cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.4145996
title: Carbon and hydrogen isotope fractionation during uncultured aerobic oxidation of short-chain alkanes that discharged from a natural hydrothermal system

description: Aerobic oxidation of short-chain alkanes was observed in gas samples from the Lutao intertidal hydrothermal vents in Taiwan, during storage without adding strains and replenishing substrates at 20 <sup>o</sup>C up to 29 months. The carbon isotope fractionation factors (<em>ε<sub>C</sub></em>) of methane (C<sub>1</sub>), ethane (C<sub>2</sub>), and propane (C<sub>3</sub>), were calculated using the Rayleigh fractionation equation to be -37.1 ± 7.5‰, -14.8 ± 4.8‰, and -4.7 ± 5.2‰, respectively. The hydrogen isotope fractionation factor (<em>ε<sub>H</sub></em>) of methane was determined to be -281 ± 187‰. DNA sequencing of the 16sRNA gene in the vent fluids suggests that aerobic oxidation is dominated by methanotrophs of the genera <em>Methylomicrobium</em> and <em>Methylophaga,</em> which use the ribulose monophosphate pathway (RuMP). The degrees of isotope fractionation (<em>ε<sub>C</sub></em> and <em>ε<sub>H</sub></em> values) herein are larger than previously reported values, possibly due to the limited O<sub>2</sub> supply and low abundance of aerobic methane-oxidizing bacteria in the experiments. Since the fractionation factor of methane is higher than those of ethane and propane, the aerobic oxidation of thermogenic or microbial alkanes could produce carbon isotope reversal, which is frequently noted as a trait of abiotic hydrocarbons. This work demonstrates that in addition to anaerobic microbial oxidation, aerobic oxidation with a low cell density can also produce significant isotope fractionation of alkanes in geological closed/semi-closed environments that are characterized by moderate temperatures and a limited supply of substrates and O<sub>2</sub>; these environments include cold seeps, mud volcanoes, and low-temperature hydrothermal aquifers/reservoirs.
DOI: 10.5281/zenodo.3813159
title: Carbon and hydrogen isotope fractionation during uncultured aerobic oxidation of short-chain alkanes that discharged from a natural hydrothermal system

description: Aerobic oxidation of short-chain alkanes was observed in gas samples from the Lutao intertidal hydrothermal vents in Taiwan, during storage without adding strains and replenishing substrates at 20 <sup>o</sup>C up to 29 months. The carbon isotope fractionation factors (<em>ε<sub>C</sub></em>) of methane (C<sub>1</sub>), ethane (C<sub>2</sub>), and propane (C<sub>3</sub>), were calculated using the Rayleigh fractionation equation to be -37.1 ± 7.5‰, -14.8 ± 4.8‰, and -4.7 ± 5.2‰, respectively. The hydrogen isotope fractionation factor (<em>ε<sub>H</sub></em>) of methane was determined to be -281 ± 187‰. DNA sequencing of the 16sRNA gene in the vent fluids suggests that aerobic oxidation is dominated by methanotrophs of the genera <em>Methylomicrobium</em> and <em>Methylophaga,</em> which use the ribulose monophosphate pathway (RuMP). The degrees of isotope fractionation (<em>ε<sub>C</sub></em> and <em>ε<sub>H</sub></em> values) herein are larger than previously reported values, possibly due to the limited O<sub>2</sub> supply and low abundance of aerobic methane-oxidizing bacteria in the experiments. Since the fractionation factor of methane is higher than those of ethane and propane, the aerobic oxidation of thermogenic or microbial alkanes could produce carbon isotope reversal, which is frequently noted as a trait of abiotic hydrocarbons. This work demonstrates that in addition to anaerobic microbial oxidation, aerobic oxidation with a low cell density can also produce significant isotope fractionation of alkanes in geological closed/semi-closed environments that are characterized by moderate temperatures and a limited supply of substrates and O<sub>2</sub>; these environments include cold seeps, mud volcanoes, and low-temperature hydrothermal aquifers/reservoirs.
DOI: 10.5281/zenodo.4141219
title: SWASH Model Files from Modeled Three-Dimensional Currents and Eddies on an Alongshore-Variable Barred Beach

