cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1325063
title: Gibberellin driven growth in <i>elf3</i> mutants requires PIF4 and PIF5

description: The regulatory connections between the circadian clock and hormone signaling are essential to understand, as these two regulatory processes work together to time growth processes relative to predictable environmental events. Gibberellins (GAs) are phytohormones that control many growth processes throughout all stages of the plant life cycle, including germination and flowering. An increasing number of examples demonstrate that the circadian clock directly influences GA biosynthesis and signaling. EARLY FLOWERING 3 (ELF3) participates in a tripartite transcriptional complex known as the Evening Complex (EC). In this capacity, ELF3 is fundamental to core circadian clock activity, as well as time-of-day specific regulation of genes directly responsible for growth control, namely the <i>PHYTOCHROME INTERACTING FACTOR 4</i> (<i>PIF4</i>) and <i>PIF5</i> genes. Here we show that the GA biosynthesis inhibitor paclobutrazol substantially reduces the long hypocotyl and petiole phenotypes of Arabidopsis <i>elf3</i> mutants. In addition, loss of ELF3 activity causes upregulation of the key GA biosynthesis genes <i>GA20ox1</i> and <i>GA20ox2</i>. Moreover, <i>GA20ox1</i> and <i>GA20ox2</i> expression depends strongly on the redundant activities of <i>PIF4</i> and <i>PIF5</i>. These findings indicate that the defining growth phenotypes of <i>elf3</i> mutants arise from altered GA biosynthesis due to misregulation of <i>PIF4</i> and <i>PIF5</i>. These observations agree with recent work linking increased GA production with the elongated growth phenotypes of the barley <i>elf3</i> mutant. Thus, the role of the EC in regulation of GA biosynthesis and signaling in eudicots is shared with monocots and, therefore, is a highly conserved mechanism for growth control.
DOI: 10.6084/m9.figshare.1324480
title: Phylogeography in Response to Reproductive Strategies and Ecogeographic Isolation in Ant Species on Madagascar: Genus Mystrium (Formicidae: Amblyoponinae)

description: Nexus file from four gene nuclear phylogeny (long-wavelength rhodopsin, 28s, wingless and abdominal-A) of the ant genus Mystrium from Madagascar. Nexus file from 790 bp mitochondrial phylogeny (cytochrome c oxidase I). MrBayes block included as seperate files for each analysis, and show partitioning sceme (by codon and/or gene) accordingly. Phylogenies generated from Mr. Bayes and RaxML analyses for both the mitochondrial and nuclear data sets are presented as well.
DOI: 10.6084/m9.figshare.1325063.v1
title: Gibberellin driven growth in <i>elf3</i> mutants requires PIF4 and PIF5

description: ABSTRACTThe regulatory connections between the circadian clock and hormone signaling are essential to understand, as these two regulatory processes work together to time growth processes relative to predictable environmental events. Gibberellins (GAs) are phytohormones that control many growth processes throughout all stages of the plant life cycle, including germination and flowering. An increasing number of examples demonstrate that the circadian clock directly influences GA biosynthesis and signaling. EARLY FLOWERING 3 (ELF3) participates in a tripartite transcriptional complex known as the Evening Complex (EC). In this capacity, ELF3 is fundamental to core circadian clock activity, as well as time-of-day specific regulation of genes directly responsible for growth control, namely the <i>PHYTOCHROME INTERACTING FACTOR 4</i> (<i>PIF4</i>) and <i>PIF5</i> genes. Here we show that the GA biosynthesis inhibitor paclobutrazol substantially reduces the long hypocotyl and petiole phenotypes of Arabidopsis <i>elf3</i> mutants. In addition, loss of ELF3 activity causes upregulation of the key GA biosynthesis genes <i>GA20ox1</i> and <i>GA20ox2</i>. Moreover, <i>GA20ox1</i> and <i>GA20ox2</i> expression depends strongly on the redundant activities of <i>PIF4</i> and <i>PIF5</i>. These findings indicate that the defining growth phenotypes of <i>elf3</i> mutants arise from altered GA biosynthesis due to misregulation of <i>PIF4</i> and <i>PIF5</i>. These observations agree with recent work linking increased GA production the elongated growth phenotypes of the barley <i>elf3</i> mutant. Thus, the role of the EC in regulation of GA biosynthesis and signaling in eudicots is shared with monocots and, therefore, is a highly conserved mechanism for growth control.
DOI: 10.6084/m9.figshare.1323384
title: Supplemental Data for "Multi-locus fossil-calibrated phylogeny of Atheriniformes"

