cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.6620358
title: Raw sequencing data for studying the colonization of soil communities after glacier retreat

description: Glaciers show a pattern of retreat at the global scale. Deglaciated areas are exposed and colonized by multiple organisms, but lack of global studies hampers a complete understanding of the future of these ecosystems. Until now, the complete reconstruction of soil communities was hampered by the complex identification of organisms, thus analyses at broad geographical and taxonomic scale have been so far impossible. The dataset used for this study represents the assemblages of Bacteria, Mycota, Eukaryota, Collembola (springtails), Oligochaeta (Earth worms), Insecta, Arthropoda and Vascular Plants obtained using environmental DNA (eDNA) metabarcoding. eDNA was extracted from soil samples collected from multiple glacier forelands representative of some of the main mountain chains of Europe, Asia, the Americas and Oceania. We investigated chronosequences of glacier retreat (i.e., the chronological sequence of specific geomorphological features along deglaciated areas for which the date of glacier retreat is known) ranging from recent years to the Little Ice Age (~1850). We used this newly assembled global DNA metabarcoding dataset to obtain a complete reconstruction of community changes in novel ecosystems after glacier retreat. Information on assemblages can be then combined with analyses of soil, landscape and climate to identify the drivers of community changes.
description: Libraries were prepared following the MetaFast protocol (Taberlet et al., 2018) and sequenced using the MiSeq (Bact02 and Fung02) or HiSeq 2500 (Arth02, Coll01, Euka02, Inse01, Olig01, Sper01) Illumina platforms (Illumina, San Diego, CA, USA) with a paired-end approach (2 × 250 bp for Bact02 and Fung02, and 2 × 150 bp for the others markers) at Fasteris (SA, Geneva, Switzerland). For each marker, the sequence depth corresponded to 10,000 reads per sample.

USAGE NOTES:
Example for Euka02 marker:

The zipped folders contains raw sequence data for seven paired-end sequenced libraries. Usually two files per library are available, corresponding to the forward and reverse reads.

Example of files for one library (GWM-671):

150703_SN234_A_L001_GWM-671_R1.fastq.gz
150703_SN234_A_L001_GWM-671_R2.fastq.gz

When more than two files are available for the the forward and reverse reads, more than one sequencing lane was needed to guarantee the desired sequencing depth (i.e. 10,000 sequences per sample). In this case, the raw sequences of the forward and reverse sequencing were concatenated prior to bioinformatics treatment.

Example of files for one library (GWM-1497):
these two files were concatenated
190503_SND405_B_L001_GWM-1497_R1.fastq.gz
190503_SND405_B_L002_GWM-1497_R1.fastq.gz
these two files were concatenated
190503_SND405_B_L001_GWM-1497_R2.fastq.gz
190503_SND405_B_L002_GWM-1497_R2.fastq.gz

See the complete bioinformatics pipeline provided and described in the "Methods" section of the related manuscript.
DOI: 10.5281/zenodo.6620359
title: Raw sequencing data for studying the colonization of soil communities after glacier retreat

description: Glaciers show a pattern of retreat at the global scale. Deglaciated areas are exposed and colonized by multiple organisms, but lack of global studies hampers a complete understanding of the future of these ecosystems. Until now, the complete reconstruction of soil communities was hampered by the complex identification of organisms, thus analyses at broad geographical and taxonomic scale have been so far impossible. The dataset used for this study represents the assemblages of Bacteria, Mycota, Eukaryota, Collembola (springtails), Oligochaeta (Earth worms), Insecta, Arthropoda and Vascular Plants obtained using environmental DNA (eDNA) metabarcoding. eDNA was extracted from soil samples collected from multiple glacier forelands representative of some of the main mountain chains of Europe, Asia, the Americas and Oceania. We investigated chronosequences of glacier retreat (i.e., the chronological sequence of specific geomorphological features along deglaciated areas for which the date of glacier retreat is known) ranging from recent years to the Little Ice Age (~1850). We used this newly assembled global DNA metabarcoding dataset to obtain a complete reconstruction of community changes in novel ecosystems after glacier retreat. Information on assemblages can be then combined with analyses of soil, landscape and climate to identify the drivers of community changes.
description: Libraries were prepared following the MetaFast protocol (Taberlet et al., 2018) and sequenced using the MiSeq (Bact02 and Fung02) or HiSeq 2500 (Arth02, Coll01, Euka02, Inse01, Olig01, Sper01) Illumina platforms (Illumina, San Diego, CA, USA) with a paired-end approach (2 × 250 bp for Bact02 and Fung02, and 2 × 150 bp for the others markers) at Fasteris (SA, Geneva, Switzerland). For each marker, the sequence depth corresponded to 10,000 reads per sample. USAGE NOTES: Example for Euka02 marker: The zipped folders contains raw sequence data for seven paired-end sequenced libraries. Usually two files per library are available, corresponding to the forward and reverse reads. Example of files for one library (GWM-671): 150703_SN234_A_L001_GWM-671_R1.fastq.gz 150703_SN234_A_L001_GWM-671_R2.fastq.gz When more than two files are available for the the forward and reverse reads, more than one sequencing lane was needed to guarantee the desired sequencing depth (i.e. 10,000 sequences per sample). In this case, the raw sequences of the forward and reverse sequencing were concatenated prior to bioinformatics treatment. Example of files for one library (GWM-1497): these two files were concatenated 190503_SND405_B_L001_GWM-1497_R1.fastq.gz 190503_SND405_B_L002_GWM-1497_R1.fastq.gz these two files were concatenated 190503_SND405_B_L001_GWM-1497_R2.fastq.gz 190503_SND405_B_L002_GWM-1497_R2.fastq.gz See the complete bioinformatics pipeline provided and described in the "Methods" section of the related manuscript.
DOI: 10.5281/zenodo.7628236
title: Raw sequencing data for studying the colonization of soil communities after glacier retreat

