cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17028/rd.lboro.6844781
title: Modular Tissue Engineered Perfusion System

description: Perfusion system for the insertion of modular tissue engineered constructs.
DOI: 10.17028/rd.lboro.6844781.v1
title: Modular Tissue Engineered Perfusion System

description: Perfusion system for the insertion of modular tissue engineered constructs.
DOI: 10.17028/rd.lboro.6844799.v1
title: Integrated Tissue Engineered Perfusion System

description: Perfusion system which incorporates integrated scaffold for tissue engineered skeletal muscle
DOI: 10.17028/rd.lboro.6844772
title: Screw Thread

description: Screw thread for monolayer and tissue engineered perfusion systems.
DOI: 10.17028/rd.lboro.6844766
title: Monolayer Perfusion System

description: Perfusion system for the culture of cells in monolayer.
DOI: 10.17028/rd.lboro.6844769
title: O-ring Mould

description: Mould for the production of PDMS O-rings at 20 mm diameters.
DOI: 10.17028/rd.lboro.6844766.v1
title: Monolayer Perfusion System

description: Perfusion system for the culture of cells in monolayer.
DOI: 10.17028/rd.lboro.6844769.v1
title: O-ring Mould

description: Mould for the production of PDMS O-rings at 20 mm diameters.
DOI: 10.6084/m9.figshare.6844730
title: An overview of systematic reviews about ibuprofen and paracetamol for treating pain in children

description: Detailed characteristics of systematic reviews included in the overview of systematic reviews about ibuprofen and paracetamol for treating pain in children
DOI: 10.6084/m9.figshare.6844730.v1
title: An overview of systematic reviews about ibuprofen and paracetamol for treating pain in children

description: Detailed characteristics of systematic reviews included in the overview of systematic reviews about ibuprofen and paracetamol for treating pain in children
DOI: 10.6084/m9.figshare.6844619
title: Mathematical structural descriptors and mutagenicity assessment: a study with congeneric and diverse datasets<sup>$</sup>

description: Quantitative bioactivity and toxicity assessment of chemical compounds plays a central role in drug discovery as it saves a substantial amount of resources. To this end, high-performance computing has enabled researchers and practitioners to leverage hundreds, or even thousands, of computed molecular descriptors for the activity prediction of candidate compounds. In this paper, we evaluate the utility of two large groups of chemical descriptors by such predictive modelling, as well as chemical structure discovery, through empirical analysis. We use a suite of commercially available and in-house software to calculate molecular descriptors for two sets of chemical mutagens – a homogeneous set of 95 amines, and a diverse set of 508 chemicals. Using calculated descriptors, we model the mutagenic activity of these compounds using a number of methods from the statistics and machine-learning literature, and use robust principal component analysis to investigate the low-dimensional subspaces that characterize these chemicals. Our results suggest that combining different sets of descriptors is likely to result in a better predictive model – but that depends on the compounds being modelled and the modelling technique being used.
DOI: 10.6084/m9.figshare.6844619.v1
title: Mathematical structural descriptors and mutagenicity assessment: a study with congeneric and diverse datasets<sup>$</sup>

description: Quantitative bioactivity and toxicity assessment of chemical compounds plays a central role in drug discovery as it saves a substantial amount of resources. To this end, high-performance computing has enabled researchers and practitioners to leverage hundreds, or even thousands, of computed molecular descriptors for the activity prediction of candidate compounds. In this paper, we evaluate the utility of two large groups of chemical descriptors by such predictive modelling, as well as chemical structure discovery, through empirical analysis. We use a suite of commercially available and in-house software to calculate molecular descriptors for two sets of chemical mutagens – a homogeneous set of 95 amines, and a diverse set of 508 chemicals. Using calculated descriptors, we model the mutagenic activity of these compounds using a number of methods from the statistics and machine-learning literature, and use robust principal component analysis to investigate the low-dimensional subspaces that characterize these chemicals. Our results suggest that combining different sets of descriptors is likely to result in a better predictive model – but that depends on the compounds being modelled and the modelling technique being used.
DOI: 10.6084/m9.figshare.6844505
title: Supplementary Material for: The Anaphylatoxin C3a Receptor Expression on Human M2 Macrophages Is Down-Regulated by Stimulating the Histamine H4 Receptor and the IL-4 Receptor

