cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10580109
title: Annotated audio of the loud nest calls of brooding female rooks in five colonies with individual-level identification

description: This data accompanies our article entitled 'Individual, but not nest cluster or colonial, vocal signatures in the nest call of female rooks (Corvus frugilegus)'.

The dataset.zip archive contains audio and annotations obtained from recording five different colonies of rooks during the breeding season. The audio was compressed losslessly to .flac files from the original wav format to save storage space. The annotations are the corresponding .txt files containing timestamps and individual identity for each call used in the article, intended for viewing in Audacity (open the flac files, then import the annotation file with the same name). Finally, the tabelau_vocs.tsv file is essentially all the .txt files aggregated for the analysis. 

Note that to run the analysis, either the .flac audio files must be converted back to .wav files, or the tableau_vocs.tsv file should be edited to point at the .flac files instead of the original .wav files.

The intermediate_results.zip archive contains all intermediate results used in the analysis. These are meant to be used with the provided .R scripts in the same archive, which reproduce the statistical analysis and the figures in the article and supplementary.

Finally, the supplementary.zip archive contains the supplementary materials provided with the article, including the supplementary.pdf file containing additional analyses, and the example_nest_calls folder containing example of nest calls from various females in the five colonies.

The example nest calls are provided at various stages of processing: raw audio extracted from the spectrogram (the .wav files without suffixes), high-pass filter above 100 Hz (.wav files with the 'filtered' suffix), audio with all the processing steps including the spectral gating-based denoising, pre-amplification, and centering (.wav files with the 'processed' suffix), and spectrograms used as inputs for the analysis after dB-scaling and Mel frequenct-scaling (.png files).

 

The rook_vocal_signatures-main.zip archive contains all the code as of the date of submission (August 21st, 2024) used in the article. This was added purely to anonymise the submission as much as possible. Up-to-date code should still be consulted from the link above (will be added after the paper is accepted.
DOI: 10.5281/zenodo.10580110
title: Dataset for 'Can we trace the social affiliation of rooks (Corvus frugilegus) through their vocal signature?': annotated audio of brooding female rooks in five colonies with individual-level identification

description: This data accompanies our article entitle 'Can we trace the social affiliation of rooks (Corvus frugilegus) through their vocal signature?'. The data is required to run the analysis code, hosted at https://gitlab.com/kimartin/rook_vocal_signature.

Included are the audio, annotations, and various intermediate results used for the article. The audio and annotations are stored in the dataset.zip archive, in the following format: five folders of audio .flac files and corresponding .txt files (each pair of files has the same name, just different extensions).

Each folder contains recordings of a different colony / recording site (three around Strasbourg, France: Strasbourg_Captive, Contades, and CNRS; two around Cambridge, UK: Cambridge Captive and Cambridge Wild). The recordings span mostly the 2022 breeding season from around March to May, except for the Strasbourg Captive colony where recordings were taken in 2020 and 2021. All recordings were taken in naturalistic conditions (i.e. with background noises and other rooks vocalising). Annotations correspond to clean instances of the 'nest call', a particular call produced only by brooding females within the nest.

Inside the dataset.zip archive is the tableau_vocs.tsv file, which aggregates the various .txt files for ease of use with the code.

The intermediate_results.zip archive stores the data used for the statistical analysis (see the GitLab repo for details on using it and the R scripts used for treatment).
DOI: 10.5281/zenodo.10829899
title: Dataset for 'Can we trace the social affiliation of rooks (Corvus frugilegus) through their vocal signature?': annotated audio of brooding female rooks in five colonies with individual-level identification

description: This data accompanies our article entitle 'Can we trace the social affiliation of rooks (Corvus frugilegus) through their vocal signature?'. The data is required to run the analysis code, hosted at https://gitlab.com/kimartin/rook_vocal_signature.

Included are the audio, annotations, and various intermediate results used for the article. The audio and annotations are stored in the dataset.zip archive, in the following format: five folders of audio .flac files and corresponding .txt files (each pair of files has the same name, just different extensions).

Each folder contains recordings of a different colony / recording site (three around Strasbourg, France: Strasbourg_Captive, Contades, and CNRS; two around Cambridge, UK: Cambridge Captive and Cambridge Wild). The recordings span mostly the 2022 breeding season from around March to May, except for the Strasbourg Captive colony where recordings were taken in 2020 and 2021. All recordings were taken in naturalistic conditions (i.e. with background noises and other rooks vocalising). Annotations correspond to clean instances of the 'nest call', a particular call produced only by brooding females within the nest.

Inside the dataset.zip archive is the tableau_vocs.tsv file, which aggregates the various .txt files for ease of use with the code.

