cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3115600
title: Fast-crawling cell types migrate to avoid the direction of periodic substratum stretching

description: To investigate the relationship between mechanical stimuli from substrata and related cell functions, one of the most useful techniques is the application of mechanical stimuli via periodic stretching of elastic substrata. In response to this stimulus, <i>Dictyostelium discoideum</i> cells migrate in a direction perpendicular to the stretching direction. The origins of directional migration, higher migration velocity in the direction perpendicular to the stretching direction or the higher probability of a switch of migration direction to perpendicular to the stretching direction, however, remain unknown. In this study, we applied periodic stretching stimuli to neutrophil-like differentiated HL-60 cells, which migrate perpendicular to the direction of stretch. Detailed analysis of the trajectories of HL-60 cells and <i>Dictyostelium</i> cells obtained in a previous study revealed that the higher probability of a switch of migration direction to that perpendicular to the direction of stretching was the main cause of such directional migration. This directional migration appears to be a strategy adopted by fast-crawling cells in which they do not migrate faster in the direction they want to go, but migrate to avoid a direction they do not want to go.
DOI: 10.6084/m9.figshare.3115600.v1
title: Fast-crawling cell types migrate to avoid the direction of periodic substratum stretching

description: To investigate the relationship between mechanical stimuli from substrata and related cell functions, one of the most useful techniques is the application of mechanical stimuli via periodic stretching of elastic substrata. In response to this stimulus, <i>Dictyostelium discoideum</i> cells migrate in a direction perpendicular to the stretching direction. The origins of directional migration, higher migration velocity in the direction perpendicular to the stretching direction or the higher probability of a switch of migration direction to perpendicular to the stretching direction, however, remain unknown. In this study, we applied periodic stretching stimuli to neutrophil-like differentiated HL-60 cells, which migrate perpendicular to the direction of stretch. Detailed analysis of the trajectories of HL-60 cells and <i>Dictyostelium</i> cells obtained in a previous study revealed that the higher probability of a switch of migration direction to that perpendicular to the direction of stretching was the main cause of such directional migration. This directional migration appears to be a strategy adopted by fast-crawling cells in which they do not migrate faster in the direction they want to go, but migrate to avoid a direction they do not want to go.
DOI: 10.6084/m9.figshare.3115585
title: Emulation of Numerical Models With Over-Specified Basis Functions

description: Mathematical models are frequently used to explore physical systems, but can be computationally expensive to evaluate. In such settings, an emulator is used as a surrogate. In this work, we propose a basis-function approach for computer model emulation. To combine field observations with a collection of runs from the numerical model, we use the proposed emulator within the Kennedy-O’Hagan framework of model calibration. A novel feature of the approach is the use of an over-specified set of basis functions where number of bases used and their inclusion probabilities are treated as unknown quantities. The new approach is found to have smaller predictive uncertainty and computational efficiency than the standard Gaussian process approach to emulation and calibration. Along with several simulation examples focusing on different model characteristics, we also use the method to analyze a dataset on laboratory experiments related to astrophysics.
DOI: 10.6084/m9.figshare.3115579
title: Germline Competent Pluripotent Mouse Stem Cells Generated by Plasmid Vectors

description: We developed nonintegrated methods to reprogram mouse embryonic fibroblast (MEF) cells into induced pluripotent stem cells (iPSCs) using pig pOct4, pSox2, and pc-Myc as well as human hKLF4, hAID, and hTDG that were carried by plasmid vectors. The 4F method employed pOct4, pSox2, pc-Myc, and hKLF4 to derive iPSC clones with naive embryonic stem cell (ESC)-like morphology. These 4F clones expressed endogenous mouse Nanog protein and could generate chimeras. In addition to the four conventional reprogramming factors used in the 4F method, hAID and hTDG were utilized in a 6F method to increase the conversion efficiency of reprogramming by approximately five-fold. One of the 6F plasmid derived iPSC (piPSC) clones was shown to be germline transmission competent.
DOI: 10.6084/m9.figshare.3115579.v1
title: Germline Competent Pluripotent Mouse Stem Cells Generated by Plasmid Vectors

