cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6389735.v1
title: Additional file 4: of Stability of gene expression by primary bronchial epithelial cells over increasing passage number

description: Figure S3. Un-normalized mRNA expression of genes related to airway remodeling by primary BECs. Un-normalized mRNA Ct values for TGFβ1 (A.), TGFβ2 (B.), MUC5AC (C.), activin A (D.), and FSTL3 (E.) by BECs at P1 (n = 6 asthma donors, n = 6 healthy donors), P2 (n = 6 asthma donors, n = 6 healthy donors), P3 (n = 4 asthma donors, n = 6 healthy donors), P4 (n = 6 asthma donors, n = 6 healthy donors), and P5 (n = 6 asthma donors, n = 6 healthy donors) are presented as individual data points for each donor cell line. To compare expression of genes at P2-P5 to expression at P1, and to compare patterns of gene expression between asthmatic and healthy donors, ordinary two-way ANOVA with Dunnett’s multiple comparisons test was used for normally distributed data, and Kruskal-Wallis ANOVA with Dunn’s multiple comparisons test was used for non-normally distributed data. (EMF 195 kb)
DOI: 10.6084/m9.figshare.6389708
title: Additional file 2: of Stability of gene expression by primary bronchial epithelial cells over increasing passage number

description: Figure S2. Comparison of gene expression between asthmatic and healthy BECs at passage 1 (P1). Expression of genes related to airway remodeling (panel A.; TGFβ1, TGFβ2, MUC5AC, activin A, and FSTL3), innate immunity and immunomodulatory genes (panel B.; CXCL10, IFIH1, IL-33, and TSLP), and expression of genes associated with airway epithelial basal cells, ciliogenesis, and epithelial tight junctions (panel C.; TP63, KRT5, TUBB4A, TJP1, OCLN, and FOXJ1) by primary asthmatic (grey plots) and healthy (white plots) BECs at P1 (n = 6 asthma donors, n = 6 healthy donors). Expression of each gene (normalized to GAPDH) relative to the median of healthy BECs are presented as box-and-whisker plots which depict the interquartile range and median (the ends of each box represent the upper and lower quartiles, error bars represent the maximum and minimum, and the horizontal line within the box represents the median). The Wilcoxon signed rank test was used to test differences in expression of specific genes between asthmatic and healthy BECs. (EMF 109 kb)
DOI: 10.6084/m9.figshare.6389708.v1
title: Additional file 2: of Stability of gene expression by primary bronchial epithelial cells over increasing passage number

description: Figure S2. Comparison of gene expression between asthmatic and healthy BECs at passage 1 (P1). Expression of genes related to airway remodeling (panel A.; TGFβ1, TGFβ2, MUC5AC, activin A, and FSTL3), innate immunity and immunomodulatory genes (panel B.; CXCL10, IFIH1, IL-33, and TSLP), and expression of genes associated with airway epithelial basal cells, ciliogenesis, and epithelial tight junctions (panel C.; TP63, KRT5, TUBB4A, TJP1, OCLN, and FOXJ1) by primary asthmatic (grey plots) and healthy (white plots) BECs at P1 (n = 6 asthma donors, n = 6 healthy donors). Expression of each gene (normalized to GAPDH) relative to the median of healthy BECs are presented as box-and-whisker plots which depict the interquartile range and median (the ends of each box represent the upper and lower quartiles, error bars represent the maximum and minimum, and the horizontal line within the box represents the median). The Wilcoxon signed rank test was used to test differences in expression of specific genes between asthmatic and healthy BECs. (EMF 109 kb)
DOI: 10.6084/m9.figshare.6389693
title: Additional file 1 of Stability of gene expression by primary bronchial epithelial cells over increasing passage number

description: Primary quantitative PCR datasets. (XLSX 37Â kb)
DOI: 10.6084/m9.figshare.6389693.v1
title: Additional file 1 of Stability of gene expression by primary bronchial epithelial cells over increasing passage number

description: Primary quantitative PCR datasets. (XLSX 37Â kb)
DOI: 10.6084/m9.figshare.6389645
title: Additional file 8 of Identification and analysis of ribosome-associated lncRNAs using ribosome profiling data

description: Table S8. Ribosome association for human and mouse lncRNAs. (XLSX 1515.52 kb)
DOI: 10.6084/m9.figshare.6389645.v1
title: Additional file 8 of Identification and analysis of ribosome-associated lncRNAs using ribosome profiling data

description: Table S8. Ribosome association for human and mouse lncRNAs. (XLSX 1515.52 kb)
DOI: 10.6084/m9.figshare.6389633
title: Additional file 4: of Landscape of copy number variations in Bos taurus: individual â and inter-breed variability

description: Table S1. SO terms classified in two, more general groups as the non-genic and genic regions. (XLSX 8 kb)
DOI: 10.6084/m9.figshare.6389633.v1
title: Additional file 4: of Landscape of copy number variations in Bos taurus: individual â and inter-breed variability

description: Table S1. SO terms classified in two, more general groups as the non-genic and genic regions. (XLSX 8 kb)
DOI: 10.6084/m9.figshare.6389558
title: Additional file 3 of Identification and analysis of ribosome-associated lncRNAs using ribosome profiling data