description: Supplemental Data from the Molecular Phylogenetics and Evolution article: Campanella, D., Hughes, L.C., Unmack, P.J., Bloom, D.D., Piller, K.R., and Orti, G. (2015). Multi-locus fossil-calibrated phylogeny of Atheriniformes (Teleostei: Ovalentaria). <em>Molecular Phylogenetics and Evolution</em>.
DOI: 10.6084/m9.figshare.1324480.v1
title: Phylogeography in Response to Reproductive Strategies and Ecogeographic Isolation in Ant Species on Madagascar: Genus Mystrium (Formicidae: Amblyoponinae)

description: Nexus file from four gene nuclear phylogeny (long-wavelength rhodopsin, 28s, wingless and abdominal-A) of the ant genus Mystrium from Madagascar. Nexus file from 790 bp mitochondrial phylogeny (cytochrome c oxidase I). MrBayes block included as seperate files for each analysis, and show partitioning sceme (by codon and/or gene) accordingly. Phylogenies generated from both Mr. Bayes and RaxML analyses for both the mitochondrial and nuclear data sets are presented as well.
DOI: 10.6084/m9.figshare.1323275
title: Dynamic Retrospective Regression for Functional Data

description: Samples of curves, or functional data, usually present phase variability in addition to amplitude variability. Existing functional regression methods do not handle phase variability in an efficient way. In this article we propose a functional regression method that incorporates phase synchronization as an intrinsic part of the model, and then attains better predictive power than ordinary linear regression in a simple and parsimonious way. The finite-sample properties of the estimators are studied by simulation. As an example of application, we analyze neuromotor data arising from a study of human lip movement. This article has supplementary materials online.
DOI: 10.6084/m9.figshare.1324480.v3
title: Phylogeography in Response to Reproductive Strategies and Ecogeographic Isolation in Ant Species on Madagascar: Genus Mystrium (Formicidae: Amblyoponinae)

description: Nexus file from four gene nuclear phylogeny (long-wavelength rhodopsin, 28s, wingless and abdominal-A) of the ant genus Mystrium from Madagascar. Nexus file from 790 bp mitochondrial phylogeny (cytochrome c oxidase I). MrBayes block included as seperate files for each analysis, and show partitioning sceme (by codon and/or gene) accordingly. Phylogenies generated from Mr. Bayes and RaxML analyses for both the mitochondrial and nuclear data sets are presented as well.
DOI: 10.6084/m9.figshare.1325063.v2
title: Gibberellin driven growth in <i>elf3</i> mutants requires PIF4 and PIF5

description: The regulatory connections between the circadian clock and hormone signaling are essential to understand, as these two regulatory processes work together to time growth processes relative to predictable environmental events. Gibberellins (GAs) are phytohormones that control many growth processes throughout all stages of the plant life cycle, including germination and flowering. An increasing number of examples demonstrate that the circadian clock directly influences GA biosynthesis and signaling. EARLY FLOWERING 3 (ELF3) participates in a tripartite transcriptional complex known as the Evening Complex (EC). In this capacity, ELF3 is fundamental to core circadian clock activity, as well as time-of-day specific regulation of genes directly responsible for growth control, namely the <i>PHYTOCHROME INTERACTING FACTOR 4</i> (<i>PIF4</i>) and <i>PIF5</i> genes. Here we show that the GA biosynthesis inhibitor paclobutrazol substantially reduces the long hypocotyl and petiole phenotypes of Arabidopsis <i>elf3</i> mutants. In addition, loss of ELF3 activity causes upregulation of the key GA biosynthesis genes <i>GA20ox1</i> and <i>GA20ox2</i>. Moreover, <i>GA20ox1</i> and <i>GA20ox2</i> expression depends strongly on the redundant activities of <i>PIF4</i> and <i>PIF5</i>. These findings indicate that the defining growth phenotypes of <i>elf3</i> mutants arise from altered GA biosynthesis due to misregulation of <i>PIF4</i> and <i>PIF5</i>. These observations agree with recent work linking increased GA production with the elongated growth phenotypes of the barley <i>elf3</i> mutant. Thus, the role of the EC in regulation of GA biosynthesis and signaling in eudicots is shared with monocots and, therefore, is a highly conserved mechanism for growth control.
DOI: 10.6084/m9.figshare.1323384.v1
title: Supplemental Data for "Multi-locus fossil-calibrated phylogeny of Atheriniformes"

