cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7037228.v1
title: Figure_4_Sulfite_Reductase_Phylogeny

description: Figure 4 of manuscript "Comparative genomics and proteomic analysis of assimilatory sulfate reduction pathways in anaerobic methanotrophic archaea"<br>Files included:Fig4_sulfite_reductase_clustalo_alignment.faa - ClustalO alignment of protein sequencesFig4_sulfite_reductase_clustalo_alignment_filtered_for_tree.faa - Filtered protein sequences (224 amino acids) used for phylogeneticsFig2_cysN_ef_clustalo_tree.png - Bayesian phylogeny of sulfite reductases with collapsed groupsFigure_S1_full_sulfite_reductase_phylogeny.png - Bayesian phylogeny of sulfite reductases fully expanded<br><br>Figure 4. Bayesian phylogeny of sulfite reductases. Two well-supported groups of Fsr were identified in exclusion of alSir and other sulfite reductases. ANME proteins are bolded and in red. The phylogenetic tree was constructed based on 224 amino acid residues of the shared catalytic and siroheme-binding region. Asterisks (*) indicate proteins that have been studied biochemically (Huynh et al., 1984; Johnson and Mukhopadhyay, 2005; Moura et al., 1986). Protein accession numbers from the NCBI database or gene IDs from the IMG database are shown in parentheses. Black dots on the branches represent Bayesian posterior probability values greater than 90%, and scale bar indicates the number of amino acid substitutions per site. The fully expanded tree can be found be found in Supplementary Figure 1.<br><br>Supplementary Figure 1. Bayesian phylogeny of sulfite reductases. ANME proteins are bolded and in red. The phylogenetic tree was constructed based on 224 amino acid residues of the shared catalytic and siroheme-binding region. Protein accession numbers from the NCBI database or gene IDs from the IMG database are shown in parentheses. Black dots on the branches represent Bayesian posterior probability values greater than 90%, and scale bar indicates the number of amino acid substitutions per site. In addition to Fsr and alSir, aSir and Group III Dsr-LP were identified in Ca. Methanoperedens. <br>
DOI: 10.6084/m9.figshare.7037228.v2
title: Figure_4_Sulfite_Reductase_Phylogeny

description: Figure 4 of manuscript "Comparative genomics and proteomic analysis of assimilatory sulfate reduction pathways in anaerobic methanotrophic archaea"<br>Files included:Fig4_sulfite_reductase_clustalo_alignment.faa - ClustalO alignment of protein sequencesFig4_sulfite_reductase_clustalo_alignment_filtered_for_tree.faa - Filtered protein sequences (224 amino acids) used for phylogeneticsFig2_cysN_ef_clustalo_tree.png - Bayesian phylogeny of sulfite reductases with collapsed groups<br>Figure 4. Bayesian phylogeny of sulfite reductases. Two well-supported groups of Fsr were identified in exclusion of alSir and other sulfite reductases. ANME proteins are bolded and in red. The phylogenetic tree was constructed based on 224 amino acid residues of the shared catalytic and siroheme-binding region. Asterisks (*) indicate proteins that have been studied biochemically (Huynh et al., 1984; Johnson and Mukhopadhyay, 2005; Moura et al., 1986). Protein accession numbers from the NCBI database or gene IDs from the IMG database are shown in parentheses. Black dots on the branches represent Bayesian posterior probability values greater than 90%, and scale bar indicates the number of amino acid substitutions per site. The fully expanded tree can be found be found in Supplementary Figure 1.<br><br>
DOI: 10.6084/m9.figshare.7036289
title: Figure_3_Assimilatory_APS_PAPS_Reductase_Phylogeny

