cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5271622.v1
title: Dataset for: Hierarchical role for transcription factors and chromatin structure in genome organization along adipogenesis

description: The three dimensional folding of mammalian genomes is cell-type specific and difficult to alter suggesting that it is an important component of gene regulation. However, given the multitude of chromatin associating factors, the mechanisms driving the co-localization of active chromosomal domains and the role of this organization in regulating the transcription program in adipocytes are not clear. Analysis of genome-wide chromosomal associations revealed cell type-specific spatial clustering of adipogenic genes in 3T3-L1 cells. Time course analysis demonstrated that the adipogenic "hub", sampled by PPARγ and Lpin1, undergoes orchestrated reorganization during adipogenesis. Coupling the dynamics of genome architecture with multiple chromatin datasets indicated that among all the transcription factors tested, RXR is central to genome reorganization at the beginning of adipogenesis. Interestingly, at the end of differentiation, the adipogenic hub was shifted to an H3K27me3 repressive environment in conjunction with attenuation of gene transcription. We propose a stage-specific hierarchy for the activity of transcription factors contributing to the establishment of an adipogenic genome architecture that brings together the adipogenic genetic program. In addition, the repositioning of this network in a H3K27me3-rich environment at the end of differentiation may contribute to the stabilization of gene transcription levels and reduce the developmental plasticity of these specialized cells.
DOI: 10.6084/m9.figshare.5271613.v1
title: Dataset for: G3BP1 interacts directly with the FMDV IRES and negatively regulates translation

description: RNA-protein interactions play a pivotal role in the function of picornavirus internal ribosome entry site (IRES) elements. Here we analysed the impact of Ras GTPase SH3 domain binding protein 1 (G3BP1) in the IRES activity of foot-and-mouth disease virus (FMDV). We found that G3BP1 interacts directly with three distinct sequences of the IRES element using RNA electrophoretic mobility-shift assays. Analysis of the interaction with domain 5 indicated that the G3BP1 binding-site is placed at the single-stranded region although it allows large sequence heterogeneity and the hairpin located upstream of this region enhances retarded complex formation. In addition, G3BP1 interacts directly with the polypyrimidine tract-binding protein (PTB) and the translation initiation factor 4B (eIF4B) through the C-terminal region. Moreover, G3BP1 is cleaved during FMDV infection yielding two fragments, Ct-G3BP1 and Nt-G3BP1. Both fragments inhibit cap- and IRES-dependent translation, but the Ct-G3BP1 fragment shows a stronger effect on IRES-dependent translation. Assembly of complexes with G3BP1 results in a significantly reduced local flexibility of the IRES element, consistent with the negative effect of this protein. Our results highlight the IRES-binding capacity of G3BP1 and illustrate its function as a translation inhibitor.
DOI: 10.6084/m9.figshare.5271577
title: KCAP Results

description: Results about an ontology learning evaluation (precision, recall, f-measure) from a semantic web corpus
DOI: 10.6084/m9.figshare.5271574
title: Supplement “Age of enlightenment: long-term effects of artificial outdoor lighting on bats in churches”. Rydell et al. 2017. from Age of enlightenment: long-term effects of outdoor aesthetic lights on bats in churches

description: Supplement 1. Rydell et al. Excel sheet showing the original data and the analysis used for the study.
DOI: 10.6084/m9.figshare.5271577.v1
title: KCAP Results

description: Results about an ontology learning evaluation (precision, recall, f-measure) from a semantic web corpus
DOI: 10.6084/m9.figshare.5271619.v1
title: Supplementary Material for: Collectin-11 Is an Important Modulator of Retinal Pigment Epithelial Cell Phagocytosis and Cytokine Production