description: Supplemental Data from the Molecular Phylogenetics and Evolution article: Campanella, D., Hughes, L.C., Unmack, P.J., Bloom, D.D., Piller, K.R., and Orti, G. (2015). Multi-locus fossil-calibrated phylogeny of Atheriniformes (Teleostei: Ovalentaria). <em>Molecular Phylogenetics and Evolution</em>.
DOI: 10.6084/m9.figshare.1323275.v1
title: Dynamic Retrospective Regression for Functional Data

description: Samples of curves, or functional data, usually present phase variability in addition to amplitude variability. Existing functional regression methods do not handle phase variability in an efficient way. In this article we propose a functional regression method that incorporates phase synchronization as an intrinsic part of the model, and then attains better predictive power than ordinary linear regression in a simple and parsimonious way. The finite-sample properties of the estimators are studied by simulation. As an example of application, we analyze neuromotor data arising from a study of human lip movement. This article has supplementary materials online.
DOI: 10.6084/m9.figshare.1324480.v2
title: Phylogeography in Response to Reproductive Strategies and Ecogeographic Isolation in Ant Species on Madagascar: Genus Mystrium (Formicidae: Amblyoponinae)

description: Nexus file from four gene nuclear phylogeny (long-wavelength rhodopsin, 28s, wingless and abdominal-A) of the ant genus Mystrium from Madagascar. Nexus file from 790 bp mitochondrial phylogeny (cytochrome c oxidase I). MrBayes block included as seperate files for each analysis, and show partitioning sceme (by codon and/or gene) accordingly. Phylogenies generated from Mr. Bayes and RaxML analyses for both the mitochondrial and nuclear data sets are presented as well.
DOI: 10.6084/m9.figshare.1325063.v3
title: Gibberellin driven growth in <i>elf3</i> mutants requires PIF4 and PIF5

description: The regulatory connections between the circadian clock and hormone signaling are essential to understand, as these two regulatory processes work together to time growth processes relative to predictable environmental events. Gibberellins (GAs) are phytohormones that control many growth processes throughout all stages of the plant life cycle, including germination and flowering. An increasing number of examples demonstrate that the circadian clock directly influences GA biosynthesis and signaling. EARLY FLOWERING 3 (ELF3) participates in a tripartite transcriptional complex known as the Evening Complex (EC). In this capacity, ELF3 is fundamental to core circadian clock activity, as well as time-of-day specific regulation of genes directly responsible for growth control, namely the <i>PHYTOCHROME INTERACTING FACTOR 4</i> (<i>PIF4</i>) and <i>PIF5</i> genes. Here we show that the GA biosynthesis inhibitor paclobutrazol substantially reduces the long hypocotyl and petiole phenotypes of Arabidopsis <i>elf3</i> mutants. In addition, loss of ELF3 activity causes upregulation of the key GA biosynthesis genes <i>GA20ox1</i> and <i>GA20ox2</i>. Moreover, <i>GA20ox1</i> and <i>GA20ox2</i> expression depends strongly on the redundant activities of <i>PIF4</i> and <i>PIF5</i>. These findings indicate that the defining growth phenotypes of <i>elf3</i> mutants arise from altered GA biosynthesis due to misregulation of <i>PIF4</i> and <i>PIF5</i>. These observations agree with recent work linking increased GA production with the elongated growth phenotypes of the barley <i>elf3</i> mutant. Thus, the role of the EC in regulation of GA biosynthesis and signaling in eudicots is shared with monocots and, therefore, is a highly conserved mechanism for growth control.
DOI: 10.6084/m9.figshare.1323273
title: Sequential Exploration of Complex Surfaces Using Minimum Energy Designs

