cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25666/dataubfc-2016-12-09-02
title: Meteorological monitoring on Forbonnet peatland
title: Suivi météorologique sur la tourbière du Forbonnet

description: Chrono-Environnement laboratory is responsible for the meteorological monitoring of an experimental station on the Frasne peatland (Tourbières du Forbonnet, Doubs) since November 2008. The meteorological parameters (temperature and humidity, rainfall, wind speed and direction , groundwater level, atmospheric pressure) are acquired every 30 min and archived as annual files. This monitoring was initiated for the PeatWarm project (ANR) and continues for the "Service National d'Observation des Tourbières".
description: Le laboratoire Chrono-Environnement assure le suivi météorologique d'une station expérimentale sur la tourbière de Frasne (Tourbières du Forbonnet, Doubs) depuis novembre 2008. Les paramètres météorologiques (température / humidité de l'air, pluviométrie, vitesse et direction du vent, niveau de nappe, pression atmosphérique) sont acquis toutes les 30 min et archivés en fichiers annuels. Ce suivi a été initié dans le cadre du projet ANR PeatWarm et se poursuit dans le cadre du Service National d'Observation des Tourbières.
description: Audience: University: master, Research, Policy maker
description: Project: Peatwarm, ANR (French National Agency for Research), PMA (Local community), Région Franche-Comté (Region Franche-Comté)
description: Label: SNO Tourbières (Service National d'Observation Tourbières)
description: Derived or compiled data: Les données sont compilées chaque année sous tableur Excel.
description: Observational data: Mesures toutes les 15 secondes et conservation des moyennes chaque demi-heure.
DOI: 10.25666/dataubfc-2016-12-14
title: Bromadiolone kinetics in common and montane water vole populations
title: Cinétique de la bromadiolone dans des populations de campagnols des champs et terrestre

description: Field measurements describing the kinetics of bromadiolone in two vole populations (Microtus arvalis and Arviola scherman) after a field control of water voles, Arvicola scherman.

Those data have been obtained during Mickael Sage's doctorate.
description: Mesures sur le terrain de la cinétique de la bromadiolone dans deux populations de campagnols (Microtus arvalis et Arvicola terrestris) après traitement contre Arvicola scherman.

Ces données ont été obtenues au cours du doctorat de Mickael Sage.
description: Audience: Research
description: UpdatePeriodicity: no update
description: Label: ZAAJ (Zone Atelier Arc Jurassien)
description: Observational data: Voir Matériel et méthode de M. Sage, M. Coeurdassier, R. Defaut, F. Gimbert, P. Berny, and P. Giraudoux. 2008. Kinetics of bromadiolone in rodent populations and implications for predators after field control of the water vole, Arvicola terrestris. Science of the Total Environment 407:211-222. (référencé dans les publications de cette fiche)
DOI: 10.5281/zenodo.10031786
title: Workflow II - Streaming Analysis - Multi-Position, Multi Timepoint Acquisition

description: This dataset contains the experimental data associated with Workflow II, a streaming analysis workflow.
DOI: 10.25381/cput.23659749
title: Occurrence and ecotoxicological effects of microplastics in the Diep river, Milnerton, Cape Town

