cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6571319
title: Supplementary Material for: Rapid Electrical Stimulation Increased Cardiac Apoptosis Through Disturbance of Calcium Homeostasis and Mitochondrial Dysfunction in Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes

description: <b><i>Background/Aims:</i></b> Heart failure induced by tachycardia, the most common arrhythmia, is frequently observed in clinical practice. This study was designed to investigate the underlying mechanisms. <b><i>Methods:</i></b> Rapid electrical stimulation (RES) at a frequency of 3 Hz was applied on human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) for 7 days, with 8 h/day and 24 h/day set to represent short-term and long-term tachycardia, respectively. Age-matched hiPSC-CMs without electrical stimulation or with slow electrical stimulation (1 Hz) were set as no electrical stimulation (NES) control or low-frequency electrical stimulation (LES) control. Following stimulation, JC-1 staining flow cytometry analysis was performed to examine mitochondrial conditions. Apoptosis in hiPSC-CMs was evaluated using Hoechst staining and Annexin V/propidium iodide (AV/PI) staining flow cytometry analysis. Calcium transients and L-type calcium currents were recorded to evaluate calcium homeostasis. Western blotting and qPCR were performed to evaluate the protein and mRNA expression levels of apoptosis-related genes and calcium homeostasis-regulated genes. <b><i>Results:</i></b> Compared to the controls, hiPSC-CMs following RES presented mitochondrial dysfunction and an increased apoptotic percentage. Amplitudes of calcium transients and L-type calcium currents were significantly decreased in hiPSC-CMs with RES. Molecular analysis demonstrated upregulated expression of Caspase3 and increased Bax/Bcl-2 ratio. Genes related to calcium re-sequence were downregulated, while phosphorylated Ca<sup>2+</sup>/calmodulin-dependent protein kinase II (CaMKII) was significantly upregulated following RES. There was no significant difference between the NES control and LES control groups in these aspects. Inhibition of CaMKII with 1 µM KN93 partly reversed these adverse effects of RES. <b><i>Conclusion:</i></b> RES on hiPSC-CMs disturbed calcium homeostasis, which led to mitochondrial stress, promoted cell apoptosis and caused electrophysiological remodeling in a time-dependent manner. CaMKII played a central role in the damages induced by RES, pharmacological inhibition of CaMKII activity partly reversed the adverse effects of RES on both structural and electrophysiological properties of cells.
DOI: 10.6084/m9.figshare.6571304
title: Supplementary Material for: RA190, a Proteasome Subunit ADRM1 Inhibitor, Suppresses Intrahepatic Cholangiocarcinoma by Inducing NF-KB-Mediated Cell Apoptosis

description: <b><i>Background/Aims:</i></b> Effective drug treatment for intrahepatic cholangiocarcinoma (ICC) is currently lacking. Therefore, there is an urgent need for new targets and new drugs that can prolong patient survival. Recently targeting the ubiquitin proteasome pathway has become an attractive anti-cancer strategy. In this study, we aimed to evaluate the therapeutic effect of and identify the potential mechanisms involved in targeting the proteasome subunit ADRM1 for ICC. <b><i>Methods:</i></b> The expression of ADRM1 and its prognostic value in ICC was analyzed using GEO and TCGA datasets, tumor tissues, and tumor tissue arrays. The effects of RA190 on the proliferation and survival of both established ICC cell lines and primary ICC cells were examined <i>in vitro</i>. Annexin V/propidium iodide staining, western blotting and immunohistochemical staining were performed. The <i>in vivo</i> anti-tumor effect of RA190 on ICC was validated in subcutaneous xenograft and patient-derived xenograft (PDX) models. <b><i>Results:</i></b> ADRM1 levels were significantly higher in ICC tissues than in normal bile duct tissues. ICC patients with high ADRM1 levels had worse overall survival (hazard ratio [HR] = 2.383, 95% confidence interval [CI] =1.357 to 4.188) and recurrence-free survival (HR = 1.710, 95% CI =1.045 to 2.796). ADRM1 knockdown significantly inhibited ICC growth <i>in vitro</i> and <i>in vivo</i>. The specific inhibitor RA190 targeting ADRM1 suppressed proliferation and reduced cell vitality of ICC cell lines and primary ICC cells significantly <i>in vitro</i>. Furthermore, RA190 significantly inhibited the proteasome by inactivating ADRM1, and the consequent accumulation of ADRM1 substrates decreased the activating levels of NF-κB to aggravate cell apoptosis. The therapeutic benefits of RA190 treatment were further demonstrated in both subcutaneous implantation and PDX models. <b><i>Conclusions:</i></b> Our findings indicate that up-regulated ADRM1 was involved in ICC progression and suggest the potential clinical application of ADRM1 inhibitors (e.g., RA190 and KDT-11) for ICC treatment.
DOI: 10.6084/m9.figshare.6570941
title: Supplementary Material for: Associations of Pulmonary Fibrosis with Peripheral Blood Th1/Th2 Cell Imbalance and EBF3 Gene Methylation in Uygur Pigeon Breeder’s Lung Patients

