cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.sjtwke
title: Occurrence Download

description: A dataset containing 1199 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is one of (Africa, Antarctica, Asia, Oceania, Europe, North America, South America)",
 "Country is one of (China, Japan, Korea, Republic of, Russian Federation, Chinese Taipei, Korea (Democratic People’s Republic of), unknown or invalid, Belgium, Mongolia, United States of America)",
 "DatasetKey is one of (2023 Contributions of Plant Specimen Data inside China, 500,000 plant Specimens from PE Herbarium in China from 1950 to 1999, Plant, Some Plant Specimens from PE Herbarium in China from 1900 to 1950, Vascular plants of the Soviet Far East (1985-2006): georeferenced records from dot maps, Local floras of Russia: records from literature, Some Plant Specimens from KUN, IBSC, NAS Herbarium in China from 1900 to 1950, 2007-2022_nibr_simpl_vp, iNaturalist Research-grade Observations)",
 "OccurrenceStatus is Present",
 "PublishingOrg is one of (a2fa5b68-3ebf-4845-abc5-f456d251386f, f5fc4e61-b7a0-414b-ab68-b41cb23e7fdc, ce3cfcc0-6d56-11db-a819-b8a03c50a862, 28eb1a3f-1c15-4a95-931a-4af90ecb574d, d6aeeb7c-db16-436f-98bb-f0d7e2c7a0db)",
 "TaxonKey is Arabis stelleri DC."
 ]
}

 The dataset includes 1199 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033583-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10572720
title: Dataset for Article: Transforming Esox lucius (Northern Pike) Monitoring with Environmental DNA based detection using CRISPR-Cas and Lateral Flow: a step closer to on-site monitoring - Idelegbagbon et al. 2024

description: Compilation of data related to published paper on the development and application of an RPA-CRISPR-Cas Assay for detecting Esox lucius (Northern Pike) in Irish Freshwaters. This encompassed species-specific detection through eDNA from collected water samples, utilising both fluorescence signal output and Lateral Flow Assay (LFA) detection. This collection includes pertinent figures, graphs, and associated raw data supporting all major steps undertaken including primer design, assay optimisation, and field application.
description: The escalating risk to freshwater fish species and the accompanying biodiversity loss in freshwater systems underscores the pressing need for sustained conservation initiatives. Human demands and activities further exacerbate these challenges, necessitating effective management strategies to curtail biodiversity decline and protect vulnerable species. In the Irish context, Esox lucius (Northern Pike) represents a non-native freshwater species notorious for its impact on indigenous fish populations. While acknowledged for its predation on native species, the Northern Pike also holds considerable economic value as a prized angling species.We have developed an environmental DNA assay that combines Recombinase Polymerase Amplification and CRISPR technologies, complemented by Lateral Flow detection. This assay enables the specific and accurate detection of Northern Pike presence or absence in Irish freshwater environments. By employing two distinct detection methods—fluorescence signal output and lateral flow visual readout—the assay successfully identified the target species across multiple locations. Field application using environmental water samples establishes a robust foundation for reliable and species-specific Northern Pike detection. The inclusion of Lateral Flow detection enhances assay performance, making it more user-friendly and simplifying result acquisition. This key feature also sets the stage for future on-site applications. The significance of this assay lies in its potential to improve the efficiency of conservation efforts focused on species monitoring and management.
DOI: 10.5281/zenodo.10572721
title: Dataset for Article: Transforming Esox lucius (Northern Pike) Monitoring with Environmental DNA based detection using CRISPR-Cas and Lateral Flow: a step closer to on-site monitoring - Idelegbagbon et al. 2024