description: The anaphylatoxin C3a triggers inflammation by binding to its specific G-protein-coupled C3a receptor (C3aR). Since the number of C3aR, which is expressed on the cell surface, affects the response to C3a, we investigated the expression levels of C3aR on human M2 macrophages in allergic situations where high levels of the Th2 cytokine IL-4 and histamine are present in a local microenvironment. The histamine H1 receptor (H1R), H2R and the H4R mRNA expressions were induced or up-regulated during the differentiation process of M2 macrophages. The presence of histamine or agonists targeting the H1R, H2R and, in particular, the H4R during in vitro differentiation from monocytes to macrophages modified the M2 phenotype by regulating the macrophage differentiation marker CD68 and CD163 expressions. In ­addition, the C3aR expression was also down-regulated by ­ST-1006 during this process. Histamine and ST-1006 down-regulated the expression of C3aR with different time kinetics on fully differentiated M2 macrophages. By analysing C3a-induced IL-6 mRNA expression, we observed a diminished response to C3a in ST-1006-treated M2 macrophages when compared to un-treated cells. Expression of C3 was not affected by histamine, whereas IL-4 strongly down-regulated C3aR and C3 expressions. Our data suggests that down-regulation of C3aR expression by mediators present in allergic situations such as IL-4 or histamine has an anti-inflammatory impact by reducing the sensitivity to C3a-induced down-stream signaling, thereby contributing to the regulation of local inflammatory responses in the skin.
DOI: 10.6084/m9.figshare.6844496
title: Supplementary Material for: Human Cervical Epithelial Cells Release Antiviral Factors and Inhibit HIV Replication in Macrophages

description: The female reproductive tract is a major site of HIV sexual transmission. We here examined whether human cervical epithelial cells (HCEs) can be immunologically activated and produce antiviral factors against HIV. We demonstrated that HCEs (End1/E6E7 cells) possess the functional toll-like receptor (TLR)3 signaling system, which could be activated by Poly I:C and induce multiple cellular HIV restriction factors. The treatment of primary human macrophages with supernatant (SN) from TLR3-activated End1/E6E7 cell cultures resulted in HIV inhibition. This SN-mediated HIV inhibition was mainly through the induction of interferons (IFN)-β and IFN-λs, as the antibodies to IFN-β or IFN-λs receptor could effectively block the SN-mediated anti-HIV effect. Further studies showed that the incubation of macrophages with SN from the activated cervical epithelial cell cultures induced the expression of a number of IFN-stimulated genes (ISGs), including IFN-stimulated gene (ISG15), ISG56, 2′, 5′-oligoadenylate synthetase 1 (OAS 1), OAS 2, Myxovirus Resistance A (MxA), MxB, and Guanylate-binding protein 5 (GBP5). In addition, TLR3-activated cells produced the CC chemokines [regulated on activation, normal T cell expressed and secreted (RANTES), Human macrophage inflammatory protein 1 alpha (MIP-1α), MIP-1β] the ligands of HIV entry co-receptor CCR5. These observations support further studies on HCEs as potentially crucial and alternative targets for immunological intervention to control and prevent HIV sexual transmission.
DOI: 10.6084/m9.figshare.6844484
title: Supplementary Material for: The Italian Version of the Brief 21-Item Prodromal Questionnaire: Field Test, Psychometric Properties and Age-Sensitive Cut-Offs

description: <b><i>Background:</i></b> The Brief, 21-item version of the Prodromal Questionnaire (PQ-B) is a promising screener for psychosis-risk states that could be implemented in routine clinical practice. In this study, we assessed psychometric properties of the Italian version of the PQ-B (iPQ-B) in a sample of 243 help-seekers, aged 13–35 years. <b><i>Sampling and Methods:</i></b> After completing the iPQ-B, participants were assessed with the Comprehensive Assessment of At-Risk Mental States (CAARMS). Diagnostic accuracy (sensitivity, specificity, positive and negative predictive values [PPV and NPV], positive and negative likelihood ratios) and concurrent validity between PQ-B and CAARMS were determined using Cronbach’s alpha and Cohen’s kappa. We also tested the validity of the adopted PQ-B cut-offs through Receiver Operating Characteristic (ROC) curves plotted against CAARMS diagnoses and the predictive validity of the iPQ-B at 1-year follow-up. <b><i>Results:</i></b> The iPQ-B showed high internal consistency (Cronbach’s alpha = 0.868), acceptable diagnostic accuracy and concurrent validity (70% sensitivity, 67% specificity, 81% PPV, Cohen’s kappa = 0.335). ROC analyses pointed to threshold of ≥20 on the PQ-B total distress score as best cut-off. After 12 months of follow-up, 11% of participants who scored ≥4 on the PQ-B distressing item total score and did not meet CAARMS psychosis criteria at baseline, developed a psychotic disorder. Interestingly, age had significant negative correlations with iPQ-B scores and adolescents (aged &lt; 18 years) showed higher iPQ-B scores than young adults. <b><i>Conclusions:</i></b> Overall, the psychometric properties of the iPQ-B were satisfactory. As iPQ-B scores appeared inversely associated to age, age-tailored cut-off scores are recommended for screening purposes in child-adolescent cohorts.
DOI: 10.6084/m9.figshare.6844193
title: Additional file 1: of Whole-body clearing, staining and screening of calcium deposits in the mdx mouse model of Duchenne muscular dystrophy