description: Glaciers show a pattern of retreat at the global scale. Deglaciated areas are exposed and colonized by multiple organisms, but lack of global studies hampers a complete understanding of the future of these ecosystems. Until now, the complete reconstruction of soil communities was hampered by the complex identification of organisms, thus analyses at broad geographical and taxonomic scale have been so far impossible. The dataset used for this study represents the assemblages of Bacteria, Mycota, Eukaryota, Collembola (springtails), Oligochaeta (Earth worms), Insecta, Arthropoda and Vascular Plants obtained using environmental DNA (eDNA) metabarcoding. eDNA was extracted from soil samples collected from multiple glacier forelands representative of some of the main mountain chains of Europe, Asia, the Americas and Oceania. We investigated chronosequences of glacier retreat (i.e., the chronological sequence of specific geomorphological features along deglaciated areas for which the date of glacier retreat is known) ranging from recent years to the Little Ice Age (~1850). We used this newly assembled global DNA metabarcoding dataset to obtain a complete reconstruction of community changes in novel ecosystems after glacier retreat. Information on assemblages can be then combined with analyses of soil, landscape and climate to identify the drivers of community changes.
description: Libraries were prepared following the MetaFast protocol (Taberlet et al., 2018) and sequenced using the MiSeq (Bact02 and Fung02) or HiSeq 2500 (Arth02, Coll01, Euka02, Inse01, Olig01, Sper01) Illumina platforms (Illumina, San Diego, CA, USA) with a paired-end approach (2 × 250 bp for Bact02 and Fung02, and 2 × 150 bp for the others markers) at Fasteris (SA, Geneva, Switzerland). For each marker, the sequence depth corresponded to 10,000 reads per sample.

USAGE NOTES:
Example for Euka02 marker:

The zipped folders contains raw sequence data for seven paired-end sequenced libraries. Usually two files per library are available, corresponding to the forward and reverse reads.

Example of files for one library (GWM-671):

150703_SN234_A_L001_GWM-671_R1.fastq.gz
150703_SN234_A_L001_GWM-671_R2.fastq.gz

When more than two files are available for the the forward and reverse reads, more than one sequencing lane was needed to guarantee the desired sequencing depth (i.e. 10,000 sequences per sample). In this case, the raw sequences of the forward and reverse sequencing were concatenated prior to bioinformatics treatment.

Example of files for one library (GWM-1497):
these two files were concatenated
190503_SND405_B_L001_GWM-1497_R1.fastq.gz
190503_SND405_B_L002_GWM-1497_R1.fastq.gz
these two files were concatenated
190503_SND405_B_L001_GWM-1497_R2.fastq.gz
190503_SND405_B_L002_GWM-1497_R2.fastq.gz

See the complete bioinformatics pipeline provided and described in the "Methods" section of the related manuscript.
DOI: 10.5281/zenodo.10074848
title: Assessing the interaction of oceanic and riverine processes on coastal phytoplankton dynamics in the East China Sea
DOI: 10.5281/zenodo.10074847
title: Assessing the interaction of oceanic and riverine processes on coastal phytoplankton dynamics in the East China Sea
DOI: 10.5281/zenodo.10074760
title: Saharan HPEs identified and described in Armon et al. (in rev.)