description: Compilation of data related to published paper on the development and application of an RPA-CRISPR-Cas Assay for detecting Esox lucius (Northern Pike) in Irish Freshwaters. This encompassed species-specific detection through eDNA from collected water samples, utilising both fluorescence signal output and Lateral Flow Assay (LFA) detection. This collection includes pertinent figures, graphs, and associated raw data supporting all major steps undertaken including primer design, assay optimisation, and field application.
description: The escalating risk to freshwater fish species and the accompanying biodiversity loss in freshwater systems underscores the pressing need for sustained conservation initiatives. Human demands and activities further exacerbate these challenges, necessitating effective management strategies to curtail biodiversity decline and protect vulnerable species. In the Irish context, Esox lucius (Northern Pike) represents a non-native freshwater species notorious for its impact on indigenous fish populations. While acknowledged for its predation on native species, the Northern Pike also holds considerable economic value as a prized angling species.We have developed an environmental DNA assay that combines Recombinase Polymerase Amplification and CRISPR technologies, complemented by Lateral Flow detection. This assay enables the specific and accurate detection of Northern Pike presence or absence in Irish freshwater environments. By employing two distinct detection methods—fluorescence signal output and lateral flow visual readout—the assay successfully identified the target species across multiple locations. Field application using environmental water samples establishes a robust foundation for reliable and species-specific Northern Pike detection. The inclusion of Lateral Flow detection enhances assay performance, making it more user-friendly and simplifying result acquisition. This key feature also sets the stage for future on-site applications. The significance of this assay lies in its potential to improve the efficiency of conservation efforts focused on species monitoring and management.
DOI: 10.5281/zenodo.12799114
title: INCIDENCE OF POVERTY AND GOVERNMENT EXPENDITURE IN NIGERIA: AN EMPIRICAL INVESTIGATION
DOI: 10.5281/zenodo.12799115
title: INCIDENCE OF POVERTY AND GOVERNMENT EXPENDITURE IN NIGERIA: AN EMPIRICAL INVESTIGATION
DOI: 10.5281/zenodo.12799130
title: Lombrisco compost 2010-2012
DOI: 10.5281/zenodo.12799131
title: Lombrisco compost 2010-2012
DOI: 10.15468/dl.t7gwe6
title: Occurrence Download

description: A dataset containing 587 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "OccurrenceStatus is Present",
 "TaxonKey is Spodoptera frugiperda J.E.Smith, 1797"
 ]
}

 The dataset includes 587 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033584-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.12698951
title: TIMCI Tanzania RCT dataset

description: This dataset contains data from the TIMCI (Tools for Integrated Management of Childhood Illness) cluster Randomized Controlled Trial (RCT) in Tanzania (NCT04910750), which was conducted by the Ifakara Health Institute (IHI) in collaboration with the Swiss Tropical & Public Health Institute (Swiss TPH). Data were collected with ODK between March 28, 2022 and March 31, 2023 (12 months) in 66 facilities.

To request access to this dataset:



Contact the TIMCI consortium directly

Clearly state your intended purpose for data analysis


When using the data, please ensure proper attribution.
DOI: 10.5281/zenodo.10423907
title: Neuroimaging data related to the study: "Midlife Dynamics of White Matter Architecture in Lexical Production"

description: See the accompanying code repository

Track-Weighted Imaging (TWI)



TW_FA_Gaussian25_155subj.mif.gz (dim 121 x 152 x 121 x 155): Track-Weighted Fractional Anisotropic images (TW-FA) generated with 25 mm neighborhood weighting (per-track smoothing) in template space.

155subj_FA_map.mif.gz (dim 128 x 128 x 88): Fractional Anistropic images (FA).

wmfod_norm_up.mif.gz (dim 121 x 152 x 121 x 45): Study template derived from white matter fiber orientation distribution (FOD), normalized, and upsampled to 1.5 mm isotropic.

SH_peaks_template.mif.gz (dim 121 x 152 x 121 x 9): Spherical Harmonics peaks derived from the study template (used to generate TOM and TOM trackings with TractSeg).


Non-Negative Matrix Factorization (NMF)



W.mat & H.mat: Solutions from NMF. The optimal solution found for this study is the one with 16 networks (i.e., in the 8th position in the mat files as there is a 2-step increment between solutions).

Network_Parcellation_NNMF.nii: 3D volume containing the part-based solution derived from NMF (i.e., 16 spatially non-overlapping networks of structurally covarying white matter areas).

Network_Parcellation_NNMF_cluster.nii: IDEM but only considering clusters of at least 25 connected voxels within each network (used to compute the overlap with TractSeg bundles).


BRAIN VISUALIZATION

For figure 2:



TW_FA_Gaussian25_155subj_mean_mesh.obj: White Matter Mesh derived from the mean image (used with the surfice software).

