cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.12626180
title: Extended rat miRNA repertoire

description: Generally, Rattus norvegicus' miRNA repertoire falls short compared to the other rodent model organism, Mus musculus.

To extend the miRNA catalogue in Rattus norvegicus, we utilized Infernal v1.1 (Nawrocki and Eddy, 2013) to derive potential rat miRNA candidates starting from all available mammalian miRNA families in miRBase. We utilized MIRfix (Yazbeck et al., 2019) to curate the extended miRNA datasets automatically. Subsequent manual inspection and curation of miRNA alignments resulted in a reliable and comprehensive update to the rat miRNA annotation.

Key facts of the extended miRNA repertoire



342 miRNA families (40 novel families)

549 miRNA sequences (56 novel miRNAs)

 11 corrected annotated miRNAs


European Nucleotide Archive

The 56 novel sequences not listed in miRBase before have been submitted to the European Nucleotide Archive at EMBL-EBI.They are accessible with the accession numbers OZ078105 - OZ078160.The sequences will be permanently available from the ENA browser at http://www.ebi.ac.uk/ena/data/view/<ACCESSION NUMBERS>.

An overview of all sequences is given here: http://www.ebi.ac.uk/ena/data/view/OZ078105-OZ078160.
DOI: 10.5281/zenodo.12626179
title: Extended rat miRNA repertoire

description: Generally, Rattus norvegicus' miRNA repertoire falls short compared to the other rodent model organism, Mus musculus.

To extend the miRNA catalogue in Rattus norvegicus, we utilized Infernal v1.1 (Nawrocki and Eddy, 2013) to derive potential rat miRNA candidates starting from all available mammalian miRNA families in miRBase. We utilized MIRfix (Yazbeck et al., 2019) to curate the extended miRNA datasets automatically. Subsequent manual inspection and curation of miRNA alignments resulted in a reliable and comprehensive update to the rat miRNA annotation.

Key facts of the extended miRNA repertoire



342 miRNA families (40 novel families)

549 miRNA sequences (56 novel miRNAs)

 11 corrected annotated miRNAs


European Nucleotide Archive

The 56 novel sequences not listed in miRBase before have been submitted to the European Nucleotide Archive at EMBL-EBI.They are accessible with the accession numbers OZ078105 - OZ078160.The sequences will be permanently available from the ENA browser at http://www.ebi.ac.uk/ena/data/view/<ACCESSION NUMBERS>.

An overview of all sequences is given here: http://www.ebi.ac.uk/ena/data/view/OZ078105-OZ078160.
DOI: 10.5281/zenodo.12571785
title: The valence electron affinity of uracil determined by anion cluster photoelectron spectroscopy

description: Connor J. Clarke, E. Michi Burrow, Jan R. R. Verlet
DOI: 10.5281/zenodo.12571786
title: The valence electron affinity of uracil determined by anion cluster photoelectron spectroscopy

description: Connor J. Clarke, E. Michi Burrow, Jan R. R. Verlet
DOI: 10.5281/zenodo.7928190
title: Data and code for "Brehm et al. (2023) The complexity of micro- and nanoplastic research in the genus Daphnia – A systematic review of study variability and a meta-analysis of immobilization rates"

description: All data and R code for


Brehm, J., Ritschar, S., Laforsch, C. and Mair, M.M. (2023). The complexity of micro- and nanoplastic research in the genus Daphnia – A systematic review of study variability and a meta-analysis of immobilization rates. Journal of Hazardous Materials 458: 131839. (https://doi.org/10.1016/j.jhazmat.2023.131839)