description: This archive contains SWASH model input, MATLAB processing scripts, and the model output used to produce the figures in “Modeled Three-Dimensional Currents and Eddies on an A longshore-Variable Barred Beach." Support was provided by the Washington Royalty Research Fund, the National Science Foundation, the Office of Naval Research, a National Defense Science and Engineering Graduate Fellowship, a Vannevar Bush Faculty Fellowship, the United States Army Corps of Engineers, the United States Coastal Research Program, Sea Grant, and the WHOI Investment in Science Fund. The model inputs, scripts, and data are contained in three zip files: model_input.zip: input files for all simulations presented in this paper model_output_processing.zip: MATLAB model output processing scripts. model_data.zip: model output used to produce the figures SWASH is an open source code and can be download at http://swash.sourceforge.net/home.htm. Please contact C.M. Baker at cmbaker9@uw.edu with questions.
DOI: 10.5281/zenodo.4091611
title: SWASH Model Files from Modeled Three-Dimensional Currents and Eddies on an Alongshore-Variable Barred Beach

description: This archive contains SWASH model input, MATLAB processing scripts, and the model output used to produce the figures in “Modeled Three-Dimensional Currents and Eddies on an A longshore-Variable Barred Beach." Support was provided by the Washington Royalty Research Fund, the National Science Foundation, the Office of Naval Research, a National Defense Science and Engineering Graduate Fellowship, a Vannevar Bush Faculty Fellowship, the United States Army Corps of Engineers, the United States Coastal Research Program, Sea Grant, and the WHOI Investment in Science Fund. The model inputs, scripts, and data are contained in three zip files: model_input.zip: input files for all simulations presented in this paper model_output_processing.zip: MATLAB model output processing scripts. model_data.zip: model output used to produce the figures SWASH is an open source code and can be download at http://swash.sourceforge.net/home.htm. Please contact C.M. Baker at cmbaker9@uw.edu with questions.
DOI: 10.25919/5f98e14bbf0f7
title: Hydraulic and Geochemical Data for Assessment of Large Scale Impacts of Groundwater Replenishment With Highly Treated Reclaimed Wastewater

description: This collection represents the hydrochemical data collected for groundwater samples from Perth Groundwater Replenishment Project Stage I, injection rates, bore locations, etc. The project was carried out at a site located near the Beenyup wastewater treatment plant, a site located ~20 km north of the city centre of Perth, by injecting treated wastewater into Leederville Formation. The data were collected to monitor the water quality under such injection.
DOI: 10.5281/zenodo.4146056
title: Marine amphipods as a new live prey for ornamental aquaculture: exploring the potential of Parhyale hawaiensis and Elasmopus pectenicrus

