cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.25101848
title: Data for Object Understanding in Ungulates

description: In their natural environment, animals face a variety of ecological and social challenges, which might be linked to the emergence of different cognitive skills. To assess inter-specific variation in cognitive skills, we used ungulates as a study model, testing a total of 26 captive individuals across 5 different species (i.e., dwarf goats, <i>Capra aegagrus hircus</i>, llamas, <i>Lama glama</i>, guanacos, <i>Lama guanicoe</i>, zebras, <i>Equus grevyi</i>, and rhinos, <i>Diceros bicornis michaeli</i>). Across species, we used the same well-established experimental procedures to test individuals’ object permanence, short-term memory, causality, understanding of object properties, and gravity. Our results revealed that study subjects showed object permanence, were able to remember the position of hidden food after up to 60 seconds, and inferred the position of hidden food from the sound produced or not produced when shaking containers. Moreover, they showed an understanding of basic object properties, being able to locate objects hidden behind occluders based on their size and inclination, and could reliably follow the trajectory of falling objects across different conditions. Finally, inter-specific differences were limited to the understanding of object properties, and suggest that domesticated species as goats might perform better than non-domesticated ones in tasks requiring these skills. These results provide new information on the cognitive skills of a still understudied taxon and confirm ungulates as a promising taxon for the comparative study of cognitive evolution.
DOI: 10.5281/zenodo.10457955
title: SI3 sea-ice hourly output for SI3-BBM and SI3-EVP simulations (Brodeau et al., 2024)

description: These netCDF files countain the simulated SI3 sea-ice hourly output for simulation SI3-BBM and SI3-EVP that are discussed in the following paper:

Implementation of a brittle sea-ice rheology in an Eulerian, finite-difference, C-grid modeling framework:       Impact on the simulated deformation of sea-ice in the Arctic

by Laurent Brodeau, Pierre Rampal, Einar Ólason and Véronique Dansereau, submitted to Geoscientific Model Development (GMD), 2024.

More specifically, they contain:



hourly sea-ice velocity (u,v) vector (m/s)

hourly sea-ice concentration

hourly  sea-ice volume per area (m)

hourly sea-ice damage


The file mesh_mask_NANUK4_L31_4.2_1stLev.nc contains the metrics of the horizontal grid of the model (NEMO regional Arctic configuration named NANUK4).
DOI: 10.5281/zenodo.10457954
title: SI3 sea-ice hourly output for SI3-BBM and SI3-EVP simulations (Brodeau et al., 2024)

description: These netCDF files countain the simulated SI3 sea-ice hourly output for simulation SI3-BBM and SI3-EVP that are discussed in the following paper:

Implementation of a brittle sea-ice rheology in an Eulerian, finite-difference, C-grid modeling framework:       Impact on the simulated deformation of sea-ice in the Arctic

by Laurent Brodeau, Pierre Rampal, Einar Ólason and Véronique Dansereau, submitted to Geoscientific Model Development (GMD), 2024.

More specifically, they contain:



hourly sea-ice velocity (u,v) vector (m/s)

hourly sea-ice concentration

hourly  sea-ice volume per area (m)

hourly sea-ice damage


The file mesh_mask_NANUK4_L31_4.2_1stLev.nc contains the metrics of the horizontal grid of the model (NEMO regional Arctic configuration named NANUK4).
DOI: 10.6084/m9.figshare.23702514
title: Preserved Whole-Brain Functional Topology Hides Local Reorganisation in Genetic Generalised Epilepsy

description: Set of files containing the connectivity matrices and associated measures (e.g. segregation, integration, hub disruption index) of 20 healthy controls and 20 GGE patients, as well as the results of different statistical tests, used in the manuscript entitled: Functional Networks In Genetic Generalised Epilepsy: Preserved Whole-Brain Topology Hides Local Reorganisation.
The README file provides a detailed description of all files.
DOI: 10.5281/zenodo.10579264
title: DOM files, positive, mzml, 2 of 2

description: DOM samples for Daniel, 20230807, pos mode, mzml, 2 of 2
DOI: 10.5281/zenodo.10579265
title: DOM files, positive, mzml, 2 of 2

description: DOM samples for Daniel, 20230807, pos mode, mzml, 2 of 2
DOI: 10.5281/zenodo.10579387
title: Animal-mediated seed dispersal and the demo-genetic configuration across plant colonization gradients

description: This is the repository (data and code) of the manuscript: 