description: We developed nonintegrated methods to reprogram mouse embryonic fibroblast (MEF) cells into induced pluripotent stem cells (iPSCs) using pig pOct4, pSox2, and pc-Myc as well as human hKLF4, hAID, and hTDG that were carried by plasmid vectors. The 4F method employed pOct4, pSox2, pc-Myc, and hKLF4 to derive iPSC clones with naive embryonic stem cell (ESC)-like morphology. These 4F clones expressed endogenous mouse Nanog protein and could generate chimeras. In addition to the four conventional reprogramming factors used in the 4F method, hAID and hTDG were utilized in a 6F method to increase the conversion efficiency of reprogramming by approximately five-fold. One of the 6F plasmid derived iPSC (piPSC) clones was shown to be germline transmission competent.
DOI: 10.6084/m9.figshare.3115585.v2
title: Emulation of Numerical Models With Over-Specified Basis Functions

description: Mathematical models are frequently used to explore physical systems, but can be computationally expensive to evaluate. In such settings, an emulator is used as a surrogate. In this work, we propose a basis-function approach for computer model emulation. To combine field observations with a collection of runs from the numerical model, we use the proposed emulator within the Kennedy-O’Hagan framework of model calibration. A novel feature of the approach is the use of an over-specified set of basis functions where number of bases used and their inclusion probabilities are treated as unknown quantities. The new approach is found to have smaller predictive uncertainty and computational efficiency than the standard Gaussian process approach to emulation and calibration. Along with several simulation examples focusing on different model characteristics, we also use the method to analyze a dataset on laboratory experiments related to astrophysics.
DOI: 10.6084/m9.figshare.3115585.v1
title: Emulation of Numerical Models with Over-specified Basis Functions

description: Mathematical models are frequently used to explore physical systems, but can be computationally expensive to evaluate. In such settings, an emulator is used as a surrogate. In this work, we propose a basis-function approach for computer model emulation. To combine field observations with a collection of runs from the numerical model, we use the proposed emulator within the Kennedy-O’Hagan framework of model calibration. A novel feature of the approach is the use of an over-specified set of basis functions where number of bases used, and their inclusion probabilities, are treated as unknown quantities. The new approach is found to have smaller predictive uncertainty and computational efficiency than the standard Gaussian process approach to emulation and calibration. Along with several simulation examples focusing on different model characteristics, we also use the method to analyze a dataset on laboratory experiments related to astrophysics.
DOI: 10.6084/m9.figshare.3115576
title: Proteome distribution between nucleoplasm and nucleolus and its relation to ribosome biogenesis in <i>Arabidopsis thaliana</i>

description: Ribosome biogenesis is an essential process initiated in the nucleolus. In eukaryotes, multiple ribosome biogenesis factors (RBFs) can be found in the nucleolus, the nucleus and in the cytoplasm. They act in processing, folding and modification of the pre-ribosomal (r)RNAs, incorporation of ribosomal proteins (RPs), export of pre-ribosomal particles to the cytoplasm, and quality control mechanisms. Ribosome biogenesis is best established for <i>Saccharomyces cerevisiae</i>. Plant ortholog assignment to yeast RBFs revealed the absence of about 30% of the yeast RBFs in plants. In turn, few plant specific proteins have been identified by biochemical experiments to act in plant ribosome biogenesis. Nevertheless, a complete inventory of plant RBFs has not been established yet. We analyzed the proteome of the nucleus and nucleolus of <i>Arabidopsis thaliana</i> and the post-translational modifications of these proteins. We identified 1602 proteins in the nucleolar and 2544 proteins in the nuclear fraction with an overlap of 1429 proteins. For a randomly selected set of proteins identified by the proteomic approach we confirmed the localization inferred from the proteomics data by the localization of GFP fusion proteins. We assigned the identified proteins to various complexes and functions and found about 519 plant proteins that have a potential to act as a RBFs, but which have not been experimentally characterized yet. Last, we compared the distribution of RBFs and RPs in the various fractions with the distribution established for yeast.
DOI: 10.6084/m9.figshare.3115576.v2
title: Proteome distribution between nucleoplasm and nucleolus and its relation to ribosome biogenesis in <i>Arabidopsis thaliana</i>

