cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5745459
title: Anthracotheriid artiodactyl <i>Anthracokeryx</i> and an upper Eocene age for the Youganwo Formation of southern China

description: The two recently collected mammalian dentary fragments from the Eocene Youganwo Formation of Guangdong Province, southern China, are referred to the anthracotheriid species <i>Anthracokeryx naduongensis</i> based on phylogenetic analysis and size comparison. One of these specimens (SYSU-M-1) is the first mammal fossil described from the Youganwo Formation. It was attributed previously to the perissodactyl genus <i>Lunania</i>. <i>Anthracokeryx naduongensis</i> was described originally from the lower upper Eocene Na Duong Formation in Northern Vietnam. The second record of this species supports a basal upper Eocene correlation for the Youganwo Formation, which was estimated previously as middle or late Eocene.
DOI: 10.6084/m9.figshare.5745459.v1
title: Anthracotheriid artiodactyl <i>Anthracokeryx</i> and an upper Eocene age for the Youganwo Formation of southern China

description: The two recently collected mammalian dentary fragments from the Eocene Youganwo Formation of Guangdong Province, southern China, are referred to the anthracotheriid species <i>Anthracokeryx naduongensis</i> based on phylogenetic analysis and size comparison. One of these specimens (SYSU-M-1) is the first mammal fossil described from the Youganwo Formation. It was attributed previously to the perissodactyl genus <i>Lunania</i>. <i>Anthracokeryx naduongensis</i> was described originally from the lower upper Eocene Na Duong Formation in Northern Vietnam. The second record of this species supports a basal upper Eocene correlation for the Youganwo Formation, which was estimated previously as middle or late Eocene.
DOI: 10.6084/m9.figshare.5745411
title: Additional file 1: Table S1. of Molecular screening of tsetse flies and cattle reveal different Trypanosoma species including T. grayi and T. theileri in northern Cameroon

description: Data for tsetse flies gut sample analysis. Sampling sites, ID code, Glossina species, PCR analysis with ITS1 primers (Table 1), accession numbers of sequences. Band sizes were determined by agarose gel electrophoresis and therefore, the sizes given are approximate. Based on sequences and data obtained in this study, size heterogeneity occurs for several species. The size ranges, in which we have to consider the corresponding Trypanosoma species are indicated in a separate column (expected). Table S2. Data for tsetse flies proboscis sample analysis. Sampling sites, ID code, flies species, PCR analysis with ITS1 primers (Table 1), accession numbers of sequences. Band sizes were determined by agarose gel electrophoresis and therefore, the sizes given are approximate. Based on sequences and data obtained in this study, size heterogeneity occurs for several species. The size ranges, in which we have to consider the corresponding Trypanosoma species are indicated in a separate column (expected). Table S3. Data for cattle blood sample analysis. Sampling sites, herd ID code, ID code, cattle breed, PCV, PCR analysis with ITS1 primers (Table 1), accession numbers of sequences. Band sizes were determined by agarose gel electrophoresis and therefore, the sizes given are approximate. Based on sequences and data obtained in this study, size heterogeneity occurs for several species. The size ranges, in which we have to consider the corresponding Trypanosoma species are indicated in a separate column (expected). Table S4. Nucleic acid sequences generated in this study and their accession numbers. (XLS 169Â kb)
DOI: 10.6084/m9.figshare.5745411.v1
title: Additional file 1: Table S1. of Molecular screening of tsetse flies and cattle reveal different Trypanosoma species including T. grayi and T. theileri in northern Cameroon

description: Data for tsetse flies gut sample analysis. Sampling sites, ID code, Glossina species, PCR analysis with ITS1 primers (Table 1), accession numbers of sequences. Band sizes were determined by agarose gel electrophoresis and therefore, the sizes given are approximate. Based on sequences and data obtained in this study, size heterogeneity occurs for several species. The size ranges, in which we have to consider the corresponding Trypanosoma species are indicated in a separate column (expected). Table S2. Data for tsetse flies proboscis sample analysis. Sampling sites, ID code, flies species, PCR analysis with ITS1 primers (Table 1), accession numbers of sequences. Band sizes were determined by agarose gel electrophoresis and therefore, the sizes given are approximate. Based on sequences and data obtained in this study, size heterogeneity occurs for several species. The size ranges, in which we have to consider the corresponding Trypanosoma species are indicated in a separate column (expected). Table S3. Data for cattle blood sample analysis. Sampling sites, herd ID code, ID code, cattle breed, PCV, PCR analysis with ITS1 primers (Table 1), accession numbers of sequences. Band sizes were determined by agarose gel electrophoresis and therefore, the sizes given are approximate. Based on sequences and data obtained in this study, size heterogeneity occurs for several species. The size ranges, in which we have to consider the corresponding Trypanosoma species are indicated in a separate column (expected). Table S4. Nucleic acid sequences generated in this study and their accession numbers. (XLS 169Â kb)
DOI: 10.6084/m9.figshare.5745360
title: RAMPs data from Puerto Rico deployment 2017