description:  Ethical Reference Number: 30085741/05/2020 <br>
  
  
Rivers play an important role in the water cycle and serve as habitats for various species in aquatic ecosystems. They also serve as a source of microplastic litter in the ocean. Microplastics are ubiquitous, with the potential for accumulation in the environment. Improperly disposed of plastics often end up in freshwater ecosystems. The Diep River runs through the City of Cape Town via neighbourhoods with different land use types into the ocean. In this study, the occurrence and ecotoxicological effects of microplastics in the Diep River and some physicochemical parameters of the river water were assessed. Water and sediment samples were collected from five sites on the Diep River and analysed for microplastics. On the field, a 100 L sample was filtered through a 250 µm mesh and 20 L was collected for processing in the laboratory. The 20 L sample was filtered through a 20 µm mesh in the laboratory. The microplastics extracted were characterized using microscopy and Fourier-transform infrared spectroscopy (FTIR). Surface water samples were evaluated to determine the ecological risk, effects of microplastic standards on the river, potential climate change effects of microplastics using three bioassays and potential for genetic toxicity. Three test organisms, each representing a trophic level, were exposed to the river water samples, river water samples with microplastics, and distilled water with microplastic at variable temperatures. The organisms used were <em>Raphidocelis subcapitata</em> (microalgae), <em>Daphnia magna</em> (crustacean), and <em>Tetrahymena thermophila</em> (protozoan). The AMES test was used to test for potential mutagenicity. There were significant relationships between microplastics and physicochemical parameters. Fibres and polyethylene were the most predominant microplastics particles identified in water and sediment samples (under microscopy and FTIR, respectively). Tourist and recreational areas had higher microplastics burden relative to non-tourist areas. There were significant differences shown in spatial and temporal microplastic distribution based on the proximity to urban/industrial areas and wastewater treatment plants. Different toxicity levels were shown over the four seasons in environmental water, and growth inhibition occurred in environmental samples with microplastics. The climate change effect studies revealed that microalgal and crustacean growth were enhanced in response to temperature rise in the presence of microplastics. A mutagenic response was observed in the investigated Diep River water samples. This study provided information for management strategies in policy development and implementation, protection, and other mitigation strategies about the microplastic burden of the Diep River. The ecotoxicological approach used can add value to hazard and risk assessment of the river and contribute to the management of water quality along the Diep River.
DOI: 10.25381/cput.23659749.v1
title: <strong>O</strong><strong>CCURRENCE AND ECOTOXICOLOGICAL EFFECTS OF MICROPLASTICS IN THE DIEP RIVER, MILNERTON, CAPE TOWN</strong>

description:  Ethical Reference Number: 30085741/05/2020 <br>
  
  
Rivers play an important role in the water cycle and serve as habitats for various species in aquatic ecosystems. They also serve as a source of microplastic litter in the ocean. Microplastics are ubiquitous, with the potential for accumulation in the environment. Improperly disposed of plastics often end up in freshwater ecosystems. The Diep River runs through the City of Cape Town via neighbourhoods with different land use types into the ocean. In this study, the occurrence and ecotoxicological effects of microplastics in the Diep River and some physicochemical parameters of the river water were assessed. Water and sediment samples were collected from five sites on the Diep River and analysed for microplastics. On the field, a 100 L sample was filtered through a 250 µm mesh and 20 L was collected for processing in the laboratory. The 20 L sample was filtered through a 20 µm mesh in the laboratory. The microplastics extracted were characterized using microscopy and Fourier-transform infrared spectroscopy (FTIR). Surface water samples were evaluated to determine the ecological risk, effects of microplastic standards on the river, potential climate change effects of microplastics using three bioassays and potential for genetic toxicity. Three test organisms, each representing a trophic level, were exposed to the river water samples, river water samples with microplastics, and distilled water with microplastic at variable temperatures. The organisms used were <em>Raphidocelis subcapitata</em> (microalgae), <em>Daphnia magna</em> (crustacean), and <em>Tetrahymena thermophila</em> (protozoan). The AMES test was used to test for potential mutagenicity. There were significant relationships between microplastics and physicochemical parameters. Fibres and polyethylene were the most predominant microplastics particles identified in water and sediment samples (under microscopy and FTIR, respectively). Tourist and recreational areas had higher microplastics burden relative to non-tourist areas. There were significant differences shown in spatial and temporal microplastic distribution based on the proximity to urban/industrial areas and wastewater treatment plants. Different toxicity levels were shown over the four seasons in environmental water, and growth inhibition occurred in environmental samples with microplastics. The climate change effect studies revealed that microalgal and crustacean growth were enhanced in response to temperature rise in the presence of microplastics. A mutagenic response was observed in the investigated Diep River water samples. This study provided information for management strategies in policy development and implementation, protection, and other mitigation strategies about the microplastic burden of the Diep River. The ecotoxicological approach used can add value to hazard and risk assessment of the river and contribute to the management of water quality along the Diep River.
DOI: 10.5281/zenodo.10589721
title: Exploiting Formal Concept Analysis for Data Modeling in Data Lakes
DOI: 10.5281/zenodo.10589722
title: Exploiting Formal Concept Analysis for Data Modeling in Data Lakes
DOI: 10.5281/zenodo.10578774
title: Probing the origin of the two-component structure of broad line region by reverberation mapping of an extremely variable quasar
DOI: 10.5281/zenodo.10578775
title: Probing the origin of the two-component structure of broad line region by reverberation mapping of an extremely variable quasar
DOI: 10.25381/cput.24718137
title: A time series analysis of fresh water quality in the Greater Plettenberg Bay Municipality, Western Cape Province

description: <b>Ethical Clearance reference number: 216277744/06/2022</b>Enter your brief data descriptionThis data is raw secondary data, obtained from the local Bitou Municipality Waterworks Department. Each sampling site has been sampled and monitored three times every from 2016 to 2020.
DOI: 10.25381/cput.24718137.v1
title: A TIME SERIES ANALYSIS OF FRESH WATER QUALITY IN THE GREATER PLETTENBERG BAY MUNICIPALITY, WESTERN CAPE PROVINCE.