description: Figure 3 of manuscript "Comparative genomics and proteomic analysis of assimilatory sulfate reduction pathways in anaerobic methanotrophic archaea"<br>Files included:Fig3_APS_PAPS_reductase_clustalo_alignment.faa - ClustalO alignment of protein sequencesFig3_APS_PAPS_reductase_clustalo_alignment_filtered_for_tree.faa - Filtered protein sequences (172 amino acids) used for phylogeneticsFig3_APS_PAPS_Reductase_Phylogeny.png - Final Bayesian Phylogeny of Assimilatory APS/PAPS Reductases<br>Figure 3. Bayesian phylogeny of assimilatory adenyl-sulfate (APS) reductases and phosphoadenylyl-sulfate (PAPS) reductases. APS reductases and putative APS reductases are in green, PAPS reductases and putative PAPS reductases are in blue, bifunctional APS and PAPS reductase of Bacillus subtilis is in teal, and ANME proteins are bolded and in red. Archaeal and Bacterial/Eukaryal sequences formed separate clusters. Asterisks (*) indicate proteins that have been studied biochemically from Archaea (Cho, 2013; Lee et al., 2011), or Bacteria/Eukaryotes (Berndt et al., 2004; Gutierrez-Marcos et al., 1996; Kim et al., 2004; Savage et al., 1997; Suter et al., 2000; Yu et al., 2008). Length of the proteins ranged from 239 to 896 amino acids with the addition of protein domains. The protein domains, if found, are shown with filled symbols. Only 172 amino acid residues of the central shared region were used for phylogenetics. Given that two copies of APS/PAPS reductases were found in each ANME-2 lineage and clustered separately, it is likely one is for APS and the other is for PAPS reduction similar to M. jannaschii (Cho, 2013; Lee et al., 2011). Ca. Methanoperedens and four other methanogens in Methanosarcinales also contained a second putative assimilatory APS reductase more closely related to the bacterial/eukaryotic homologs, while ANME-1b contained a gene that does not cluster with assimilatory APS or PAPS reductases of known substrate. Protein accession numbers from the NCBI database or gene IDs from the IMG database are shown in parentheses. Black dots on the branches represent Bayesian posterior probability values greater than 90%, and scale bar indicates the number of amino acid substitutions per site.<br>
DOI: 10.6084/m9.figshare.7035917
title: Figure_2_cysDN_phylogeny

description: Figure 2 of manuscript "Comparative genomics and proteomic analysis of assimilatory sulfate reduction pathways in anaerobic methanotrophic archaea"<br>Files included:Fig2_cysN_ef_clustalo_alignment.faa - ClustalO alignment of protein sequencesFig2_cysN_ef_clustalo_alignment_filtered_for_tree.faa - Filtered protein sequences (416 amino acids) used for phylogeneticsFig2_cysN_ef_clustalo_tree.png - Final Bayesian Phylogeny of CysN and Elongation FactorFig2_cysD_clustalo_alignment.faa - ClustalO alignment of protein sequencesFig2_cysD_clustalo_alignment_filtered_for_tree.faa - Filtered protein sequences (416 amino acids) used for phylogeneticsFig2_cysD_clustalo_tree.png - Final Bayesian Phylogeny of CysN and Elongation Factor<br>Figure 2. Phylogeny of heterodimeric ATP sulfurylase subunits (CysDN). (a) Bayesian phylogeny of 416 amino acid residues of sulfate adenylyltransferase subunit 1 (CysN) and elongation factor 1 alpha (EF-1A) or elongation factor thermo unstable (EF-Tu) proteins. CysN, in green, formed a separate phylogenetic cluster from the homologous EF-1A and EF-Tu in blue. ANME proteins are bolded in red. The phylogenetic analysis distinguished CysN from their homologous elongation factor in ANME. (b) Bayesian phylogeny of 270 amino acid residues of sulfate adenylyltransferase subunit 2 (CysD) in green. They are found in ANME genomes next to CysN confirming that they are the heterodimeric ATP sulfurylase subunits. Asterisks (*) indicate proteins that have been studied biochemically or structurally (Andersen et al., 2000; Kobayashi et al., 2010; Liu et al., 1994; Mougous et al., 2006; Schmeing et al., 2009; Thirup et al., 2015; Vitagliano et al., 2001). Protein accession numbers from the NCBI database or gene IDs from the IMG database are shown in parentheses. Black dots on the branches represent Bayesian posterior probability values greater than 90%, and scale bar indicates the number of amino acid substitutions per site.<br>
DOI: 10.6084/m9.figshare.7036289.v1
title: Figure_3_Assimilatory_APS_PAPS_Reductase_Phylogeny