Animal-mediated seed dispersal and the demo-genetic makeup across plant colonization gradients

Jorge Isla, Miguel Jácome-Flores, Cristina Rigueiro, Juan Miguel Arroyo, Pedro Jordano & Cristina García

Corresponding author: Jorge Isla (jorgeislaescudero1992@gmail.com)

 

Ecologists have long recognized that seed dispersal mutualisms trigger natural regeneration and expansion of animal-dispersed trees, but we lack empirical studies addressing whether frugivore activity counteract founder effects, which reduce genetic diversity at the colonization front of rapidly expanding populations. Here we evaluate the contribution of a complex assemblage of frugivores dispersing juniper seeds across an expansion gradient. We used DNA barcoding for frugivores identification and highly polymorphic genetic markers (SSRs) for maternal seed analysis to investigate how (1) stand maturity, (2) microhabitat types, and (3) foraging patterns shape the distribution of the maternal progenies along this gradient. Contrary to our expectations, we found that frugivores generated dense, genetically diverse seed rains across the entire expansion gradient, even at the colonization front with scarcity of local fruiting trees. Through our findings, we shed light on the fundamental and applied implications of plant-frugivore interactions in shaping diverse second growth forests.
DOI: 10.5281/zenodo.10579388
title: Animal-mediated seed dispersal and the demo-genetic configuration across plant colonization gradients

description: This is the repository (data and code) of the manuscript: 

Animal-mediated seed dispersal and the demo-genetic makeup across plant colonization gradients

Jorge Isla, Miguel Jácome-Flores, Cristina Rigueiro, Juan Miguel Arroyo, Pedro Jordano & Cristina García

Corresponding author: Jorge Isla (jorgeislaescudero1992@gmail.com)

 

Ecologists have long recognized that seed dispersal mutualisms trigger natural regeneration and expansion of animal-dispersed trees, but we lack empirical studies addressing whether frugivore activity counteract founder effects, which reduce genetic diversity at the colonization front of rapidly expanding populations. Here we evaluate the contribution of a complex assemblage of frugivores dispersing juniper seeds across an expansion gradient. We used DNA barcoding for frugivores identification and highly polymorphic genetic markers (SSRs) for maternal seed analysis to investigate how (1) stand maturity, (2) microhabitat types, and (3) foraging patterns shape the distribution of the maternal progenies along this gradient. Contrary to our expectations, we found that frugivores generated dense, genetically diverse seed rains across the entire expansion gradient, even at the colonization front with scarcity of local fruiting trees. Through our findings, we shed light on the fundamental and applied implications of plant-frugivore interactions in shaping diverse second growth forests.
DOI: 10.5281/zenodo.10560074
title: Inter-phylum circulation of a beta-lactamase - encoding gene: a rare but observable event

description: Sequence data associated with the publication : Inter-phylum circulation of a beta-lactamase - encoding gene: a rare but observable event

Escherichia coli strain displayed two morphotypes labelled as: white and grey.

Chromosomes assembly are found in the White_Chromosome.fasta and Grey_Chromosome.fasta.

Each morphotypes had a IncF plasmid: IncF.fasta

Only the white morphotype had a p0111 phage plasmid: White_p0111.fasta

The blaMUN-1 gene was found in each morphotype on the chromosome and on the p0111 phage plasmid from the white morphotype: blaMUN-1.fasta

Each copy of this gene was found on a 7.6 kb genomic island: 7_6kb_genomic_island.fasta

It encoded for MUN-1, an extended spectrum beta-lactamase: MUN-1.faa

Variants of the gene and of the beta-lactamase can be found here: variants_MUN_an.fasta and variants_MUN_aa.fasta
DOI: 10.5281/zenodo.10560075
title: Inter-phylum circulation of a beta-lactamase - encoding gene: a rare but observable event

description: Sequence data associated with the publication : Inter-phylum circulation of a beta-lactamase - encoding gene: a rare but observable event

Escherichia coli strain displayed two morphotypes labelled as: white and grey.

