cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9913040
title: Interatomic Distances Chi-Squared Test

description: Models <i>in silico</i> were developed using Molecular Modelling Pro Plus, version 6.22, and ChemSite, version 5.10, produced by ChemSW (Accelrys Inc., San Diego, USA), as described in <i>Methods</i>. For EPL001’s <sub>9</sub>KEFNNI<sub>14</sub>, nine atoms were selected from side chains and two from the peptide backbone, thus: a = nitrogen in the side-chain of K9; b = delta carbon in E; c = hydroxyl oxygen in the side-chain of E; d = beta carbon in F; e = gamma carbon of F; f = peptide bond carbon of I; g = delta carbon of I; h = gamma carbon of N13; i = nitrogen of the side-chain of N13; j = peptide bond carbon of N12, k = nitrogen of side-chain of N12. This permitted 46 measurements, each atom to every other atom: a-b, a-c etc. Distances between the same atoms were calculated for KEFNNI as a free peptide, with comparisons reducing in number for free EFNNI through free FNNI to free NNI. The peptide MKPVFNNI has also been modelled. A chi-squared test was used, with measurements from the EPL001 model in silico representing Expected (E) and measurements from the modelled free peptides as Observed (O). Chi-squared values were calculated on the basis of (O-E)<sup>2</sup>/E. dof = degrees of freedom.
DOI: 10.6084/m9.figshare.9913043
title: <sup>68</sup>Ga-PSMA-PET/CT-directed IGRT/SBRT for oligometastases of recurrent prostate cancer after initial surgery

description: <b>Background:</b> We evaluated efficacy and toxicity of <sup>68</sup>Ga-PSMA-Positron Emission Tomography/Computed Tomography (PET/CT)-directed stereotactic body radiotherapy and image-guided radiotherapy (SBRT/IGRT) for oligometastases of prostate cancer recurrences after previous surgery. <b>Methods:</b> Nineteen patients were analyzed within a prospective PET-registry study (064/2013BO1) and retrospectively analyzed (807/2017BO2) fulfilling the following inclusion criteria: biochemical recurrence after radical prostatectomy, ≤five <sup>68</sup>Ga-PSMA-PET/CT positive lesions. Biochemical control was evaluated with EORTC (European Organization for Research and Treatment of Cancer)- and Phenix-definitions. Toxicity was scored according to CTCAE-criteria v. 4.03. <b>Results:</b> A total of 38 oligometastases (19 patients, 2 with re-treatment) were treated with SBRT/IGRT from October 2014 to July 2017. <sup>68</sup>Ga-PSMA-PET/CT-positive lesions were detected on average 39 months (5–139) after prostatectomy (pT2b-3b pN0-1 cM0). Mean PSA (Prostate-specific antigen)-level at time of imaging reached 2.2 ng/mL (range 0.2–10.1). PET/CT-positive lesions were treated with different fractionation schedules reaching biological equivalent doses (BED) of 116.7–230.0 Gy. Concomitant androgen deprivation therapy (ADT) was given in seven patients. After a median follow-up of 17 months (4–42) all patients were alive. Estimated 1-year PSA- control (<i>n</i> = 19) reached 80.8% (Phenix) and 67.5% (EORTC). A PSA-decline (≥50%) was detected in 16/19 patients after radiotherapy. Higher graded G3+-acute toxicity did not occur. Temporary late G3-proctitis was detected in one patient. <b>Conclusions:</b> Reaching of nadir ≤0.1 or 0.2 ng/mL was associated by improved DMFS (distant metastases free survival) and could serve as a surrogate endpoint for RT of oligometastases after initial prostatectomy. Short term effects of <sup>68</sup>Ga-PSMA-PET/CT-based ablative radiotherapy for oligometastases demonstrated an acceptable toxicity profile and favorable biochemical response.
DOI: 10.6084/m9.figshare.9913043.v1
title: <sup>68</sup>Ga-PSMA-PET/CT-directed IGRT/SBRT for oligometastases of recurrent prostate cancer after initial surgery

