cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.21206663
title: An updated dataset of published carbon and nitrogen trophic enrichment factors (Δ13C and Δ15N) for aquatic crustacean taxa

description: Stable isotopes of nitrogen and carbon (δ<sup>15</sup>N and δ<sup>13</sup>C) represent an important tool in food web ecology, useful for the determination of consumers’ diet and trophic position. One of the key requirements for an appropriate and reliable use of this methodology is represented by the application of species-specific trophic enrichment factors (TEFs, also defined as diet-tissue discrimination factors, DTDFs). Here we present an updated synthesis of carbon and nitrogen TEFs for aquatic crustaceans collated from literature sources. Specifically, on September 20th, 2022 the online databases ISI Web of Science and Scopus were searched for publications by a multiple search criterion using the terms “trophic enrichment factor” or “discrimination factor” in conjunction with “stable isotopes” and “crustacean”. The results were complemented with those obtained from queries on Google Scholar (https://scholar.google.com/) using identical keywords and subsequently saved using the freeware Harzings’s Publish or Perish ver. 7.27.284953. The literature search resulted in a total of 564 entries; subsequently, their titles and abstracts were screened in order to remove field investigations and laboratory studies not performed on aquatic crustacean species or estimating TEFs values on blood. The full text of the remaining 87 sources was examined in detail to select those where TEFs or DTDFs were reported explicitly at least for nitrogen, together with information on the taxonomy of the consumer and dietary resource, the consumer life stage, the analysed tissues, lipid extraction treatment, duration and temperature at which the experiment was performed. 23 eligible literature sources matching the aforementioned criteria were eventually selected, published between 1978 and 2019. The dataset is contained in Table 1; it includes, together with TEFs values, the literature source, the consumer and prey species scientific or common names, information on the environment (M = marine, F = Freshwater), information on the species life stage, the analysed tissue, the treatment used for lipids extraction (N = no treatment; Y = chemical extraction or mathematical normalization), the duration (in days) and temperature at which the experiment was performed (in °C), and the type and the isotopic values of the diet (δ<sup>13</sup>C and δ<sup>15</sup>N). complementary information regarding the the literature sources used to extract the data including permanent identifiers (bibliographic Citation DOI) if available are reported in Table 2.
DOI: 10.34740/kaggle/dsv/4251565
title: 2021 World Population (updated daily)
DOI: 10.5281/zenodo.7112893
title: Abramov glacier firn data

description: Historical and recent firn data for Abramov glacier, Pamir Alay compiled and measured in the context of the PhD Thesis 'Changing glacier firn in Central Asia and its impact on glacier mass balance' by Marlene Kronenberg (2022). This repository contains firn data measured in 2018 consisting of GPR measurements (zip folder), subsurface temperature measurements (zip folder) and firn core data from three drill sites as well as historical firn profile data digitized from Kislov (1982) and Suslov and Krenke (1980). Refer to abra_firn_cores_overview.xlsx for an overview of the core data. The data are described in Kronenberg et al. (2021) and Kronenberg (2022). Please refer to these studies when using the data. References: Kislov BV (1982) Formation and regime of the firn-ice stratum of a mountain glacier [in Russian] (Ph.D. thesis). SARNIGMI Tashkent. Kronenberg M, Machguth H, Eichler A, Schwikowski M, Hoelzle M (2021). Comparison of historical and recent accumulation rates on Abramov Glacier, Pamir Alay. Journal of Glaciology 67(262), 253–268. https://doi.org/10.1017/jog.2020.103 Kronenberg Marlene. (2022). Changing glacier firn in Central Asia and its impact on glacier mass balance. PhD thesis, University of Fribourg. Suslov VF and Krenke AN (1980) Abaramov Glacier (Alay Range) [in Russian]. St. Petersburg: Gidrometeoizdat.
description: The measurements were financed by the Swiss National Science Foundation (SNSF), grant 200021_169453 and the Project CICADA (Cryospheric Climate Services for improved Adaptation, contract no. 81049674 between the Swiss Agency for Development and Cooperation and the University of Fribourg).
description: {"references": ["Kislov BV (1982) Formation and regime of the firn-ice stratum of a mountain glacier [in Russian] (Ph.D. thesis). SARNIGMI Tashkent.", "Kronenberg M, Machguth H, Eichler A, Schwikowski M, Hoelzle M (2021). Comparison of historical and recent accumulation rates on Abramov Glacier, Pamir Alay. Journal of Glaciology 67(262), 253\u2013268. https://doi.org/10.1017/jog.2020.103", "Kronenberg Marlene. (2022). Changing glacier firn in Central Asia and its impact on glacier mass balance. PhD thesis, University of Fribourg.", "Suslov VF and Krenke AN (1980) Abaramov Glacier (Alay Range) [in Russian]. St. Petersburg: Gidrometeoizdat.", "Walther, S. Accumulation distribution on Abramov Glacier from GPR measurements. MSc thesis, University of Fribourg, 2018."]}
DOI: 10.5281/zenodo.7113350
title: PROCRAFT_Form B_Dewoitine D.520_B2