description: This dataset represents heavy precipitation events (HPEs) identified and described in Armon et al. (in rev., Weather and Climate Extremes). 
It contains two files, both similar to Table 1 in the manuscript: 
(a)  'Sahara_HPEs.csv' contains details of 41,978 HPEs throughout the Sahara
(b) 'Sahara_Core_HPEs.csv' contains details of 650 HPEs identified over the core of the Sahara.
Please note, coordinates represent the centre-of-mass of precipitation for every HPE.
DOI: 10.5281/zenodo.10074759
title: Saharan HPEs identified and described in Armon et al. (in rev.)

description: This dataset represents heavy precipitation events (HPEs) identified and described in Armon et al. (in rev., Weather and Climate Extremes). 
It contains two files, both similar to Table 1 in the manuscript: 
(a)  'Sahara_HPEs.csv' contains details of 41,978 HPEs throughout the Sahara
(b) 'Sahara_Core_HPEs.csv' contains details of 650 HPEs identified over the core of the Sahara.
Please note, coordinates represent the centre-of-mass of precipitation for every HPE.
DOI: 10.5281/zenodo.10074832
title: Radiomics and machine learning analysis by computed tomography and magnetic resonance imaging in colorectal liver metastases prognostic assessment

description: We uploaded the raw data related to extracted features of the manuscript "Granata V, Fusco R, De Muzio F, Brunese MC, Setola SV, Ottaiano A, Cardone C, Avallone A, Patrone R, Pradella S, Miele V, Tatangelo F, Cutolo C, Maggialetti N, Caruso D, Izzo F, Petrillo A. Radiomics and machine learning analysis by computed tomography and magnetic resonance imaging in colorectal liver metastases prognostic assessment. Radiol Med. 2023 Nov;128(11):1310-1332. doi: 10.1007/s11547-023-01710-w. Epub 2023 Sep 11. PMID: 37697033."
DOI: 10.5281/zenodo.10074831
title: Radiomics and machine learning analysis by computed tomography and magnetic resonance imaging in colorectal liver metastases prognostic assessment

description: We uploaded the raw data related to extracted features of the manuscript "Granata V, Fusco R, De Muzio F, Brunese MC, Setola SV, Ottaiano A, Cardone C, Avallone A, Patrone R, Pradella S, Miele V, Tatangelo F, Cutolo C, Maggialetti N, Caruso D, Izzo F, Petrillo A. Radiomics and machine learning analysis by computed tomography and magnetic resonance imaging in colorectal liver metastases prognostic assessment. Radiol Med. 2023 Nov;128(11):1310-1332. doi: 10.1007/s11547-023-01710-w. Epub 2023 Sep 11. PMID: 37697033."
DOI: 10.17632/rx6kpwmvtf.1
title: Illumination and gaze effects on face evaluation: the Bi-AGI Database

description: Face evaluation and first impression generation can be affected by multiple face elements such as invariant facial features, gaze direction and environmental context; however, the composite modulation of eye gaze and illumination on faces of different gender and ages has not been previously investigated. We aimed at testing how these different facial and contextual features affect ratings of social attributes. Thus, we created and validated the Bi-AGI Database, a freely available new set of male and female face stimuli varying in age across lifespan from 18 to 87 years, gaze direction and illumination conditions. Judgments on attractiveness, femininity-masculinity, dominance and trustworthiness were collected for each stimulus. Results evidence the interaction of the different variables in modulating social trait attribution, in particular illumination differently affects ratings across age, gaze and gender, with less impact on older adults and greater effect on young faces.
DOI: 10.5281/zenodo.10074471
title: Pix2pix training dataset for predicting nuclei form brightfield images

description: Dataset for training pix2pix model to predict nuclei from brightfield images of MDA-MB-231. 
This dataset contains 1600 brightfield and 1600 nuclei images. 
The nuclei were labeled using sir-DNA (Cytoskeleton). Cells were imaged live (37 °C, 5% CO2) using a Nikon Eclipse Ti2-E microscope (Nikon) equipped with an sCMOS Orca Flash4.0 camera (Hamamatsu) and controlled by the NIS-Elements software (Nikon, v 5.11.01). MDA-MB-231 cells were imaged using a 20× Nikon CFI Plan Apo Lambda objective (NA 0.75), either 1 frame per minute for 2 hours or 1 frame every 5 minutes for 17 hours. In these experiments, a camera binning of 2 × 2 was used.
DOI: 10.5281/zenodo.10074470
title: Pix2pix training dataset for predicting nuclei form brightfield images