The intermediate_results.zip archive stores the data used for the statistical analysis, along with the R scripts needed for the statistical analysis and for creating the figures. All scripts should run out-of-the-box with the results stored in the same folder and reproduce the same results as the article, however up-to-date versions can still be found on the GitLab repository if needed.
DOI: 10.5281/zenodo.11048542
title: Dataset for 'Individual, but not nest cluster or colonial, signature in the loud nest call of captive and wild female rooks (Corvus frugilegus)': annotated audio of brooding female rooks in five colonies with individual-level identification

description: This data accompanies our article entitle 'Can we trace the social affiliation of rooks (Corvus frugilegus) through their vocal signature?'. The data is required to run the analysis code, hosted at https://gitlab.com/kimartin/rook_vocal_signature.

Included are the audio, annotations, and various intermediate results used for the article. The audio and annotations are stored in the dataset.zip archive, in the following format: five folders of audio .flac files and corresponding .txt files (each pair of files has the same name, just different extensions).

Each folder contains recordings of a different colony / recording site (three around Strasbourg, France: Strasbourg_Captive, Contades, and CNRS; two around Cambridge, UK: Cambridge Captive and Cambridge Wild). The recordings span mostly the 2022 breeding season from around March to May, except for the Strasbourg Captive colony where recordings were taken in 2020 and 2021. All recordings were taken in naturalistic conditions (i.e. with background noises and other rooks vocalising). Annotations correspond to clean instances of the 'nest call', a particular call produced only by brooding females within the nest.

Inside the dataset.zip archive is the tableau_vocs.tsv file, which aggregates the various .txt files for ease of use with the code.

The intermediate_results.zip archive stores the data used for the statistical analysis, along with the R scripts needed for the statistical analysis and for creating the figures. All scripts should run out-of-the-box with the results stored in the same folder and reproduce the same results as the article, however up-to-date versions can still be found on the GitLab repository if needed. By default the scripts will use the file with "dfw" in their names, corresponding to the DFTW results (i.e. with frequency and time alignment of the spectrograms). Each script can be modified to use the files with "dtw" in their names to instead replicate the results in the Supplementary for the article, using DTW (i.e. with only time alignment of the spectrograms), or "d.w" to use both (the scripts keep them separate, but this can be useful for easy comparison between DFTW and DTW).
DOI: 10.5281/zenodo.13353672
title: Annotated audio of the loud nest calls of brooding female rooks in five colonies with individual-level identification

description: This data accompanies our article entitle 'The loud nest call of female rooks (Corvus frugilegus) shows a vocal signature at the individual level, but not at the nest cluster or colony levels'. See here for details. The data is required to run the analysis code, hosted here.

The dataset.zip archive contains audio and annotations obtained from recording five different colonies of rooks during the breeding season. The audio was compressed losslessly to .flac files from the original wav format to save storage space. The annotations are the corresponding .txt files containing timestamps and individual identity for each call used in the article, intended for viewing in Audacity (open the flac files, then import the annotation file with the same name). Finally, the tabelau_vocs.tsv file is essentially all the .txt files aggregated for the analysis. 

Note that to run the analysis, either the .flac audio files must be converted back to .wav files, or the tableau_vocs.tsv file should be edited to point at the .flac files instead of the original .wav files.

The intermediate_results.zip archive contains various intermediate results used in the analysis. These are meant to be used with the provided .R scripts in the same archive (up-to-date versions of these scripts may be found in the gitlab repo above), which reproduce the statistical analysis and the figures in the article and supplementary.

Finally, the supplementary.zip archive contains the supplementary materials provided with the article, including the supplementary.pdf file containing additional analyses, and the example_nest_calls folder containing example of nest calls from various females in the five colonies.

The example nest calls are provided at various stages of processing: raw audio extracted from the spectrogram (the .wav files without suffixes), high-pass filter above 100 Hz (.wav files with the 'filtered' suffix), audio with all the processing steps including the spectral gating-based denoising, pre-amplification, and centering (.wav files with the 'processed' suffix), and spectrograms used as inputs for the analysis after dB-scaling and Mel frequenct-scaling (.png files).
DOI: 10.5281/zenodo.13355056
title: Annotated audio of the loud nest calls of brooding female rooks in five colonies with individual-level identification

description: This data accompanies our article entitle 'The loud nest call of female rooks (Corvus frugilegus) shows a vocal signature at the individual level, but not at the nest cluster or colony levels'.

The dataset.zip archive contains audio and annotations obtained from recording five different colonies of rooks during the breeding season. The audio was compressed losslessly to .flac files from the original wav format to save storage space. The annotations are the corresponding .txt files containing timestamps and individual identity for each call used in the article, intended for viewing in Audacity (open the flac files, then import the annotation file with the same name). Finally, the tabelau_vocs.tsv file is essentially all the .txt files aggregated for the analysis. 