Chromosomes assembly are found in the White_Chromosome.fasta and Grey_Chromosome.fasta.

Each morphotypes had a IncF plasmid: IncF.fasta

Only the white morphotype had a p0111 phage plasmid: White_p0111.fasta

The blaMUN-1 gene was found in each morphotype on the chromosome and on the p0111 phage plasmid from the white morphotype: blaMUN-1.fasta

Each copy of this gene was found on a 7.6 kb genomic island: 7_6kb_genomic_island.fasta

It encoded for MUN-1, an extended spectrum beta-lactamase: MUN-1.faa

Variants of the gene and of the beta-lactamase can be found here: variants_MUN_an.fasta and variants_MUN_aa.fasta
DOI: 10.5281/zenodo.10513368
title: Data and code for "Do the rain calls of chaffinches indicate rain?"

description: For more than 300 years, the rain call of the Common Chaffinch (Fringilla coelebs) has been thought to herald rain – hence the name. However, the biological function of this vocalisation still remains unknown. Because rain calls are produced only by males during the breeding season, it has been suggested that the call serves a territorial function and that it may replace song in adverse situations, such as bad weather. However, it is unclear whether rain calls are linked to precipitation at all. Here, we explored the relationship between the occurrence of rain calls and the weather, based on the hypothesis that rain calls are produced instead of song during rainfall. For that purpose, we conducted three studies on different geographical and temporal scales: a large-scale analysis across Europe (relating 242 audio recordings from the Xeno-Canto archive to weather data) and two observational studies in Germany (one cross-sectional study surveying 509 chaffinches and one longitudinal study on 49 selected males over a period of two weeks). We make available here the data for each of the three analyses, as well as the R code used to perform statistical analyses. Refer to the ReadMe file for more detail.
DOI: 10.5281/zenodo.10513369
title: Data and code for "Do the rain calls of chaffinches indicate rain?"

description: For more than 300 years, the rain call of the Common Chaffinch (Fringilla coelebs) has been thought to herald rain – hence the name. However, the biological function of this vocalisation still remains unknown. Because rain calls are produced only by males during the breeding season, it has been suggested that the call serves a territorial function and that it may replace song in adverse situations, such as bad weather. However, it is unclear whether rain calls are linked to precipitation at all. Here, we explored the relationship between the occurrence of rain calls and the weather, based on the hypothesis that rain calls are produced instead of song during rainfall. For that purpose, we conducted three studies on different geographical and temporal scales: a large-scale analysis across Europe (relating 242 audio recordings from the Xeno-Canto archive to weather data) and two observational studies in Germany (one cross-sectional study surveying 509 chaffinches and one longitudinal study on 49 selected males over a period of two weeks). We make available here the data for each of the three analyses, as well as the R code used to perform statistical analyses. Refer to the ReadMe file for more detail.
DOI: 10.21227/8wbz-7e29
title: Reflection Server Tuning Dataset

description: The Reflection Server Tuning dataset contains HiPerConTracer latency measurements performed in a lab setup.The purpose of the dataset is to measure the latency and jitter effects of  firewalls and Linux kernel tuning. The details of each test are published in the paper Evang, Jan Marius and Dreibholz, Thomas: «Optimizing Network Latency: Unveiling the Impact of Reflection Server Tuning» (), in Proceedings of the 6th International Workshop on Recent Advances for Multi-Clouds and Mobile Edge Computing (M2EC) in conjunction with the 38th International Conference on Advanced Information Networking and Applications (AINA), Kitakyushu, Fukuoka/Japan, April 2024.
DOI: 10.5281/zenodo.7414955
title: Data accompanying "Calibrated microphone array recordings reveal that a gleaning bat emits low-intensity echolocation calls even in open-space habitat"

description: Introduction to the dataset: 