description: Figure S1. Implementation of apparatus for macroscopic imaging using light-sheet illumination. (a) General view. (b) Side view. (c) Front view. (1) camera, (2) stepper motor, (3) z-axis line module (here light microscope body, Zeiss), (4) base holder, (5) glass container, (6) line lasers, (7) metal block, (8) laser power supply. Figure S2. Perfusion-based CUBIC cleared rat organs stained with propidium iodide. Bright field images of whole rat organs (a) intestine, (b) kidney, (c) heart, (d) cerebellum and (e) spleen. Single squares in all panels - 5 × 5 mm. This figure has been adapted from the original article “Optimized perfusion-based CUBIC protocol for the efficient whole-body clearing and imaging of rat organs” by P. Matryba et al., J Biophotonics 2017, doi./10.1002/jbio.201700248 . Reproduced with permission 4358370973288. Figure S3. Comparison between optical and standard histopathology sectioning of Alizarin red S stained mdx mouse muscles. (a) Representative optical sections acquired during imaging with custom-made LSFM. Control animals present no staining-positive tissue. (b) Representative histopathology 4 μm sections observed with low and (c) high magnification. It has to be noted that histopathology images stay in line with optical sectioning, presenting petite deposits in triceps brachii and similar amount of deposits between quadriceps femoris and spinalis pars lumborum. White scale bar, 1 mm, black scale bar, 200 μm. Figure S4. Quantitative volume analysis of calcified deposits in mdx mouse. (a) Triceps brachii muscles from left and right side of the animals were compared. Differences between left vs. right side presented as % mineralization of muscle volume were not statistically significant (Wilcoxon test (W = 0.0, number of pairs = 3), p &gt; 0.999). (b) Analysis of volume of muscles replaced by calcific deposits. Percent of mineralization in triceps brachii, quadriceps femoris and spinalis pars lumborum muscles was significantly different (Kruskal-Wallis test (K-W statistic = 5.6), p = 0.05, n = 3 per each muscle group). Figure S5. Perfusion-based CUBIC clearing does not alter microstructure of muscle. Perfusion-based CUBIC cleared triceps brachii and quadriceps femoris muscles of mdx and C57BL/10 control animals were subjected to standard hematoxylin and eosin histological staining. Low (10×) and high (20×) magnification representative images present microstructure preservation. It has to be noted that centrally positioned nuclei, a prominent feature of dystrophy, is maintained during mdx clearing. Scale bar, 100 μm. (ZIP 12014 kb)
DOI: 10.6084/m9.figshare.6844193.v1
title: Additional file 1: of Whole-body clearing, staining and screening of calcium deposits in the mdx mouse model of Duchenne muscular dystrophy

description: Figure S1. Implementation of apparatus for macroscopic imaging using light-sheet illumination. (a) General view. (b) Side view. (c) Front view. (1) camera, (2) stepper motor, (3) z-axis line module (here light microscope body, Zeiss), (4) base holder, (5) glass container, (6) line lasers, (7) metal block, (8) laser power supply. Figure S2. Perfusion-based CUBIC cleared rat organs stained with propidium iodide. Bright field images of whole rat organs (a) intestine, (b) kidney, (c) heart, (d) cerebellum and (e) spleen. Single squares in all panels - 5 × 5 mm. This figure has been adapted from the original article “Optimized perfusion-based CUBIC protocol for the efficient whole-body clearing and imaging of rat organs” by P. Matryba et al., J Biophotonics 2017, doi./10.1002/jbio.201700248 . Reproduced with permission 4358370973288. Figure S3. Comparison between optical and standard histopathology sectioning of Alizarin red S stained mdx mouse muscles. (a) Representative optical sections acquired during imaging with custom-made LSFM. Control animals present no staining-positive tissue. (b) Representative histopathology 4 μm sections observed with low and (c) high magnification. It has to be noted that histopathology images stay in line with optical sectioning, presenting petite deposits in triceps brachii and similar amount of deposits between quadriceps femoris and spinalis pars lumborum. White scale bar, 1 mm, black scale bar, 200 μm. Figure S4. Quantitative volume analysis of calcified deposits in mdx mouse. (a) Triceps brachii muscles from left and right side of the animals were compared. Differences between left vs. right side presented as % mineralization of muscle volume were not statistically significant (Wilcoxon test (W = 0.0, number of pairs = 3), p &gt; 0.999). (b) Analysis of volume of muscles replaced by calcific deposits. Percent of mineralization in triceps brachii, quadriceps femoris and spinalis pars lumborum muscles was significantly different (Kruskal-Wallis test (K-W statistic = 5.6), p = 0.05, n = 3 per each muscle group). Figure S5. Perfusion-based CUBIC clearing does not alter microstructure of muscle. Perfusion-based CUBIC cleared triceps brachii and quadriceps femoris muscles of mdx and C57BL/10 control animals were subjected to standard hematoxylin and eosin histological staining. Low (10×) and high (20×) magnification representative images present microstructure preservation. It has to be noted that centrally positioned nuclei, a prominent feature of dystrophy, is maintained during mdx clearing. Scale bar, 100 μm. (ZIP 12014 kb)
DOI: 10.6084/m9.figshare.6844187
title: MOESM8 of A year of monitoring 20 mesophilic full-scale bioreactors reveals the existence of stable but different core microbiomes in bio-waste and wastewater anaerobic digestion systems

