cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8158049
title: Supplementary Material for: Proteomic Profiling of Signaling Networks Modulated by G-CSF/Plerixafor/Busulfan-Fludarabine Conditioning in Acute Myeloid Leukemia Patients in Remission or with Active Disease prior to Allogeneic Stem Cell Transplantation

description: To characterize intracellular signaling in peripheral blood (PB) cells of acute myeloid leukemia (AML) patients undergoing pretransplant conditioning with CXCR4 inhibitor plerixafor, granulocyte colony-stimulating factor (G-CSF), and busulfan plus fludarabine (Bu+Flu) chemotherapy, we profiled 153 proteins in 33 functional groups using reverse phase protein array. CXCR4 inhibition mobilized AML progenitors and clonal AML cells, and this was associated with molecular markers of cell cycle progression. G-CSF/plerixafor and G-CSF/plerixafor/Bu+Flu modulated distinct signaling networks in AML blasts of patients undergoing conditioning with active disease compared to nonleukemic PB cells of patients in remission. We identified AML-specific proteins that remained aberrantly expressed after chemotherapy, representing putative chemoresistance markers in AML.
DOI: 10.6084/m9.figshare.8158049.v1
title: Supplementary Material for: Proteomic Profiling of Signaling Networks Modulated by G-CSF/Plerixafor/Busulfan-Fludarabine Conditioning in Acute Myeloid Leukemia Patients in Remission or with Active Disease prior to Allogeneic Stem Cell Transplantation

description: To characterize intracellular signaling in peripheral blood (PB) cells of acute myeloid leukemia (AML) patients undergoing pretransplant conditioning with CXCR4 inhibitor plerixafor, granulocyte colony-stimulating factor (G-CSF), and busulfan plus fludarabine (Bu+Flu) chemotherapy, we profiled 153 proteins in 33 functional groups using reverse phase protein array. CXCR4 inhibition mobilized AML progenitors and clonal AML cells, and this was associated with molecular markers of cell cycle progression. G-CSF/plerixafor and G-CSF/plerixafor/Bu+Flu modulated distinct signaling networks in AML blasts of patients undergoing conditioning with active disease compared to nonleukemic PB cells of patients in remission. We identified AML-specific proteins that remained aberrantly expressed after chemotherapy, representing putative chemoresistance markers in AML.
DOI: 10.6084/m9.figshare.8158022
title: Discussion of: Ortega-Flores et al. (2018) Provenance analysis of Oligocene sandstone from the Cerro Pelón area, southern Gulf of Mexico.https://doi.org/10.1080/00206814.2018.1476922

description: We discuss the 2018 publication that reports petrographic, heavy mineral data, mineral chemistry, and zircon geochronology for Oligocene sandstones in the Cerro Pelón area in southern Mexico Sureste basin. As the title of their paper says, the goal of their study is to establish the source (s) of the voluminous Cenozoic section in this region, reaching several kilometres in thickness and important as a petroleum system. These authors conclude that Oligocene sandstones of La Laja Formation were mostly sourced from eclogite- to greenschist-facies metasedimentary, metaigneous, and ultramafic rocks of the Guatemala suture complex. Minor contributions from the Chiapas Massif Complex, exposed directly to the south ~60 km of the Cerro Pelón area, were also suggested by the authors. They thus conclude that the Palaeogene stratigraphic record in southeastern Mexico was mostly controlled by the development of the Caribbean–North America plate boundary rather than by orogenic processes at the Pacific margin of North America. Presently, we do not agree with the conclusions of Ortega Flores and colleagues who studied the Cerro Pelón section, thus some discussion is required. Serpentinite bearing Nanchital Conglomerate is well exposed in the Cerro Pelón area, and high- to low-grade metamorphic rocks experienced an uplift in the vicinity of the Cerro Pelón area at the time of deposition of the La Laja Formation. We believe the data are better explained by multiple local sources in southern and eastern Oaxaca as well as sources to the south and southwest, which include the Cenozoic coastal batholith, the Grenvillean/Guichicovi basement complexes, the Chiapas Massif, the Mazatlán schist and other units in the Cuicateco Belt, as well as the Mesozoic cover of these areas (Todos Santos Formation, Cretaceous carbonate rocks, and Paleogene strata such as the Soyaló and Bosque Formations).
DOI: 10.6084/m9.figshare.8158022.v1
title: Discussion of: Ortega-Flores et al. (2018) Provenance analysis of Oligocene sandstone from the Cerro Pelón area, southern Gulf of Mexico.https://doi.org/10.1080/00206814.2018.1476922