description: <b><i>Background/Aims</i></b> Pigeon breeder’s lung (PBL) results from Th1/Th2 cell imbalance. B cells inhibit the immune activity of Th1, and EBF3 is a key B cell factor. This study explored the relationship between EBF3 and Th1/Th2 imbalance in chronic PBL cases complicated with pulmonary fibrosis (PF). <b><i>Methods</i></b> Twenty Uygur PBL+PF patients, 20 pigeon breeders without PBL or PF, and 20 healthy individuals without pigeon breeding history constituted the patient I, negative control, and normal control groups, respectively. Peripheral blood specimens and case backgrounds were collected between June 2016 and March 2017. EBF3 gene methylation was analyzed by matrix assisted laser desorption ionization-time of flight mass spectrometry. To compare different mechanisms of PF progression in PBL, samples from 20 Uygur PBL patients without PF (at acute and sub-acute stages) were collected between October 2017 and February 2018, constituting the patient II group. EBF3 mRNA expression was evaluated by real-time polymerase chain reaction. IFN-γ, IL-4 and IL-10 expression and Th1/Th2 imbalance in PBL were evaluated by enzyme-linked immunosorbent assay and flow cytometry. <b><i>Results</i></b> CpG-2 and general methylation rates in the patient I group were lower than those in the control groups (P˂0.017). The level of EBF3 mRNA expression in the patient I group was significantly higher than that in any other group. Compared with the control groups, the patient I group showed a significantly higher level of IL-4, whereas the patient II group showed a significantly lower level. IL-10 was also expressed more highly in the patient I group than in any other group (P&lt; 0.01). Flow cytometry showed INF-γ dominance (Th1 cytokine) in PBL at the acute/sub-acute stage and IL-4 dominance (Th2 cytokine) at the chronic stage after PF occurred. The general methylation rate was negatively correlated with the mRNA level, with the latter being positively correlated with the IL-10 level and number of pigeons bred in the past 3 months. IL-4 expression was negatively correlated with INF-γ but positively correlated with PF area and duration of pigeon breeding history. <b><i>Conclusions</i></b> After PF occurs in chronic PBL, the inflammation type changes from Th1 dominance to Th2 dominance. During PBL development, IL-10 increases before IL-4 does, which may be associated with EBF3 hypomethylation and the involvement of B lymphocytes.
DOI: 10.6084/m9.figshare.6570926
title: Normative data for the Digit Symbol Substitution Test in a population-based sample aged 65–79 years: Results from the German Health Interview and Examination Survey for Adults (DEGS1)