description: Supplementary data from the scientific paper contribution " Marine amphipods as a new live prey for ornamental aquaculture: exploring the potential of Parhyale hawaiensis and Elasmopus pectenicrus". Marine amphipods are gaining attention in aquaculture as a natural live food alternative to traditional preys such as <em>Artemia</em>, as they are rich in essential nutrients such as the lipids eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), are an important natural diet of many marine fish of commercial interest, and are relatively easy to culture in large numbers. However, there are no established culture techniques and a deeper knowledge on the reproductive biology, nutritional profiles and culture methodologies is still needed to potentiate the optimization of mass production. The present study assessed for the first time the aquaculture potential of <em>Parhyale hawaiensis</em> and <em>Elasmopus pectenicrus</em>, two cosmopolitan marine gammarids (as per traditional schemes of classification) that naturally proliferate in the wild and in aquaculture facilities. For that purpose, aspects of the population and reproductive biology of wild populations were characterized and then a series of laboratory-scale experiments were conducted to determine the amphipod productivity, the time needed to reach sexual maturity by the newborns (generation time), cannibalism degree, the effects of sex ratio on fecundity and the effects of diet (shrimp diet, plant-based diet and commercial fish diet) on fecundity and the juvenile growth. <em>P. hawaiensis</em>, unlike <em>E. pectenicrus</em>, was easily kept and propagated in laboratory conditions, performing exceedingly better than <em>E. pectenicrus</em>. <em>P. hawaiensis </em>showed a higher total length (9.3 ± 1.3 mm), wet weight (14.4 ± 6.2 mg), dry weight (10.5 ± 4.4 mg), females/males sex ratio in the wild (2.24), fecundity (12.8 ± 5.7 embryos per female), and gross energy content (16.71 ± 0.67 kJ g-1) with respect to <em>E. pectenicrus</em>. Although the <em>P. hawaiensis</em> juvenile growth was slightly reduced (marginally significant) by the use of a plant-based diet compared to a commercial shrimp and fish diet, fecundity was not affected, supporting the possible use of inexpensive diets to mass produce amphipods as live or frozen food. Possible limitations identified were their quite long generation times (50.9 ± 5.8 days) and relatively low fecundity levels (12.8 ± 5.7 embryos per female). With an observed productivity rate of 0.36 ± 0.08 juveniles per amphipod couple per day, <em>P. hawaiensis</em> could become a specialty feed for species that cannot easily transition to a formulated diet such as seahorses and other highly-priced marine ornamental species. Future studies should assess the nutritional value and to explore optimized medium- and large-scale production as well as self-producing biofloc systems taking advantage of the great dietary plasticity and environmental tolerance of the species.
DOI: 10.5281/zenodo.4146055
title: Marine amphipods as a new live prey for ornamental aquaculture: exploring the potential of Parhyale hawaiensis and Elasmopus pectenicrus

description: Supplementary data from the scientific paper contribution " Marine amphipods as a new live prey for ornamental aquaculture: exploring the potential of Parhyale hawaiensis and Elasmopus pectenicrus". Marine amphipods are gaining attention in aquaculture as a natural live food alternative to traditional preys such as <em>Artemia</em>, as they are rich in essential nutrients such as the lipids eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), are an important natural diet of many marine fish of commercial interest, and are relatively easy to culture in large numbers. However, there are no established culture techniques and a deeper knowledge on the reproductive biology, nutritional profiles and culture methodologies is still needed to potentiate the optimization of mass production. The present study assessed for the first time the aquaculture potential of <em>Parhyale hawaiensis</em> and <em>Elasmopus pectenicrus</em>, two cosmopolitan marine gammarids (as per traditional schemes of classification) that naturally proliferate in the wild and in aquaculture facilities. For that purpose, aspects of the population and reproductive biology of wild populations were characterized and then a series of laboratory-scale experiments were conducted to determine the amphipod productivity, the time needed to reach sexual maturity by the newborns (generation time), cannibalism degree, the effects of sex ratio on fecundity and the effects of diet (shrimp diet, plant-based diet and commercial fish diet) on fecundity and the juvenile growth. <em>P. hawaiensis</em>, unlike <em>E. pectenicrus</em>, was easily kept and propagated in laboratory conditions, performing exceedingly better than <em>E. pectenicrus</em>. <em>P. hawaiensis </em>showed a higher total length (9.3 ± 1.3 mm), wet weight (14.4 ± 6.2 mg), dry weight (10.5 ± 4.4 mg), females/males sex ratio in the wild (2.24), fecundity (12.8 ± 5.7 embryos per female), and gross energy content (16.71 ± 0.67 kJ g-1) with respect to <em>E. pectenicrus</em>. Although the <em>P. hawaiensis</em> juvenile growth was slightly reduced (marginally significant) by the use of a plant-based diet compared to a commercial shrimp and fish diet, fecundity was not affected, supporting the possible use of inexpensive diets to mass produce amphipods as live or frozen food. Possible limitations identified were their quite long generation times (50.9 ± 5.8 days) and relatively low fecundity levels (12.8 ± 5.7 embryos per female). With an observed productivity rate of 0.36 ± 0.08 juveniles per amphipod couple per day, <em>P. hawaiensis</em> could become a specialty feed for species that cannot easily transition to a formulated diet such as seahorses and other highly-priced marine ornamental species. Future studies should assess the nutritional value and to explore optimized medium- and large-scale production as well as self-producing biofloc systems taking advantage of the great dietary plasticity and environmental tolerance of the species.
DOI: 10.6084/m9.figshare.12925652
title: Verde para que(m) te quero: análise da relação entre fatores socioeconômicos e a distribuição espacial de praças nos bairros de Fortaleza - Script em linguagem R e planilha de parâmetros analisados