description: We discuss the 2018 publication that reports petrographic, heavy mineral data, mineral chemistry, and zircon geochronology for Oligocene sandstones in the Cerro Pelón area in southern Mexico Sureste basin. As the title of their paper says, the goal of their study is to establish the source (s) of the voluminous Cenozoic section in this region, reaching several kilometres in thickness and important as a petroleum system. These authors conclude that Oligocene sandstones of La Laja Formation were mostly sourced from eclogite- to greenschist-facies metasedimentary, metaigneous, and ultramafic rocks of the Guatemala suture complex. Minor contributions from the Chiapas Massif Complex, exposed directly to the south ~60 km of the Cerro Pelón area, were also suggested by the authors. They thus conclude that the Palaeogene stratigraphic record in southeastern Mexico was mostly controlled by the development of the Caribbean–North America plate boundary rather than by orogenic processes at the Pacific margin of North America. Presently, we do not agree with the conclusions of Ortega Flores and colleagues who studied the Cerro Pelón section, thus some discussion is required. Serpentinite bearing Nanchital Conglomerate is well exposed in the Cerro Pelón area, and high- to low-grade metamorphic rocks experienced an uplift in the vicinity of the Cerro Pelón area at the time of deposition of the La Laja Formation. We believe the data are better explained by multiple local sources in southern and eastern Oaxaca as well as sources to the south and southwest, which include the Cenozoic coastal batholith, the Grenvillean/Guichicovi basement complexes, the Chiapas Massif, the Mazatlán schist and other units in the Cuicateco Belt, as well as the Mesozoic cover of these areas (Todos Santos Formation, Cretaceous carbonate rocks, and Paleogene strata such as the Soyaló and Bosque Formations).
DOI: 10.6084/m9.figshare.8157980
title: Koala_data_Submission.csv

description: Dataset from video analysis of six koalas moving across habitat structures from their natural environment. Data points on speed, subjects, kinematics and antero posterior sequences of gait are represented.
DOI: 10.6084/m9.figshare.8157980.v1
title: Koala_data_Submission.csv

description: Dataset from video analysis of six koalas moving across habitat structures from their natural environment. Data points on speed, subjects, kinematics and antero posterior sequences of gait are represented.
DOI: 10.6084/m9.figshare.8157938
title: CUE_pred_1982_2011_EcoT2.nc

description: This is a grid dataset for global carbon use efficiency with a half degree from 1982 to 2011, predicted by Random Forest using observations from publications. For more detail: Tang, X., Carvalhais, N., Moura, C., Ahrens, B., Koirala, S., Fan, S., Guan, F., Zhang, W., Gao, S., Magliulo, V., Buysse, P., Liu, S., Chen, G., Yang, W., Yu, Z., Liang, J., Shi, L., Pu, S., and Reichstein, M.: Global variability of carbon use efficiency in terrestrial ecosystems, Biogeosciences Discuss., 2019, 1-19, DOI: 10.5194/bg-2019-37.
DOI: 10.6084/m9.figshare.8157938.v1
title: CUE_pred_1982_2011_EcoT2.nc

description: This is a grid dataset for global carbon use efficiency with a half degree, predicted by Random Forest using observations from publications. For more detail: Tang, X., Carvalhais, N., Moura, C., Ahrens, B., Koirala, S., Fan, S., Guan, F., Zhang, W., Gao, S., Magliulo, V., Buysse, P., Liu, S., Chen, G., Yang, W., Yu, Z., Liang, J., Shi, L., Pu, S., and Reichstein, M.: Global variability of carbon use efficiency in terrestrial ecosystems, Biogeosciences Discuss., 2019, 1-19, DOI: 10.5194/bg-2019-37.
DOI: 10.6084/m9.figshare.8157932
title: CUE_dataset.csv