Abstract


In recent years, the number of publications on nano- and microplastic particles (NMPs) effects on freshwater organisms has increased rapidly. Freshwater crustaceans of the genus Daphnia are widely used in ecotoxicological research as model organisms for assessing the impact of NMPs. However, the diversity of experimental designs in these studies makes conclusions about the general impact of NMPs on Daphnia challenging. To approach this, we systematically reviewed the literature on NMP effects on Daphnia and summarized the diversity of test organisms, experimental conditions, NMP properties and measured endpoints to identify gaps in our knowledge of NMP effects on Daphnia. We use a meta-analysis on mortality and immobilization rates extracted from the compiled literature to illustrate how NMP properties, study parameters and the biology of Daphnia can impact outcomes in toxicity bioassays. In addition, we investigate the extent to which the available data can be used to predict the toxicity of untested NMPs based on the extracted parameters. Based on our results, we argue that focusing on a more diverse set of NMP properties combined with a more detailed characterization of the particles in future studies will help to fill current research gaps, improve predictive models and allow the identification of NMP properties linked to toxicity.
description: This study was funded by the Deutsche Forschungsgemeinschaft (DFG; German Research Foundation) – Project Number 391977956-SFB 1357.
DOI: 10.5281/zenodo.7928191
title: Data and code for "Brehm et al. (2023) The complexity of micro- and nanoplastic research in the genus Daphnia – A systematic review of study variability and a meta-analysis of immobilization rates"

description: All data and R code for


Brehm, J., Ritschar, S., Laforsch, C. and Mair, M.M. (2023). The complexity of micro- and nanoplastic research in the genus Daphnia – A systematic review of study variability and a meta-analysis of immobilization rates. Journal of Hazardous Materials 458: 131839. (https://doi.org/10.1016/j.jhazmat.2023.131839)


Abstract


In recent years, the number of publications on nano- and microplastic particles (NMPs) effects on freshwater organisms has increased rapidly. Freshwater crustaceans of the genus Daphnia are widely used in ecotoxicological research as model organisms for assessing the impact of NMPs. However, the diversity of experimental designs in these studies makes conclusions about the general impact of NMPs on Daphnia challenging. To approach this, we systematically reviewed the literature on NMP effects on Daphnia and summarized the diversity of test organisms, experimental conditions, NMP properties and measured endpoints to identify gaps in our knowledge of NMP effects on Daphnia. We use a meta-analysis on mortality and immobilization rates extracted from the compiled literature to illustrate how NMP properties, study parameters and the biology of Daphnia can impact outcomes in toxicity bioassays. In addition, we investigate the extent to which the available data can be used to predict the toxicity of untested NMPs based on the extracted parameters. Based on our results, we argue that focusing on a more diverse set of NMP properties combined with a more detailed characterization of the particles in future studies will help to fill current research gaps, improve predictive models and allow the identification of NMP properties linked to toxicity.
description: This study was funded by the Deutsche Forschungsgemeinschaft (DFG; German Research Foundation) – Project Number 391977956-SFB 1357.
DOI: 10.5281/zenodo.12632228
title: Intergroup cooperation in the lab: asymmetric power relations and redistributive policies

description: Dataset and analysis script to recreate the figures and tables for the paper.
DOI: 10.5281/zenodo.12632229
title: Intergroup cooperation in the lab: asymmetric power relations and redistributive policies

description: Dataset and analysis script to recreate the figures and tables for the paper.
DOI: 10.5281/zenodo.11477724
title: Data and code for "Salomon et al. 2024: Effects of dissolved organic matter on the toxicity of micro- and nanoplastic particles to Daphnia - a meta-analysis."

description: All data and R code for

Salomon S, Grubmüller E, Kropf P, Nickl E, Rühl A, Weigel S, Becker F, Antonio Vital AL, Laforsch C, Schott M, Mair MM. (2024). Effects of dissolved organic matter on the toxicity of micro- and nanoplastic particles to Daphnia - a meta-analysis. Microplastics and Nanoplastics. (https://doi.org/10.1186/s43591-024-00088-4)