description: Information and condition state of one part of the Dewoitine D.520 wreck (related to PROCRAFT_Form A_Dewoitine D.520_Encausse)
description: Paint
DOI: 10.5281/zenodo.7113349
title: PROCRAFT_Form B_Dewoitine D.520_B2

description: Information and condition state of one part of the Dewoitine D.520 wreck (related to PROCRAFT_Form A_Dewoitine D.520_Encausse)
description: Paint
DOI: 10.5281/zenodo.5762767
title: Sige_model_subduction_data_basic_dense

description: This dataset includes the raw data of hydraulic modeling in subduction zones, which are used in the manuscript submitted to JGR by Kaneki & Noda. Details of the dataset can be found in Readme_data_basic_dence.txt.
DOI: 10.5281/zenodo.5762768
title: Pe_model_subduction_data_basic_dense

description: This dataset includes the raw data of hydraulic modeling in subduction zones, which are used in the manuscript submitted to JGR by Kaneki & Noda. Details of the dataset can be found in Readme_data_basic_dence.txt.
DOI: 10.5281/zenodo.7113149
title: Sige_model_subduction_data_basic_dense

description: This dataset includes the raw data of hydraulic modeling in subduction zones, which are used in the manuscript submitted to JGR by Kaneki & Noda. Details of the dataset can be found in Readme_data_basic_dence.txt.
DOI: 10.6084/m9.figshare.21206810
title: Response time in different conditions

description: Trial type: norisk (high-payoff choice), risk(low-payoff choice), prerisk (prelow-payoff choice), postrisk(choice after low-payoff) Feedback cur - type of the current feedback (positive, negative) Feedback prev - type of the feedback in the previous trial (positive, negative)
DOI: 10.6084/m9.figshare.21206810.v1
title: Response time in different conditions

description: Trial type: norisk (high-payoff choice), risk(low-payoff choice), prerisk (prelow-payoff choice), postrisk(choice after low-payoff) Feedback cur - type of the current feedback (positive, negative) Feedback prev - type of the feedback in the previous trial (positive, negative)
DOI: 10.6084/m9.figshare.21206837
title: Additional file 10 of A global phylogenomic and metabolic reconstruction of the large intestine bacterial community of domesticated cattle

description: Additional file 10: Table S10. Overview of virulence genes detected in the 2114 MAGs using the virulence genes of interest in the six pathogenic genera (A) and in all taxa (B). From left to right: the percentage, E-value and bitscore of diamond BLAST comparisons, the VFdb identifier, the VFdb preferred gene name, the VFdb taxon, MAG name and alternative name, the metagenomics sample, the country and the study the MAG came from, the dRep cluster identified and the average abundance of the MAG in the 436 samples. The subtable to the right presents the gene prevalence based on occurrence (the times a VFdb gene gave a positive match to the dataset).
DOI: 10.6084/m9.figshare.21206837.v1
title: Additional file 10 of A global phylogenomic and metabolic reconstruction of the large intestine bacterial community of domesticated cattle

description: Additional file 10: Table S10. Overview of virulence genes detected in the 2114 MAGs using the virulence genes of interest in the six pathogenic genera (A) and in all taxa (B). From left to right: the percentage, E-value and bitscore of diamond BLAST comparisons, the VFdb identifier, the VFdb preferred gene name, the VFdb taxon, MAG name and alternative name, the metagenomics sample, the country and the study the MAG came from, the dRep cluster identified and the average abundance of the MAG in the 436 samples. The subtable to the right presents the gene prevalence based on occurrence (the times a VFdb gene gave a positive match to the dataset).
DOI: 10.6084/m9.figshare.21206849
title: Additional file 1 of A global phylogenomic and metabolic reconstruction of the large intestine bacterial community of domesticated cattle