description: Figure 3 of manuscript "Comparative genomics and proteomic analysis of assimilatory sulfate reduction pathways in anaerobic methanotrophic archaea"<br>Files included:Fig3_APS_PAPS_reductase_clustalo_alignment.faa - ClustalO alignment of protein sequencesFig3_APS_PAPS_reductase_clustalo_alignment_filtered_for_tree.faa - Filtered protein sequences (172 amino acids) used for phylogeneticsFig3_APS_PAPS_Reductase_Phylogeny.png - Final Bayesian Phylogeny of Assimilatory APS/PAPS Reductases<br>Figure 3. Bayesian phylogeny of assimilatory adenyl-sulfate (APS) reductases and phosphoadenylyl-sulfate (PAPS) reductases. APS reductases and putative APS reductases are in green, PAPS reductases and putative PAPS reductases are in blue, bifunctional APS and PAPS reductase of Bacillus subtilis is in teal, and ANME proteins are bolded and in red. Archaeal and Bacterial/Eukaryal sequences formed separate clusters. Asterisks (*) indicate proteins that have been studied biochemically from Archaea (Cho, 2013; Lee et al., 2011), or Bacteria/Eukaryotes (Berndt et al., 2004; Gutierrez-Marcos et al., 1996; Kim et al., 2004; Savage et al., 1997; Suter et al., 2000; Yu et al., 2008). Length of the proteins ranged from 239 to 896 amino acids with the addition of protein domains. The protein domains, if found, are shown with filled symbols. Only 172 amino acid residues of the central shared region were used for phylogenetics. Given that two copies of APS/PAPS reductases were found in each ANME-2 lineage and clustered separately, it is likely one is for APS and the other is for PAPS reduction similar to M. jannaschii (Cho, 2013; Lee et al., 2011). Ca. Methanoperedens and four other methanogens in Methanosarcinales also contained a second putative assimilatory APS reductase more closely related to the bacterial/eukaryotic homologs, while ANME-1b contained a gene that does not cluster with assimilatory APS or PAPS reductases of known substrate. Protein accession numbers from the NCBI database or gene IDs from the IMG database are shown in parentheses. Black dots on the branches represent Bayesian posterior probability values greater than 90%, and scale bar indicates the number of amino acid substitutions per site.<br>
DOI: 10.6084/m9.figshare.7036289.v2
title: Figure_3_Assimilatory_APS_PAPS_Reductase_Phylogeny

description: Figure 3 of manuscript "Comparative genomics and proteomic analysis of assimilatory sulfate reduction pathways in anaerobic methanotrophic archaea"<br>Files included:Fig3_APS_PAPS_reductase_clustalo_alignment.faa - ClustalO alignment of protein sequencesFig3_APS_PAPS_reductase_clustalo_alignment_filtered_for_tree.faa - Filtered protein sequences (172 amino acids) used for phylogeneticsFig3_APS_PAPS_Reductase_Phylogeny.png - Final Bayesian Phylogeny of Assimilatory APS/PAPS Reductases<br>Figure 3. Bayesian phylogeny of assimilatory adenyl-sulfate (APS) reductases and phosphoadenylyl-sulfate (PAPS) reductases. APS reductases and putative APS reductases are in green, PAPS reductases and putative PAPS reductases are in blue, bifunctional APS and PAPS reductase of Bacillus subtilis is in teal, and ANME proteins are bolded and in red. Archaeal and Bacterial/Eukaryal sequences formed separate clusters. Asterisks (*) indicate proteins that have been studied biochemically from Archaea (Cho, 2013; Lee et al., 2011), or Bacteria/Eukaryotes (Berndt et al., 2004; Gutierrez-Marcos et al., 1996; Kim et al., 2004; Savage et al., 1997; Suter et al., 2000; Yu et al., 2008). Length of the proteins ranged from 239 to 896 amino acids with the addition of protein domains. The protein domains, if found, are shown with filled symbols. Only 172 amino acid residues of the central shared region were used for phylogenetics. Given that two copies of APS/PAPS reductases were found in each ANME-2 lineage and clustered separately, it is likely one is for APS and the other is for PAPS reduction similar to M. jannaschii (Cho, 2013; Lee et al., 2011). Ca. Methanoperedens and four other methanogens in Methanosarcinales also contained a second putative assimilatory APS reductase more closely related to the bacterial/eukaryotic homologs, while ANME-1b contained a gene that does not cluster with assimilatory APS or PAPS reductases of known substrate. Protein accession numbers from the NCBI database or gene IDs from the IMG database are shown in parentheses. Black dots on the branches represent Bayesian posterior probability values greater than 90%, and scale bar indicates the number of amino acid substitutions per site.<br>
DOI: 10.6084/m9.figshare.7035917.v1
title: Figure_2_cysDN_phylogeny