Note that to run the analysis, either the .flac audio files must be converted back to .wav files, or the tableau_vocs.tsv file should be edited to point at the .flac files instead of the original .wav files.

The intermediate_results.zip archive contains various intermediate results used in the analysis. These are meant to be used with the provided .R scripts in the same archive (up-to-date versions of these scripts may be found in the gitlab repo above), which reproduce the statistical analysis and the figures in the article and supplementary.

Finally, the supplementary.zip archive contains the supplementary materials provided with the article, including the supplementary.pdf file containing additional analyses, and the example_nest_calls folder containing example of nest calls from various females in the five colonies.

The example nest calls are provided at various stages of processing: raw audio extracted from the spectrogram (the .wav files without suffixes), high-pass filter above 100 Hz (.wav files with the 'filtered' suffix), audio with all the processing steps including the spectral gating-based denoising, pre-amplification, and centering (.wav files with the 'processed' suffix), and spectrograms used as inputs for the analysis after dB-scaling and Mel frequenct-scaling (.png files).

 

The rook_vocal_signatures-main.zip archive contains all the code as of the date of submission (August 21st, 2024) used in the article. This was added purely to anonymise the submission as much as possible. Up-to-date code should still be consulted from the link above (will be added after the paper is accepted.
DOI: 10.5281/zenodo.15609846
title: Annotated audio of the loud nest calls of brooding female rooks in five colonies with individual-level identification

description: This data accompanies our article entitled 'Individual, but not nest cluster or colonial, vocal signatures in the nest call of female rooks (Corvus frugilegus)'.

The dataset.zip archive contains audio and annotations obtained from recording five different colonies of rooks during the breeding season. The audio was compressed losslessly to .flac files from the original wav format to save storage space. The annotations are the corresponding .txt files containing timestamps and individual identity for each call used in the article, intended for viewing in Audacity (open the flac files, then import the annotation file with the same name). Finally, the tabelau_vocs.tsv file is essentially all the .txt files aggregated for the analysis. 

Note that to run the analysis, either the .flac audio files must be converted back to .wav files, or the tableau_vocs.tsv file should be edited to point at the .flac files instead of the original .wav files.

The intermediate_results.zip archive contains all intermediate results used in the analysis. These are meant to be used with the provided .R scripts in the same archive, which reproduce the statistical analysis and the figures in the article and supplementary.

Finally, the supplementary.zip archive contains the supplementary materials provided with the article, including the supplementary.pdf file containing additional analyses, and the example_nest_calls folder containing example of nest calls from various females in the five colonies.

The example nest calls are provided at various stages of processing: raw audio extracted from the spectrogram (the .wav files without suffixes), high-pass filter above 100 Hz (.wav files with the 'filtered' suffix), audio with all the processing steps including the spectral gating-based denoising, pre-amplification, and centering (.wav files with the 'processed' suffix), and spectrograms used as inputs for the analysis after dB-scaling and Mel frequenct-scaling (.png files).

 

The rook_vocal_signatures-main.zip archive contains all the code as of the date of submission (August 21st, 2024) used in the article. This was added purely to anonymise the submission as much as possible. Up-to-date code should still be consulted from the link above (will be added after the paper is accepted.
DOI: 10.17632/sg2cr99j5m
title: Differential warming and rainfall in Ballarat vs. Bendigo, South East Victoria, Australia

description: To evaluate wind farms' impact on local climate, we compared temperature and rainfall data from Ballarat, with recent wind farm installations, and Bendigo, without, in southwest Victoria, Australia. Both regions share similar population, growth, and meteorological station settings. Wind energy infrastructure maps are available at Aneroid Energy (Fig. 1, 2).

Australian Bureau of Meteorology data since November 1991 show Ballarat’s monthly mean minimum temperatures rising at 0.508°C per decade, similar to Bendigo’s 0.471°C. Over the last decade, coinciding with Ballarat’s wind farm operations, Ballarat’s warming rate increased to 1.287°C per decade, while Bendigo’s was 0.814°C, yielding a 0.473°C differential (Fig. 3, 4). This aligns with Zhou et al. (2012), reporting 0.72°C per decade warming in a Texas wind farm region (Nature Climate Change, 2(7), 539–543).