description: This is a dataset for global carbon use efficiency in terrestrial ecosystems. For more details, please see:Tang, X., Carvalhais, N., Moura, C., Ahrens, B., Koirala, S., Fan, S., Guan, F., Zhang, W., Gao, S., Magliulo, V., Buysse, P., Liu, S., Chen, G., Yang, W., Yu, Z., Liang, J., Shi, L., Pu, S., and Reichstein, M.: Global variability of carbon use efficiency in terrestrial ecosystems, Biogeosciences Discuss., 2019, 1-19, 10.5194/bg-2019-37.
DOI: 10.6084/m9.figshare.8157932.v1
title: CUE_dataset.csv

description: This is a dataset for global carbon use efficiency in terrestrial ecosystems. For more details, please see:Tang, X., Carvalhais, N., Moura, C., Ahrens, B., Koirala, S., Fan, S., Guan, F., Zhang, W., Gao, S., Magliulo, V., Buysse, P., Liu, S., Chen, G., Yang, W., Yu, Z., Liang, J., Shi, L., Pu, S., and Reichstein, M.: Global variability of carbon use efficiency in terrestrial ecosystems, Biogeosciences Discuss., 2019, 1-19, 10.5194/bg-2019-37.
DOI: 10.6084/m9.figshare.8157920
title: Supplementary Material for: The Colorful Diversity of Thyroid Hormone Metabolites

description: Since the discovery of L-thyroxine, the main secretory product of the thyroid gland, and its major metabolite T3, which exerts the majority of thyroid hormone action via ligand-dependent modulation of the function of T3 receptors in nuclei, mitochondria, and other subcellular compartments, various other T4-derived endogenous metabolites have been identified in blood and tissues of humans, animals, and early protochordates. This review addresses major historical milestones and experimental findings resulting in the discovery of the key enzymes of thyroid hormone metabolism, the three selenoprotein deiodinases, as well as the decarboxylases and amine oxidases involved in formation and degradation of recently identified endogenous thyroid hormone metabolites, i.e. 3-iodothyronamine and 3-thyroacetic acid. The concerted action of deiodinases 2 and 3 in regulation of local T3 availability is discussed. Special attention is given to the role of the thyromimetic “hot” metabolite 3,5-T2 and the “cool” 3-iodothyronamine, especially after administration of pharmacological doses of these endogenous thyroid hormone metabolites in various animal experimental models. In addition, available information on the biological roles of the two major acetic acid derivatives of thyroid hormones, i.e. Tetrac and Triac, as well as sulfated metabolites of thyroid hormones is reviewed. This review addresses the consequences of the existence of this broad spectrum of endogenous thyroid hormone metabolites, the “thyronome,” beyond the classical thyroid hormone profile comprising T4, T3, and rT3 for appropriate analytical coverage and clinical diagnostics using mass spectrometry versus immunoassays for determination of total and free concentrations of thyroid hormone metabolites in blood and tissues.
DOI: 10.6084/m9.figshare.8157920.v1
title: Supplementary Material for: The Colorful Diversity of Thyroid Hormone Metabolites

description: Since the discovery of L-thyroxine, the main secretory product of the thyroid gland, and its major metabolite T3, which exerts the majority of thyroid hormone action via ligand-dependent modulation of the function of T3 receptors in nuclei, mitochondria, and other subcellular compartments, various other T4-derived endogenous metabolites have been identified in blood and tissues of humans, animals, and early protochordates. This review addresses major historical milestones and experimental findings resulting in the discovery of the key enzymes of thyroid hormone metabolism, the three selenoprotein deiodinases, as well as the decarboxylases and amine oxidases involved in formation and degradation of recently identified endogenous thyroid hormone metabolites, i.e. 3-iodothyronamine and 3-thyroacetic acid. The concerted action of deiodinases 2 and 3 in regulation of local T3 availability is discussed. Special attention is given to the role of the thyromimetic “hot” metabolite 3,5-T2 and the “cool” 3-iodothyronamine, especially after administration of pharmacological doses of these endogenous thyroid hormone metabolites in various animal experimental models. In addition, available information on the biological roles of the two major acetic acid derivatives of thyroid hormones, i.e. Tetrac and Triac, as well as sulfated metabolites of thyroid hormones is reviewed. This review addresses the consequences of the existence of this broad spectrum of endogenous thyroid hormone metabolites, the “thyronome,” beyond the classical thyroid hormone profile comprising T4, T3, and rT3 for appropriate analytical coverage and clinical diagnostics using mass spectrometry versus immunoassays for determination of total and free concentrations of thyroid hormone metabolites in blood and tissues.
DOI: 10.6084/m9.figshare.8157911
title: droso_exons.tar from The perils of intralocus recombination for inferences of molecular convergence