In this manuscript, we analyse recordings of brown long-eared bats in the wild collected with a 4-microphone array, which we use to measure the distance between the bat and the microphone.
The distance is then used to correct the recordings for distance-dependent frequency and amplitude attenuation.
To ensure that our measurements and corrections are correct, we fully calibrated the microphone array and analysis set-up. 
The calibration includes a comparison between real distances and calculated distances between a loudspeaker and the microphone array as well as comparisons between the real amplitude and the calculated amplitude of the loudspeaker.
To obtain the original amplitude of the calibration recording, we calibrated the loudspeaker as well


In this folder, we provide the original bat recordings as well as the datasheet with all analysed call measurements, and the original data from the microphone calibration.


DATA & FILE OVERVIEW


Folder list: 
    - Bat data: folder containing the original Plecotus recordings and raw call parameters
    - Calibration data : folder containing the array calibration raw data, as well as codes and recordings necessary to calibrate the loudspeaker.
DOI: 10.5281/zenodo.7414956
title: Data accompanying "Calibrated microphone array recordings reveal that a gleaning bat emits low-intensity echolocation calls even in open-space habitat"

description: Introduction to the dataset: 


In this manuscript, we analyse recordings of brown long-eared bats in the wild collected with a 4-microphone array, which we use to measure the distance between the bat and the microphone.
The distance is then used to correct the recordings for distance-dependent frequency and amplitude attenuation.
To ensure that our measurements and corrections are correct, we fully calibrated the microphone array and analysis set-up. 
The calibration includes a comparison between real distances and calculated distances between a loudspeaker and the microphone array as well as comparisons between the real amplitude and the calculated amplitude of the loudspeaker.
To obtain the original amplitude of the calibration recording, we calibrated the loudspeaker as well


In this folder, we provide the original bat recordings as well as the datasheet with all analysed call measurements, and the original data from the microphone calibration.


DATA & FILE OVERVIEW


Folder list: 
    - Bat data: folder containing the original Plecotus recordings and raw call parameters
    - Calibration data : folder containing the array calibration raw data, as well as codes and recordings necessary to calibrate the loudspeaker.
DOI: 10.12751/g-node.q82cjj
title: Automated quality control of small animal MR neuroimaging data

description: MRI is a valuable tool for studying brain structure and function in animal and clinical studies. With the growth of public MRI repositories, access to data has finally become easier. However, filtering large data sets for potential poor quality outliers can be a challenge. We present AIDAqc, a machine learning-assisted automated Python-based command-line tool for the quality assessment of small animal MRI data. Quality control features include signal-to-noise ratio (SNR), temporal SNR, and motion. All features are automatically calculated and no regions of interest are needed. Automated outlier detection is based on the combination of interquartile range and the machine learning methods one-class support vector machine, isolation forest, local outlier factor, and elliptic envelope. AIDAqc was challenged in a large heterogeneous dataset collected from 18 international laboratories, including data from mice, rats, rabbits, hamsters, and gerbils, obtained with different hardware and at different field strengths. The results show that the manual inter-rater variability (mean Fleiss Kappa score 0.17) is high when identifying poor quality data. A direct comparison of AIDAqc results therefore showed only low to moderate concordance. In a manual post-hoc validation of AIDAqc output, agreement was high (&gt;70%). The outlier data can have a significant impact on further post-processing, as shown in representative functional and structural connectivity analysis. In summary, this pipeline optimized for small animal MRI provides researchers with a valuable tool to efficiently and effectively assess the quality of their MRI data, which is essential for improved reliability and reproducibility.
description: IsSupplementTo: Kalantari, Aref et. al 2024, Automated quality control of small animal MR neuroimaging data, Imaging Neuroscience, first submission on 23.12.2023.
DOI: 10.6084/m9.figshare.24311929
title: Electrophysiological data from control experiment

description: Zip folder contains two folders which correspond to two recording days.<br>PFC spike times are contained in PFCSpikes.mat. <br>Use GitHub code referenced in the paper to align the spikes to stimuli using the LOG files.
DOI: 10.6084/m9.figshare.24311929.v1
title: Electrophysiological data from control experiment