description: <b>Objective:</b> To provide normative data for the Digit Symbol Substitution Test (DSST) of the Wechsler Adult Intelligence Scale, 3rd edition (WAIS-III) in a population-based sample of community-dwelling older adults in Germany according to age, sex, and level of education. <b>Method:</b> The sample comprised 1385 participants aged 65–79 years from the nationwide representative ‘German Health Interview and Examination Survey for Adults’ (DEGS1, 2008–2011). Participants with known cognitive impairment or dementia, other medical conditions affecting cognition, or currently using psychotropic drugs were excluded. Educational level was categorized as low, medium, and high according to the Comparative Analyses of Social Mobility in Industrial Nations (CASMIN) scale. Normative values for the DSST according to age, sex, and level of education were estimated by multiple linear regression using population weights. <b>Results:</b> Mean age was 71.1 years, 48.6% were men and low, medium, and high education levels were 62.8, 24.6, and 12.6%, respectively. Younger age, female sex, and higher level of education were significantly associated with higher DSST scores. Regression-based normative data for the DSST is provided according to age, sex, and level of education. In addition, a normative score calculator is provided. <b>Conclusions:</b> These are the first age-, sex-, and education-specific normative data for older individuals for the DSST of the WAIS-III in Germany. These normative data will enable future population-level analyses on impaired cognitive function according to DSST.
DOI: 10.6084/m9.figshare.6570704
title: Symbiodinium morphology data and statistics

description: Coral bleaching is the dysfunction of the coral-algal endosymbiosis and is characterized as a loss of <i>Symbiodinium</i>cells from host tissues or the loss of photosynthetic pigments. Symbiosis breakdown occurs as a result elevated temperature beyond the meta-organism’s thermal threshold. Despite the impacts of coral bleaching we have not resolved the tipping points and the mechanisms underlying bleaching responses. This study characterized the cellular responses of <i>Symbiodinium</i>sp. (C3) within <i>Acropora aspera</i>exposed to thermal stress. Thermally stressed corals experienced significant declines in <i>Symbiodinium</i>density and dark-adapted yield following exposure to bleaching at 34 °C for four consecutive days, equating to an ecological thermal stress of 4-degree heating weeks (DHW). However large impacts on <i>Symbiodinium</i>morphology and cell division were seen following exposure to temperatures between 2-3 °C (2 DHW) below the bleaching threshold, and by 4 DHW over 90% of <i>Symbiodinium</i>were degraded. While these sub-bleaching levels will not trigger bleaching alerts it is vital that we begin to quantify how these significant sub-bleaching levels will impact the fitness of <i>Symbiodinium</i>populations, their coral hosts and subsequently reefs worldwide.
DOI: 10.6084/m9.figshare.6570572
title: Meta data

description: List of molecular descriptors and odorants used in the paper.
DOI: 10.6084/m9.figshare.6570572.v1
title: Meta data

description: List of molecular descriptors and odorants used in the paper.
DOI: 10.6084/m9.figshare.6570566
title: Predicted glomerular responses

description: Predicted glomerular responses using the proposed neural network model. Values in each cell represents the standardized glomerular activity (z-score). Each cell is assigned to the 2D grid with the value "1" shown in the modPos file in the order from upper-left to lower-right.
DOI: 10.6084/m9.figshare.6570563
title: Additional file 9: of The evolution of a series of behavioral traits is associated with autism-risk genes in cavefish

description: ASD genes under diversification/positive selection and under QTL intervals. (XLSX 71 kb)
DOI: 10.6084/m9.figshare.6570563.v1
title: Additional file 9: of The evolution of a series of behavioral traits is associated with autism-risk genes in cavefish

description: ASD genes under diversification/positive selection and under QTL intervals. (XLSX 71 kb)
DOI: 10.6084/m9.figshare.6570557
title: Additional file 7: of The evolution of a series of behavioral traits is associated with autism-risk genes in cavefish

description: Divergence outliers within the SFARI ASD-risk genes between cavefish and surface fish based on three metrics (i.e. top 5% for FST, top 20% for DXY, and Pâ
DOI: 10.6084/m9.figshare.6570557.v1
title: Additional file 7: of The evolution of a series of behavioral traits is associated with autism-risk genes in cavefish