description: A new space-filling design, called minimum energy design (MED), is proposed to explore unknown regions of the design space of particular interest to an experimenter. The key ideas involved in constructing the MED are the visualization of each design point as a charged particle inside a box, and minimization of the total potential energy of these particles. It is shown through theoretical arguments and simulations that with a proper choice of the charge function, the MED can asymptotically generate any arbitrary probability density function. A version of the MED, which adaptively updates the design by “learning” about the unknown response surface sequentially, is proposed and implemented. Two potential applications of MED in simulation of complex probability densities and optimization of complex response surfaces are discussed and demonstrated with examples. This article has supplementary material online.
DOI: 10.6084/m9.figshare.1323274
title: Approximate Model Spaces for Model-Robust Experiment Design

description: Optimal designs depend upon a prespecified model form. A popular and effective model-robust alternative is to design with respect to a set of models instead of just one. However, model spaces associated with experiments of interest are often prohibitively large and so algorithmically generated designs are infeasible. Here, we present a simple method that largely eliminates this problem by choosing a small set of models that approximates the full set and finding designs that are explicitly robust for this small set. We build our procedure on a restricted columnwise-pairwise algorithm, and explore its effectiveness for two model spaces in the literature. For smaller full model spaces, we find that the designs constructed with the new method compare favorably with robust designs that use the full model space, with construction times reduced by orders of magnitude. We also construct designs that heretofore have been unobtainable due to the size of their model spaces. Supplementary material (available online) includes code, designs, and additional results.
DOI: 10.6084/m9.figshare.1323384.v2
title: Supplemental Data for "Multi-locus fossil-calibrated phylogeny of Atheriniformes"

description: Supplemental Data from the Molecular Phylogenetics and Evolution article: Campanella, D., Hughes, L.C., Unmack, P.J., Bloom, D.D., Piller, K.R., and Orti, G. (2015). Multi-locus fossil-calibrated phylogeny of Atheriniformes (Teleostei: Ovalentaria). <em>Molecular Phylogenetics and Evolution</em>.
DOI: 10.6084/m9.figshare.1325063.v4
title: Gibberellin driven growth in <i>elf3</i> mutants requires PIF4 and PIF5

description: The regulatory connections between the circadian clock and hormone signaling are essential to understand, as these two regulatory processes work together to time growth processes relative to predictable environmental events. Gibberellins (GAs) are phytohormones that control many growth processes throughout all stages of the plant life cycle, including germination and flowering. An increasing number of examples demonstrate that the circadian clock directly influences GA biosynthesis and signaling. EARLY FLOWERING 3 (ELF3) participates in a tripartite transcriptional complex known as the Evening Complex (EC). In this capacity, ELF3 is fundamental to core circadian clock activity, as well as time-of-day specific regulation of genes directly responsible for growth control, namely the <i>PHYTOCHROME INTERACTING FACTOR 4</i> (<i>PIF4</i>) and <i>PIF5</i> genes. Here we show that the GA biosynthesis inhibitor paclobutrazol substantially reduces the long hypocotyl and petiole phenotypes of Arabidopsis <i>elf3</i> mutants. In addition, loss of ELF3 activity causes upregulation of the key GA biosynthesis genes <i>GA20ox1</i> and <i>GA20ox2</i>. Moreover, <i>GA20ox1</i> and <i>GA20ox2</i> expression depends strongly on the redundant activities of <i>PIF4</i> and <i>PIF5</i>. These findings indicate that the defining growth phenotypes of <i>elf3</i> mutants arise from altered GA biosynthesis due to misregulation of <i>PIF4</i> and <i>PIF5</i>. These observations agree with recent work linking increased GA production with the elongated growth phenotypes of the barley <i>elf3</i> mutant. Thus, the role of the EC in regulation of GA biosynthesis and signaling in eudicots is shared with monocots and, therefore, is a highly conserved mechanism for growth control.
DOI: 10.6084/m9.figshare.1323274.v2
title: Approximate Model Spaces for Model-Robust Experiment Design

description: Optimal designs depend upon a prespecified model form. A popular and effective model-robust alternative is to design with respect to a set of models instead of just one. However, model spaces associated with experiments of interest are often prohibitively large and so algorithmically generated designs are infeasible. Here, we present a simple method that largely eliminates this problem by choosing a small set of models that approximates the full set and finding designs that are explicitly robust for this small set. We build our procedure on a restricted columnwise-pairwise algorithm, and explore its effectiveness for two model spaces in the literature. For smaller full model spaces, we find that the designs constructed with the new method compare favorably with robust designs that use the full model space, with construction times reduced by orders of magnitude. We also construct designs that heretofore have been unobtainable due to the size of their model spaces. Supplementary material (available online) includes code, designs, and additional results.
DOI: 10.6084/m9.figshare.1325063.v6
title: Gibberellin driven growth in <i>elf3</i> mutants requires PIF4 and PIF5