description: Figure 2 of manuscript "Comparative genomics and proteomic analysis of assimilatory sulfate reduction pathways in anaerobic methanotrophic archaea"<br>Files included:Fig2_cysN_ef_clustalo_alignment.faa - ClustalO alignment of protein sequencesFig2_cysN_ef_clustalo_alignment_filtered_for_tree.faa - Filtered protein sequences (416 amino acids) used for phylogeneticsFig2_cysN_ef_clustalo_tree.png - Final Bayesian Phylogeny of CysN and Elongation FactorFig2_cysD_clustalo_alignment.faa - ClustalO alignment of protein sequencesFig2_cysD_clustalo_alignment_filtered_for_tree.faa - Filtered protein sequences (416 amino acids) used for phylogeneticsFig2_cysD_clustalo_tree.png - Final Bayesian Phylogeny of CysN and Elongation Factor<br>Figure 2. Phylogeny of heterodimeric ATP sulfurylase subunits (CysDN). (a) Bayesian phylogeny of 416 amino acid residues of sulfate adenylyltransferase subunit 1 (CysN) and elongation factor 1 alpha (EF-1A) or elongation factor thermo unstable (EF-Tu) proteins. CysN, in green, formed a separate phylogenetic cluster from the homologous EF-1A and EF-Tu in blue. ANME proteins are bolded in red. The phylogenetic analysis distinguished CysN from their homologous elongation factor in ANME. (b) Bayesian phylogeny of 270 amino acid residues of sulfate adenylyltransferase subunit 2 (CysD) in green. They are found in ANME genomes next to CysN confirming that they are the heterodimeric ATP sulfurylase subunits. Asterisks (*) indicate proteins that have been studied biochemically or structurally (Andersen et al., 2000; Kobayashi et al., 2010; Liu et al., 1994; Mougous et al., 2006; Schmeing et al., 2009; Thirup et al., 2015; Vitagliano et al., 2001). Protein accession numbers from the NCBI database or gene IDs from the IMG database are shown in parentheses. Black dots on the branches represent Bayesian posterior probability values greater than 90%, and scale bar indicates the number of amino acid substitutions per site.<br>
DOI: 10.6084/m9.figshare.7035917.v2
title: Figure_2_cysDN_phylogeny

description: Figure 2 of manuscript "Comparative genomics and proteomic analysis of assimilatory sulfate reduction pathways in anaerobic methanotrophic archaea"<br>Files included:Fig2_cysN_ef_clustalo_alignment.faa - ClustalO alignment of protein sequencesFig2_cysN_ef_clustalo_alignment_filtered_for_tree.faa - Filtered protein sequences (416 amino acids) used for phylogeneticsFig2_cysN_ef_clustalo_tree.png - Final Bayesian Phylogeny of CysN and Elongation FactorFig2_cysD_clustalo_alignment.faa - ClustalO alignment of protein sequencesFig2_cysD_clustalo_alignment_filtered_for_tree.faa - Filtered protein sequences (416 amino acids) used for phylogeneticsFig2_cysD_clustalo_tree.png - Final Bayesian Phylogeny of CysN and Elongation Factor<br>Figure 2. Phylogeny of heterodimeric ATP sulfurylase subunits (CysDN). (a) Bayesian phylogeny of 416 amino acid residues of sulfate adenylyltransferase subunit 1 (CysN) and elongation factor 1 alpha (EF-1A) or elongation factor thermo unstable (EF-Tu) proteins. CysN, in green, formed a separate phylogenetic cluster from the homologous EF-1A and EF-Tu in blue. ANME proteins are bolded in red. The phylogenetic analysis distinguished CysN from their homologous elongation factor in ANME. (b) Bayesian phylogeny of 270 amino acid residues of sulfate adenylyltransferase subunit 2 (CysD) in green. They are found in ANME genomes next to CysN confirming that they are the heterodimeric ATP sulfurylase subunits. Asterisks (*) indicate proteins that have been studied biochemically or structurally (Andersen et al., 2000; Kobayashi et al., 2010; Liu et al., 1994; Mougous et al., 2006; Schmeing et al., 2009; Thirup et al., 2015; Vitagliano et al., 2001). Protein accession numbers from the NCBI database or gene IDs from the IMG database are shown in parentheses. Black dots on the branches represent Bayesian posterior probability values greater than 90%, and scale bar indicates the number of amino acid substitutions per site.<br>
DOI: 10.6084/m9.figshare.7035866
title: Supplemental Material for Bellot, de los Campos and Pérez-Enciso, 2018