description: Divergence outliers within the SFARI ASD-risk genes between cavefish and surface fish based on three metrics (i.e. top 5% for FST, top 20% for DXY, and Pâ
DOI: 10.6084/m9.figshare.6570548
title: Additional file 4: of The evolution of a series of behavioral traits is associated with autism-risk genes in cavefish

description: The direction of gene regulation (up or down) seen in A. mexicanus with that seen in ASD patients versus controls. (XLSX 559 kb)
DOI: 10.6084/m9.figshare.6570548.v1
title: Additional file 4: of The evolution of a series of behavioral traits is associated with autism-risk genes in cavefish

description: The direction of gene regulation (up or down) seen in A. mexicanus with that seen in ASD patients versus controls. (XLSX 559 kb)
DOI: 10.6084/m9.figshare.6570524
title: Additional file 1: of The evolution of a series of behavioral traits is associated with autism-risk genes in cavefish

description: Gene expression changes in A. mexicanus orthologs of SFARI genes (Category 1 to 4 and Category S in in March 2017). (XLSX 217 kb)
DOI: 10.6084/m9.figshare.6570524.v1
title: Additional file 1: of The evolution of a series of behavioral traits is associated with autism-risk genes in cavefish

description: Gene expression changes in A. mexicanus orthologs of SFARI genes (Category 1 to 4 and Category S in in March 2017). (XLSX 217 kb)
DOI: 10.6084/m9.figshare.6570482
title: Mol files

description: Mol files to compute molecular descriptors by Dragon (Kode srl, Italy)
DOI: 10.6084/m9.figshare.6566855
title: Theoretical ribosomal protein mass fingerprint of Hafnia alvei

description: This is a dataset containing the theoretical molecular mass of various ribosomal proteins in the large and small ribosome subunit of <i>Hafnia alvei</i>.<br><br>
DOI: 10.6084/m9.figshare.6566855.v1
title: Theoretical ribosomal protein mass fingerprint of Hafnia alvei

description: This is a dataset containing the theoretical molecular mass of various ribosomal proteins in the large and small ribosome subunit of <i>Hafnia alvei</i>.<br><br>
DOI: 10.6084/m9.figshare.6566651
title: Theoretical ribosomal protein mass fingerprint of Escherichia coli

description: This is a dataset containing the theoretical molecular mass of various ribosomal proteins in the large and small ribosome subunit of <i>Escherichia coli.</i><br><br>
DOI: 10.6084/m9.figshare.6566651.v1
title: Theoretical ribosomal protein mass fingerprint of Escherichia coli

description: This is a dataset containing the theoretical molecular mass of various ribosomal proteins in the large and small ribosome subunit of <i>Escherichia coli.</i><br><br>
DOI: 10.6084/m9.figshare.6566177
title: Theoretical ribosomal protein mass fingerprint of Enterobacter hormaechei

description: This is a dataset containing the theoretical molecular mass of various ribosomal proteins in the large and small ribosome subunit of <i>Enterobacter hormaechei.</i><br><br>
DOI: 10.6084/m9.figshare.6566177.v1
title: Theoretical ribosomal protein mass fingerprint of Enterobacter hormaechei

description: This is a dataset containing the theoretical molecular mass of various ribosomal proteins in the large and small ribosome subunit of <i>Enterobacter hormaechei.</i><br><br>
DOI: 10.6084/m9.figshare.6561914
title: Evaluation Criteria of ERP Systems

description: Presenting a diversity of criteria that can be used to guide the selection of ERP systems. The criteria covers seven main groups including: i) Cost-Related, ii) Implementation Time, iii) Vendor-Related, iv) User-Related, v) Technology-Related, vi) System-Related, and vii)Organizational Requirements. The paper below can be kindly cited in case of using the criteria. Hegazy, A. E. F. A., ElBattah, M., & Kadry, M. (2012, October). Fuzzy-Based Framework for Enterprise Resource Planning System Selection. In Proceedings of the <i>22nd International Conference on Computer Theory and Applications (ICCTA), </i>(pp. 139-147). IEEE. <br>
DOI: 10.6084/m9.figshare.6561914.v2
title: Evaluation Criteria of ERP Systems