description: Dataset for training pix2pix model to predict nuclei from brightfield images of MDA-MB-231. 
This dataset contains 1600 brightfield and 1600 nuclei images. 
The nuclei were labeled using sir-DNA (Cytoskeleton). Cells were imaged live (37 °C, 5% CO2) using a Nikon Eclipse Ti2-E microscope (Nikon) equipped with an sCMOS Orca Flash4.0 camera (Hamamatsu) and controlled by the NIS-Elements software (Nikon, v 5.11.01). MDA-MB-231 cells were imaged using a 20× Nikon CFI Plan Apo Lambda objective (NA 0.75), either 1 frame per minute for 2 hours or 1 frame every 5 minutes for 17 hours. In these experiments, a camera binning of 2 × 2 was used.
DOI: 10.15151/esrf-es-1334151285
title: The origin of the blue colour of protohistoric vitreous materials from Paduli (Colli sul Velino, Rieti, Italy)

description: The present study aims at ascertain the valence state speciation of the transition elements (Cu and Co) suspected to play a role in the origin of the blue colour of protohistoic vitreous materials. The case study is provided by 5 different glass artefacts coming from Paduli (Colli sul Velino, Rieti, Italy), where a relevant ability in controlling chromatic effects has been reached by opportunely mixing the two elements, and controlling the thermal process. Only an accurate X-ray Absorption Spectroscopy (XAS) investigation could allow to ascertain the effective metal speciations in the artefacts, thus providing a clue in the understanding of the technological process active in the area.
DOI: 10.5281/zenodo.10074787
title: Mushroom Species: Diversity, Utility, and Conservation

description: Mushrooms, as a taxonomically diverse group of fungi, have garnered increasing scientific interest due to their ecological significance and extensive utility in various industries. This review contributes a comprehensive analysis that integrates the ecological, economic, and medicinal aspects of mushrooms, shedding light on the novel and holistic understanding of these remarkable organisms. It emphasizes the urgent requirement for a more cohesive approach to studying and preserving mushroom diversity, considering their integral role in ecosystems and their potential to address pressing global challenges. The primary aim of this paper is to provide a holistic assessment of mushroom species diversity, delve into their diverse utilities across various sectors, and emphasize the imperative need for their conservation. The article is based on an extensive examination of scientific literature, encompassing research articles, reports, and databases. The paper showcases the extraordinary diversity of mushroom species, with countless yet-to-be-identified species. Despite their ecological and economic importance, mushroom populations face formidable threats from habitat degradation, overharvesting, and climate change. Mushrooms, often overshadowed by more charismatic organisms, are indispensable components of ecosystems and hold tremendous potential for various industries. To ensure their sustained existence, comprehensive conservation strategies are imperative, including the establishment of protected areas, sustainable harvesting practices, and the promotion of cultivation techniques. Additionally, raising awareness among the public and policymakers about the multifaceted significance of mushrooms is essential. Finally, the paper recommends fostering interdisciplinary collaborations to explore untapped mushroom potential, incorporating mushroom conservation into biodiversity plans, and launching educational initiatives to heighten public awareness. This review serves as a foundational resource for future studies and initiatives aimed at preserving mushroom diversity and harnessing their manifold benefits for society and the environment.
DOI: 10.5281/zenodo.10074786
title: Mushroom Species: Diversity, Utility, and Conservation

description: Mushrooms, as a taxonomically diverse group of fungi, have garnered increasing scientific interest due to their ecological significance and extensive utility in various industries. This review contributes a comprehensive analysis that integrates the ecological, economic, and medicinal aspects of mushrooms, shedding light on the novel and holistic understanding of these remarkable organisms. It emphasizes the urgent requirement for a more cohesive approach to studying and preserving mushroom diversity, considering their integral role in ecosystems and their potential to address pressing global challenges. The primary aim of this paper is to provide a holistic assessment of mushroom species diversity, delve into their diverse utilities across various sectors, and emphasize the imperative need for their conservation. The article is based on an extensive examination of scientific literature, encompassing research articles, reports, and databases. The paper showcases the extraordinary diversity of mushroom species, with countless yet-to-be-identified species. Despite their ecological and economic importance, mushroom populations face formidable threats from habitat degradation, overharvesting, and climate change. Mushrooms, often overshadowed by more charismatic organisms, are indispensable components of ecosystems and hold tremendous potential for various industries. To ensure their sustained existence, comprehensive conservation strategies are imperative, including the establishment of protected areas, sustainable harvesting practices, and the promotion of cultivation techniques. Additionally, raising awareness among the public and policymakers about the multifaceted significance of mushrooms is essential. Finally, the paper recommends fostering interdisciplinary collaborations to explore untapped mushroom potential, incorporating mushroom conservation into biodiversity plans, and launching educational initiatives to heighten public awareness. This review serves as a foundational resource for future studies and initiatives aimed at preserving mushroom diversity and harnessing their manifold benefits for society and the environment.
DOI: 10.14469/hpc/13105
title: FAIR Table: Calculated isotope effects for the SWERN oxidation