description: Ribosome biogenesis is an essential process initiated in the nucleolus. In eukaryotes, multiple ribosome biogenesis factors (RBFs) can be found in the nucleolus, the nucleus and in the cytoplasm. They act in processing, folding and modification of the pre-ribosomal (r)RNAs, incorporation of ribosomal proteins (RPs), export of pre-ribosomal particles to the cytoplasm, and quality control mechanisms. Ribosome biogenesis is best established for <i>Saccharomyces cerevisiae</i>. Plant ortholog assignment to yeast RBFs revealed the absence of about 30% of the yeast RBFs in plants. In turn, few plant specific proteins have been identified by biochemical experiments to act in plant ribosome biogenesis. Nevertheless, a complete inventory of plant RBFs has not been established yet. We analyzed the proteome of the nucleus and nucleolus of <i>Arabidopsis thaliana</i> and the post-translational modifications of these proteins. We identified 1602 proteins in the nucleolar and 2544 proteins in the nuclear fraction with an overlap of 1429 proteins. For a randomly selected set of proteins identified by the proteomic approach we confirmed the localization inferred from the proteomics data by the localization of GFP fusion proteins. We assigned the identified proteins to various complexes and functions and found about 519 plant proteins that have a potential to act as a RBFs, but which have not been experimentally characterized yet. Last, we compared the distribution of RBFs and RPs in the various fractions with the distribution established for yeast.
DOI: 10.6084/m9.figshare.3115573
title: The presence of LC3B puncta and HMGB1 expression in malignant cells correlate with the immune infiltrate in breast cancer

description: Several cell-intrinsic alterations have poor prognostic features in human breast cancer, as exemplified by the absence of MAP1LC3B/LC3B (microtubule-associated protein 1 light chain 3 β)-positive puncta in the cytoplasm (which indicates reduced autophagic flux) or the loss of nuclear HMGB1 expression by malignant cells. It is well established that breast cancer is under strong immunosurveillance, as reflected by the fact that scarce infiltration of the malignant lesion by CD8<sup>+</sup> cytotoxic T lymphocytes or comparatively dense infiltration by immunosuppressive cell types (such as FOXP3<sup>+</sup> regulatory T cells or CD68<sup>+</sup> tumor-associated macrophages), resulting in low CD8<sup>+</sup>:FOXP3<sup>+</sup> or CD8<sup>+</sup>:CD68<sup>+</sup> ratios, has a negative prognostic impact. Here, we reveal the surprising finding that cell-intrinsic features may influence the composition of the immune infiltrate in human breast cancer. Thus, the absence of LC3B puncta is correlated with intratumoral (but not peritumoral) infiltration by fewer CD8<sup>+</sup> cells and more FOXP3<sup>+</sup> or CD68<sup>+</sup> cells, resulting in a major drop in the CD8<sup>+</sup>:FOXP3<sup>+</sup> or CD8<sup>+</sup>:CD68<sup>+</sup> ratios. Moreover, absence of HMGB1 expression in nuclei correlated with a general drop in all immune effectors, in particular FOXP3<sup>+</sup> and CD68<sup>+</sup> cells, both within the tumor and close to it. Combined analysis of LC3B puncta and HMGB1 expression allowed for improved stratification of patients with respect to the characteristics of their immune infiltrate as well as overall and metastasis-free survival. It can be speculated that blocked autophagy in, or HMGB1 loss from, cancer cells may favor tumor progression due to their negative impact on anticancer immunosurveillance.
DOI: 10.6084/m9.figshare.3115576.v1
title: Proteome distribution between nucleoplasm and nucleolus and its relation to ribosome biogenesis in <i>A. thaliana</i>