description: <b>Ethical Clearance reference number: 216277744/06/2022</b>Enter your brief data descriptionThis data is raw secondary data, obtained from the local Bitou Municipality Waterworks Department. Each sampling site has been sampled and monitored three times every from 2016 to 2020.
DOI: 10.25381/cput.24718137.v2
title: A time series analysis of fresh water quality in the Greater Plettenberg Bay Municipality, Western Cape Province

description: <b>Ethical Clearance reference number: 216277744/06/2022</b>Enter your brief data descriptionThis data is raw secondary data, obtained from the local Bitou Municipality Waterworks Department. Each sampling site has been sampled and monitored three times every from 2016 to 2020.
DOI: 10.5281/zenodo.10589686
title: Evolution of microRNAs in Amoebozoa and implications for the origin of multicellularity

description: Evolution of microRNAs in Amoebozoa and implications for the origin of multicellularity

Repository accompanying "Evolution of microRNAs in Amoebozoa and implications for the origin of multicellularity" manuscript

 

microRNA curation

Potential miRNA clusters, generated using Shortstack (https://github.com/MikeAxtell/ShortStack), are analyzed with miRNA_curation.py. An example run of the miRNA curation can be performed by running the 'example_run/explore_all.sh' and 'example_run/refine_all.sh' scripts in order. A sample of the sRNA sequences from D. discoideum is included in the 'example/example_sizeselected_data' folder. A sample of miRNA candidates are included in 'example_run/pot-miRNAs_merged.fa' to facilitate the example run.

Prerequisites: Python 3, Biopython, RNAlib, matplotlib, numpy

 

microRNA analysis

Following miRNA curation, high confidence miRNAs are identified and further analysed in amoeba_miRNAevo.Rmd. The data for the analysis is located in  'data_in' and are mostly derived from the miRNA_curation.py script and other scripts located in the 'helper_scripts' folder. The plots generated in the analysis is located in the 'plots' folder. Tables and other data generated from the analysis are located in the 'data_out' folder. In order to perform the miRNA conservation search, refer to the 'helper_scripts/miRNA_conservation_search/' folder.

Prerequisites: R, Blast, bash

 

Access genomes/annotations

For Dictyostelium firmibasis, the genome was de-novo sequenced and assembled and is located in 'data_in/novel_assembly'. Assembly was done using Flye v2.9.1 in nano-hq mode, and two rounds of long-read polishing were done using Medaka v1.7.2. The filtered reads used for assembly can be accessed from NCBI BioProject PRJNA972620. The Acanthamoeba castellanii genome and annotation were accessed at https://www.doi.org/10.5281/zenodo.680005. The other genomes and annotations for this study were accessed from NCBI and can be downloaded using the 'get_references.sh' script located in the helper_scripts folder.
DOI: 10.5281/zenodo.7937210
title: Evolution of microRNAs in Amoebozoa and implications for the origin of multicellularity

description: Evolution of microRNAs in Amoebozoa and implications for the origin of multicellularity
Repository accompanying "Evolution of microRNAs in Amoebozoa and implications for the origin of multicellularity" manuscript
 
microRNA curation
Potential miRNA clusters, generated using Shortstack (https://github.com/MikeAxtell/ShortStack), are analyzed with miRNA_curation.py. An example run of the miRNA curation can be performed by running the 'example_run/explore_all.sh' and 'example_run/refine_all.sh' scripts in order. A sample of the sRNA sequences from D. discoideum is included in the 'example/example_sizeselected_data' folder. A sample of miRNA candidates are included in 'example_run/pot-miRNAs_merged.fa' to facilitate the example run.
Prerequisites: Python 3, Biopython, RNAlib, matplotlib, numpy
 