description: Air quality data from San Juan Metro Area.
DOI: 10.6084/m9.figshare.5745360.v1
title: RAMPs data from Puerto Rico deployment 2017

description: Air quality data from San Juan Metro Area.
DOI: 10.6084/m9.figshare.5743656
title: Roles of auxin and ethylene in aerenchyma formation in sugarcane roots

description: Although the cross-talk between auxin and ethylene has been described during plant development, the role played by auxin upon gene expression during aerenchyma formation is poorly understood. Root aerenchyma formation results from the opening of gas spaces in the cortex. It is part of a developmental program (constitutive) or due to ethylene treatment or abiotic stress (induced) such as flooding and nutrient starvation. This process relies on programmed cell death and cell wall modifications. Here we followed development of aerenchyma formation in sugarcane along 5 cm from the root apex. As a constitutive process, the aerenchyma formation was observed in the cortex from the 3<sup>rd</sup> cm onwards. This occurred despite 1-methylcyclepropene (1-MCP) treatment, an inhibitor of ethylene perception. However, this process occurred while ethylene (and auxin) levels decreased. Within the aerenchyma formation zone, the concentration of ethylene is lower in comparison to the concentration in maize. Besides, the ratio between both hormones (ethylene and auxin) was around 1:1. These pieces of evidence suggest that ethylene sensitivity and ethylene-auxin balance may play a role in the formation of aerenchyma. Furthermore, the transcriptional analysis showed that genes related to cell expansion are up-regulated due to 1-MCP treatment. Our results help explaining the regulation of the formation constitutive aerenchyma in sugarcane.
DOI: 10.6084/m9.figshare.5743656.v2
title: Roles of auxin and ethylene in aerenchyma formation in sugarcane roots

description: Although the cross-talk between auxin and ethylene has been described during plant development, the role played by auxin upon gene expression during aerenchyma formation is poorly understood. Root aerenchyma formation results from the opening of gas spaces in the cortex. It is part of a developmental program (constitutive) or due to ethylene treatment or abiotic stress (induced) such as flooding and nutrient starvation. This process relies on programmed cell death and cell wall modifications. Here we followed development of aerenchyma formation in sugarcane along 5 cm from the root apex. As a constitutive process, the aerenchyma formation was observed in the cortex from the 3<sup>rd</sup> cm onwards. This occurred despite 1-methylcyclepropene (1-MCP) treatment, an inhibitor of ethylene perception. However, this process occurred while ethylene (and auxin) levels decreased. Within the aerenchyma formation zone, the concentration of ethylene is lower in comparison to the concentration in maize. Besides, the ratio between both hormones (ethylene and auxin) was around 1:1. These pieces of evidence suggest that ethylene sensitivity and ethylene-auxin balance may play a role in the formation of aerenchyma. Furthermore, the transcriptional analysis showed that genes related to cell expansion are up-regulated due to 1-MCP treatment. Our results help explaining the regulation of the formation constitutive aerenchyma in sugarcane.
DOI: 10.6084/m9.figshare.5743656.v1
title: Roles of Auxin and Ethylene in Aerenchyma Formation in Sugarcane Roots