description: The regulatory connections between the circadian clock and hormone signaling are essential to understand, as these two regulatory processes work together to time growth processes relative to predictable environmental events. Gibberellins (GAs) are phytohormones that control many growth processes throughout all stages of the plant life cycle, including germination and flowering. An increasing number of examples demonstrate that the circadian clock directly influences GA biosynthesis and signaling. EARLY FLOWERING 3 (ELF3) participates in a tripartite transcriptional complex known as the Evening Complex (EC). In this capacity, ELF3 is fundamental to core circadian clock activity, as well as time-of-day specific regulation of genes directly responsible for growth control, namely the <i>PHYTOCHROME INTERACTING FACTOR 4</i> (<i>PIF4</i>) and <i>PIF5</i> genes. Here we show that the GA biosynthesis inhibitor paclobutrazol substantially reduces the long hypocotyl and petiole phenotypes of Arabidopsis <i>elf3</i> mutants. In addition, loss of ELF3 activity causes upregulation of the key GA biosynthesis genes <i>GA20ox1</i> and <i>GA20ox2</i>. Moreover, <i>GA20ox1</i> and <i>GA20ox2</i> expression depends strongly on the redundant activities of <i>PIF4</i> and <i>PIF5</i>. These findings indicate that the defining growth phenotypes of <i>elf3</i> mutants arise from altered GA biosynthesis due to misregulation of <i>PIF4</i> and <i>PIF5</i>. These observations agree with recent work linking increased GA production with the elongated growth phenotypes of the barley <i>elf3</i> mutant. Thus, the role of the EC in regulation of GA biosynthesis and signaling in eudicots is shared with monocots and, therefore, is a highly conserved mechanism for growth control.
DOI: 10.6084/m9.figshare.1323274.v1
title: Approximate Model Spaces for Model-Robust Experiment Design

description: Optimal designs depend upon a prespecified model form. A popular and effective model-robust alternative is to design with respect to a set of models instead of just one. However, model spaces associated with experiments of interest are often prohibitively large and so algorithmically generated designs are infeasible. Here, we present a simple method that largely eliminates this problem by choosing a small set of models that approximates the full set and finding designs that are explicitly robust for this small set. We build our procedure on a restricted columnwise-pairwise algorithm, and explore its effectiveness for two model spaces in the literature. For smaller full model spaces, we find that the designs constructed with the new method compare favorably with robust designs that use the full model space, with construction times reduced by orders of magnitude. We also construct designs that heretofore have been unobtainable due to the size of their model spaces. Supplementary material (available online) includes code, designs, and additional results.
DOI: 10.6084/m9.figshare.1323271
title: Inverse Gaussian Processes With Random Effects and Explanatory Variables for Degradation Data

description: Degradation models are widely used to assess the lifetime information of highly reliable products. This study proposes a degradation model based on an inverse normal-gamma mixture of an inverse Gaussian process. This article presents the properties of the lifetime distribution and parameter estimation using the EM-type algorithm, in addition to providing a simple model-checking procedure to assess the validity of different stochastic processes. Several case applications are performed to demonstrate the advantages of the proposed model with random effects and explanatory variables. Technical details, data, and R code are available online as supplementary materials.
DOI: 10.6084/m9.figshare.1323273.v1
title: Sequential Exploration of Complex Surfaces Using Minimum Energy Designs

description: A new space-filling design, called minimum energy design (MED), is proposed to explore unknown regions of the design space of particular interest to an experimenter. The key ideas involved in constructing the MED are the visualization of each design point as a charged particle inside a box, and minimization of the total potential energy of these particles. It is shown through theoretical arguments and simulations that with a proper choice of the charge function, the MED can asymptotically generate any arbitrary probability density function. A version of the MED, which adaptively updates the design by “learning” about the unknown response surface sequentially, is proposed and implemented. Two potential applications of MED in simulation of complex probability densities and optimization of complex response surfaces are discussed and demonstrated with examples. This article has supplementary material online.