description: Presenting a diversity of criteria that can be used to guide the selection of ERP systems. The criteria covers seven main groups including: i) Cost-Related, ii) Implementation Time, iii) Vendor-Related, iv) User-Related, v) Technology-Related, vi) System-Related, and vii)Organizational Requirements. The paper below can be kindly cited in case of using the criteria. Hegazy, A. E. F. A., ElBattah, M., & Kadry, M. (2012, October). Fuzzy-Based Framework for Enterprise Resource Planning System Selection. In Proceedings of the <i>22nd International Conference on Computer Theory and Applications (ICCTA), </i>(pp. 139-147). IEEE. <br>
DOI: 10.6084/m9.figshare.6561914.v1
title: Evaluation Criteria of ERP Systems

description: Presenting a diversity of criteria that can be used to guide the selection of ERP systems. The criteria covers seven main groups including: i) Cost-Related, ii) Implementation Time, iii) Vendor-Related, iv) User-Related, v) Technology-Related, vi) System-Related, and vii)Organizational Requirements. The paper below can be kindly cited in case of using the criteria. Hegazy, A. E. F. A., ElBattah, M., & Kadry, M. (2012, October). Fuzzy-Based Framework for Enterprise Resource Planning System Selection. In Proceedings of the <i>22nd International Conference on Computer Theory and Applications (ICCTA), </i>(pp. 139-147). IEEE. <br>
DOI: 10.6084/m9.figshare.6561905
title: Evolution of pre-service teachers’ attitudes towards learning science during an introductory science unit

description: Primary teachers, despite their critical role in fostering student interest in science, lack confidence and have negative attitudes towards teaching science, with this trend starting during initial teacher education. Though research on attitudes towards teaching science is well established, less is known about attitudes towards learning science. In order to advance our understanding in this area, this study mapped the entry and evolution of attitudinal profiles towards learning science of 108 primary education pre-service teachers undertaking a first-year science unit. Participants completed an online survey tapping on self-determination, grade motivation, self-efficacy, difficulty, interest, anxiety and enjoyment in science before the commencement of the unit (T1) and at the end of it (T2). Clustering methods were used to group participants into homogenous attitudinal profiles at both points in time. Subsequently, daughter profile analysis was used to examine qualitative changes in final profiles respective to entry. Four distinct attitudinal profiles were identified with 47% of the participants exhibiting the least favourable profiles at the start of the science unit. Migration (T1 to T2) was more prevalent from the least to the most favourable profiles, however, it did occur in the opposite direction. Findings revealed that, though pre-service teachers increased their confidence in their ability to learn science, their self-determination decreased in all but one of the eight resulting daughter profiles.
DOI: 10.6084/m9.figshare.6561890
title: Yrr2_haplotype_diversity.tar.gz

description: Haplotype diversity at the <i>Yrr2</i> locus with a range of accessions of <i>Brachypodium distachyon</i> based on the reference genome of accession Bd21.<br>
DOI: 10.6084/m9.figshare.6561890.v1
title: Yrr2_haplotype_diversity.tar.gz

description: Haplotype diversity at the <i>Yrr2</i> locus with a range of accessions of <i>Brachypodium distachyon</i> based on the reference genome of accession Bd21.<br>
DOI: 10.6084/m9.figshare.6561887
title: Yrr1_haplotype_diversity.tar.gz

description: Haplotype diversity at the <i>Yrr1</i> locus with a range of accessions of <i>Brachypodium distachyon</i> based on the reference genome of accession Bd21.<br>
DOI: 10.6084/m9.figshare.6561887.v1
title: Yrr1_haplotype_diversity.tar.gz