description: Calculated using Kinisot.py
DOI: 10.5281/zenodo.10074874
title: Information and Bargaining through Agents: Experimental Evidence from Mexico's Labor Courts

description: Sadka, Joyce, Enrique Seira and Christopher Woodruff, "Information and Bargaining through Agents: Experimental Evidence from Mexico’s Labor Courts", Review of Economic Studies, accepted.
DOI: 10.5281/zenodo.8143345
title: Information and Bargaining through Agents: Experimental Evidence from Mexico's Labor Courts

description: Sadka, Joyce, Enrique Seira and Christopher Woodruff, "Information and Bargaining through Agents: Experimental Evidence from Mexico’s Labor Courts", Review of Economic Studies, accepted.
DOI: 10.5281/zenodo.8143346
title: Information and Bargaining through Agents: Experimental Evidence from Mexico's Labor Courts

description: Sadka, Joyce, Enrique Seira and Christopher Woodruff, "Information and Bargaining through Agents: Experimental Evidence from Mexico’s Labor Courts", Review of Economic Studies, accepted.
DOI: 10.5281/zenodo.8340216
title: Information and Bargaining through Agents: Experimental Evidence from Mexico's Labor Courts

description: Sadka, Joyce, Enrique Seira and Christopher Woodruff, "Information and Bargaining through Agents: Experimental Evidence from Mexico’s Labor Courts", Review of Economic Studies, accepted.
DOI: 10.5281/zenodo.10069577
title: Input data for boreal tip analysis code

description: Input data for analysis code of boreal tip repository.Includes central European geographical subsets of CRU TS, MOD44B, GLC2000, MPI-ESM and CHELSA-TraCE21k data products as well as paths for download of complete data sets.
DOI: 10.5281/zenodo.10069578
title: Input data for boreal tip analysis code

description: Input data for analysis code of boreal tip repository.Includes central European geographical subsets of CRU TS, MOD44B, GLC2000, MPI-ESM and CHELSA-TraCE21k data products as well as paths for download of complete data sets.
DOI: 10.5281/zenodo.10074865
title: Input data for boreal tip analysis code

description: Input data for analysis code of boreal tip repository.Includes central European geographical subsets of CRU TS, MOD44B, GLC2000, MPI-ESM and CHELSA-TraCE21k data products as well as paths for download of complete data sets.
DOI: 10.5281/zenodo.10044678
title: NLRP3 inflammasome activation and symptom burden in KRAS-mutated CMML patients is reverted by IL-1 blocking therapy
DOI: 10.5281/zenodo.10014194
title: Multilevel Interventions for Mental Health in SMEs and Public Workplaces - H-Work EU Project Dataset (Only for Partners)

description: This Dataset includes data collected as part of the H-Work project, at timepoints T1-T7. It contains data from each timepoint per site in single files and merged Data from multiple sites and timepoints, for more information see info file.
DOI: 10.5281/zenodo.10014195
title: Multilevel Interventions for Mental Health in SMEs and Public Workplaces - H-Work EU Project Dataset (Only for Partners)

description: This Dataset includes data collected as part of the H-Work project, at timepoints T1-T7. It contains data from each timepoint per site in single files and merged Data from multiple sites and timepoints, for more information see info file.
DOI: 10.6084/m9.figshare.24511243
title: Paediatric TB treatment Outcome.xls

description: The research focused on paediatric tuberculosis treatment outcomes.
DOI: 10.6084/m9.figshare.24511306
title: <b>Drivers of biogenic volatile organic compound emissions in hygrophytic bryophytes (DATASET)</b>

description: Dataset and R script used to produce the results shown in the paper: <b>Drivers of biogenic volatile organic compound emissions in hygrophytic bryophytes</b>.
DOI: 10.17633/rd.brunel.23905842
title: A modelling workflow for quantification of photobioreactor performance dataset

description: Excel spreadsheet containing experimental data-set showing two-phase flow measurements and experimental growth data for the diatom <i>Phaeodactylum tricornutum</i>.