NMF_age_networks_composition.xlsx: Dataset containing the spatial, connectivity, and composite score used to determine the composition of each NMF-derived network.

*_track_overlay.tck: The 6 Tractography files to overlay onto the mesh for visualizating the bundles most contributing to the middle-age-related NMF networks.


For figure 3 & 4:



TW_FA_Gaussian25_155subj_mean.nii: Mean TW-FA image across all subjects.

TW_FA_Gaussian25_155subj_mean_mask_95.nii: Binary group mask containing only the voxels that had a non-null TW-FA value across at least 95% of subjects.

*LC1_BSR_saliences.nii & *LC2_BSR_saliences.nii: Voxel-level salience map of the 1st and 2nd latent component (unthresholded; please note that only BSR +/- 2.58 signified a robust contribution in our study).

NNMF_BSR_LC1.nii: Network-level salience map.

*res & save_opts.mat: Partial Least Squares (PLS) results and parameters.
DOI: 10.5281/zenodo.10423906
title: Neuroimaging data related to the study: "Midlife Dynamics of White Matter Architecture in Lexical Production"

description: See the accompanying code repository

Track-Weighted Imaging (TWI)



TW_FA_Gaussian25_155subj.mif.gz (dim 121 x 152 x 121 x 155): Track-Weighted Fractional Anisotropic images (TW-FA) generated with 25 mm neighborhood weighting (per-track smoothing) in template space.

155subj_FA_map.mif.gz (dim 128 x 128 x 88): Fractional Anistropic images (FA).

wmfod_norm_up.mif.gz (dim 121 x 152 x 121 x 45): Study template derived from white matter fiber orientation distribution (FOD), normalized, and upsampled to 1.5 mm isotropic.

SH_peaks_template.mif.gz (dim 121 x 152 x 121 x 9): Spherical Harmonics peaks derived from the study template (used to generate TOM and TOM trackings with TractSeg).


Non-Negative Matrix Factorization (NMF)



W.mat & H.mat: Solutions from NMF. The optimal solution found for this study is the one with 16 networks (i.e., in the 8th position in the mat files as there is a 2-step increment between solutions).

Network_Parcellation_NNMF.nii: 3D volume containing the part-based solution derived from NMF (i.e., 16 spatially non-overlapping networks of structurally covarying white matter areas).

Network_Parcellation_NNMF_cluster.nii: IDEM but only considering clusters of at least 25 connected voxels within each network (used to compute the overlap with TractSeg bundles).


BRAIN VISUALIZATION

For figure 2:



TW_FA_Gaussian25_155subj_mean_mesh.obj: White Matter Mesh derived from the mean image (used with the surfice software).

NMF_age_networks_composition.xlsx: Dataset containing the spatial, connectivity, and composite score used to determine the composition of each NMF-derived network.

*_track_overlay.tck: The 6 Tractography files to overlay onto the mesh for visualizating the bundles most contributing to the middle-age-related NMF networks.


For figure 3 & 4:



TW_FA_Gaussian25_155subj_mean.nii: Mean TW-FA image across all subjects.

TW_FA_Gaussian25_155subj_mean_mask_95.nii: Binary group mask containing only the voxels that had a non-null TW-FA value across at least 95% of subjects.

*LC1_BSR_saliences.nii & *LC2_BSR_saliences.nii: Voxel-level salience map of the 1st and 2nd latent component (unthresholded; please note that only BSR +/- 2.58 signified a robust contribution in our study).

NNMF_BSR_LC1.nii: Network-level salience map.

*res & save_opts.mat: Partial Least Squares (PLS) results and parameters.
DOI: 10.15468/dl.tykbsh
title: Occurrence Download

description: A dataset containing 8630 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Panthera onca (Linnaeus, 1758)"
 ]
}