description: Script em linguagem R e planilha de parâmetros para análise da relação entre fatores socioeconômicos e a distribuição espacial de praças.<br>Este arquivo é parte da monografia "Verde para que(m) te quero: análise da relação entre fatores socioeconômicos e a distribuição espacial de praças nos bairros de Fortaleza", defendido por Laymara Xavier-Sampaio no Curso de Ciências Ambientais da Universidade Federal do Ceará em dezembro de 2019.<br> O arquivo possibilita ao público interessado uma melhor compreensão e da metodologia e auxilia na sua reprodução em pesquisas de tema similar com outros recortes espaciais. Além disso, viabiliza a validação dos dados e verificação dos resultados.<br>Legenda e fonte dos dados, na ordem das colunas, com visualização partindo da esquerda para a direita.<br>• Bairro e ID do bairro: Fortaleza em Mapas (https://mapas.fortaleza.ce.gov.br/#/) e ajustado em acordo com as alterações nos limites dos bairros identificadas.<br><br>• Área relativa de praças por bairro: Soma da área de todas as praças em um bairro dividido pela extensão deste bairro. Produto desta pesquisa, calculado a partir de dados do Canal Infocidade - Secretaria de Urbanismo e Meio Ambiente de Fortaleza (https://urbanismoemeioambiente.fortaleza.ce.gov.br/infocidade/11-arquivos-kml-s-e-kmz-s).<br>• Área relativa de favelas por bairro: Soma da área de todas as regiões catalogadas como favelas em um bairro dividido pela extensão deste bairro. Produto desta pesquisa, calculado a partir de dados do Fortaleza em Mapas (https://mapas.fortaleza.ce.gov.br/#/).<br>• Distância média: distância média de cada pixel (5m²) no bairro até praça mais próxima. Produto desta pesquisa, calculado a partir de dados do Fortaleza em Mapas (https://mapas.fortaleza.ce.gov.br/#/).<br>• EVI médio das praças por bairro: produto desta pesquisa, calculado a partir de dados do Google Engine.<br><br>• EVI médio geral por bairro: produto desta pesquisa, calculado a partir de dados do Google Engine.<br>• IDH: base de informações Dados Abertos Fortaleza. (https://dados.fortaleza.ce.gov.br/catalogo/dataset/desenvolvimento-humano-por-bairro-de-fortaleza)<br>• Renda média: arquivo dbf. associado ao shapefile "renda média" na base de dados Fortaleza em Mapas (https://mapas.fortaleza.ce.gov.br/#/).<br>• Percentual da população branca ou da população parda somada à preta: SIDRA/IBGE (https://sidra.ibge.gov.br/territorio#/N6/2304400)<br>
DOI: 10.6084/m9.figshare.13139294.v1
title: Tables.xls

description: Table S1. Mo and B isotopic compositions of the adakitic rocks from the Dexing and MLYR areas in central-eastern China.Table S2. Parameters for mixing calculation of the La/Yb ratios and REEs during melt–mantle interaction.Table S3. Comparison of measured δ98/95Mo values of the reference materials analyzed in this study to the literature values. Table S4. Comparison of measured δ11B values of the reference materials analyzed in this study to the literature values.
DOI: 10.21227/gr11-j254
title: Ear-EEG Recording for Brain Computer Interface of Motor Task

