, but diagnostic COI divergence. A very few cases (13) involved species whose members fell into both categories. Most of the remaining 140 species show a split into two or three BINs per species, while Virbia ferruginosa was divided into 16. The overall results confirm that DNA barcodes are effective for the identification of Canadian noctuoids. This study also affirms that BINs are a strong proxy for species, providing a pathway for a rapid, accurate estimation of animal diversity.
Extracted statement — lower number estimated species (Method): BINs