description: Ribosome biogenesis is an essential process initiated in the nucleolus. In eukaryotes, multiple ribosome biogenesis factors (RBFs) can be found in the nucleolus, the nucleus and in the cytoplasm. They act in processing, folding and modification of the pre-ribosomal (r)RNAs, incorporation of ribosomal proteins (RPs), export of pre-ribosomal particles to the cytoplasm, and quality control mechanisms. Ribosome biogenesis is best established for <i>Saccharomyces cerevisiae</i>. Plant orthologue assignment to yeast RBFs revealed the absence of about 30% of the yeast RBFs in plants. In turn, few plant specific proteins have been identified by biochemical experiments to act in plant ribosome biogenesis. Nevertheless, a complete inventory of plant RBFs has not been established yet. We analysed the proteome of the nucleus and nucleolus of <i>Arabidopsis thaliana</i> and the post-translational modifications of these proteins. We identified 1602 proteins in the nucleolar and 2544 proteins in the nuclear fraction with an overlap of 1429 proteins. For a randomly selected set of proteins identified by the proteomic approach we confirmed the localization inferred from the proteomics data by the localization of GFP fusion proteins. We assigned the identified proteins to various complexes and functions and found about 519 plant proteins that have a potential to act as a RBFs, but which have not been experimentally characterized yet. Last, we compared the distribution of RBFs and RPs in the various fractions with the distribution established for yeast.
DOI: 10.6084/m9.figshare.3115552
title: Hong_figshare

description: Additional table:The compositional variation of the Formula Diet fed to the experimental mice (Table 1), Differentially expressed genes by effect of RS, DJ, and DJ526 (Table 2), The most highly significant up-regulated and down-regulated pathways in the livers of mice on RS, DJ and DJ526 towards those on Ctrl groups (Table 3)Excel file: Globally normalized data (Fold change raw data), Z transformed data (Z-ratio raw data), and GSEA results
DOI: 10.6084/m9.figshare.3115573.v2
title: The presence of LC3B puncta and HMGB1 expression in malignant cells correlate with the immune infiltrate in breast cancer

description: Several cell-intrinsic alterations have poor prognostic features in human breast cancer, as exemplified by the absence of MAP1LC3B/LC3B (microtubule-associated protein 1 light chain 3 β)-positive puncta in the cytoplasm (which indicates reduced autophagic flux) or the loss of nuclear HMGB1 expression by malignant cells. It is well established that breast cancer is under strong immunosurveillance, as reflected by the fact that scarce infiltration of the malignant lesion by CD8<sup>+</sup> cytotoxic T lymphocytes or comparatively dense infiltration by immunosuppressive cell types (such as FOXP3<sup>+</sup> regulatory T cells or CD68<sup>+</sup> tumor-associated macrophages), resulting in low CD8<sup>+</sup>:FOXP3<sup>+</sup> or CD8<sup>+</sup>:CD68<sup>+</sup> ratios, has a negative prognostic impact. Here, we reveal the surprising finding that cell-intrinsic features may influence the composition of the immune infiltrate in human breast cancer. Thus, the absence of LC3B puncta is correlated with intratumoral (but not peritumoral) infiltration by fewer CD8<sup>+</sup> cells and more FOXP3<sup>+</sup> or CD68<sup>+</sup> cells, resulting in a major drop in the CD8<sup>+</sup>:FOXP3<sup>+</sup> or CD8<sup>+</sup>:CD68<sup>+</sup> ratios. Moreover, absence of HMGB1 expression in nuclei correlated with a general drop in all immune effectors, in particular FOXP3<sup>+</sup> and CD68<sup>+</sup> cells, both within the tumor and close to it. Combined analysis of LC3B puncta and HMGB1 expression allowed for improved stratification of patients with respect to the characteristics of their immune infiltrate as well as overall and metastasis-free survival. It can be speculated that blocked autophagy in, or HMGB1 loss from, cancer cells may favor tumor progression due to their negative impact on anticancer immunosurveillance.
DOI: 10.6084/m9.figshare.3115546
title: Additional Table 1-3.docx