description: Additional file 8: Table S7. The 16S rRNA gene amplicon sequencing results of 1-year monthly time series of 20 AD reactors located in Luxembourg and Belgium. Blast search results for bOTUs analysed in this study against the 8000 metagenome-reconstructed genomes from the study by Parks et al. [54].
DOI: 10.6084/m9.figshare.6844187.v1
title: MOESM8 of A year of monitoring 20 mesophilic full-scale bioreactors reveals the existence of stable but different core microbiomes in bio-waste and wastewater anaerobic digestion systems

description: Additional file 8: Table S7. The 16S rRNA gene amplicon sequencing results of 1-year monthly time series of 20 AD reactors located in Luxembourg and Belgium. Blast search results for bOTUs analysed in this study against the 8000 metagenome-reconstructed genomes from the study by Parks et al. [54].
DOI: 10.6084/m9.figshare.6844184
title: MOESM7 of A year of monitoring 20 mesophilic full-scale bioreactors reveals the existence of stable but different core microbiomes in bio-waste and wastewater anaerobic digestion systems

description: Additional file 7: Table S6. The 16S rRNA gene amplicon sequencing results of 1-year monthly time series of 20 AD reactors located in Luxembourg and Belgium. Spearman correlation matrix between operational data and dominant microbial groups/ OTUs.
DOI: 10.6084/m9.figshare.6844184.v1
title: MOESM7 of A year of monitoring 20 mesophilic full-scale bioreactors reveals the existence of stable but different core microbiomes in bio-waste and wastewater anaerobic digestion systems

description: Additional file 7: Table S6. The 16S rRNA gene amplicon sequencing results of 1-year monthly time series of 20 AD reactors located in Luxembourg and Belgium. Spearman correlation matrix between operational data and dominant microbial groups/ OTUs.
DOI: 10.6084/m9.figshare.6844160
title: MOESM5 of A year of monitoring 20 mesophilic full-scale bioreactors reveals the existence of stable but different core microbiomes in bio-waste and wastewater anaerobic digestion systems

description: Additional file 5: Table S5. The 16S rRNA gene amplicon sequencing results of 1-year monthly time series of 20 AD reactors located in Luxembourg and Belgium. Relative abundance (%, normalised number of reads) and taxonomic affiliation of the 16S rRNA amplicon sequencing OTUs for bacteria and archaea.
DOI: 10.6084/m9.figshare.6844160.v1
title: MOESM5 of A year of monitoring 20 mesophilic full-scale bioreactors reveals the existence of stable but different core microbiomes in bio-waste and wastewater anaerobic digestion systems

description: Additional file 5: Table S5. The 16S rRNA gene amplicon sequencing results of 1-year monthly time series of 20 AD reactors located in Luxembourg and Belgium. Relative abundance (%, normalised number of reads) and taxonomic affiliation of the 16S rRNA amplicon sequencing OTUs for bacteria and archaea.
DOI: 10.6084/m9.figshare.6844097
title: MOESM2 of A year of monitoring 20 mesophilic full-scale bioreactors reveals the existence of stable but different core microbiomes in bio-waste and wastewater anaerobic digestion systems