Rainfall data since 1991 show Ballarat’s monthly rainfall decreasing by 1 mm per decade, while Bendigo’s increased by 0.9 mm. Over the past decade, Ballarat’s rainfall rose by 12.7 mm, compared to Bendigo’s 6.1 mm (Fig. 5, 6), suggesting a potential link to wind farm development. Further research is needed.
DOI: 10.17632/sg2cr99j5m.1
title: Differential warming and rainfall in Ballarat vs. Bendigo, South East Victoria, Australia

description: To evaluate wind farms' impact on local climate, we compared temperature and rainfall data from Ballarat, with recent wind farm installations, and Bendigo, without, in southwest Victoria, Australia. Both regions share similar population, growth, and meteorological station settings. Wind energy infrastructure maps are available at Aneroid Energy (Fig. 1, 2).

Australian Bureau of Meteorology data since November 1991 show Ballarat’s monthly mean minimum temperatures rising at 0.508°C per decade, similar to Bendigo’s 0.471°C. Over the last decade, coinciding with Ballarat’s wind farm operations, Ballarat’s warming rate increased to 1.287°C per decade, while Bendigo’s was 0.814°C, yielding a 0.473°C differential (Fig. 3, 4). This aligns with Zhou et al. (2012), reporting 0.72°C per decade warming in a Texas wind farm region (Nature Climate Change, 2(7), 539–543).

Rainfall data since 1991 show Ballarat’s monthly rainfall decreasing by 1 mm per decade, while Bendigo’s increased by 0.9 mm. Over the past decade, Ballarat’s rainfall rose by 12.7 mm, compared to Bendigo’s 6.1 mm (Fig. 5, 6), suggesting a potential link to wind farm development. Further research is needed.
DOI: 10.5281/zenodo.15609897
title: Concentration of DMT and DMiP present in the studied PET
DOI: 10.5281/zenodo.15609898
title: Concentration of DMT and DMiP present in the studied PET
DOI: 10.17632/4xw445msth
title: Zhao-ECE

description: Data
DOI: 10.17632/4xw445msth.1
title: Zhao-ECE

description: Data
DOI: 10.15468/dl.y2hh4r
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Labeobarbus aeneus (Burchell, 1822)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((32.064 -28.9416,32.4847 -28.5786,30.5701 -28.5786,30.5701 -30.7329,30.6252 -30.6659,31.4179 -29.4257,31.8178 -29.0299,32.064 -28.9416))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025283-250525065834625/datasets/export for details.
DOI: 10.15468/dl.gfwnvt
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Material sample)"
 ]
 }
 },
 "TaxonKey is Viverra cristata Sparrman, 1783",
 "Continent is one of (Africa)",
 "Year is greater than or equal to 1900"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025282-250525065834625/datasets/export for details.
DOI: 10.17632/r3t9jm798y
title: Metatranscriptomics Uncover Diurnal Functional Shifts in Bacterial Transgenes with Profound Metabolic Effects

description: This dataset contains code and processed data used to perform analysis and generate figures for our manuscript "Diurnal Characterization of Metatranscriptomics Yields Bacterial Transgenes with Pronounced Metabolic Effects" . The main folder are "code", "data", and "figures". Within each folder, it is organized as follows:

- diversity_analysis: contains the code, data, or figures for the diversity analysis comparing 16S, metagenomics genes, and metatranscriptomic transcripts. Related to Figure 1.
- DE_analysis: contains the code, data, or figures for the differential abundance analysis for the metagenomics genes and metatranscriptomic transcripts. Related to Figure 2.
- cycling_analysis: contains the code, data, or figures for the cycling analysis for the metagenomics genes and metatranscriptomic transcripts. Related to Figure 3.
- bsh_analysis: contains the code, data, or figures for the bsh differential expression analysis using the targeted and untargeted search for bsh in the metatranscriptomics. Related to Figure 4.
- ENB_invitro_metab: contains the code, data, or figures the bile acid quantification from the cultures of ENBs. Related to Figure 5.
- ENB_invivo_metab: contains the code, data, or figures for the phenotypic measurements of mice gavaged with ENBs. Also contains the fecal bile acid quantification of these mice. Related to Figure 6.
- replotting_AZ2014_CD2022: contains the code, data, or figures for weight and glucose measurements from Zarrinpar 2014 and ileum bile acid quantification from Dantas Machado, 2022 we replotted in Figure S1 and S4, respectively.

Under "code" we also include:
- processing_metaG: contains the code used to process the metagenomic data from fastq to counts table.
- processing_metaT: contains the code used to process the metatranscriptomics data from fastq to counts table.

Under "data" we also include:
- m16s: contains the processed 16s counts data from Zarrinpar 2014
- genome_metaG: contains woltka processed metagenomic counts data at the genome level
- genome_metaT: contains woltka processed metatranscriptomics counts data at the genome level
- pfam_metaG: contains woltka processed metagenomic counts data collapsed to pfam functions
- pfam_metaT: contains woltka processed metatranscriptomics counts data collapsed to pfam functions