description: In this paper, we report previously unknown roles for collectin-11 (CL-11, a soluble C-type lectin) in modulating the retinal pigment epithelial (RPE) cell functions of phagocytosis and cytokine production. We found that CL-11 and its carbohydrate ligand are expressed in both the murine and human neural retina; these resemble each other in terms of RPE and photoreceptor cells. Functional analysis of murine RPE cells showed that CL-11 facilitates the opsonophagocytosis of photoreceptor outer segments and apoptotic cells, and also upregulates IL-10 production. Mechanistic analysis revealed that calreticulin on the RPE cells is required for CL-11-mediated opsonophagocytosis whereas signal-regulatory protein α and mannosyl residues on the cells are involved in the CL-11-mediated upregulation of IL-10 production. This study is the first to demonstrate the role of CL-11 and the molecular mechanisms involved in modulating RPE cell phagocytosis and cytokine production. It provides a new insight into retinal health and disease and has implications for other phagocytic cells.
DOI: 10.6084/m9.figshare.5271574.v1
title: Supplement “Age of enlightenment: long-term effects of artificial outdoor lighting on bats in churches”. Rydell et al. 2017. from Age of enlightenment: long-term effects of outdoor aesthetic lights on bats in churches

description: Supplement 1. Rydell et al. Excel sheet showing the original data and the analysis used for the study.
DOI: 10.6084/m9.figshare.5271463
title: Chapter_2_Supplementary_tables_SCA 160105.xlsx

description: Supplementary tables for chapter two on house sparrow invasion history<br>
DOI: 10.6084/m9.figshare.5271469
title: Chapter_3_Sup_data_Andrew_et_al_HOSP_170615.xlsx

description: Supplementary data for chapter three on house sparrow body size. <br>
DOI: 10.6084/m9.figshare.5271463.v1
title: Chapter_2_Supplementary_tables_SCA 160105.xlsx

description: Supplementary tables for chapter two on house sparrow invasion history<br>
DOI: 10.6084/m9.figshare.5271469.v1
title: Chapter_3_Sup_data_Andrew_et_al_HOSP_170615.xlsx

description: Supplementary data for chapter three on house sparrow body size. <br>
DOI: 10.6084/m9.figshare.5271445
title: Normalized expression levels of unigenes

description: Gene expression level was estimated by mapping clean reads without rRNA to the clustered assembly using RSEM (ver. 1.3.0), and was normalized by TMM (trimmed mean of M values) method.<br>All unigenes were aligned using BLAST+ (ver. 2.5.0) against the NCBI’s non-redundant nucleotide (nt) database (downloaded on December 27, 2016), COG (clusters of orthologous groups) database (2003 COGs, 2014 update), and the Swissprot database (downloaded on December 15, 2016) with an E-value cutoff of 10<sup>-5</sup>.<br>
DOI: 10.34760/5f4755d384ac8
title: Skeleton 3572 
title: 1
DOI: 10.6084/m9.figshare.5271436
title: The assembled cDNA sequences of Grandidierella japonica

description: Sequences assembled by Trinity and clustered by CD-HIT. A total of 78,572 sequences with an average length of 488 bp.
DOI: 10.6084/m9.figshare.5271436.v2
title: The assembled cDNA sequences of Grandidierella japonica

description: Sequences assembled by Trinity and clustered by CD-HIT. A total of 78,572 sequences with an average length of 488 bp.
DOI: 10.6084/m9.figshare.5271436.v1
title: The assembled sequences

description: Assembled and clustered sequences using Trinity and CD-HIT softwares. A total of 78,572 sequences with an average length of 488 bp.
DOI: 10.6084/m9.figshare.5271046
title: Analysis of core protein clusters identifies candidate variable sites conferring metronidazole resistance in Helicobacter pylori

description: Prokka-annotated draft genomes in GenBank format and alignments of core protein clusters using MAFFT
DOI: 10.6084/m9.figshare.5271001
title: Yuri Kriel - article data: Mode

description: Yuri Kriel - article data: Mode
DOI: 10.6084/m9.figshare.5270992
title: Yuri Kriel - HIIT versus CMIE

description: Data for research article: HIIT vs CMIE
DOI: 10.6084/m9.figshare.5270983
title: Dataset - Solving the Manufacturing Cell Design Problem using the Artificial Bee Colony.

description: Dataset - Solving the Manufacturing Cell Design Problem using the Artificial Bee Colony.
DOI: 10.6084/m9.figshare.5270983.v1
title: Dataset - Solving the Manufacturing Cell Design Problem using the Artificial Bee Colony.