description: The compositional variation of the Formula Diet fed to the experimental mice (Table 1), Differentially expressed genes by effect of RS, DJ, and DJ526 (Table 2), The most highly significant up-regulated and down-regulated pathways in the livers of mice on RS, DJ and DJ526 towards those on Ctrl groups (Table 3)
DOI: 10.6084/m9.figshare.3115531
title: Phylogenetic analysis of the diatom genus Rhoicosphenia Supplemental phylogenetic trees

description: Supplemental phylogenetic trees from the paper "Historical and Current Perspectives on the Systematics of the ‘Enigmatic’ Diatom Genus <i>Rhoicosphenia</i> (Bacillariophyta), with Single and Multi-Molecular Marker and Morphological Analyses and Discussion on the Monophyly of ‘Monoraphid’ Diatoms" Thomas et al. 2016 PLOS ONE. DOI: 10.1371/journal.pone.0152797<br>
DOI: 10.6084/m9.figshare.3115546.v1
title: Additional Table 1-3.docx

description: The compositional variation of the Formula Diet fed to the experimental mice (Table 1), Differentially expressed genes by effect of RS, DJ, and DJ526 (Table 2), The most highly significant up-regulated and down-regulated pathways in the livers of mice on RS, DJ and DJ526 towards those on Ctrl groups (Table 3)
DOI: 10.6084/m9.figshare.3115522
title: Phylogenetic analysis of the diatom genus Rhoicosphenia Alignments

description: Alignments from the paper "Historical and Current Perspectives on the Systematics of the ‘Enigmatic’ Diatom Genus <i>Rhoicosphenia</i> (Bacillariophyta), with Single and Multi-Molecular Marker and Morphological Analyses and Discussion on the Monophyly of ‘Monoraphid’ Diatoms" Thomas et al. PLOS ONE. DOI: 10.1371/journal.pone.0152797
DOI: 10.6084/m9.figshare.3115531.v1
title: Phylogenetic analysis of the diatom genus Rhoicosphenia Supplemental phylogenetic trees

description: Supplemental phylogenetic trees from the paper "Historical and Current Perspectives on the Systematics of the ‘Enigmatic’ Diatom Genus <i>Rhoicosphenia</i> (Bacillariophyta), with Single and Multi-Molecular Marker and Morphological Analyses and Discussion on the Monophyly of ‘Monoraphid’ Diatoms" Thomas et al. 2016 PLOS ONE. DOI: 10.1371/journal.pone.0152797<br>
DOI: 10.6084/m9.figshare.3115522.v2
title: Phylogenetic analysis of the diatom genus Rhoicosphenia Alignments

description: Alignments from the paper "Historical and Current Perspectives on the Systematics of the ‘Enigmatic’ Diatom Genus <i>Rhoicosphenia</i> (Bacillariophyta), with Single and Multi-Molecular Marker and Morphological Analyses and Discussion on the Monophyly of ‘Monoraphid’ Diatoms" Thomas et al. PLOS ONE. DOI: 10.1371/journal.pone.0152797
DOI: 10.6084/m9.figshare.3115522.v1
title: Phylogenetic analysis of the diatom genus Rhoicosphenia Alignments

description: Alignments from the paper "Historical and Current Perspectives on the Systematics of the ‘Enigmatic’ Diatom Genus <i>Rhoicosphenia</i> (Bacillariophyta), with Single and Multi-Molecular Marker and Morphological Analyses and Discussion on the Monophyly of ‘Monoraphid’ Diatoms" Thomas et al. (in revision) PLOS ONE<br>
DOI: 10.6084/m9.figshare.3115552.v1
title: New draft item