 The dataset includes 8630 records from 272 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033582-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.24763251
title: Data Note related to the article "Gender perspectives on a flipped classroom environment"

description: The research investigates the gender perspective of flipped classroom.In particular, it considers how the collaborative setting of in-class group-work affect the female population of students. The paper draws on an in-depth analysis of the interview with one such student. The focus of this interview was on interactional collaboration between peers during group work activities in a mathematics course. Such work is vital in a flipped classroom arrangement. The student, called Sofia, highlighted arguments of value for a deeper investigation. The analysis draws on Bjerrum Nielsen’s framework with four different gender perspectives (2003). Our analysis illuminates a number of arguments about interactions and interpretations of gender and challenges when collaborating in groups in a flipped classroom setting. Arguments informs both context and individual levels of the setting. What is realised in the case of Sofia is that there are dualistic viewpoints raised within all gender perspectives, sometimes conflicting each other. Result is that guidance from a teacher in formation of groups is necessary but will need careful considerations.
DOI: 10.6084/m9.figshare.26355158
title: Crocodile CTA data from Taste aversion training can educate free-ranging crocodiles against toxic invaders

description: Data used in all analyses within this study
DOI: 10.6084/m9.figshare.26355158.v1
title: Crocodile CTA data from Taste aversion training can educate free-ranging crocodiles against toxic invaders

description: Data used in all analyses within this study
DOI: 10.5281/zenodo.5078071
title: ENGAGE Global Scenarios

description: This data set includes global climate change mitigation scenarios as summarized by Riahi et al., 2021. The scenarios are developed as part of the ENGAGE project and were assessed in terms of the their investment implications (Bertram et al., 2021), their land-use dynamics (Hasegawa et al., 2021) as we all as with respect to their costs and benefits (Drouret et al., 2021). The scenarios include a current national policies scenario and an NDC scenario that depict relevant near-term GHG emission tends and targets. In the long-term, two types of CO2 emission budgets are implemented, so called “net-zero budgets” and “end-of-century” budgets. The “net-zero-budget” scenarios assume climate policies that limit the remaining cumulative CO2 emissions until net zero CO2 emissions are reached. These scenarios limit the temperature overshoot and do not rely on global net-negative CO2 emissions to keep warming below the intended temperature limit. In contrast, the “end-of-century budget” scenarios assume long-term climate policies that limit cumulative CO2 emissions over the full course of the 21st century. Depending on the availability of carbon dioxide removal options, these scenarios may comprise high temperature overshoot and global net negative CO2 emissions in the second half of the century. The near-term dimension of current national policies until 2020 or NDCs until 2030 is then combined with reaching the net-zero and full-century CO2 emissions budgets. To cover a relevant range of temperature outcomes (which in addition to the budgets themselves also determined by mitigation of non-CO2 GHG and aerosol emissions), the budgets are varied between 200 and 3000 GtCO2 in steps of 50 – 500 GtCO2.

The data is available for download at the ENGAGE Scenario Explorer. The license permits use of the scenario ensemble for scientific research and science communication, but restricts redistribution of substantial parts of the data. Please refer to the FAQ and legal code for more information.
DOI: 10.5281/zenodo.5078072
title: ENGAGE Global Scenarios

description: This data set includes global climate change mitigation scenarios as summarized by Riahi et al., 2021. The scenarios are developed as part of the ENGAGE project and were assessed in terms of the their investment implications (Bertram et al., 2021), their land-use dynamics (Hasegawa et al., 2021) as we all as with respect to their costs and benefits (Drouret et al., 2021). The scenarios include a current national policies scenario and an NDC scenario that depict relevant near-term GHG emission tends and targets. In the long-term, two types of CO<sub>2</sub> emission budgets are implemented, so called “net-zero budgets” and “end-of-century” budgets. The “net-zero-budget”<strong> </strong>scenarios assume climate policies that limit the remaining cumulative CO<sub>2</sub> emissions until net zero CO<sub>2</sub> emissions are reached. These scenarios limit the temperature overshoot and do not rely on global net-negative CO<sub>2 </sub>emissions to keep warming below the intended temperature limit. In contrast, the “end-of-century budget”<strong> </strong>scenarios assume long-term climate policies that limit cumulative CO<sub>2</sub> emissions over the full course of the 21<sup>st</sup> century. Depending on the availability of carbon dioxide removal options, these scenarios may comprise high temperature overshoot and global net negative CO<sub>2</sub> emissions in the second half of the century. The near-term dimension of current national policies until 2020 or NDCs until 2030 is then combined with reaching the net-zero and full-century CO<sub>2</sub> emissions budgets. To cover a relevant range of temperature outcomes (which in addition to the budgets themselves also determined by mitigation of non-CO<sub>2</sub> GHG and aerosol emissions), the budgets are varied between 200 and 3000 GtCO<sub>2</sub> in steps of 50 – 500 GtCO<sub>2</sub>. The data is available for download at the ENGAGE Scenario Explorer. The license permits use of the scenario ensemble for scientific research and science communication, but restricts redistribution of substantial parts of the data. Please refer to the FAQ and legal code for more information.
DOI: 10.5281/zenodo.5553932
title: ENGAGE Global Scenarios