description: Dataset - Solving the Manufacturing Cell Design Problem using the Artificial Bee Colony.
DOI: 10.6084/m9.figshare.5270974
title: Dataset for: A Comprehensive Pipeline for Multi-Resolution Modeling of the Mitral Valve: Validation, Computational Efficiency, and Predictive Capability

description: Multiple studies have demonstrated that the pathological geometries unique to each patient can affect the durability of mitral valve (MV) repairs. While computational modeling of the MV is a promising approach to improve the surgical outcomes, the complex MV geometry precludes use of simplified models. Moreover, the lack of complete in-vivo geometric information presents significant challenges in the development of patient-specific computational models. There is thus a need to determine the level of detail necessary for predictive MV models. To address this issue, we developed a novel pipeline for building attribute-rich computational models of MV with varying fidelity directly from the in-vitro imaging data. The approach combines high-resolution geometric information from loaded and unloaded states to achieve a high level of anatomic detail, followed by mapping and parametric embedding of tissue attributes to build a high resolution, attribute-rich computational models. Subsequent lower resolution models were then developed, and evaluated by comparing the displacements and surface strains to those extracted from the imaging data. We then identified the critical levels of fidelity for building predictive MV models in the dilated and repaired states. We demonstrated that a model with a feature size of ~5 mm and mesh size of ~1 mm was sufficient to predict the overall MV shape, stress, and strain distributions with high accuracy. However, we also noted that more detailed models were found to be needed to simulate microstructural events. We conclude that the developed pipeline enables sufficiently complex models for biomechanical simulations of MV in different states
DOI: 10.6084/m9.figshare.5270974.v1
title: Dataset for: A Comprehensive Pipeline for Multi-Resolution Modeling of the Mitral Valve: Validation, Computational Efficiency, and Predictive Capability

description: Multiple studies have demonstrated that the pathological geometries unique to each patient can affect the durability of mitral valve (MV) repairs. While computational modeling of the MV is a promising approach to improve the surgical outcomes, the complex MV geometry precludes use of simplified models. Moreover, the lack of complete in-vivo geometric information presents significant challenges in the development of patient-specific computational models. There is thus a need to determine the level of detail necessary for predictive MV models. To address this issue, we developed a novel pipeline for building attribute-rich computational models of MV with varying fidelity directly from the in-vitro imaging data. The approach combines high-resolution geometric information from loaded and unloaded states to achieve a high level of anatomic detail, followed by mapping and parametric embedding of tissue attributes to build a high resolution, attribute-rich computational models. Subsequent lower resolution models were then developed, and evaluated by comparing the displacements and surface strains to those extracted from the imaging data. We then identified the critical levels of fidelity for building predictive MV models in the dilated and repaired states. We demonstrated that a model with a feature size of ~5 mm and mesh size of ~1 mm was sufficient to predict the overall MV shape, stress, and strain distributions with high accuracy. However, we also noted that more detailed models were found to be needed to simulate microstructural events. We conclude that the developed pipeline enables sufficiently complex models for biomechanical simulations of MV in different states
DOI: 10.6084/m9.figshare.5270923
title: Sleep Condition Indicator

description: Data of participants' scores on Sleep Condition Indicator, together with descriptive information about the participants - their age & sex. Lower scores on Sleep Condition Indicator indicate poorer sleep quality.
DOI: 10.6084/m9.figshare.5270890
title: Attractiveness ratings

description: The data set containing attractiveness ratings by the participants for tired and neutral stimuli pictures.
DOI: 10.6084/m9.figshare.5270896
title: Trustworthiness ratings

description: The data set containing trustworthiness ratings by the participants for tired and neutral stimuli pictures.
DOI: 10.6084/m9.figshare.12901784
title: Supplementation of rice husk activated charcoal in feed and its effects on growth and histology of the stomach and intestines from giant trevally Caranx ignobilis

description: Data of daily growth rate (DGR), specific growth rate (SGR), absolute growth rate (AGR), feed conversion ratio (FCR), feed efficiency (FE) and survival rate (SR) of Caranx ignobilis
DOI: 10.6084/m9.figshare.5270854
title: Forkhead Box M1 positively regulates UBE2C and protects glioma cells from autophagic death