description: Although the cross-talk between auxin and ethylene has been described during plant development, the role played by auxin upon gene expression during aerenchyma formation is poorly understood. Root aerenchyma formation results from the opening of gas spaces in the cortex. It is part of a developmental program (constitutive) or due to ethylene treatment or abiotic stress (induced) such as flooding and nutrient starvation. This process relies on programmed cell death and cell wall modifications. Here we followed development of aerenchyma formation in sugarcane along 5 cm from the root apex. As a constitutive process, the aerenchyma formation was observed in the cortex from the 3<sup>rd</sup> cm onwards. This occurred despite 1-methylcyclepropene (1-MCP) treatment, an inhibitor of ethylene perception. However, this process occurred while ethylene (and auxin) levels decreased. Within the aerenchyma formation zone, the concentration of ethylene is lower in comparison to the concentration in maize. Besides, the ratio between both hormones (ethylene and auxin) was around 1:1. These pieces of evidence suggest that ethylene sensitivity and ethylene-auxin balance may play a role in the formation of aerenchyma. Furthermore, the transcriptional analysis showed that genes related to cell expansion are up-regulated due to 1-MCP treatment. Our results help explaining the regulation of the formation constitutive aerenchyma in sugarcane.
DOI: 10.6084/m9.figshare.5743545
title: A common toad hybrid zone that runs from the Atlantic to the Mediterranean. Supplementary Material

description: We document the distribution of the common toad <i>Bufo bufo </i>and the spined toad <i>B. spinosus </i>at their contact zone across France with data from a mitochondrial DNA RFLP assay, complementing similar work including nuclear markers in the northwest and southeast of France and in Italy. We also reconstruct geographical clines across the species’ contact zone in central France. <i>Bufo bufo </i>is found in the north-eastern half of France. <i>Bufo spinosus </i>is found in the south-western complement. The contact zone they form runs from the Atlantic coast near Caen, France, to the Mediterranean coast near Savona, Italy, and has a length of over 900 km. In central France <i>B. bufo </i>and <i>B. spinosus </i>engage in a hybrid zone with a unimodal genetic signature. Hybrid zone width is ca. 10 km at mitochondrial DNA and averages at 61 km for four nuclear loci. The hybrid zone is distinctly asymmetric with a signature of <i>B. spinosus </i>in <i>B. bufo </i>and not the other way round. We attribute this observation to <i>B. bufo </i>moving southwards at the expense of <i>B. spinosus</i>, with introgression in the direction of the advancing species. We noted substantial geographic variation in characters for species identification. Morphological species identification performs well in France, but breaks down in Italy. Mitochondrial DNA is inconclusive in south-eastern France and Italy. The nuclear genetic markers perform consistently well but have not yet been applied to the zone in full. Possible, but surely heterogeneous ecological correlates for the position of the hybrid zone are mountains and rivers.
DOI: 10.6084/m9.figshare.5743545.v1
title: A common toad hybrid zone that runs from the Atlantic to the Mediterranean. Supplementary Material

description: We document the distribution of the common toad <i>Bufo bufo </i>and the spined toad <i>B. spinosus </i>at their contact zone across France with data from a mitochondrial DNA RFLP assay, complementing similar work including nuclear markers in the northwest and southeast of France and in Italy. We also reconstruct geographical clines across the species’ contact zone in central France. <i>Bufo bufo </i>is found in the north-eastern half of France. <i>Bufo spinosus </i>is found in the south-western complement. The contact zone they form runs from the Atlantic coast near Caen, France, to the Mediterranean coast near Savona, Italy, and has a length of over 900 km. In central France <i>B. bufo </i>and <i>B. spinosus </i>engage in a hybrid zone with a unimodal genetic signature. Hybrid zone width is ca. 10 km at mitochondrial DNA and averages at 61 km for four nuclear loci. The hybrid zone is distinctly asymmetric with a signature of <i>B. spinosus </i>in <i>B. bufo </i>and not the other way round. We attribute this observation to <i>B. bufo </i>moving southwards at the expense of <i>B. spinosus</i>, with introgression in the direction of the advancing species. We noted substantial geographic variation in characters for species identification. Morphological species identification performs well in France, but breaks down in Italy. Mitochondrial DNA is inconclusive in south-eastern France and Italy. The nuclear genetic markers perform consistently well but have not yet been applied to the zone in full. Possible, but surely heterogeneous ecological correlates for the position of the hybrid zone are mountains and rivers.
DOI: 10.6084/m9.figshare.5743347
title: Fractionation, physicochemical, and structural characterization of winged bean seed protein fractions with reference to soybean