description: <b>Background:</b> We evaluated efficacy and toxicity of <sup>68</sup>Ga-PSMA-Positron Emission Tomography/Computed Tomography (PET/CT)-directed stereotactic body radiotherapy and image-guided radiotherapy (SBRT/IGRT) for oligometastases of prostate cancer recurrences after previous surgery. <b>Methods:</b> Nineteen patients were analyzed within a prospective PET-registry study (064/2013BO1) and retrospectively analyzed (807/2017BO2) fulfilling the following inclusion criteria: biochemical recurrence after radical prostatectomy, ≤five <sup>68</sup>Ga-PSMA-PET/CT positive lesions. Biochemical control was evaluated with EORTC (European Organization for Research and Treatment of Cancer)- and Phenix-definitions. Toxicity was scored according to CTCAE-criteria v. 4.03. <b>Results:</b> A total of 38 oligometastases (19 patients, 2 with re-treatment) were treated with SBRT/IGRT from October 2014 to July 2017. <sup>68</sup>Ga-PSMA-PET/CT-positive lesions were detected on average 39 months (5–139) after prostatectomy (pT2b-3b pN0-1 cM0). Mean PSA (Prostate-specific antigen)-level at time of imaging reached 2.2 ng/mL (range 0.2–10.1). PET/CT-positive lesions were treated with different fractionation schedules reaching biological equivalent doses (BED) of 116.7–230.0 Gy. Concomitant androgen deprivation therapy (ADT) was given in seven patients. After a median follow-up of 17 months (4–42) all patients were alive. Estimated 1-year PSA- control (<i>n</i> = 19) reached 80.8% (Phenix) and 67.5% (EORTC). A PSA-decline (≥50%) was detected in 16/19 patients after radiotherapy. Higher graded G3+-acute toxicity did not occur. Temporary late G3-proctitis was detected in one patient. <b>Conclusions:</b> Reaching of nadir ≤0.1 or 0.2 ng/mL was associated by improved DMFS (distant metastases free survival) and could serve as a surrogate endpoint for RT of oligometastases after initial prostatectomy. Short term effects of <sup>68</sup>Ga-PSMA-PET/CT-based ablative radiotherapy for oligometastases demonstrated an acceptable toxicity profile and favorable biochemical response.
DOI: 10.6084/m9.figshare.9912938
title: Systematic assessment of commercially available low-input miRNA library preparation kits

description: High-throughput sequencing is increasingly favoured to assay the presence and abundance of microRNAs (miRNAs) in biological samples, even from low RNA amounts, and a number of commercial vendors now offer kits that allow miRNA sequencing from sub-nanogram (ng) inputs. Although biases introduced during library preparation have been documented, the relative performance of current reagent kits has not been investigated in detail. Here, six commercial kits capable of handling &lt;100ng total RNA input were used for library preparation, performed by kit manufactures, on synthetic miRNAs of known quantities and human total RNA samples. We compared the performance of miRNA detection sensitivity, reliability, titration response and the ability to detect differentially expressed miRNAs. In addition, we assessed the use of unique molecular identifiers (UMI) sequence tags in one kit. We observed differences in detection sensitivity and ability to identify differentially expressed miRNAs between the kits, but none were able to detect the full repertoire of synthetic miRNAs. The reliability within the replicates of all kits was good, while larger differences were observed between the kits, although none could accurately quantify the relative levels of the majority of miRNAs. UMI tags, at least within the input ranges tested, offered little advantage to improve data utility. In conclusion, biases in miRNA abundance are heavily influenced by the kit used for library preparation, suggesting that comparisons of datasets prepared by different procedures should be made with caution. This article is intended to assist researchers select the most appropriate kit for their experimental conditions.
DOI: 10.6084/m9.figshare.9912932
title: Plasma CCN2 is independently related to subsequent need for abdominal aorta aneurysm repair

description: The objective of this study was to determine if plasma CCN2 is associated with abdominal aorta aneurysm (AAA), and future need for AAA repair, and further to assess the potential clinical value of CCN2 in predicting disease outcome. CCN2 was quantified in plasma samples obtained from a cohort of 679 men aged 65–74 at initial ultrasound screening for AAA in the Viborg Vascular (VIVA) screening trial. Plasma CCN2 was correlated with need for future surgical repair in the whole study population (HR = 1.457 (1.081–1.962), <i>p</i> = .013) and in the AAA group alone (HR = 1.431 (1.064–1.926), <i>p</i> = .018), yet the predictive value (CCN2 &gt; 0 and &lt;0 of 0.52 and 0.55, respectively) disqualified its use in clinically relevant AAA repair prediction. In conclusion, CCN2 is independently related to subsequent need for AAA repair, but has negligible predictive power for clinical use.
DOI: 10.6084/m9.figshare.9912926
title: Supplementary Material for: Proteomic Analysis Reveals Allergen Variability among Breeds of the Dust Mite <b><i>Blomia tropicalis</i></b>