description: This data set includes global climate change mitigation scenarios as summarized by Riahi et al., 2021. The scenarios are developed as part of the ENGAGE project and were assessed in terms of the their investment implications (Bertram et al., 2021), their land-use dynamics (Hasegawa et al., 2021) as we all as with respect to their costs and benefits (Drouret et al., 2021). The scenarios include a current national policies scenario and an NDC scenario that depict relevant near-term GHG emission tends and targets. In the long-term, two types of CO<sub>2</sub> emission budgets are implemented, so called “net-zero budgets” and “end-of-century” budgets. The “net-zero-budget”<strong> </strong>scenarios assume climate policies that limit the remaining cumulative CO<sub>2</sub> emissions until net zero CO<sub>2</sub> emissions are reached. These scenarios limit the temperature overshoot and do not rely on global net-negative CO<sub>2 </sub>emissions to keep warming below the intended temperature limit. In contrast, the “end-of-century budget”<strong> </strong>scenarios assume long-term climate policies that limit cumulative CO<sub>2</sub> emissions over the full course of the 21<sup>st</sup> century. Depending on the availability of carbon dioxide removal options, these scenarios may comprise high temperature overshoot and global net negative CO<sub>2</sub> emissions in the second half of the century. The near-term dimension of current national policies until 2020 or NDCs until 2030 is then combined with reaching the net-zero and full-century CO<sub>2</sub> emissions budgets. To cover a relevant range of temperature outcomes (which in addition to the budgets themselves also determined by mitigation of non-CO<sub>2</sub> GHG and aerosol emissions), the budgets are varied between 200 and 3000 GtCO<sub>2</sub> in steps of 50 – 500 GtCO<sub>2</sub>. The data is available for download at the ENGAGE Scenario Explorer. The license permits use of the scenario ensemble for scientific research and science communication, but restricts redistribution of substantial parts of the data. Please refer to the FAQ and legal code for more information.
DOI: 10.5281/zenodo.11498006
title: Metagenomic insights into microbial community structure and metabolism in alpine permafrost on the Tibetan Plateau

description: Microbes in Tibetan permafrost

 



This project repository associated with the following manuscript:




Luyao Kang, Yutong Song, Rachel Mackelprang, Dianye Zhang, Shuqi Qin, Leiyi Chen, Linwei Wu, Yunfeng Peng and Yuanhe Yang*. Metagenomic insights into microbial community structure and metabolism in alpine permafrost on the Tibetan Plateau.


Abstract

        Permafrost, characterized by its frozen soil, serves as a unique habitat for diverse microorganisms. Understanding these microbial communities is crucial for predicting the response of permafrost ecosystems to climate change. However, large-scale evidence regarding stratigraphic variations in microbial profiles remains limited. Here, we analyze microbial community structure and functional potential based on 16S rRNA gene amplicon sequencing and metagenomic data obtained from a ∼1,000 km permafrost transect on the Tibetan Plateau. We find that microbial alpha diversity declines but beta diversity increases down the soil profile. Microbial assemblages are primarily governed by dispersal limitation and drift; the importance of drift decreases but that of dispersal limitation increases with soil depth. Moreover, genes related to reduction reactions (e.g., ferric iron reduction, dissimilatory nitrate reduction, and denitrification) are enriched in the subsurface and permafrost layers. In addition, microbial groups involved in alternative electron accepting processes are more diverse and contribute highly to community-level metabolic profiles in the subsurface and permafrost layers, likely reflecting the lower redox potential and more complicated trophic strategies for microorganisms in deeper soils. Overall, these findings provide comprehensive insights into large-scale stratigraphic profiles of microbial community structure and functional potentials in permafrost regions.

        For the description of the files, please see README.md file.