description: Proteins from defatted flour winged bean seed (<i>Psophocarpus tetragonolobus</i>) were sequentially fractionated with reference to soybean seed (<i>Glycine max</i>) using distilled water, 25 g/kg sodium chloride solution, 0.1 M NaOH, and 70% alcohol and subjected to physicochemical, functional, and structural analysis. Winged bean seed had globulin (31.94%) and albumin (26.46%), with denaturation temperatures (<i>T</i><sub>d</sub>) of 92.82 and 82.76°C, and surface hydrophobicities (SHs) of 214.51 and 189.32, respectively, whereas soybean seed had 34.95% globulin and 32.82% albumin, with respective <i>T</i><sub>d</sub> of 81.68 and 90.63°C, and SH of 210.80 and 204.66. This indicates that winged bean albumin could perform better at water/oil interface in an oil-in-water emulsion system because of it higher hydrophobicity, although soybean albumin had higher extraction rate. Both legumes’ proteins showed comparable gelation when employed for their gelling ability to form three-dimensional network in food systems. Soybean proteins had significantly (<i>P</i> P <b>Abbreviations:</b> WB: Winged bean; SB: soybean; <i>T</i><sub>d</sub>: denaturation temperature; SH: surface hydrophobicity; SH: surface hydrophobicity; W-ALB: winged bean albumin; W-GLO: winged bean globulin; W-GLU: winged bean glutelin; W-PRO: winged bean prolamin; W-ISO: winged bean isolate; S-ALB: soy albumin; S-GLO: soy globulin; S-GLU: glutelin; S-ISO: soy glutelin and S-PRO: soy prolamin.
DOI: 10.6084/m9.figshare.5743347.v1
title: Fractionation, physicochemical, and structural characterization of winged bean seed protein fractions with reference to soybean

description: Proteins from defatted flour winged bean seed (<i>Psophocarpus tetragonolobus</i>) were sequentially fractionated with reference to soybean seed (<i>Glycine max</i>) using distilled water, 25 g/kg sodium chloride solution, 0.1 M NaOH, and 70% alcohol and subjected to physicochemical, functional, and structural analysis. Winged bean seed had globulin (31.94%) and albumin (26.46%), with denaturation temperatures (<i>T</i><sub>d</sub>) of 92.82 and 82.76°C, and surface hydrophobicities (SHs) of 214.51 and 189.32, respectively, whereas soybean seed had 34.95% globulin and 32.82% albumin, with respective <i>T</i><sub>d</sub> of 81.68 and 90.63°C, and SH of 210.80 and 204.66. This indicates that winged bean albumin could perform better at water/oil interface in an oil-in-water emulsion system because of it higher hydrophobicity, although soybean albumin had higher extraction rate. Both legumes’ proteins showed comparable gelation when employed for their gelling ability to form three-dimensional network in food systems. Soybean proteins had significantly (<i>P</i> P <b>Abbreviations:</b> WB: Winged bean; SB: soybean; <i>T</i><sub>d</sub>: denaturation temperature; SH: surface hydrophobicity; SH: surface hydrophobicity; W-ALB: winged bean albumin; W-GLO: winged bean globulin; W-GLU: winged bean glutelin; W-PRO: winged bean prolamin; W-ISO: winged bean isolate; S-ALB: soy albumin; S-GLO: soy globulin; S-GLU: glutelin; S-ISO: soy glutelin and S-PRO: soy prolamin.
DOI: 10.6084/m9.figshare.5743326
title: Fe(III) Reducing Microorganisms from Iron Ore Caves Demonstrate Fermentative Fe(III) Reduction and Promote Cave Formation

description: The banded iron formations (BIF) of Brazil are composed of silica and Fe(III) oxide lamina, and are largely covered by a rock cap of BIF fragments in a goethite matrix (canga). Despite both BIF and canga being highly resistant to erosion and poorly soluble, &gt;3,000 iron ore caves (IOCs) have formed at their interface. Fe(III) reducing microorganisms (FeRM) can reduce the Fe(III) oxides present in the BIF and canga, which could account for the observed speleogenesis. Here, we show that IOCs contain a variety of microbial taxa with member species capable of dissimilatory Fe(III) reduction, including the <i>Chloroflexi, Acidobacteria</i> and the <i>Alpha</i>- <i>Beta</i>- and <i>Gammaproteobacteria</i>; however, Fe(III) reducing enrichment cultures from IOCs indicate the predominance of <i>Firmicutes</i> and <i>Enterobacteriaceae</i>, despite varying the carbon/electron donor, Fe(III) type, and pH. We used model-based inference to evaluate multiple candidate hypotheses that accounted for the variation in medium chemistry and culture composition. Model selection indicated that none of the tested variables account for the dominance of the <i>Firmicutes</i> in these cultures. The addition of H<sub>2</sub> to the headspace of the enrichment cultures enhanced Fe(III) reduction, while addition of N<sub>2</sub> resulted in diminished Fe(III) reduction, indicating that these <i>Enterobacteriaceae</i> and <i>Firmicutes</i> were reducing Fe(III) during fermentative growth. These results suggest that fermentative reduction of Fe(III) may play a larger role in iron-rich environments than expected. Our findings also demonstrate that FeRM are present within the IOCs, and that their reductive dissolution of Fe(III) oxides, combined with mass transport of solubilized Fe(II) by groundwater, could contribute to IOC formation.
DOI: 10.6084/m9.figshare.5743326.v1
title: Fe(III) Reducing Microorganisms from Iron Ore Caves Demonstrate Fermentative Fe(III) Reduction and Promote Cave Formation