description: Zip folder contains two folders which correspond to two recording days.<br>PFC spike times are contained in PFCSpikes.mat. <br>Use GitHub code referenced in the paper to align the spikes to stimuli using the LOG files.
DOI: 10.6084/m9.figshare.24311767
title: Electrophysiological data from the local-global experiment

description: Pandas dataframes contain PFC spike times of either 96 recording channels or isolated single units (SU). Each row corresponds to one stimulus item of a trial specified in trialID in the recording specified by the date column. <br>Spike times are aligned to stimulus onset.
DOI: 10.6084/m9.figshare.24311767.v1
title: Electrophysiological data from the local-global experiment

description: Pandas dataframes contain PFC spike times of either 96 recording channels or isolated single units (SU). Each row corresponds to one stimulus item of a trial specified in trialID in the recording specified by the date column. <br>Spike times are aligned to stimulus onset.
DOI: 10.5517/ccdc.csd.cc2d6c33
title: CCDC 2210644: Experimental Crystal Structure Determination

description: Related Article: Moyna Das, Vishakha Jaswal, Himanshi Bhambri, Prasenjit Das, Suvendu Maity, Prasanta Ghosh, Sanjay K. Mandal, Madhushree Sarkar|2023|Dalton Trans.|52|1449|doi:10.1039/D2DT04106E
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2d6c44
title: CCDC 2210645: Experimental Crystal Structure Determination

description: Related Article: Moyna Das, Vishakha Jaswal, Himanshi Bhambri, Prasenjit Das, Suvendu Maity, Prasanta Ghosh, Sanjay K. Mandal, Madhushree Sarkar|2023|Dalton Trans.|52|1449|doi:10.1039/D2DT04106E
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.6084/m9.figshare.25102082
title: Metadata and OTU table for Slovenian meadow samples

description: The ecological impacts of long-term (press) disturbance on mechanisms regulating the relative abundance (i.e. commonness or rarity) and temporal dynamics of species within a community remains largely unknown. This is particularly true for the functionally important arbuscular mycorrhizal (AM) fungi; obligate plant-root endosymbionts that colonise more than two-thirds of terrestrial plant species. Here we use high-resolution amplicon sequencing to examine how AM fungal communities in a specific extreme ecosystem – mofettes or natural CO<sub>2</sub>springs caused by geological CO<sub>2</sub>exhalations – are affected by long-term stress. We found that in mofettes, specific and temporally stable communities form as a subset of the local metacommunity. These communities are less diverse and dominated by adapted, ‘stress tolerant’ taxa. Those taxa are rare in control locations and more benign environments worldwide, but show a stable temporal pattern in the extreme sites, consistently dominating the communities in grassland mofettes. This pattern of lower diversity and high dominance of specific taxa has been confirmed as relatively stable over several sampling years and is independently observed across multiple geographic locations (mofettes in different countries). This study implies that the response of soil microbial community composition to long-term stress is relatively predictable, which can reflect also the community response to other anthropogenic stressors (e.g. heavy metal pollution or land use change). Moreover, as AM fungi are functionally differentiated, with different taxa providing different benefits to host plants, changes in community structure in response to long-term environmental change have the potential to impact terrestrial plant communities and their productivity.<br><b>IMPORTANCE</b>Arbuscular mycorrhizal (AM) fungi form symbiotic relationships with more than two-thirds of plant species. In return for using plant carbon as their sole energy source, AM fungi improve plant mineral supply, water balance, and protection against pathogens. This work demonstrates the importance of long-term experiments to understand the effects of long-term environmental change and long-term disturbance on terrestrial ecosystems. We demonstrated a consistent response of the AM fungal community to a long-term stress, with lower diversity and a less variable AM fungal community over time under stress conditions compared to the surrounding controls. We have also identified, for the first time, a suite of AM fungal taxa that are consistently observed across broad geographic scales in stressed and anthropogenically heavily influenced ecosystems. This is critical because global environmental change in terrestrial ecosystems requires an integrative approach that considers both above- and below-ground changes and examines patterns over a longer geographic and temporal scale, rather than just single sampling events.