description: Ear-EEG recording collects brain signals from electrodes placed in the ear canal. Compared with existing scalp-EEG, ear-EEG is more wearable and user-comfortable compared with existing scalp-EEG.In this dataset, we collected ear-EEG signals and the scalp-EEG signals when subjects were performing a left/right hand grasping motor task. We first validated the ear-EEG recordings by measuring the similarity of power ratio and channel correlation between ear-EEG and scalp-EEG signals. Then we applied EEG compact network (EEGNet) for classification of left/right-hand motor tasks using ear-EEG signals and scalp EEG signals separately. Our results showed motor task classification based on ear-EEG has a high potential for the practical BCI applications in motor task.
DOI: 10.5517/ccdc.csd.cc25l0d6
title: CCDC 2013307: Experimental Crystal Structure Determination

description: Related Article: Harrison J. Barnett, Anthony F. Hill|2020|Chem.Commun.|56|12593|doi:10.1039/D0CC05106C
DOI: 10.21227/49db-xz77
title: Ear-EEG Recording for Brain Computer Interface of Motor Task

description: Ear-EEG recording collects brain signals from electrodes placed in the ear canal. Compared with existing scalp-EEG, ear-EEG is more wearable and user-comfortable compared with existing scalp-EEG.In this dataset, we collected ear-EEG signals and the scalp-EEG signals when subjects were performing a left/right hand grasping motor task. We first validated the ear-EEG recordings by measuring the similarity of power ratio and channel correlation between ear-EEG and scalp-EEG signals. Then we applied EEG compact network (EEGNet) for classification of left/right-hand motor tasks using ear-EEG signals and scalp EEG signals separately. Our results showed motor task classification based on ear-EEG has a high potential for the practical BCI applications in motor task.
DOI: 10.7302/6pja-rp18
title: Village health team (VHT) key informant interviews dataset
DOI: 10.5281/zenodo.4087510
title: Supplementary files for Silva et al. 2020 "Reptiles on the wrong track?": R Code, data and figures

description: Datasets, R code and figures pertaining to the manuscript: Silva, I., Crane, M., Marshall, B.M., & Strine, C.T. (2020).<em> </em> <em>Reptiles on the wrong track? Moving beyond traditional estimators with dynamic Brownian Bridge Movement Models.</em> Movement Ecology 8, 43 DOI: 10.1186/s40462-020-00229-3 Article available at: https://movementecologyjournal.biomedcentral.com/articles/10.1186/s40462-020-00229-3
DOI: 10.5281/zenodo.3660795
title: Supplementary files for Silva et al. 2020 "Reptiles on the wrong track?": R Code, data and figures

description: Datasets, R code and figures pertaining to the manuscript: Silva, I., Crane, M., Marshall, B.M., & Strine, C.T. (2020).<em> </em> <em>Reptiles on the wrong track? Moving beyond traditional estimators with dynamic Brownian Bridge Movement Models.</em> Movement Ecology 8, 43 DOI: 10.1186/s40462-020-00229-3 Article available at: https://movementecologyjournal.biomedcentral.com/articles/10.1186/s40462-020-00229-3
DOI: 10.6084/m9.figshare.13151688
title: Additional file 2 of Genetic, transcriptional, and regulatory landscape of monolignol biosynthesis pathway in Miscanthus × giganteus

description: Additional file 2. Additional tables.
DOI: 10.6084/m9.figshare.13151688.v1
title: Additional file 2 of Genetic, transcriptional, and regulatory landscape of monolignol biosynthesis pathway in Miscanthus × giganteus

description: Additional file 2. Additional tables.
DOI: 10.6084/m9.figshare.13151692.v1
title: Additional file 2 of Genome sequencing, assembly, and annotation of the self-flocculating microalga Scenedesmus obliquus AS-6-11

description: Additional file 2:. Assessing genome completeness with BUSCO. (TXT 880 bytes)
DOI: 10.6084/m9.figshare.13151701
title: Additional file 5 of Genome sequencing, assembly, and annotation of the self-flocculating microalga Scenedesmus obliquus AS-6-11