description: Ubiquitin-conjugating enzyme E2C (UBE2C) is characterized as a crucial molecule in cancer cell growth that plays an essential role in the development of gliomas, but the detailed mechanisms have not been fully elucidated. In this study, we found that Forkhead box transcription factor M1 (FoxM1) overexpression increased UBE2C expression, whereas FoxM1 suppression inhibited UBE2C expression in glioma cells. In addition, high FoxM1/UBE2C expression was significantly correlated with poor prognosis in glioma. We subsequently demonstrated that UBE2C was a direct transcriptional target of FoxM1, and site-directed mutations markedly down-regulated UBE2C promoter activity. Moreover, UBE2C siRNA (si-UBE2C) significantly induced glioma cell autophagy and increased both mCherry-LC3 punctate fluorescence and LC3B-II/LC3-I expression. Notably, the si-UBE2C-induced decrease in cell viability was markedly inhibited by the autophagy inhibitor bafilomycin A1. The silencing of UBE2C resulted in a distinct inhibition of the PI3K-Akt-mTOR pathway, which functions in the negative modulation of autophagy. Collectively, our findings provide clinical and molecular evidence that FoxM1 promotes glioma progression by enhancing UBE2C transcription and that the inhibition of UBE2C partially induces autophagic glioma cell death. Thus, targeting the FoxM1-UBE2C axis has therapeutic potential in the treatment of gliomas.
DOI: 10.6084/m9.figshare.12901784.v1
title: Supplementation of rice husk activated charcoal in feed and its effects on growth and histology of the stomach and intestines from giant trevally Caranx ignobilis

description: Data of daily growth rate (DGR), specific growth rate (SGR), absolute growth rate (AGR), feed conversion ratio (FCR), feed efficiency (FE) and survival rate (SR) of Caranx ignobilis
DOI: 10.6084/m9.figshare.5270770
title: VOI_of_fracture_prediction_methods_final_model.xlsx

description: This is a user-friendly spreadsheet model to calculate the VOI of fracture prediction methods using play-specific geologic and cost parameters. This is part of my MSc thesis at the University of Texas at Austin titled: A Value of Information Analysis of Fracture Prediction Methods.
DOI: 10.6084/m9.figshare.5270854.v1
title: Forkhead Box M1 positively regulates UBE2C and protects glioma cells from autophagic death

description: Ubiquitin-conjugating enzyme E2C (UBE2C) is characterized as a crucial molecule in cancer cell growth that plays an essential role in the development of gliomas, but the detailed mechanisms have not been fully elucidated. In this study, we found that Forkhead box transcription factor M1 (FoxM1) overexpression increased UBE2C expression, whereas FoxM1 suppression inhibited UBE2C expression in glioma cells. In addition, high FoxM1/UBE2C expression was significantly correlated with poor prognosis in glioma. We subsequently demonstrated that UBE2C was a direct transcriptional target of FoxM1, and site-directed mutations markedly down-regulated UBE2C promoter activity. Moreover, UBE2C siRNA (si-UBE2C) significantly induced glioma cell autophagy and increased both mCherry-LC3 punctate fluorescence and LC3B-II/LC3-I expression. Notably, the si-UBE2C-induced decrease in cell viability was markedly inhibited by the autophagy inhibitor bafilomycin A1. The silencing of UBE2C resulted in a distinct inhibition of the PI3K-Akt-mTOR pathway, which functions in the negative modulation of autophagy. Collectively, our findings provide clinical and molecular evidence that FoxM1 promotes glioma progression by enhancing UBE2C transcription and that the inhibition of UBE2C partially induces autophagic glioma cell death. Thus, targeting the FoxM1-UBE2C axis has therapeutic potential in the treatment of gliomas.
DOI: 10.6084/m9.figshare.5270926
title: Transcriptomic characterization of MRI contrast with focus on the T1-w/T2-w ratio in the cerebral cortex