microRNA analysis
Following miRNA curation, high confidence miRNAs are identified and further analysed in amoeba_miRNAevo.Rmd. The data for the analysis is located in  'data_in' and are mostly derived from the miRNA_curation.py script and other scripts located in the 'helper_scripts' folder. The plots generated in the analysis is located in the 'plots' folder. Tables and other data generated from the analysis are located in the 'data_out' folder. In order to perform the miRNA conservation search, refer to the 'helper_scripts/miRNA_conservation_search/' folder.
Access genomes/annotations
For Dictyostelium firmibasis, the genome was de-novo sequenced and is located in 'data_in/novel_assembly'. Assembly was done using Flye v2.9.1 in nano-hq mode, and two rounds of long-read polishing were done using Medaka v1.7.2. The filtered reads used for assembly can be accessed from NCBI BioProject PRJNA972620. The Acanthamoeba castellanii genome and annotation were accessed at https://www.doi.org/10.5281/zenodo.680005. The other genomes and annotations for this study were accessed from NCBI and can be downloaded using the 'get_references.sh' script located in the helper_scripts folder.
DOI: 10.5281/zenodo.10144907
title: Evolution of microRNAs in Amoebozoa and implications for the origin of multicellularity

description: Evolution of microRNAs in Amoebozoa and implications for the origin of multicellularity
Repository accompanying "Evolution of microRNAs in Amoebozoa and implications for the origin of multicellularity" manuscript
 
microRNA curation
Potential miRNA clusters, generated using Shortstack (https://github.com/MikeAxtell/ShortStack), are analyzed with miRNA_curation.py. An example run of the miRNA curation can be performed by running the 'example_run/explore_all.sh' and 'example_run/refine_all.sh' scripts in order. A sample of the sRNA sequences from D. discoideum is included in the 'example/example_sizeselected_data' folder. A sample of miRNA candidates are included in 'example_run/pot-miRNAs_merged.fa' to facilitate the example run.
Prerequisites: Python 3, Biopython, RNAlib, matplotlib, numpy
 
microRNA analysis
Following miRNA curation, high confidence miRNAs are identified and further analysed in amoeba_miRNAevo.Rmd. The data for the analysis is located in  'data_in' and are mostly derived from the miRNA_curation.py script and other scripts located in the 'helper_scripts' folder. The plots generated in the analysis is located in the 'plots' folder. Tables and other data generated from the analysis are located in the 'data_out' folder. In order to perform the miRNA conservation search, refer to the 'helper_scripts/miRNA_conservation_search/' folder.
Access genomes/annotations
For Dictyostelium firmibasis, the genome was de-novo sequenced and is located in 'data_in/novel_assembly'. Assembly was done using Flye v2.9.1 in nano-hq mode, and two rounds of long-read polishing were done using Medaka v1.7.2. The filtered reads used for assembly can be accessed from NCBI BioProject PRJNA972620. The Acanthamoeba castellanii genome and annotation were accessed at https://www.doi.org/10.5281/zenodo.680005. The other genomes and annotations for this study were accessed from NCBI and can be downloaded using the 'get_references.sh' script located in the helper_scripts folder.
DOI: 10.5281/zenodo.7937209
title: Evolution of microRNAs in Amoebozoa and implications for the origin of multicellularity

description: Evolution of microRNAs in Amoebozoa and implications for the origin of multicellularity

Repository accompanying "Evolution of microRNAs in Amoebozoa and implications for the origin of multicellularity" manuscript

 

microRNA curation

Potential miRNA clusters, generated using Shortstack (https://github.com/MikeAxtell/ShortStack), are analyzed with miRNA_curation.py. An example run of the miRNA curation can be performed by running the 'example_run/explore_all.sh' and 'example_run/refine_all.sh' scripts in order. A sample of the sRNA sequences from D. discoideum is included in the 'example/example_sizeselected_data' folder. A sample of miRNA candidates are included in 'example_run/pot-miRNAs_merged.fa' to facilitate the example run.

Prerequisites: Python 3, Biopython, RNAlib, matplotlib, numpy

 

microRNA analysis

Following miRNA curation, high confidence miRNAs are identified and further analysed in amoeba_miRNAevo.Rmd. The data for the analysis is located in  'data_in' and are mostly derived from the miRNA_curation.py script and other scripts located in the 'helper_scripts' folder. The plots generated in the analysis is located in the 'plots' folder. Tables and other data generated from the analysis are located in the 'data_out' folder. In order to perform the miRNA conservation search, refer to the 'helper_scripts/miRNA_conservation_search/' folder.