description: Additional table:The compositional variation of the Formula Diet fed to the experimental mice (Table 1), Differentially expressed genes by effect of RS, DJ, and DJ526 (Table 2), The most highly significant up-regulated and down-regulated pathways in the livers of mice on RS, DJ and DJ526 towards those on Ctrl groups (Table 3)Excel file: Globally normalized data (Fold change raw data), Z transformed data (Z-ratio raw data), and GSEA results
DOI: 10.6084/m9.figshare.3115552.v3
title: Hong_figshare

description: Additional table:The compositional variation of the Formula Diet fed to the experimental mice (Table 1), Differentially expressed genes by effect of RS, DJ, and DJ526 (Table 2), The most highly significant up-regulated and down-regulated pathways in the livers of mice on RS, DJ and DJ526 towards those on Ctrl groups (Table 3)Excel file: Globally normalized data (Fold change raw data), Z transformed data (Z-ratio raw data), and GSEA results
DOI: 10.6084/m9.figshare.3115486
title: supp1.doc

description: Table S1 Changes in the expression levels of genes induced by sevoflurane
DOI: 10.6084/m9.figshare.3115552.v2
title: Hong_figshare

description: Additional table:The compositional variation of the Formula Diet fed to the experimental mice (Table 1), Differentially expressed genes by effect of RS, DJ, and DJ526 (Table 2), The most highly significant up-regulated and down-regulated pathways in the livers of mice on RS, DJ and DJ526 towards those on Ctrl groups (Table 3)Excel file: Globally normalized data (Fold change raw data), Z transformed data (Z-ratio raw data), and GSEA results
DOI: 10.6084/m9.figshare.3115483
title: 1.pdf

description: Changes in prevalence of periodontal disease from 2002 to 2013.
DOI: 10.6084/m9.figshare.3115486.v1
title: supp1.doc

description: Table S1 Changes in the expression levels of genes induced by sevoflurane
DOI: 10.6084/m9.figshare.3115483.v1
title: 1.pdf

description: Changes in prevalence of periodontal disease from 2002 to 2013.
DOI: 10.6084/m9.figshare.3115408
title: The effect of noseband tightening on horses' behaviour, eye temperature and cardiac responses

description: The effect of noseband tightening on horses' behaviour, eye temperature and cardiac responses
DOI: 10.6084/m9.figshare.3115465
title: Stauffer_Olsen_B_tricaudatus_alignment.nex

description: Alignment of the Baetis tricaudatus COI sequences I generated.
DOI: 10.6084/m9.figshare.3115336
title: Chapter 11 Data File

description: Data for Chapter 11 (n-level SEM).
DOI: 10.6084/m9.figshare.3115465.v1
title: Stauffer_Olsen_B_tricaudatus_alignment.nex

description: Alignment of the Baetis tricaudatus COI sequences I generated.
DOI: 10.6084/m9.figshare.3115303
title: Chapter 7 Data File

description: Data File for Chapter 7 (Item Response Theory)
DOI: 10.6084/m9.figshare.3115267
title: Chapter 5 Data File

description: Chapter 5 data (modeling dichotomous outcomes)
DOI: 10.6084/m9.figshare.3115471.v1
title: 16eao_first_announcement.pdf

description: test
DOI: 10.6084/m9.figshare.3115264
title: Chapter 4 Data File

description: Chapter 4 data (Multilevel)
DOI: 10.6084/m9.figshare.3115264.v1
title: Chapter 4 Data File

description: Chapter 4 data (Multilevel)
DOI: 10.6084/m9.figshare.3115303.v1
title: Chapter 7 Data File

description: Data File for Chapter 7 (Item Response Theory)
DOI: 10.6084/m9.figshare.3115252
title: Chapter 1 Data File

description: This is the data file associated with Chapter 1 (Quantile Regression)