cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5938846.v1
title: Supplementary Material for: A Comparative Study of Albumin-Bilirubin Score with Child-Pugh Score, Model for End-Stage Liver Disease Score and Indocyanine Green R15 in Predicting Posthepatectomy Liver Failure for Hepatocellular Carcinoma Patients

description: <b><i>Background:</i></b> The albumin-bilirubin (ALBI) grade is a newly proposed model for assessing the hepatic function. This study aimed to compare the value of the ALBI score with Child-Pugh score, model for end-stage liver disease (MELD) score and indocyanine green (ICG) R15 in predicting posthepatectomy liver failure (PHLF). <b><i>Methods:</i></b> Patients undergoing curative resection for hepatocellular carcinoma (HCC) between January 2014 and June 2017 were enrolled. The values of the Child-Pugh score, MELD score, ICG R15 and ALBI score in predicting PHLF were evaluated. <b><i>Results:</i></b> A total of 473 HCC patients were enrolled. The ALBI score was identified as an independent predictor of PHLF. The AUCs for the Child-Pugh score, MELD score, ICG R15 and ALBI score in predicting PHLF were 0.665, 0.649, 0.668, and 0.745 respectively. Multivariable analyses revealed that the ALBI score was an independent predictor of PHLF regardless of the hepatectomy subgroups, but the Child-Pugh score and MELD score were not significant predictors of PHLF both in major and minor hepatectomy subgroups, and ICG R15 was only a significant predictor of PHLF in minor hepatectomy subgroup. <b><i>Conclusion:</i></b> The ALBI score showed superior predictive value of PHLF over Child-Pugh score, MELD score and ICG R15. We propose to use the ALBI score to evaluate surgical risk for HCC patients undergoing hepatic resection.
DOI: 10.6084/m9.figshare.5938777
title: Supplementary Material for: Hidradenitis Suppurativa: Disease Burden and Etiology in Skin of Color

description: Hidradenitis suppurativa (HS) is a chronic, debilitating skin disease. Although most studies on HS are conducted in largely Caucasian populations, evidence demonstrates a higher prevalence in patients with skin of color, including African and Hispanic populations. These racial subgroups are likely at risk for greater disease burden due to a higher prevalence of components of the metabolic syndrome, comorbid depression, and low socioeconomic status; however, there is a paucity of research in these populations. Additionally, studies examining the genetic and anatomical basis for HS, as well as the response to HS therapies, are lacking for patients with skin of color. Complicating this issue is the limited access to effective medical care, including dermatologists, for African and Hispanic populations as well as other minority groups. In this review, we identify gaps in the knowledge base, highlight the association between HS and patients with skin of color, and provide direction for much needed research into this condition.
DOI: 10.6084/m9.figshare.5938771
title: The pro-α1(V) collagen gene (<i>Col5a1</i>) is coordinately regulated by miR-29b with core promoter in cultured cells

description: <b><i>Aims</i></b><i>: Col5a1</i> encodes the α1 chain of type V collagen, a quantitatively minor fibrillar collagen that is critical for the formation and function of the organs in the body. MicroRNAs (miRNAs) are small noncoding RNAs that posttranscriptionally regulate biological functions by binding to the 3ʹ-untranslated region (3ʹUTR) of specific target mRNA. In this study, we investigated the posttranscriptional regulation of miRNAs on the <i>Col5a1</i> gene expression. <b><i>Materials and Methods</i></b>: We cultured osteoblasts and fibroblasts of cell lines. To examine the 3ʹUTR activity of the <i>Col5a1</i> gene, chimeric plasmids constructs containing the core promoter and 3ʹUTR of <i>Col5a1</i> were generated and luciferase assays were performed. We also evaluated the role of miRNA using constructs that were mutated at the putative binding sites of miRNA. In addition, we evaluated the endogenous mRNA and protein, and luciferase activity of the <i>Col5a1</i> gene after miRNA overexpression/knockdown or CRISPR/Cas9-induced knockout. <b><i>Results</i></b>: The luciferase assay showed a decreased activity of the 3ʹUTR of <i>Col5a1</i> gene. However, the expression of the mutant constructs of miRNA-binding sites was restored. The overexpression of miRNA inhibited the <i>Col5a1</i> gene not only with regard to the luciferase activity and endogenous mRNA but also at the protein level. In contrast, the RNAi-mediated knockdown or CRISPR/Cas9 system increased the expression of the <i>Col5a1</i> gene. <b><i>Conclusion</i></b>: These results provided evidence that miR-29b regulates the <i>Col5a1</i> gene expression through binding to the 3ʹUTR, which might play an important role in the pathogenesis of disease related to bone metabolism and fibrogenic reactions.
DOI: 10.6084/m9.figshare.5938771.v1
title: The pro-α1(V) collagen gene (<i>Col5a1</i>) is coordinately regulated by miR-29b with core promoter in cultured cells