description: Additional file 1: Table S1. Shotgun metagenomic data used in this study. From left to right: accession and bioproject numbers, study, location, sample type, diet, age, farm id and size (whenever available). The table is also accessible at www.fecobiome.com/resources/data by entering the keyword “shotgun” in the “search our database” box. Samples can be further filtered by location or farm name (e.g. using the keywords «Theix» or «Saint-Gene-Champagnelle» will only list the samples sequenced in our study).
DOI: 10.6084/m9.figshare.21206852.v1
title: Additional file 2 of A global phylogenomic and metabolic reconstruction of the large intestine bacterial community of domesticated cattle

description: Additional file 2: Table S2. Summary of the contigs assembly. From left to right: sample name (accession number), number of contigs and number of base pairs, minimum, maximum and average contig length, N50 and mean coverage of contigs (estimated by mapping filtered reads to contigs using Bowtie2).
DOI: 10.6084/m9.figshare.21206849.v1
title: Additional file 1 of A global phylogenomic and metabolic reconstruction of the large intestine bacterial community of domesticated cattle

description: Additional file 1: Table S1. Shotgun metagenomic data used in this study. From left to right: accession and bioproject numbers, study, location, sample type, diet, age, farm id and size (whenever available). The table is also accessible at www.fecobiome.com/resources/data by entering the keyword “shotgun” in the “search our database” box. Samples can be further filtered by location or farm name (e.g. using the keywords «Theix» or «Saint-Gene-Champagnelle» will only list the samples sequenced in our study).
DOI: 10.6084/m9.figshare.21206852
title: Additional file 2 of A global phylogenomic and metabolic reconstruction of the large intestine bacterial community of domesticated cattle

description: Additional file 2: Table S2. Summary of the contigs assembly. From left to right: sample name (accession number), number of contigs and number of base pairs, minimum, maximum and average contig length, N50 and mean coverage of contigs (estimated by mapping filtered reads to contigs using Bowtie2).
DOI: 10.6084/m9.figshare.21206855
title: Additional file 3 of A global phylogenomic and metabolic reconstruction of the large intestine bacterial community of domesticated cattle

description: Additional file 3: Table S3. A: Summary of the assembled contig classification: Number and proportion of contigs assigned to each domain, for each sample. The absolute figures are shown at the left and the percentages at the right. The average percentage for each domain is also presented in the small subtable to the right. B: Archaeal sequences abundance estimate: Number of reads properly paired to the 155 RUGs previously presented [53] and the assembled contigs identified as archaea in our study. The absolute numbers and percentages are presented for each sample. Mean percentages and medians across all samples are presented to the right.
DOI: 10.6084/m9.figshare.21206855.v1
title: Additional file 3 of A global phylogenomic and metabolic reconstruction of the large intestine bacterial community of domesticated cattle

description: Additional file 3: Table S3. A: Summary of the assembled contig classification: Number and proportion of contigs assigned to each domain, for each sample. The absolute figures are shown at the left and the percentages at the right. The average percentage for each domain is also presented in the small subtable to the right. B: Archaeal sequences abundance estimate: Number of reads properly paired to the 155 RUGs previously presented [53] and the assembled contigs identified as archaea in our study. The absolute numbers and percentages are presented for each sample. Mean percentages and medians across all samples are presented to the right.
DOI: 10.6084/m9.figshare.21206858
title: Additional file 4 of A global phylogenomic and metabolic reconstruction of the large intestine bacterial community of domesticated cattle