description: Supplemental material contains a summary of main DL parameters, a description of the genetic algorithm used for hyperparameter optimization, and additional MLP and CNN results.
DOI: 10.6084/m9.figshare.7035866.v1
title: Supplemental Material for Bellot, de los Campos and Pérez-Enciso, 2018

description: Supplemental material contains a summary of main DL parameters, a description of the genetic algorithm used for hyperparameter optimization, and additional MLP and CNN results.
DOI: 10.6084/m9.figshare.7035827
title: File F2 from Halloween genes in panarthropods and the evolution of the early moulting pathway in Ecdysozoa

description: Alignment of 238 bilaterian cytochrome P450 family genes, 173 bilaterian nuclear hormone receptor genes, 58 bilaterian ETS family genes including <i>E74</i> and 59 bilaterian Rieske-domain containing genes including <i>neverland</i>.
DOI: 10.6084/m9.figshare.7035827.v1
title: File F2 from Halloween genes in panarthropods and the evolution of the early moulting pathway in Ecdysozoa

description: Alignment of 238 bilaterian cytochrome P450 family genes, 173 bilaterian nuclear hormone receptor genes, 58 bilaterian ETS family genes including <i>E74</i> and 59 bilaterian Rieske-domain containing genes including <i>neverland</i>.
DOI: 10.6084/m9.figshare.7035815
title: File F1 from Halloween genes in panarthropods and the evolution of the early moulting pathway in Ecdysozoa

description: List of species names and genes with NCBI or UniProt accession number used for phylogenetic analyses of <i>neverland</i>, Halloween genes, nuclear receptor genes, Early genes, and <i>CYP18A1</i>. Identified sequences of <i>Euperipatoides rowelli</i> (Onychophora) and <i>Hypsibius exemplaris</i> (Tardigrada) are included on table 7 and 8, respectively.
DOI: 10.6084/m9.figshare.7035698
title: InputtilesMODIS.txt

description: input tiles required to calculate start of season for Aedes albopictus
DOI: 10.6084/m9.figshare.7035698.v1
title: InputtilesMODIS.txt

description: input tiles required to calculate start of season for Aedes albopictus
DOI: 10.6084/m9.figshare.7035695
title: Running calibration data.xlsx

description: These data were used in Liverakos K, McIntosh K, Moulin CJA, O’Connor AR (2018) How accurate are runners’ prospective predictions of their race times? PLoS ONE 13(8): e0200744. https://doi.org/10.1371/journal.pone.0200744<br>The spreadsheets contain (1) data that were used to examine the effects of experience, gender, and age on running calibration; and (2) data that were used to examined the effects of race repetition on running calibration.
DOI: 10.6084/m9.figshare.7035695.v2
title: Running calibration data.xlsx

description: These data were used in Liverakos K, McIntosh K, Moulin CJA, O’Connor AR (2018) How accurate are runners’ prospective predictions of their race times? PLoS ONE 13(8): e0200744. https://doi.org/10.1371/journal.pone.0200744<br>The spreadsheets contain (1) data that were used to examine the effects of experience, gender, and age on running calibration; and (2) data that were used to examined the effects of race repetition on running calibration.
DOI: 10.6084/m9.figshare.7035695.v1
title: Running calibration data.xlsx

description: These data were used in Liverakos K, McIntosh K, Moulin CJA, O’Connor AR (2018) How accurate are runners’ prospective predictions of their race times? PLoS ONE 13(8): e0200744. https://doi.org/10.1371/journal.pone.0200744<br>The spreadsheets contain (1) data that were used to examine the effects of experience, gender, and age on running calibration; and (2) data that were used to examined the effects of race repetition on running calibration.
DOI: 10.6084/m9.figshare.7035527
title: 15E0469 Ticknick Park plant id.csv