description: Accurate inferences of convergence require that the appropriate tree topology be used. If there is a mismatch between the tree a trait has evolved along and the tree used for analysis, then false inferences of convergence (‘hemiplasy’) can occur. To avoid problems of hemiplasy when there are high levels of gene tree discordance with the species tree, researchers have begun to construct tree topologies from individual loci. However, due to intralocus recombination, even locus-specific trees may contain multiple topologies within them. This implies that the use of individual tree topologies discordant with the species tree can still lead to incorrect inferences about molecular convergence. Here, we examine the frequency with which single exons and single protein-coding genes contain multiple underlying tree topologies, in primates and <i>Drosophila</i>, and quantify the effects of hemiplasy when using trees inferred from individual loci. In both clades, we find that there are most often multiple diagnosable topologies within single exons and whole genes, with 91% of <i>Drosophila</i> protein-coding genes containing multiple topologies. Because of this underlying topological heterogeneity, even using trees inferred from individual protein-coding genes results in 25% and 38% of substitutions falsely labelled as convergent in primates and <i>Drosophila</i>, respectively. While constructing local trees can reduce the problem of hemiplasy, our results suggest that it will be difficult to completely avoid false inferences of convergence. We conclude by suggesting several ways forward in the analysis of convergent evolution, for both molecular and morphological characters.This article is part of the theme issue ‘Convergent evolution in the genomics era: new insights and directions’.
DOI: 10.6084/m9.figshare.8157911.v1
title: droso_exons.tar from The perils of intralocus recombination for inferences of molecular convergence

description: Accurate inferences of convergence require that the appropriate tree topology be used. If there is a mismatch between the tree a trait has evolved along and the tree used for analysis, then false inferences of convergence (‘hemiplasy’) can occur. To avoid problems of hemiplasy when there are high levels of gene tree discordance with the species tree, researchers have begun to construct tree topologies from individual loci. However, due to intralocus recombination, even locus-specific trees may contain multiple topologies within them. This implies that the use of individual tree topologies discordant with the species tree can still lead to incorrect inferences about molecular convergence. Here, we examine the frequency with which single exons and single protein-coding genes contain multiple underlying tree topologies, in primates and <i>Drosophila</i>, and quantify the effects of hemiplasy when using trees inferred from individual loci. In both clades, we find that there are most often multiple diagnosable topologies within single exons and whole genes, with 91% of <i>Drosophila</i> protein-coding genes containing multiple topologies. Because of this underlying topological heterogeneity, even using trees inferred from individual protein-coding genes results in 25% and 38% of substitutions falsely labelled as convergent in primates and <i>Drosophila</i>, respectively. While constructing local trees can reduce the problem of hemiplasy, our results suggest that it will be difficult to completely avoid false inferences of convergence. We conclude by suggesting several ways forward in the analysis of convergent evolution, for both molecular and morphological characters.This article is part of the theme issue ‘Convergent evolution in the genomics era: new insights and directions’.
DOI: 10.6084/m9.figshare.8157908
title: primates_cdss.tar from The perils of intralocus recombination for inferences of molecular convergence