Abstract

Effects of micro- and nanoplastic particles (MNP) on organisms have been increasingly reported in recent years, with a large number of studies conducted on water fleas of the genus Daphnia. Most of the available studies used pristine particles that have not been exposed to the environment or to organic substances. In natural environments, however, organic substances like dissolved organic matter (DOM) attach to the MNP, forming an ecocorona on the particles’ surface. How the formation of an ecocorona influences MNP toxicity is still uncertain. While some studies suggest that DOM can mitigate the negative effects of MNP on organisms, other studies did not find such associations. In addition, it is unclear whether the DOM attached to the particles’ surface is attenuating the effects of MNP directly or whether co-exposure with DOM solved in the medium attenuates MNP toxicity indirectly, for instance by increasing Daphnia‘s resilience to stressors in general. To draw more solid conclusions about the direction and size of the mediating effect of DOM on MNP-associated immobilization in Daphnia spp., we synthesized evidence from the published literature and compiled 305 data points from 13 independent studies. The results of our meta-analysis show that the toxic effects of MNP are likely reduced in the presence of certain types of DOM in the exposure media. We found similar mediating effects when MNP were incubated in media containing DOM before the exposure experiments, although to a lesser extent. Future studies designed to disentangle the effects of DOM attached to the MNP from the general effects of DOM in the exposure medium will contribute to a deeper mechanistic understanding of MNP toxicity in nature and enhance the reliability of MNP risk assessment.
description: This study was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – SFB 1357 – 391977956.
DOI: 10.5281/zenodo.11477725
title: Data and code for "Salomon et al. 2024: Effects of dissolved organic matter on the toxicity of micro- and nanoplastic particles to Daphnia - a meta-analysis."

description: All data and R code for

Salomon S, Grubmüller E, Kropf P, Nickl E, Rühl A, Weigel S, Becker F, Antonio Vital AL, Laforsch C, Schott M, Mair MM. (2024). Effects of dissolved organic matter on the toxicity of micro- and nanoplastic particles to Daphnia - a meta-analysis. Microplastics and Nanoplastics. (https://doi.org/10.1186/s43591-024-00088-4)

Abstract

Effects of micro- and nanoplastic particles (MNP) on organisms have been increasingly reported in recent years, with a large number of studies conducted on water fleas of the genus Daphnia. Most of the available studies used pristine particles that have not been exposed to the environment or to organic substances. In natural environments, however, organic substances like dissolved organic matter (DOM) attach to the MNP, forming an ecocorona on the particles’ surface. How the formation of an ecocorona influences MNP toxicity is still uncertain. While some studies suggest that DOM can mitigate the negative effects of MNP on organisms, other studies did not find such associations. In addition, it is unclear whether the DOM attached to the particles’ surface is attenuating the effects of MNP directly or whether co-exposure with DOM solved in the medium attenuates MNP toxicity indirectly, for instance by increasing Daphnia‘s resilience to stressors in general. To draw more solid conclusions about the direction and size of the mediating effect of DOM on MNP-associated immobilization in Daphnia spp., we synthesized evidence from the published literature and compiled 305 data points from 13 independent studies. The results of our meta-analysis show that the toxic effects of MNP are likely reduced in the presence of certain types of DOM in the exposure media. We found similar mediating effects when MNP were incubated in media containing DOM before the exposure experiments, although to a lesser extent. Future studies designed to disentangle the effects of DOM attached to the MNP from the general effects of DOM in the exposure medium will contribute to a deeper mechanistic understanding of MNP toxicity in nature and enhance the reliability of MNP risk assessment.
description: This study was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – SFB 1357 – 391977956.
DOI: 10.5281/zenodo.12623855
title: Multi-survey data collection on Finnish household waste sorting and recycling

description: This dataset consists of surveys that have been marked with letters from A to L.



Surveys A, B, D, E, F, G, H, I, K and L have at least one questionnaire. Each questionnaire, presented with questions in both Finnish and English, has its results displayed in the dataset table. Dataset tables haven't been translated, they are in Finnish.

Survey C is an interview based study. Questions have been translated into English, but the interview data is in Finnish only.

Survey J is an experiment on how to target communication in social media. The dataset shows how many times each post has been watched, which hastags were used etc.


The work was carried out by groups of students as part of the Sustainable Product Development Project course in November-December 2023. All the surveys are interconnected in one way or another with the promotion of household waste sorting and recycling, as the topic of the assignment came from HAMK Smart research group's KOTILO project (Participatory Design of Source Separation in Recycling). For more information, go to hamk.fi/kotilo

Each survey is licensed under CC BY 4.0 Attribution 4.0 International for the respective group of students, the names of the students are at the beginning of each dataset.
DOI: 10.5281/zenodo.12623856
title: Multi-survey data collection on Finnish household waste sorting and recycling

description: This dataset consists of surveys that have been marked with letters from A to L.