description: Additional file 5: The amino acid sequences of the potential flocculation proteins of S. obliquus AS-6-11. (TXT 2 kb)
DOI: 10.6084/m9.figshare.13151701.v1
title: Additional file 5 of Genome sequencing, assembly, and annotation of the self-flocculating microalga Scenedesmus obliquus AS-6-11

description: Additional file 5: The amino acid sequences of the potential flocculation proteins of S. obliquus AS-6-11. (TXT 2 kb)
DOI: 10.6084/m9.figshare.13151692
title: Additional file 2 of Genome sequencing, assembly, and annotation of the self-flocculating microalga Scenedesmus obliquus AS-6-11

description: Additional file 2:. Assessing genome completeness with BUSCO. (TXT 880 bytes)
DOI: 10.6084/m9.figshare.13151718.v1
title: Additional file 4 of The evolution of fruit scent: phylogenetic and developmental constraints

description: Additional file 4: Table S1. VOCs and RIs. Table S2. Madagascar—RNP2016. Table S3. Madagascar—RNP2017. Table S4. Uganda—KNP. Table S5. Germany—Ulm. Table S6. RNP Unripe 2016. Table S7. RNP Unripe 2017. Table S8. N individuals per spec.
DOI: 10.6084/m9.figshare.13151718
title: Additional file 4 of The evolution of fruit scent: phylogenetic and developmental constraints

description: Additional file 4: Table S1. VOCs and RIs. Table S2. Madagascar—RNP2016. Table S3. Madagascar—RNP2017. Table S4. Uganda—KNP. Table S5. Germany—Ulm. Table S6. RNP Unripe 2016. Table S7. RNP Unripe 2017. Table S8. N individuals per spec.
DOI: 10.6084/m9.figshare.13151805.v1
title: Additional file 1 of Diversity of mucoid to non-mucoid switch among carbapenemase-producing Klebsiella pneumoniae

description: Additional file 1.
DOI: 10.6084/m9.figshare.13151805
title: Additional file 1 of Diversity of mucoid to non-mucoid switch among carbapenemase-producing Klebsiella pneumoniae

description: Additional file 1.
DOI: 10.6084/m9.figshare.13151883
title: Additional file 2 of Microbial signature in IgE-mediated food allergies

description: Additional file 2: Table S1. Differential abundance statistics of KEGG pathways in FA and non-allergic; Table S2. Taxonomic contributions to shifts in acetate-related pathways enriched in non-allergic compared to FA; Table S3. Taxonomic contributions to shifts in acetate-related pathway enriched in FA compared to non-allergic; Table S4. Taxonomic contributions to shifts in acetate-related pathways enriched in peanut FA compared to milk FA; Table S5. Taxonomic contributions to shifts in acetate-related pathway enriched in milk FA compared to peanut FA; Table S6. Taxonomic contributions to shifts in acetate-related pathways enriched in sesame FA compared to milk FA; Table S7. Taxonomic contributions to shifts in acetate-related pathway enriched in sesame FA compared to tree nuts FA.
DOI: 10.6084/m9.figshare.13151883.v1
title: Additional file 2 of Microbial signature in IgE-mediated food allergies

description: Additional file 2: Table S1. Differential abundance statistics of KEGG pathways in FA and non-allergic; Table S2. Taxonomic contributions to shifts in acetate-related pathways enriched in non-allergic compared to FA; Table S3. Taxonomic contributions to shifts in acetate-related pathway enriched in FA compared to non-allergic; Table S4. Taxonomic contributions to shifts in acetate-related pathways enriched in peanut FA compared to milk FA; Table S5. Taxonomic contributions to shifts in acetate-related pathway enriched in milk FA compared to peanut FA; Table S6. Taxonomic contributions to shifts in acetate-related pathways enriched in sesame FA compared to milk FA; Table S7. Taxonomic contributions to shifts in acetate-related pathway enriched in sesame FA compared to tree nuts FA.