description: <b><i>Aims</i></b><i>: Col5a1</i> encodes the α1 chain of type V collagen, a quantitatively minor fibrillar collagen that is critical for the formation and function of the organs in the body. MicroRNAs (miRNAs) are small noncoding RNAs that posttranscriptionally regulate biological functions by binding to the 3ʹ-untranslated region (3ʹUTR) of specific target mRNA. In this study, we investigated the posttranscriptional regulation of miRNAs on the <i>Col5a1</i> gene expression. <b><i>Materials and Methods</i></b>: We cultured osteoblasts and fibroblasts of cell lines. To examine the 3ʹUTR activity of the <i>Col5a1</i> gene, chimeric plasmids constructs containing the core promoter and 3ʹUTR of <i>Col5a1</i> were generated and luciferase assays were performed. We also evaluated the role of miRNA using constructs that were mutated at the putative binding sites of miRNA. In addition, we evaluated the endogenous mRNA and protein, and luciferase activity of the <i>Col5a1</i> gene after miRNA overexpression/knockdown or CRISPR/Cas9-induced knockout. <b><i>Results</i></b>: The luciferase assay showed a decreased activity of the 3ʹUTR of <i>Col5a1</i> gene. However, the expression of the mutant constructs of miRNA-binding sites was restored. The overexpression of miRNA inhibited the <i>Col5a1</i> gene not only with regard to the luciferase activity and endogenous mRNA but also at the protein level. In contrast, the RNAi-mediated knockdown or CRISPR/Cas9 system increased the expression of the <i>Col5a1</i> gene. <b><i>Conclusion</i></b>: These results provided evidence that miR-29b regulates the <i>Col5a1</i> gene expression through binding to the 3ʹUTR, which might play an important role in the pathogenesis of disease related to bone metabolism and fibrogenic reactions.
DOI: 10.6084/m9.figshare.5938669
title: Stabilizing ultrasmall Au clusters for enhanced photoredox catalysis

description: Recently, loading ligand-protected gold (Au) clusters as visible light photosensitizers onto various supports for photoredox catalysis has attracted considerable attention. However, the efficient control of long-term photostability of Au clusters on the metal-support interface remains challenging. Herein, we report a simple and efficient method for enhancing the photostability of glutathione-protected Au clusters (Au GSH clusters) loaded on the surface of SiO<sub>2</sub> sphere by utilizing multifunctional branched poly-ethylenimine (BPEI) as a surface charge modifying, reducing and stabilizing agent. The sequential coating of thickness controlled TiO<sub>2</sub> shells can further significantly improve the photocatalytic efficiency, while such structurally designed core-shell SiO<sub>2</sub>-Au GSH clusters-BPEI@TiO<sub>2</sub> composites maintain high photostability during longtime light illumination conditions. This joint strategy <i>via</i> interfacial modification and composition engineering provides a facile guideline for stabilizing ultrasmall Au clusters and rational design of Au clusters-based composites with improved activity toward targeting applications in photoredox catalysis.
DOI: 10.6084/m9.figshare.5938651
title: Calcium plus magnesium indicates digestibility: the significance of the second major axis of plant chemical variation for ecological processes

description: Data file contains 2 sheets with following information: (1) simultaneous measurements of plant biomass properties and vegetation records from field sampling of two long-term grassland management experiments in 2011-2012; plant species abbreviations consist of first three letters from the genus name and first three letters from the species name; community weighted traits were calculated from species biomass proportions and their respective trait values extracted from databases or literature (can be found in supporting information of the article: Appendix S1); (2) List of species abbreviations and respective scientific names. Plant names follow nomenclature: Kubát, K., Hrouda, L., Chrtek, J., Kaplan, Z., Kirschner, J. & Štěpánek, J. (2002) Key to the Flora of the Czech Republic. Academia, Praha, Czech Republic.
DOI: 10.6084/m9.figshare.5938651.v2
title: Calcium plus magnesium indicates digestibility: the significance of the second major axis of plant chemical variation for ecological processes