description: <b><i>Background:</i></b> The dawn of the “omics” technologies has changed allergy research, increasing the knowledge and identification of new allergens. However, these studies have been almost restricted to <i>Dermatophagoides</i> spp. Although <i>Blomia tropicalis</i> has long been established as a clinically important source of allergens, a thorough proteomic characterization is still lacking for this dust mite. <b><i>Objective:</i></b> To increase knowledge of <i>B. tropicalis</i> allergens through proteomic analysis. <b><i>Methods:</i></b> Eleven in-bred lineages of <i>B. tropicalis</i> were obtained from 11 unique different pregnant females. Their somatic extracts were analyzed and compared with a commercially available extract by liquid chromatography tandem mass spectrometry (LC-MS/MS). <b><i>Results:</i></b> Considerable differences in the protein expression profiles were found among the breeds, and most of them displayed higher expression levels of major allergens than the commercially available extract. Blo t 2 was the most prominent allergenic protein in the analyzed extracts. Six identified allergens and 14 isoforms have not yet been recognized by IUIS. Conversely, 3 previously recognized <i>B. tropicalis</i> allergens were not found. <b><i>Conclusions:</i></b> The clear impact of inbreeding on allergen content shown by our study leads us to conclude that the quantification and/or identification of allergens from in-bred lines should be routinely considered for mite cultivation in order to select breeds with higher amounts of major allergens. In this sense, LC-MS/MS may be a useful method to achieve this quality control for research and commercial purposes.
DOI: 10.6084/m9.figshare.9912932.v1
title: Plasma CCN2 is independently related to subsequent need for abdominal aorta aneurysm repair

description: The objective of this study was to determine if plasma CCN2 is associated with abdominal aorta aneurysm (AAA), and future need for AAA repair, and further to assess the potential clinical value of CCN2 in predicting disease outcome. CCN2 was quantified in plasma samples obtained from a cohort of 679 men aged 65–74 at initial ultrasound screening for AAA in the Viborg Vascular (VIVA) screening trial. Plasma CCN2 was correlated with need for future surgical repair in the whole study population (HR = 1.457 (1.081–1.962), <i>p</i> = .013) and in the AAA group alone (HR = 1.431 (1.064–1.926), <i>p</i> = .018), yet the predictive value (CCN2 &gt; 0 and &lt;0 of 0.52 and 0.55, respectively) disqualified its use in clinically relevant AAA repair prediction. In conclusion, CCN2 is independently related to subsequent need for AAA repair, but has negligible predictive power for clinical use.
DOI: 10.6084/m9.figshare.9912938.v1
title: Systematic assessment of commercially available low-input miRNA library preparation kits

description: High-throughput sequencing is increasingly favoured to assay the presence and abundance of microRNAs (miRNAs) in biological samples, even from low RNA amounts, and a number of commercial vendors now offer kits that allow miRNA sequencing from sub-nanogram (ng) inputs. Although biases introduced during library preparation have been documented, the relative performance of current reagent kits has not been investigated in detail. Here, six commercial kits capable of handling &lt;100ng total RNA input were used for library preparation, performed by kit manufactures, on synthetic miRNAs of known quantities and human total RNA samples. We compared the performance of miRNA detection sensitivity, reliability, titration response and the ability to detect differentially expressed miRNAs. In addition, we assessed the use of unique molecular identifiers (UMI) sequence tags in one kit. We observed differences in detection sensitivity and ability to identify differentially expressed miRNAs between the kits, but none were able to detect the full repertoire of synthetic miRNAs. The reliability within the replicates of all kits was good, while larger differences were observed between the kits, although none could accurately quantify the relative levels of the majority of miRNAs. UMI tags, at least within the input ranges tested, offered little advantage to improve data utility. In conclusion, biases in miRNA abundance are heavily influenced by the kit used for library preparation, suggesting that comparisons of datasets prepared by different procedures should be made with caution. This article is intended to assist researchers select the most appropriate kit for their experimental conditions.
DOI: 10.6084/m9.figshare.9912836
title: Metadata record for: A cone-beam X-ray computed tomography data collection designed for machine learning