description: Additional file 4: Table S4. Overview and characteristics of the 2114 MAGs, the 74 Hungate and the 102 RefSeq genomes used to reconstruct phylogenies in our study. From left to right: the internal code (a derivative of the accession number the data came from and the autometa id); the alternative name, which we either generated by identifying the closest match following BLAST comparisons with RefSeq or the assigned strain name (for reference genomes downloaded from databases); the accession number the MAG came from (when relevant); country where the sample was collected; author; dRep clustering and checkm (estimated completeness and contamination) and mean contig coverage (estimated by mapping filtered reads to contigs using Bowtie2). The overall mean and median are presented as well. The MAGs with the same drep clustering id are &gt;99% identical. The last column indicates the 1232 MAGs that were selected for the dereplicated dataset. The sequences of the 2114 MAGs are available here: doi.org/10.15454/UIJTJA . B: Mapping of filtered reads to contigs and the core MAGs. From left to right: Sample names, the total number of reads for each sample and the number of reads successfully mapped to contigs, the percentage of the number of reads mapped to contigs, the number of reads mapped to MAGs, and the percentage of reads mapped to MAGs. The smaller subtable to the right presents: the average percentage of reads successful mapping to contigs and to MAGs (top); the average percentage of reads mapped only to bacterial contigs (based on the classification from Autometa; NR database); the percentage of bacterial reads (based on the bacterial contig estimate) mapped to MAGs.
DOI: 10.6084/m9.figshare.21206861
title: Additional file 5 of A global phylogenomic and metabolic reconstruction of the large intestine bacterial community of domesticated cattle

description: Additional file 5: Table S5. PERMANOVA tests examining the impact of the different study and sample type (in two independent studies) on the fifteen class-specific reconstructed MAG phylogenies. Dissimilarity matrices were created using AA alignments, built from the phylogenies presented in Sup. Res. 1. Two independent PERMANOVA tests were performed on each matrix, using the study identifier (author) and sample source type as explanatory variables.
DOI: 10.6084/m9.figshare.21206861.v1
title: Additional file 5 of A global phylogenomic and metabolic reconstruction of the large intestine bacterial community of domesticated cattle

description: Additional file 5: Table S5. PERMANOVA tests examining the impact of the different study and sample type (in two independent studies) on the fifteen class-specific reconstructed MAG phylogenies. Dissimilarity matrices were created using AA alignments, built from the phylogenies presented in Sup. Res. 1. Two independent PERMANOVA tests were performed on each matrix, using the study identifier (author) and sample source type as explanatory variables.
DOI: 10.6084/m9.figshare.21206864.v1
title: Additional file 6 of A global phylogenomic and metabolic reconstruction of the large intestine bacterial community of domesticated cattle

description: Additional file 6: Table S6. Common KEGG metabolic pathways in the microbiome of cattle feces. A: List of KEGG pathways along with the 175 pathways (marked with an asterisk) we chose to examine as relevant (see Methods) for our analyses. B: Most common pathways based on contigs present in at least 80% of individually collected fecal samples (N = 210) and the most abundant 1000. From left to right: the metabolic pathway KEGG id, the number of predicted KOs identified in that pathway, the pathway name, additional notes inferring the function of their study based on our analysis, and the MAGs carrying most enzymes in the common contigs. C: KEGG modules complete in at least one MAG. For this analysis, the 450 predicted modules (KAAs) were examined against the dereplicated set of our core MAGs and we present the modules that were complete (all their enzymes present) in at least one MAG. From left to right: the module description (including the KEGG pathway/s it is linked to), and the KEGG subcategory and category it belongs to.
DOI: 10.6084/m9.figshare.21206864
title: Additional file 6 of A global phylogenomic and metabolic reconstruction of the large intestine bacterial community of domesticated cattle

description: Additional file 6: Table S6. Common KEGG metabolic pathways in the microbiome of cattle feces. A: List of KEGG pathways along with the 175 pathways (marked with an asterisk) we chose to examine as relevant (see Methods) for our analyses. B: Most common pathways based on contigs present in at least 80% of individually collected fecal samples (N = 210) and the most abundant 1000. From left to right: the metabolic pathway KEGG id, the number of predicted KOs identified in that pathway, the pathway name, additional notes inferring the function of their study based on our analysis, and the MAGs carrying most enzymes in the common contigs. C: KEGG modules complete in at least one MAG. For this analysis, the 450 predicted modules (KAAs) were examined against the dereplicated set of our core MAGs and we present the modules that were complete (all their enzymes present) in at least one MAG. From left to right: the module description (including the KEGG pathway/s it is linked to), and the KEGG subcategory and category it belongs to.
DOI: 10.6084/m9.figshare.21206867
title: Additional file 7 of A global phylogenomic and metabolic reconstruction of the large intestine bacterial community of domesticated cattle