description: Data file contains 2 sheets with following information: (1) simultaneous measurements of plant biomass properties and vegetation records from field sampling of two long-term grassland management experiments in 2011-2012; plant species abbreviations consist of first three letters from the genus name and first three letters from the species name; community weighted traits were calculated from species biomass proportions and their respective trait values extracted from databases or literature (can be found in supporting information of the article: Appendix S1); (2) List of species abbreviations and respective scientific names. Plant names follow nomenclature: Kubát, K., Hrouda, L., Chrtek, J., Kaplan, Z., Kirschner, J. & Štěpánek, J. (2002) Key to the Flora of the Czech Republic. Academia, Praha, Czech Republic.
DOI: 10.6084/m9.figshare.5938651.v1
title: Calcium plus magnesium indicates digestibility: the significance of the second major axis of plant chemical variation for ecological processes

description: Data file contains 2 sheets with following information: (1) simultaneous measurements of plant biomass properties and vegetation records from field sampling of two long-term management experiments in 2011-2012; plant species abbreviations consist of first three letters from the genus name and first three letters from the species name; community weighted traits were calculated from species biomass proportions and their respective trait values extracted from databases or literature (can be found in supporting information of the article: Appendix S1); (2) List of species abbreviations and respective scientific names. Plant names follow nomenclature: Kubát, K., Hrouda, L., Chrtek, J., Kaplan, Z., Kirschner, J. & Štěpánek, J. (2002) Key to the Flora of the Czech Republic. Academia, Praha, Czech Republic.
DOI: 10.6084/m9.figshare.5938615
title: Experimental data of Edmaier et al. (2015) from Resilience of riverbed vegetation to uprooting by flow

description: The data refers to the uprooting by flow of <i>Avena sativa</i>, under four different flow rates and rooting length. The relevant output is the time to uprooting.
DOI: 10.6084/m9.figshare.5938615.v1
title: Experimental data of Edmaier et al. (2015) from Resilience of riverbed vegetation to uprooting by flow

description: The data refers to the uprooting by flow of <i>Avena sativa</i>, under four different flow rates and rooting length. The relevant output is the time to uprooting.
DOI: 10.6084/m9.figshare.5938606
title: Attached to the submitted files in the name "Data" from Nanostructured mesoporous silica: influence of the preparation conditions on the physical-surface properties for organic dye uptake efficiency

description: A series of ordered mesoporous silica such as MCM-41, SBA-3 and SBA-15, in addition to silica micro- (SM) and nano- (SN) mesoporous particles, were prepared. The preparation conditions were found to greatly influence the physical-surface properties including morphological structure, porosity, particle size, aggregate average size, surface area, pore size, pore volume and zeta potential of the prepared silica, while the chemical structure, predicted from FT-IR spectra, and the diffraction patterns, predicted from wide-angle X-ray diffraction spectra, were identical. Surface areas of approximately 1500, 1027, 600, 552 and 317 m<sup>2</sup> g<sup>−1</sup>, pore volumes of 0.93, 0.56, 0.82, 0.72 and 0.5 cm<sup>3</sup> g<sup>−1</sup>, radii of 2.48, 2.2, 5.66, 6.6 and 8.98 nm, average aggregate sizes of 56, 65.4, 220.9, 73, 61.1 and 261 nm and zeta potential values of −32.8, −46.1, −26.3, −31.4 and −25.9 mV were obtained for MCM-41, SBA-3, SBA-15, SN and SM, respectively. Methylene blue dye uptake capacity of the prepared silica types was investigated using the batch technique and in addition, the most effective material was further studied by the column flow system. The kinetics and isotherms of the uptake process were studied. The morphological structure, surface area, pore radius and zeta potential values were the most correlated factors.
DOI: 10.6084/m9.figshare.5938606.v1
title: Attached to the submitted files in the name "Data" from Nanostructured mesoporous silica: influence of the preparation conditions on the physical-surface properties for organic dye uptake efficiency