description: This dataset contains key characteristics about the data described in the Data Descriptor A cone-beam X-ray computed tomography data collection designed for machine learning. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format<br><br>Versioning Note:Version 2 was generated when the metadata format was updated from JSON to JSON-LD. This was an automatic process that changed only the format, not the contents, of the metadata.
DOI: 10.17028/rd.lboro.9912821
title: Supplementary information files for 'Improving energy efficiency in manufacturing using peer benchmarking to influence machine design innovation'

description: Supplementary information files for 'Improving energy efficiency in manufacturing using peer benchmarking to influence machine design innovation'<br>Abstract:Energy efficiency in manufacturing is important for overall sustainability of society. This paper combines three observations to improve an overlooked part of the energy efficiency support infrastructure in food and drink manufacturing: innovation capability. First, variations in machine and process design produce significant differences in energy efficiency; second, these differences are not widely known or valued because comparable machine energy data are not gathered for the vast majority of products, so machine and process design is under-used as a route to efficiency improvement; third, peer benchmarking has proved to be an effective tool for stimulating change in other contexts, but has not been used at machine level in manufacturing. This paper describes and makes the case for a self-sustaining system in which machines would be validly compared on energy consumption and peer benchmarking would stimulate innovation in machine and process design for food manufacturing. The system, to be tested in a feasibility study, would benefit both food manufacturers and stakeholders. It would avoid dependence on public funding and enable stakeholders to provide value from the data. The paper contains the academic underpinning for the system and sets out an effective means of using it to achieve practical change.<br>
DOI: 10.6084/m9.figshare.9912815
title: Supplementary Material for: Are Conditioned Open Placebos Feasible as an Adjunctive Treatment to Opioids? Results from a Single-Group Dose-Extender Pilot Study with Acute Pain Patients

description: Medicine
DOI: 10.6084/m9.figshare.9912836.v2
title: Metadata record for: A cone-beam X-ray computed tomography data collection designed for machine learning

description: This dataset contains key characteristics about the data described in the Data Descriptor A cone-beam X-ray computed tomography data collection designed for machine learning. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format<br><br>Versioning Note:Version 2 was generated when the metadata format was updated from JSON to JSON-LD. This was an automatic process that changed only the format, not the contents, of the metadata.
DOI: 10.6084/m9.figshare.9912836.v1
title: Metadata record for: A cone-beam X-ray computed tomography data collection designed for machine learning

description: This dataset contains key characteristics about the data described in the Data Descriptor A cone-beam X-ray computed tomography data collection designed for machine learning. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format
DOI: 10.17028/rd.lboro.9912761
title: Supplementary information files for 'A variability taxonomy to support automation decision-making for manufacturing processes'

description: Supplementary information files for 'A variability taxonomy to support automation decision-making for manufacturing processes'<br>Abstract:Although many manual operations have been replaced by automation in the manufacturing domain, in various industries skilled operators still carry out critical manual tasks such as final assembly. The business case for automation in these areas is difficult to justify due to increased complexity and costs arising out of process variabilities associated with those tasks. The lack of understanding of process variability in automation design means that industrial automation often does not realise the full benefits at the first attempt, resulting in the need to spend additional resource and time, to fully realise the potential. This article describes a taxonomy of variability when considering automation of manufacturing processes. Three industrial case studies were analysed to develop the proposed taxonomy. The results obtained from the taxonomy are discussed with a further case study to demonstrate its value in supporting automation decision-making.<br>
DOI: 10.6084/m9.figshare.9912734
title: 10X protein and mRNA counts

description: Dataset for "RNA velocity and protein acceleration from single-cell multiomics experiments." Source data from 10X Genomics at https://support.10xgenomics.com/single-cell-gene-expression/datasets/3.0.0/pbmc_1k_protein_v3 and https://support.10xgenomics.com/single-cell-gene-expression/datasets/3.0.0/pbmc_10k_protein_v3.
DOI: 10.6084/m9.figshare.9912701
title: Supplementary Material for: Cold Atmospheric Plasma Disarms M1 Protein, an Important Streptococcal Virulence Factor