description: Dataset from a medieval Irish archaeological site, archaeobotanical data <br>
DOI: 10.6084/m9.figshare.7035524
title: 15E0471 Laughanstown and Brenanstown plant id.csv

description: Early medieval dataset, Irish archaeobotany<br>
DOI: 10.6084/m9.figshare.7035524.v1
title: 15E0471 Laughanstown and Brenanstown plant id.csv

description: Early medieval dataset, Irish archaeobotany<br>
DOI: 10.6084/m9.figshare.7035527.v1
title: 15E0469 Ticknick Park plant id.csv

description: Dataset from a medieval Irish archaeological site, archaeobotanical data <br>
DOI: 10.6084/m9.figshare.7035476
title: Postpartum Depression Urban Slum Data, Bangladesh

description: Prevalence and risk factors of postpartum depression.
DOI: 10.6084/m9.figshare.7035200
title: Data and code from Assessing gaps in reporting non-target mortality in island rodent eradication operations

description: Data and R code for analyses & figures from Ward et al. Assessing gaps in reporting non-target mortality in island rodent eradication operations
DOI: 10.6084/m9.figshare.7035476.v1
title: Untitled Item

description: Prevalence and risk factors of postpartum depression.
DOI: 10.6084/m9.figshare.7035200.v1
title: Data and code from Assessing gaps in reporting non-target mortality in island rodent eradication operations

description: Data and R code for analyses & figures from Ward et al. Assessing gaps in reporting non-target mortality in island rodent eradication operations
DOI: 10.6084/m9.figshare.7035476.v2
title: Postpartum Depression Urban Slum Data, Bangladesh

description: Prevalence and risk factors of postpartum depression.
DOI: 10.6084/m9.figshare.7035179
title: 5. Comparison of China's emission trends with atmospheric observations

description: The satellite-retrieved PM<sub>2.5</sub> concentrations are compared with emission trends of PM<sub>2.5</sub> precursors. The 2010–2017 trends in SO<sub>2</sub> and NO<sub>x</sub> emissions are compared with OMI SO<sub>2</sub> and NO<sub>2</sub> tropospheric columns for Eastern China, respectively. Eastern China here includes the provinces of Beijing, Tianjin, Hebei, Shanxi, Shaanxi, Shandong, Henan, Hubei, Anhui, Jiangsu, Shanghai, and Zhejiang. Besides, the 2013–2017 trends in ground-based observations of SO<sub>2</sub>, NO<sub>2</sub>, and PM<sub>2.5</sub> are also presented.
DOI: 10.6084/m9.figshare.7035179.v1
title: 5. Comparison of China's emission trends with atmospheric observations

description: The satellite-retrieved PM<sub>2.5</sub> concentrations are compared with emission trends of PM<sub>2.5</sub> precursors. The 2010–2017 trends in SO<sub>2</sub> and NO<sub>x</sub> emissions are compared with OMI SO<sub>2</sub> and NO<sub>2</sub> tropospheric columns for Eastern China, respectively. Eastern China here includes the provinces of Beijing, Tianjin, Hebei, Shanxi, Shaanxi, Shandong, Henan, Hubei, Anhui, Jiangsu, Shanghai, and Zhejiang. Besides, the 2013–2017 trends in ground-based observations of SO<sub>2</sub>, NO<sub>2</sub>, and PM<sub>2.5</sub> are also presented.
DOI: 10.6084/m9.figshare.7035170
title: 3. Energy consumption of hydrocarbon fuels in China during 2010–2017

description: China's fuel consumption of coal, oil, natural gas, and traditional biofuel from 2010 to 2017.
DOI: 10.6084/m9.figshare.7035176
title: 4. Drivers of 2010–2017 emission changes

description: The species plotted here include SO<sub>2</sub>, NO<sub>x</sub>, CO, PM<sub>2.5</sub>, BC, and OC. For each pollutant, the changes in emissions from 2010 to 2017 are decomposed into drivers of activity growth and pollution control by source sector.