description: A series of ordered mesoporous silica such as MCM-41, SBA-3 and SBA-15, in addition to silica micro- (SM) and nano- (SN) mesoporous particles, were prepared. The preparation conditions were found to greatly influence the physical-surface properties including morphological structure, porosity, particle size, aggregate average size, surface area, pore size, pore volume and zeta potential of the prepared silica, while the chemical structure, predicted from FT-IR spectra, and the diffraction patterns, predicted from wide-angle X-ray diffraction spectra, were identical. Surface areas of approximately 1500, 1027, 600, 552 and 317 m<sup>2</sup> g<sup>−1</sup>, pore volumes of 0.93, 0.56, 0.82, 0.72 and 0.5 cm<sup>3</sup> g<sup>−1</sup>, radii of 2.48, 2.2, 5.66, 6.6 and 8.98 nm, average aggregate sizes of 56, 65.4, 220.9, 73, 61.1 and 261 nm and zeta potential values of −32.8, −46.1, −26.3, −31.4 and −25.9 mV were obtained for MCM-41, SBA-3, SBA-15, SN and SM, respectively. Methylene blue dye uptake capacity of the prepared silica types was investigated using the batch technique and in addition, the most effective material was further studied by the column flow system. The kinetics and isotherms of the uptake process were studied. The morphological structure, surface area, pore radius and zeta potential values were the most correlated factors.
DOI: 10.6084/m9.figshare.5938597
title: Alu exaptation enriches the human transcriptome by introducing new gene ends

description: In mammals, transposable elements are largely silenced, but under fortuitous circumstances may be co-opted to play a functional role. Here, we show that when Alu elements are inserted within or nearby genes in sense orientation, they may contribute to the transcriptome diversity by forming new cleavage and polyadenylation sites. We mapped these new gene ends in human onto the Alu sequence and identified three hotspots of cleavage and polyadenylation site formation. Interestingly, the native Alu sequence does not contain any canonical polyadenylation signal. We therefore studied what evolutionary processes might explain the formation of these specific hotspots of novel gene ends. We show that two of the three hotspots might have emerged from mutational processes that turned sequences that resemble polyadenylation signals into full-blown canonical signals, whereas one hotspot is tightly linked to the process of Alu insertion into the genome. Overall, Alu elements may lie behind the formation of 302 new gene end variants, affecting a total of 243 genes. Intergenic Alu elements may elongate genes by creating a downstream cleavage site, intronic Alu elements may lead to gene variants which code for truncated proteins, and 3′UTR Alu elements may result in gene variants with alternative 3′UTR.
DOI: 10.6084/m9.figshare.5938597.v1
title: Alu exaptation enriches the human transcriptome by introducing new gene ends

description: In mammals, transposable elements are largely silenced, but under fortuitous circumstances may be co-opted to play a functional role. Here, we show that when Alu elements are inserted within or nearby genes in sense orientation, they may contribute to the transcriptome diversity by forming new cleavage and polyadenylation sites. We mapped these new gene ends in human onto the Alu sequence and identified three hotspots of cleavage and polyadenylation site formation. Interestingly, the native Alu sequence does not contain any canonical polyadenylation signal. We therefore studied what evolutionary processes might explain the formation of these specific hotspots of novel gene ends. We show that two of the three hotspots might have emerged from mutational processes that turned sequences that resemble polyadenylation signals into full-blown canonical signals, whereas one hotspot is tightly linked to the process of Alu insertion into the genome. Overall, Alu elements may lie behind the formation of 302 new gene end variants, affecting a total of 243 genes. Intergenic Alu elements may elongate genes by creating a downstream cleavage site, intronic Alu elements may lead to gene variants which code for truncated proteins, and 3′UTR Alu elements may result in gene variants with alternative 3′UTR.
DOI: 10.6084/m9.figshare.5938282
title: University of St Andrews APC data 2016-2017

description: This spreadsheet lists the publication level data which details how the University of St Andrews has spent centrally managed Open Access (OA) funds. Article Processing Charges (APCs) are reported from the Research Councils UK (RCUK) OA Block Grant, Charity Open Access Fund (COAF), and from a small Library OA Fund. <br><br>The data covers the new reporting period* for RCUK from 1 April 2016 to 31 March 2017, and the transactions from COAF and LOAF during the same period. The Library OA Fund is limited to fully OA journals only, where researchers have no other source of funds to pay APCs.<br><i><br>(*The previous reporting period was Aug-July so this data overlaps with previous year's data)</i><br>
DOI: 10.6084/m9.figshare.5938282.v1
title: University of St Andrews APC data 2016-2017