description: Haplotype diversity at the <i>Yrr1</i> locus with a range of accessions of <i>Brachypodium distachyon</i> based on the reference genome of accession Bd21.<br>
DOI: 10.6084/m9.figshare.6561860
title: Dataset Moulis Cort.xlsx

description: Data from the following article: <br><br> title: Do wild-caught urban house sparrows show desensitized stress responses to a novel stressor?<br>authors: Noraine Salleh Hudin, Aimeric Teyssier, Johan Aerts, Graham D. Fairhurst, Diederik Strubbe, Joël White, Liesbeth De Neve, Luc Lens<br>Published in Biology Open 2018 7: bio031849 doi: 10.1242/bio.031849 Published 15 June 2018 <br>
DOI: 10.6084/m9.figshare.6561860.v1
title: Dataset Moulis Cort.xlsx

description: Data from the following article: <br><br> title: Do wild-caught urban house sparrows show desensitized stress responses to a novel stressor?<br>authors: Noraine Salleh Hudin, Aimeric Teyssier, Johan Aerts, Graham D. Fairhurst, Diederik Strubbe, Joël White, Liesbeth De Neve, Luc Lens<br>Published in Biology Open 2018 7: bio031849 doi: 10.1242/bio.031849 Published 15 June 2018 <br>
DOI: 10.6084/m9.figshare.6561845
title: dataset_Longo2015.zip

description: Subjective usability (System Usability Scale) and Subjective Mental Workload (Nasa-TLX and Workload Profile) of web-based tasks and interfaces
DOI: 10.6084/m9.figshare.6561830.v1
title: cv-hirak-kashyap

description: CV of Hirak J Kashyap.
DOI: 10.6084/m9.figshare.6561704
title: Understanding standardisation of asymmetric tools from the Late Middle Palaeolithic: use-wear analysis to test morpho-functional interpretations

description: *Poster<br>Schunk, L., Jöris, O., Marreiros, J. 2018. Understanding standardisaiton of asymmetric tools from the Late<br>Middle Palaeolithic: use-wear analysis to test morpho-functional interpretations. „60th Annual Meeiting of the<br>Hugo Obermaier Society for Quaternary Research and Archaeology of the Stone Age“, Tarragona, pp. 50-51. <br>
DOI: 10.6084/m9.figshare.6561647
title: Measuring autophagosome flux

description: Macroautophagy/autophagy is a proteolytic pathway that is involved in both bulk degradation of cytoplasmic proteins as well as in selective degradation of cytoplasmic organelles. Autophagic flux is often defined as a measure of autophagic degradation activity, and many techniques exist to assess autophagic flux. Although these techniques have generated invaluable information about the autophagic system, the quest continues for developing methods that not only enhance sensitivity and provide a means of quantification, but also accurately reflect the dynamic character of the pathway. Based on the theoretical framework of metabolic control analysis, where the autophagosome flux is the quantitative description of the rate a flow along a pathway, here we treat the autophagy system as a multi-step pathway. We describe a single-cell fluorescence live-cell imaging-based approach that allows the autophagosome flux to be accurately measured. This method characterizes autophagy in terms of its complete autophagosome and autolysosome pool size, the autophagosome flux, J, and the transition time, τ, for autophagosomes and autolysosomes at steady state. This approach provides a sensitive quantitative method to measure autophagosome flux, pool sizes and transition time in cells and tissues of clinical relevance. <b>Abbreviations</b>: ATG5/APG5, autophagy-related 5; GFP, green fluorescent protein; LAMP1, lysosomal-associated membrane protein 1; MAP1LC3/LC3, microtubule-associated protein 1 light chain 3; J, flux; MEF, mouse embryonic fibroblast; MTOR, mechanistic target of rapamycin kinase; <i>nA</i>, number of autophagosomes; <i>nAL</i>, number of autolysosomes; <i>nL</i>, number of lysosomes; p-MTOR, phosphorylated mechanistic target of rapamycin kinase; RFP, red fluorescent protein; siRNA, small interfering RNA; τ, transition time; TEM, transmission electron microscopy.