Surveys A, B, D, E, F, G, H, I, K and L have at least one questionnaire. Each questionnaire, presented with questions in both Finnish and English, has its results displayed in the dataset table. Dataset tables haven't been translated, they are in Finnish.

Survey C is an interview based study. Questions have been translated into English, but the interview data is in Finnish only.

Survey J is an experiment on how to target communication in social media. The dataset shows how many times each post has been watched, which hastags were used etc.


The work was carried out by groups of students as part of the Sustainable Product Development Project course in November-December 2023. All the surveys are interconnected in one way or another with the promotion of household waste sorting and recycling, as the topic of the assignment came from HAMK Smart research group's KOTILO project (Participatory Design of Source Separation in Recycling). For more information, go to hamk.fi/kotilo

Each survey is licensed under CC BY 4.0 Attribution 4.0 International for the respective group of students, the names of the students are at the beginning of each dataset.
DOI: 10.5281/zenodo.12632096
title: Seasonal Variations of Microbial Communities and Viral Diversity in Fishery-Enhanced Marine Ranching Sediments: Insights into Metabolic Potentials and Ecological Interactions

description: Sediment samples were collected in four seasons from May 2022 to January 2023 from the Tian coastal marine ranching (36°91′ N and 122°15′ E) located along Jinghai Bay in Weihai City, Shandong Province, China. We employed amplicon (16S and 18S) and metagenomic approaches aiming to reveal the seasonal patterns of microbial communities, bacterial-eukaryotic interactions, whole metabolic potential, and their coupling mechanisms with carbon (C), nitrogen (N), and sulfur (S) cycling in marine ranching sediments. Additionally, the characterization and diversity of viral communities in different seasons were explored in marine ranching sediments.  This dataset mainly includes amplicon sequencing (16S and 18S) generated ASV tables (after rarefied), corresponding taxonomic classification tables, metagenome assembly (Single assembly and Co-assembly), metagenome-assembled genomes (MAGs) sequences, and viral operational taxonomic units (vOTUs) sequences.
DOI: 10.5281/zenodo.12632097
title: Seasonal Variations of Microbial Communities and Viral Diversity in Fishery-Enhanced Marine Ranching Sediments: Insights into Metabolic Potentials and Ecological Interactions

description: Sediment samples were collected in four seasons from May 2022 to January 2023 from the Tian coastal marine ranching (36°91′ N and 122°15′ E) located along Jinghai Bay in Weihai City, Shandong Province, China. We employed amplicon (16S and 18S) and metagenomic approaches aiming to reveal the seasonal patterns of microbial communities, bacterial-eukaryotic interactions, whole metabolic potential, and their coupling mechanisms with carbon (C), nitrogen (N), and sulfur (S) cycling in marine ranching sediments. Additionally, the characterization and diversity of viral communities in different seasons were explored in marine ranching sediments.  This dataset mainly includes amplicon sequencing (16S and 18S) generated ASV tables (after rarefied), corresponding taxonomic classification tables, metagenome assembly (Single assembly and Co-assembly), metagenome-assembled genomes (MAGs) sequences, and viral operational taxonomic units (vOTUs) sequences.
DOI: 10.5281/zenodo.12632730
title: Supplementary materials to the article "Practices and attitudes toward replication in empirical translation and interpreting studies"

description: Abstract of the paper:

This article presents the results of three studies on practices in and attitudes toward replication in empirical translation and interpreting studies. The first study reports on a survey in which 52 researchers in translation and interpreting with experience in empirical research answered questions about their practices in and attitudes toward replication. The survey data were complemented by a bibliometric study of publications indexed in the Bibliography of Interpreting and Translation (BITRA) (Franco Aixelá 2001–2019) that explicitly stated in the title or abstract that they were derived from a replication. In a second bibliometric study, a conceptual replication of Yeung’s (2017) study on the acceptance of replications in neuroscience journals was conducted by analyzing 131 translation and interpreting journals. The article aims to provide evidence-based arguments for initiating a debate about the need for replication in empirical translation and interpreting studies and its implications for the development of the discipline.