description: The banded iron formations (BIF) of Brazil are composed of silica and Fe(III) oxide lamina, and are largely covered by a rock cap of BIF fragments in a goethite matrix (canga). Despite both BIF and canga being highly resistant to erosion and poorly soluble, &gt;3,000 iron ore caves (IOCs) have formed at their interface. Fe(III) reducing microorganisms (FeRM) can reduce the Fe(III) oxides present in the BIF and canga, which could account for the observed speleogenesis. Here, we show that IOCs contain a variety of microbial taxa with member species capable of dissimilatory Fe(III) reduction, including the <i>Chloroflexi, Acidobacteria</i> and the <i>Alpha</i>- <i>Beta</i>- and <i>Gammaproteobacteria</i>; however, Fe(III) reducing enrichment cultures from IOCs indicate the predominance of <i>Firmicutes</i> and <i>Enterobacteriaceae</i>, despite varying the carbon/electron donor, Fe(III) type, and pH. We used model-based inference to evaluate multiple candidate hypotheses that accounted for the variation in medium chemistry and culture composition. Model selection indicated that none of the tested variables account for the dominance of the <i>Firmicutes</i> in these cultures. The addition of H<sub>2</sub> to the headspace of the enrichment cultures enhanced Fe(III) reduction, while addition of N<sub>2</sub> resulted in diminished Fe(III) reduction, indicating that these <i>Enterobacteriaceae</i> and <i>Firmicutes</i> were reducing Fe(III) during fermentative growth. These results suggest that fermentative reduction of Fe(III) may play a larger role in iron-rich environments than expected. Our findings also demonstrate that FeRM are present within the IOCs, and that their reductive dissolution of Fe(III) oxides, combined with mass transport of solubilized Fe(II) by groundwater, could contribute to IOC formation.
DOI: 10.6084/m9.figshare.5743212
title: MASCOT generated reports for the identification of cell wall proteins in the pir32 null strain

description: In this study, we applied tandem mass spectrometry combined with bioinformatics to generate the cell wall proteome profiles of the pir32 null and wild type strains in order to compare them and subsequently detect differential proteins between both strains grown under filamentous and nonfilamentous conditions. Differentially detected proteins explain the varying phenotypes between the studied strains with respect to virulence, resistance to stresses, chitin deposition, and filamentation. The attached files show the MASCOT generated reports that include protein hits of matched sequences pertaining to the pir32 null strain. The unmatched sequences presented at the end of each report were then BLAST searched in candidagenome.org.
DOI: 10.6084/m9.figshare.5743212.v1
title: MASCOT generated reports for the identification of cell wall proteins in the pir32 null strain

description: In this study, we applied tandem mass spectrometry combined with bioinformatics to generate the cell wall proteome profiles of the pir32 null and wild type strains in order to compare them and subsequently detect differential proteins between both strains grown under filamentous and nonfilamentous conditions. Differentially detected proteins explain the varying phenotypes between the studied strains with respect to virulence, resistance to stresses, chitin deposition, and filamentation. The attached files show the MASCOT generated reports that include protein hits of matched sequences pertaining to the pir32 null strain. The unmatched sequences presented at the end of each report were then BLAST searched in candidagenome.org.
DOI: 10.6084/m9.figshare.5743059
title: Additional file 2: Table S7. of Transcriptome analysis reveals key roles of AtLBR-2 in LPS-induced defense responses in plants

description: The FPKM of all transcripts in each data sets. (XLSX 4687 kb)
DOI: 10.6084/m9.figshare.5743059.v1
title: Additional file 2: Table S7. of Transcriptome analysis reveals key roles of AtLBR-2 in LPS-induced defense responses in plants

description: The FPKM of all transcripts in each data sets. (XLSX 4687 kb)