description: Cold atmospheric plasma (CAP) has been demonstrated to be a successful antiseptic for chronic and infected wounds. Although experimental work has focused on elucidation of the curative power of CAP for wound healing, the molecular mechanisms behind this ability are less understood. To date, the direct effect of CAP on the activity of microbial virulence factors has not been investigated. In the present study, we therefore examined whether CAP can modulate the detrimental activity of M1 protein, one of the most studied <i>Streptococcus pyogenes</i> virulence determinant. Our results show that CAP abolishes the ability of M1 protein to trigger inflammatory host responses. Subsequent mass spectrometric analysis revealed that this effect was caused by oxidation of Met81 and Trp128 located at the sub-N-terminal region of M1 protein provoking a conformational change. Notably, our results also show that CAP has an insignificant effect on the host immune system, supporting the benefits of using CAP to combat infections. Considering the growing number of antibiotic-resistant bacteria, novel antimicrobial therapeutic approaches are urgently needed that do not bear the risk of inducing additional resistance. Our study therefore may open new research avenues for the development of novel approaches for the treatment of skin and wound infections caused by <i>S. pyogenes</i>.
DOI: 10.17028/rd.lboro.9912761.v1
title: Supplementary information files for 'A variability taxonomy to support automation decision-making for manufacturing processes'

description: Supplementary information files for 'A variability taxonomy to support automation decision-making for manufacturing processes'<br>Abstract:Although many manual operations have been replaced by automation in the manufacturing domain, in various industries skilled operators still carry out critical manual tasks such as final assembly. The business case for automation in these areas is difficult to justify due to increased complexity and costs arising out of process variabilities associated with those tasks. The lack of understanding of process variability in automation design means that industrial automation often does not realise the full benefits at the first attempt, resulting in the need to spend additional resource and time, to fully realise the potential. This article describes a taxonomy of variability when considering automation of manufacturing processes. Three industrial case studies were analysed to develop the proposed taxonomy. The results obtained from the taxonomy are discussed with a further case study to demonstrate its value in supporting automation decision-making.<br>
DOI: 10.6084/m9.figshare.9912683
title: Untitled Item

description: The three IgBlast databases<br>
DOI: 10.6084/m9.figshare.9912689
title: Supplementary Material for: Factors Associated with Unsuccessful Recanalization in Mechanical Thrombectomy for Acute Ischemic Stroke

description: <b><i>Introduction:</i></b> Mechanical thrombectomy (MT) for acute ischemic stroke has become a standard therapy, and the recanalization rate has significantly improved. However, some cases of unsuccessful recanalization still occur. We aimed to clarify patient factors associated with unsuccessful recanalization after MT for acute ischemic stroke. <b><i>Methods:</i></b> This was a single-center, retrospective study of 119 consecutive patients with anterior circulation acute ischemic stroke who underwent MT at our hospital between April 2015 and March 2019. Successful recanalization after MT was defined as modified Treatment in Cerebral Ischemia (mTICI) grade 2b or 3, and unsuccessful recanalization was defined as mTICI grades 0–2a. Several factors were analyzed to assess their effect on recanalization rates. <b><i>Results:</i></b> Successful recanalization was achieved in 88 patients (73.9%). The univariate analysis showed that female sex (38.6 vs. 67.7%, <i>p</i> = 0.007), a history of hypertension (53.4 vs. 83.9%, <i>p</i> = 0.003), and a longer time from groin puncture to recanalization (median 75 vs. 124 min, <i>p</i> &lt; 0.001) were significantly associated with unsuccessful recanalization. The multivariate analysis confirmed that female sex (OR 3.18; 95% CI 1.12–9.02, <i>p</i> = 0.030), a history of hypertension (OR 4.84; 95% CI 1.32–17.8, <i>p</i> = 0.018), M2–3 occlusion (OR 4.26; 95% CI 1.36–13.3, <i>p</i> = 0.013), and the time from groin puncture to recanalization (per 10-min increase, OR 1.22; 95% CI 1.09–1.37, <i>p</i> &lt; 0.001) were independently associated with unsuccessful recanalization. <b><i>Conclusion:</i></b> Female sex and a history of hypertension might be predictors of unsuccessful recanalization after MT for anterior circulation acute ischemic stroke. Further studies are needed to fully evaluate predictors of recanalization.
DOI: 10.6084/m9.figshare.9912683.v1
title: Untitled Item

description: The three IgBlast databases<br>