Description of the supplementary materials:



Material 1: questionnaire in English

Material 2: questionnaire in Spanish

Material 3: results of both questionnaires

Material 4: corpus of identified replications in Translation and Interpreting Studies (TIS)

Material 5: acceptance of replications in TIS journals
DOI: 10.5281/zenodo.12632731
title: Supplementary materials to the article "Practices and attitudes toward replication in empirical translation and interpreting studies"

description: Abstract of the paper:

This article presents the results of three studies on practices in and attitudes toward replication in empirical translation and interpreting studies. The first study reports on a survey in which 52 researchers in translation and interpreting with experience in empirical research answered questions about their practices in and attitudes toward replication. The survey data were complemented by a bibliometric study of publications indexed in the Bibliography of Interpreting and Translation (BITRA) (Franco Aixelá 2001–2019) that explicitly stated in the title or abstract that they were derived from a replication. In a second bibliometric study, a conceptual replication of Yeung’s (2017) study on the acceptance of replications in neuroscience journals was conducted by analyzing 131 translation and interpreting journals. The article aims to provide evidence-based arguments for initiating a debate about the need for replication in empirical translation and interpreting studies and its implications for the development of the discipline.

Description of the supplementary materials:



Material 1: questionnaire in English

Material 2: questionnaire in Spanish

Material 3: results of both questionnaires

Material 4: corpus of identified replications in Translation and Interpreting Studies (TIS)

Material 5: acceptance of replications in TIS journals
DOI: 10.48366/r703591
title: A Systematic Review of Equine-Assisted Interventions in Military Veterans Diagnosed with PTSD

description: Military veterans transitioning from active duty to civilian life often face challenges during the reintegration process. Reintegration can become more difficult when a veteran is coping with posttraumatic stress disorder (PTSD) and its sequelae. Interventions are urgently needed to support veterans during times of transition. Animal-assisted interventions (AAI) show promise in reducing stress, depression, and improving wellbeing in marginalized populations. Equine-assisted interventions (EAI), in particular, are gaining momentum as a treatment option for veterans with PTSD. To synthesize current evidence on the use of EAI as a treatment option in military veterans formally diagnosed with PTSD. A comprehensive, electronic review of the literature was performed. Inclusion criteria were original quantitative or qualitative research, written in English, use of human participants, published through July 2019. The total number of studies included was nine. Main findings were that the efficacy of EAI on PTSD symptoms were equally mixed with both significant and non-significant findings. Data largely trended in the hypothesized direction for improving mental health states, resiliency, social function, quality of life, biological and behavioral measures, however, overall findings did not reach statistical significance. The investigation of EAI as an adjunct treatment for PTSD in military veterans may be effective, however, we cannot make a clear determination based on current evidence. Although findings largely trended in the hypothesized direction, most were not significant (except for PTSD symptoms) and warrant additional research to understand the effectiveness of EAI as an adjunct treatment in military veterans with PTSD.
DOI: 10.5281/zenodo.12632758
title: Research productivity in the post-independence period in Portuguese-speaking African countries, a case of Mozambique: Bibliometric analysis of four decades of Health Research and Higher Education

description: The following datasets were used to build the bibliometric analysis of most productive institutions and frequent keywords in Mozambique.
DOI: 10.5281/zenodo.12632759
title: Research productivity in the post-independence period in Portuguese-speaking African countries, a case of Mozambique: Bibliometric analysis of four decades of Health Research and Higher Education

description: The following datasets were used to build the bibliometric analysis of most productive institutions and frequent keywords in Mozambique.
DOI: 10.5281/zenodo.10802848
title: OI 630.0 nm post-sunset emission enhancement as an effect of tidal activity over low-latitudes [Dataset]
DOI: 10.5281/zenodo.12632528
title: OI 630.0 nm post-sunset emission enhancement as an effect of tidal activity over low-latitudes [Dataset]
DOI: 10.15468/dl.3fyjbz
title: Occurrence Download

description: A dataset containing 54 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is DEU.3_1",
 "Month is one of (May, June)",
 "TaxonKey is Falco subbuteo Linnaeus, 1758",
 "Year 2000-2024"
 ]
}

 The dataset includes 54 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009615-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.