description: Magnetic resonance (MR) images of the brain are of immense clinical and research utility. At the atomic and subatomic levels, the sources of MR signals are well understood. However, we lack a comprehensive understanding of the macromolecular correlates of MR signal contrast. To address this gap, we used genome-wide measurements to correlate gene expression with MR signal intensity across the cerebral cortex in the Allen Human Brain Atlas (AHBA). We focused on the ratio of T1-weighted and T2-weighted intensities (T1-w/T2-w ratio image) which is considered to be a useful proxy for myelin content. As expected, we found enrichment of positive correlations between myelin-associated genes and the ratio image, supporting its use as a myelin marker. Genome-wide, there was an association with protein mass, with genes coding for heavier proteins expressed in regions with high T1-w/T2-w values. Oligodendrocyte gene markers were strongly correlated with the T1-w/T2-w ratio, but this was not driven by myelin-associated genes. Mitochondrial genes have the strongest relationship, showing higher expression in regions with low T1-w/T2-w ratio. This may be due to the pH gradient in mitochondria as genes up-regulated by pH in the brain were also highly correlated with the ratio. While we corroborate associations with myelin and synaptic plasticity, differences in the T1-w/T2-w ratio across the cortex are more strongly linked to molecule size, oligodendrocyte markers, mitochondria, and pH. We evaluate correlations between AHBA transcriptomic measurements and a group averaged T1-w/T2-w ratio image, showing agreement with in-sample results. Expanding our analysis to the whole brain results in strong positive T1-w/T2-w correlations for immune system, inflammatory disease, and microglia marker genes. Genes with negative correlations were enriched for neuron markers and synaptic plasticity genes. Lastly, our findings are similar when performed on T1-w or inverted T2-w intensities alone. These results provide a molecular characterization of MR contrast that will aid interpretation of future MR studies of the brain.<br>
DOI: 10.6084/m9.figshare.5270695
title: Sherlock movie-watching fMRI atlas data

description: Data from 17 subjects watching the first episode of BBC's Sherlock - for more details, see:<br>J. Chen, Y.C. Leong, C.J. Honey, C.H. Yong, K.A. Norman, U. Hasson (2017). Shared memories reveal shared structure in neural activity across individuals. Nature Neuroscience.<br>C. Baldassano, J. Chen, A. Zadbood, J.W. Pillow, U. Hasson, K.A. Norman (2017). Discovering event structure in continuous narrative perception and memory. Neuron.
DOI: 10.6084/m9.figshare.5268649
title: iRF scripts and data

description: This repository contains all scripts and data used in the case studies and simulations of <i>iterative Random Forests to discover predictive and stable high-order interactions</i>.
DOI: 10.6084/m9.figshare.12849959
title: Metformin reduces autoimmune antibody levels in patients with Hashimoto’s thyroiditis: A systematic review and meta-analysis

description: In the past few years, an increasing number of studies have proposed the idea of extending the therapeutic range of metformin from traditional hypoglycaemic to autoimmune diseases, and confirmed in a variety of autoimmune diseases. However, whether metformin can be used to treat Hashimoto’s thyroiditis (HT), which is characterised by thyroid peroxidase antibody (TPOAb) and thyroglobulin antibody (TgAb), is unknown. Therefore, we conducted a systematic review and meta-analysis to evaluate whether metformin can reduce the levels of TPOAb and TgAb in patients with HT or subclinical hypothyroidism (SH), so as to provide a theoretical basis for metformin treatment of these diseases. PubMed, Web Of Science and Embase were searched for observational studies investigating the changes of TPOAb and TgAb in patients with HT after metformin treatment. Two authors extracted data from eligible studies and classified them as HT and subclinical hypothyroidism subgroups. The calculation was then performed by weighted mean difference (WMD) combined with a fixed-effects model analysis or standard mean difference (SMD) with a random-effects model analysis, based on the measurement of the outcome. Metformin significantly reduced TPOAb levels and TgAb levels in patients with HT and SH, especially TPOAb (HT: <i>p</i> <sub>TPOAb</sub> = .009, <i>p</i> <sub>TgAb</sub> = .046; SH: <i>p</i> <sub>TPOAb</sub> = .034, <i>p</i> <sub>TgAb</sub> = .066). In addition, metformin also reduced the levels of thyroid stimulating hormone (TSH), homeostasis model assessment of insulin resistance (HOMA-IR) in patients with HT and SH (HT: <i>p</i> <sub>TSH</sub> = .000 and <i>p</i> <sub>HOMA-IR</sub> = .000; SH: <i>p</i> <sub>TSH</sub> = .000 and <i>p</i> <sub>HOMA-IR</sub> = .000, respectively). Metformin significantly reduces TPOAb level and TgAb level in patients with HT and SH, especially TPOAb. This study is the first to provide a preliminary theoretical basis for the clinical application of metformin in the treatment of HT.