description: Additional file 7: Table S7. Count software analysis of the 15 taxonomic classes (A) and list of the most influential KOs (B) identified by the principal coordinate analysis presented in Fig. 2B. A: From left to right: the KO id, the number of gains and expansions for the given ortholog (overall) and their the sum, the gains and expansions in RefSeq genomes, the gains and expansions in fecal MAGs and the taxonomic class the analysis was conducted for. In the last two columns, the overall gene losses and contractions are presented as well but are grayed out on account of not examining them because we used MAGs. On the smaller subtable to the right, we present the KOs that were identified multiple times in the independent Count analyses (we performed 15 analyses one for each class that we built a phylogeny). B: From left to right: the KO id, the coordinates and the contribution of each feature based on which we selected the top twenty (as most influential) to present in Fig. 2. For the top hundred most influential vectors (a.k.a. features) we present the KO description as well. Bold font indicates features that were identified both in the Count analysis for the Bacteroidia, Clostridia or Spirochaetia classes and among the top 100 most influential features in the PCoA analysis.
DOI: 10.6084/m9.figshare.21206867.v1
title: Additional file 7 of A global phylogenomic and metabolic reconstruction of the large intestine bacterial community of domesticated cattle

description: Additional file 7: Table S7. Count software analysis of the 15 taxonomic classes (A) and list of the most influential KOs (B) identified by the principal coordinate analysis presented in Fig. 2B. A: From left to right: the KO id, the number of gains and expansions for the given ortholog (overall) and their the sum, the gains and expansions in RefSeq genomes, the gains and expansions in fecal MAGs and the taxonomic class the analysis was conducted for. In the last two columns, the overall gene losses and contractions are presented as well but are grayed out on account of not examining them because we used MAGs. On the smaller subtable to the right, we present the KOs that were identified multiple times in the independent Count analyses (we performed 15 analyses one for each class that we built a phylogeny). B: From left to right: the KO id, the coordinates and the contribution of each feature based on which we selected the top twenty (as most influential) to present in Fig. 2. For the top hundred most influential vectors (a.k.a. features) we present the KO description as well. Bold font indicates features that were identified both in the Count analysis for the Bacteroidia, Clostridia or Spirochaetia classes and among the top 100 most influential features in the PCoA analysis.
DOI: 10.6084/m9.figshare.21206870
title: Additional file 8 of A global phylogenomic and metabolic reconstruction of the large intestine bacterial community of domesticated cattle

description: Additional file 8: Table S8. Overview of the comparisons between groups of samples to identify differentially represented (DifRep) metabolic features. The four sheets present comparisons for the dairy cow samples coming from Theix (our study) separated in winter (Theix-winter) and summer samples (Theix-summer); and for the calf samples coming from the Salaheen et al. [31] study, separated into samples from animals fed exclusively milk (Salaheen-milk) and samples from calves that after the introduction of solid feed in their diets (Salaheen-solid). For each tab, from left to right, we present the metabolic pathway id; the pathway description; the number of enzymes of that pathway that were identified in the focal contigs. The rest of the columns present the number of predicted enzymes discovered in group-specific (winter-specific, summer-specific, solid-specific or milk-specific) MAGs identified by our analysis (i.e. MAGs that had &gt;25% -for summer or solid group- or &gt;10% -for milk or winter group- of their contigs DifRep; see also Results).
DOI: 10.6084/m9.figshare.21206870.v1
title: Additional file 8 of A global phylogenomic and metabolic reconstruction of the large intestine bacterial community of domesticated cattle

description: Additional file 8: Table S8. Overview of the comparisons between groups of samples to identify differentially represented (DifRep) metabolic features. The four sheets present comparisons for the dairy cow samples coming from Theix (our study) separated in winter (Theix-winter) and summer samples (Theix-summer); and for the calf samples coming from the Salaheen et al. [31] study, separated into samples from animals fed exclusively milk (Salaheen-milk) and samples from calves that after the introduction of solid feed in their diets (Salaheen-solid). For each tab, from left to right, we present the metabolic pathway id; the pathway description; the number of enzymes of that pathway that were identified in the focal contigs. The rest of the columns present the number of predicted enzymes discovered in group-specific (winter-specific, summer-specific, solid-specific or milk-specific) MAGs identified by our analysis (i.e. MAGs that had &gt;25% -for summer or solid group- or &gt;10% -for milk or winter group- of their contigs DifRep; see also Results).