description: Accurate inferences of convergence require that the appropriate tree topology be used. If there is a mismatch between the tree a trait has evolved along and the tree used for analysis, then false inferences of convergence (‘hemiplasy’) can occur. To avoid problems of hemiplasy when there are high levels of gene tree discordance with the species tree, researchers have begun to construct tree topologies from individual loci. However, due to intralocus recombination, even locus-specific trees may contain multiple topologies within them. This implies that the use of individual tree topologies discordant with the species tree can still lead to incorrect inferences about molecular convergence. Here, we examine the frequency with which single exons and single protein-coding genes contain multiple underlying tree topologies, in primates and <i>Drosophila</i>, and quantify the effects of hemiplasy when using trees inferred from individual loci. In both clades, we find that there are most often multiple diagnosable topologies within single exons and whole genes, with 91% of <i>Drosophila</i> protein-coding genes containing multiple topologies. Because of this underlying topological heterogeneity, even using trees inferred from individual protein-coding genes results in 25% and 38% of substitutions falsely labelled as convergent in primates and <i>Drosophila</i>, respectively. While constructing local trees can reduce the problem of hemiplasy, our results suggest that it will be difficult to completely avoid false inferences of convergence. We conclude by suggesting several ways forward in the analysis of convergent evolution, for both molecular and morphological characters.This article is part of the theme issue ‘Convergent evolution in the genomics era: new insights and directions’.
DOI: 10.6084/m9.figshare.8157908.v1
title: primates_cdss.tar from The perils of intralocus recombination for inferences of molecular convergence

description: Accurate inferences of convergence require that the appropriate tree topology be used. If there is a mismatch between the tree a trait has evolved along and the tree used for analysis, then false inferences of convergence (‘hemiplasy’) can occur. To avoid problems of hemiplasy when there are high levels of gene tree discordance with the species tree, researchers have begun to construct tree topologies from individual loci. However, due to intralocus recombination, even locus-specific trees may contain multiple topologies within them. This implies that the use of individual tree topologies discordant with the species tree can still lead to incorrect inferences about molecular convergence. Here, we examine the frequency with which single exons and single protein-coding genes contain multiple underlying tree topologies, in primates and <i>Drosophila</i>, and quantify the effects of hemiplasy when using trees inferred from individual loci. In both clades, we find that there are most often multiple diagnosable topologies within single exons and whole genes, with 91% of <i>Drosophila</i> protein-coding genes containing multiple topologies. Because of this underlying topological heterogeneity, even using trees inferred from individual protein-coding genes results in 25% and 38% of substitutions falsely labelled as convergent in primates and <i>Drosophila</i>, respectively. While constructing local trees can reduce the problem of hemiplasy, our results suggest that it will be difficult to completely avoid false inferences of convergence. We conclude by suggesting several ways forward in the analysis of convergent evolution, for both molecular and morphological characters.This article is part of the theme issue ‘Convergent evolution in the genomics era: new insights and directions’.
DOI: 10.6084/m9.figshare.8157905
title: primates_exons.tar from The perils of intralocus recombination for inferences of molecular convergence

description: Accurate inferences of convergence require that the appropriate tree topology be used. If there is a mismatch between the tree a trait has evolved along and the tree used for analysis, then false inferences of convergence (‘hemiplasy’) can occur. To avoid problems of hemiplasy when there are high levels of gene tree discordance with the species tree, researchers have begun to construct tree topologies from individual loci. However, due to intralocus recombination, even locus-specific trees may contain multiple topologies within them. This implies that the use of individual tree topologies discordant with the species tree can still lead to incorrect inferences about molecular convergence. Here, we examine the frequency with which single exons and single protein-coding genes contain multiple underlying tree topologies, in primates and <i>Drosophila</i>, and quantify the effects of hemiplasy when using trees inferred from individual loci. In both clades, we find that there are most often multiple diagnosable topologies within single exons and whole genes, with 91% of <i>Drosophila</i> protein-coding genes containing multiple topologies. Because of this underlying topological heterogeneity, even using trees inferred from individual protein-coding genes results in 25% and 38% of substitutions falsely labelled as convergent in primates and <i>Drosophila</i>, respectively. While constructing local trees can reduce the problem of hemiplasy, our results suggest that it will be difficult to completely avoid false inferences of convergence. We conclude by suggesting several ways forward in the analysis of convergent evolution, for both molecular and morphological characters.This article is part of the theme issue ‘Convergent evolution in the genomics era: new insights and directions’.