Prerequisites: R, Blast, bash

 

Access genomes/annotations

For Dictyostelium firmibasis, the genome was de-novo sequenced and assembled and is located in 'data_in/novel_assembly'. Assembly was done using Flye v2.9.1 in nano-hq mode, and two rounds of long-read polishing were done using Medaka v1.7.2. The filtered reads used for assembly can be accessed from NCBI BioProject PRJNA972620. The Acanthamoeba castellanii genome and annotation were accessed at https://www.doi.org/10.5281/zenodo.680005. The other genomes and annotations for this study were accessed from NCBI and can be downloaded using the 'get_references.sh' script located in the helper_scripts folder.
DOI: 10.25381/cput.23791530.v1
title: Dataset: <b>The effect of the fungus </b><i><b>Beauveria bassiana </b></i><b>(Hypocreales) on the growth of </b><i><b>Tulbaghia violacea </b></i><b>and its ability to synthesize nano-particle insecticidal to mealybug</b>

description: Can the entomopathogenic fungus <i>Beauveria bassiana</i> colonize wild garlic and induce enhanced bioactivity of the plant extracts? This study aimed to evaluate the effect of the entomopathogenic fungus <i>Beauveria bassiana</i> (Hypocreales) on the growth and ability of <i>Tulbaghia violacea</i> (wild garlic) to synthesise nanoparticles. <i>T. violacea </i>Harv.<i> </i>plants were inoculated by drenching with different concentrations of <i>B. bassiana</i> conidia. This dataset improves our understanding of the relationship between plants and endophytic fungi. This Faculty Research Ethics Committee of the Faculty of Applied Sciences granted ethics approval for this study, Reference no 212274759/1/2019.
DOI: 10.5281/zenodo.10579819
title: WP6 - Decentralised public intervention data
DOI: 10.5281/zenodo.10579820
title: WP6 - Decentralised public intervention data
DOI: 10.5285/0ec17274-7a64-2b28-e063-6c86abc0ee02
title: ATOMIX shear probes benchmark data: a dissipation profile from Minas Passage, Nova Scotia, Canada, obtained with a moored horizontal microstructure profiler in September 2016.

description: This is a profile collected using a moored microstructure profiler, prepared as a benchmark shear-probe data example for the Scientific Committee on Oceanographic Research (SCOR) Working Group number 160, "Analyzing ocean turbulence observations to quantify mixing" (ATOMIX). The profile was collected in Minas Passage, Nova Scotia, Canada on 10 September 2016 from an Nemo moored horizontal microstructure profiler (MR-1000-TE, Rockland Scientific, Canada), located nominally 15 m above the bottom of Minas Passage in an area where the water depth was 80 m. The MicroRider turbulence measurement system carried four shear probes, one FP07 thermistor, and two piezo vibrations sensors. Additional sensors include a pressure transducer, a 2-axis inclinometer, a 3-axis magnetometer, a 3-axis accelerometer, a 3-axis rotation sensor, and a 3-axis acoustic current meter. The turbulence and vibration channels were configured to sample at a rate of 2048 per second, and had anti-aliasing filters set for 392 Hz. The gains of the differentiators were reduced to 0.01 second to accommodate the expected strong shear signals due to vigorous turbulence and fast streaming (around 3 m/s). The dataset has been processed and formatted in accordance with ATOMIX guidelines and recommendations. The provided file is organised in four hierarchical groups including L1_converted: continuous time series of data converted into physical units, L2_cleaned: cleaned time series used for spectral analysis, L3_spectra: wavenumber spectra, and L4_dissipation: dissipation rate estimates. For more detailed information, please refer to the comments within the data file.
DOI: 10.25381/cput.24524866
title: Hydrochemical assessment of groundwater quality and its suitability for irrigation and domestic purposes in Breede water management area, Western Cape

description: <strong>Ethics Clerance number is 220164711/10/2021 </strong>
<br>
The study was conducted in the Breede Water Management Area in the Western Cape province in South Africa. The aim was to assess the status of groundwater quality, the suitability of the water for domestic and irrigation purposes and factors contributing to the groundwater chemistry. Twelve (12) monitoring boreholes were selected for sample collection. The samples were analysed for major ions such as potassium (K+), magnesium (Mg2+), sodium (Na+), calcium (Ca2+), chloride (Cl-), sulfate (SO42-), bicarbonate (HCO3-), nitrate (NO3-), fluoride (F-) and physical variables like pH, electrical conductivity (EC), total dissolved solids (TDS) and temperature.