description: This spreadsheet lists the publication level data which details how the University of St Andrews has spent centrally managed Open Access (OA) funds. Article Processing Charges (APCs) are reported from the Research Councils UK (RCUK) OA Block Grant, Charity Open Access Fund (COAF), and from a small Library OA Fund. <br><br>The data covers the new reporting period* for RCUK from 1 April 2016 to 31 March 2017, and the transactions from COAF and LOAF during the same period. The Library OA Fund is limited to fully OA journals only, where researchers have no other source of funds to pay APCs.<br><i><br>(*The previous reporting period was Aug-July so this data overlaps with previous year's data)</i><br>
DOI: 10.6084/m9.figshare.5938264
title: Supplementary Material for: Response of Retinoic Acid in Patients with Radioactive Iodine-Refractory Thyroid Cancer: A Meta-Analysis

description: <b><i>Purpose</i></b>: The purpose of this study was to evaluate the response of retinoic acid (RA) in radioactive iodine (RAI)-refractory differentiated thyroid cancer (DTC). <b><i>Methods:</i></b> Systematic searches of MEDLINE (from inception to December 2016) and of EMBASE (from inception to December 2016) were performed for English-language publications on thyroid cancer treated with RA. Studies were classified according to the response criteria used: (1) <sup>123</sup>I or <sup>131</sup>I whole body scintigraphy (WBS), (2) serum thyroglobulin (Tg) level, (3) the response evaluation criteria in solid tumors (RECIST) version 1.0, and (4) World Health Organization (WHO) criteria. <b><i>Results:</i></b> Disease response rates as determined by WBS ranged widely between 6.2% and 46.1% with a pooled disease response rate of 27.6% (95% confidence interval: 21.7-34.0%). Response rates as determined by Tg level ranged from 56.6% to 83.3% (pooled response rate 61.3% (51.0-70.9%)), RECIST response rates from 0% to 45.5% (pooled response rate 17.0% (1.4-44.5%)), and according to WHO criteria, the pooled response rate was 30.8% (12.7-52.7%). <b><i>Conclusions:</i></b> A minority of patients with RAI-refractory DTC respond to RA treatment.
DOI: 10.6084/m9.figshare.5938255
title: Weapon Grade Plutonium Burning

description: Helios input and output files for WGP study, Excel evaluation and Python script to run the code
DOI: 10.6084/m9.figshare.5938255.v1
title: Weapon Grade Plutonium Burning

description: Helios input and output files for WGP study, Excel evaluation and Python script to run the code
DOI: 10.6084/m9.figshare.5938252
title: Supplementary Material for: Endocrine Treatment with 2 Years of Tamoxifen versus 2 Years of Exemestane in Postmenopausal Patients with High-Risk Early Breast Cancer and Persisting Circulating Tumor Cells - First Results of the SUCCESS C Endocrine Treatment Sub-Study

description: <b><i>Background:</i></b> Optimal choice and sequence of endocrine treatment following adjuvant chemotherapy in postmenopausal early breast cancer patients are still under discussion and treatment stratification factors are missing. <b><i>Patients and Methods:</i></b> Postmenopausal women with HER2-negative, hormone receptor-positive tumors and persisting circulating tumor cells (CTCs; assessed using the FDA-approved CellSearch® System, Janssen Diagnostics, LLC) after chemotherapy were randomized to 2 years of tamoxifen followed by 3 years of exemestane (tamoxifen-exemestane group, n = 54) or 5 years of exemestane (exemestane-only group, n = 54). CTCs were again assessed after the first 2 years of endocrine treatment. In addition, safety data were compared between the 2 groups. <b><i>Results:</i></b> The 2 groups were well-balanced with regard to baseline characteristics. The CTC clearance rate after 2 years was 89% in the exemestane-only group and 97% in the tamoxifen-exemestane group (exact Fisher test, p = 0.36). The safety profile showed good tolerability with few grade 3 or 4 adverse events in both groups. <b><i>Conclusion:</i></b> The similar CTC clearance rate after 2 years of endocrine therapy with exemestane or tamoxifen, and the safety profiles obtained may indicate comparable efficacy and tolerability of both endocrine treatment regimens. However, these results have to be confirmed by final survival and safety analysis.