description: Additional file 2: Table S1. Characterisation of the studied AD reactors. Detailed (per sample) characterisation of the studied AD reactors.
DOI: 10.6084/m9.figshare.6844097.v1
title: MOESM2 of A year of monitoring 20 mesophilic full-scale bioreactors reveals the existence of stable but different core microbiomes in bio-waste and wastewater anaerobic digestion systems

description: Additional file 2: Table S1. Characterisation of the studied AD reactors. Detailed (per sample) characterisation of the studied AD reactors.
DOI: 10.6084/m9.figshare.6844091
title: MOESM3 of Increasing the economic value of lignocellulosic stillage through medium-chain fatty acid production

description: Additional file 3. Data used for development of the technoeconomic analysis (TEA). Table S11. Summary of process modeling for liquid-liquid extraction, solvent distillation, and MCFA separation with ASPEN. Table S12. Summary of capitol expenses added to the NREL TEA. Table S13. Summary of operating expenses and additional product revenues added to NREL TEA. Table S14. 30 year cash flow from NREL TEA updated to include MCFA production expenses and revenues. Table S15. Calculations for additional capital expenses. Table S16. Chemical costs for octanoic acid, hexanoic acid and 2-octanol obtained from Zauba.
DOI: 10.6084/m9.figshare.6844091.v1
title: MOESM3 of Increasing the economic value of lignocellulosic stillage through medium-chain fatty acid production

description: Additional file 3. Data used for development of the technoeconomic analysis (TEA). Table S11. Summary of process modeling for liquid-liquid extraction, solvent distillation, and MCFA separation with ASPEN. Table S12. Summary of capitol expenses added to the NREL TEA. Table S13. Summary of operating expenses and additional product revenues added to NREL TEA. Table S14. 30 year cash flow from NREL TEA updated to include MCFA production expenses and revenues. Table S15. Calculations for additional capital expenses. Table S16. Chemical costs for octanoic acid, hexanoic acid and 2-octanol obtained from Zauba.
DOI: 10.6084/m9.figshare.6844073
title: MOESM2 of Increasing the economic value of lignocellulosic stillage through medium-chain fatty acid production

description: Additional file 2. Rarefied tables of operational taxonomic units (OTUs) and classification with Silva. Table S9. OTU table for 6d experiments testing different pH conditions. Table S10. OTU table for 252 days of reactor operation at pH 5.5.
DOI: 10.6084/m9.figshare.6844073.v1
title: MOESM2 of Increasing the economic value of lignocellulosic stillage through medium-chain fatty acid production

description: Additional file 2. Rarefied tables of operational taxonomic units (OTUs) and classification with Silva. Table S9. OTU table for 6d experiments testing different pH conditions. Table S10. OTU table for 252 days of reactor operation at pH 5.5.
DOI: 10.6084/m9.figshare.6844061
title: MOESM1 of Increasing the economic value of lignocellulosic stillage through medium-chain fatty acid production

description: Additional file 1. Chemical analyses of stillage production and mixed culture fermentation reactor. Table S1. Results from two fermentations of switchgrass hydrolysate with Saccharomyces cerevisiae Y128. Table S2. Soluble COD results for fermented switchgrass hydrolysate. Table S3. Summary of organic components in switchgrass stillage and the mixed culture fermentation reactor. Table S4. Total soluble COD in switchgrass stillage and mixed culture fermentation reactor. Table S5. Components in stillage and mixed culture fermentation reactor samples measured by GC-MS and HPLC analyses. Table S6. Total soluble carbohydrates measured in stillage and mixed culture fermentation reactor with the anthrone method. Table S7. Total soluble proteins in stillage and mixed culture fermentation reactor measured with the BCA assay. Table S8. Summary of aromatic compounds in stillage.
DOI: 10.6084/m9.figshare.6844061.v1
title: MOESM1 of Increasing the economic value of lignocellulosic stillage through medium-chain fatty acid production

description: Additional file 1. Chemical analyses of stillage production and mixed culture fermentation reactor. Table S1. Results from two fermentations of switchgrass hydrolysate with Saccharomyces cerevisiae Y128. Table S2. Soluble COD results for fermented switchgrass hydrolysate. Table S3. Summary of organic components in switchgrass stillage and the mixed culture fermentation reactor. Table S4. Total soluble COD in switchgrass stillage and mixed culture fermentation reactor. Table S5. Components in stillage and mixed culture fermentation reactor samples measured by GC-MS and HPLC analyses. Table S6. Total soluble carbohydrates measured in stillage and mixed culture fermentation reactor with the anthrone method. Table S7. Total soluble proteins in stillage and mixed culture fermentation reactor measured with the BCA assay. Table S8. Summary of aromatic compounds in stillage.