description: Table S6. Mapping statistics for RNA-seq and Ribo-seq reads. (XLSX 51.4 kb)
DOI: 10.6084/m9.figshare.6389558.v1
title: Additional file 3 of Identification and analysis of ribosome-associated lncRNAs using ribosome profiling data

description: Table S6. Mapping statistics for RNA-seq and Ribo-seq reads. (XLSX 51.4 kb)
DOI: 10.6084/m9.figshare.6389510
title: Additional file 19 of Identification and analysis of ribosome-associated lncRNAs using ribosome profiling data

description: Table S12. Fold change values for NMD analysis in HeLa cells. (XLSX 147 kb)
DOI: 10.6084/m9.figshare.6389510.v1
title: Additional file 19 of Identification and analysis of ribosome-associated lncRNAs using ribosome profiling data

description: Table S12. Fold change values for NMD analysis in HeLa cells. (XLSX 147 kb)
DOI: 10.6084/m9.figshare.6389495
title: Additional file 2 of Bias due to censoring of deaths when calculating extra length of stay for patients acquiring a hospital infection

description: The document is the complete R script used in section 4 for the data analysis. (R 6 kb)
DOI: 10.6084/m9.figshare.6389495.v1
title: Additional file 2 of Bias due to censoring of deaths when calculating extra length of stay for patients acquiring a hospital infection

description: The document is the complete R script used in section 4 for the data analysis. (R 6 kb)
DOI: 10.6084/m9.figshare.6389489
title: Additional file 18 of Identification and analysis of ribosome-associated lncRNAs using ribosome profiling data

description: Table S11. Fold change values for cellular localization analysis in HeLa cells. (XLSX 154 kb)
DOI: 10.6084/m9.figshare.6389489.v1
title: Additional file 18 of Identification and analysis of ribosome-associated lncRNAs using ribosome profiling data

description: Table S11. Fold change values for cellular localization analysis in HeLa cells. (XLSX 154 kb)
DOI: 10.6084/m9.figshare.12893927
title: ROE data - Hybrid vs Wild

description: Data associated with evolutionary rates in populations of wild and crop-wild hybrid radish (Raphanus spp.) in Ontario, Canada. Data are associated with:- emergence and flowering frequency(binary data)- days to emergence, days to flowering, leaf length, stem diameter (means and haldanes)- chlorophyll fluorescence (means)- pollen fertility (means)- white flower colour (mean and haldanes)
DOI: 10.6084/m9.figshare.6389456
title: Additional file 16 of Identification and analysis of ribosome-associated lncRNAs using ribosome profiling data

description: Table S15. Putative ORFs in mouse lncRNAs. (TSV 5478.4 kb)
DOI: 10.6084/m9.figshare.6389456.v1
title: Additional file 16 of Identification and analysis of ribosome-associated lncRNAs using ribosome profiling data

description: Table S15. Putative ORFs in mouse lncRNAs. (TSV 5478.4 kb)
DOI: 10.6084/m9.figshare.6389441
title: Additional file 15 of Identification and analysis of ribosome-associated lncRNAs using ribosome profiling data

description: Table S14. Putative ORFs in human lncRNAs. (TSV 7987.2 kb)
DOI: 10.6084/m9.figshare.6389441.v1
title: Additional file 15 of Identification and analysis of ribosome-associated lncRNAs using ribosome profiling data

description: Table S14. Putative ORFs in human lncRNAs. (TSV 7987.2 kb)
DOI: 10.6084/m9.figshare.6389423
title: Additional file 14 of Identification and analysis of ribosome-associated lncRNAs using ribosome profiling data

description: Table S10. Alignment of mass spectrometry data to mouse trans-lncRNAs. (TSV 5.97 kb)
DOI: 10.6084/m9.figshare.6389423.v1
title: Additional file 14 of Identification and analysis of ribosome-associated lncRNAs using ribosome profiling data

description: Table S10. Alignment of mass spectrometry data to mouse trans-lncRNAs. (TSV 5.97 kb)
DOI: 10.6084/m9.figshare.6389402
title: Additional file 13 of Identification and analysis of ribosome-associated lncRNAs using ribosome profiling data

description: Table S9. Alignment of mass spectrometry data to human trans-lncRNAs. (TSV 9.83 kb)
DOI: 10.6084/m9.figshare.6389402.v1
title: Additional file 13 of Identification and analysis of ribosome-associated lncRNAs using ribosome profiling data

description: Table S9. Alignment of mass spectrometry data to human trans-lncRNAs. (TSV 9.83 kb)
DOI: 10.6084/m9.figshare.6389336
title: Additional file 3: of Predictors of latent tuberculosis infection treatment completion in the US private sector: an analysis of administrative claims data

description: Results of logistic regression models which examine associations between patient characteristics and the completion of at least 5Â months of daily-dose isoniazid treatment for latent tuberculosis infection (Nâ =â 1072). (XLS 31 kb)
DOI: 10.6084/m9.figshare.6389336.v1
title: Additional file 3: of Predictors of latent tuberculosis infection treatment completion in the US private sector: an analysis of administrative claims data

description: Results of logistic regression models which examine associations between patient characteristics and the completion of at least 5Â months of daily-dose isoniazid treatment for latent tuberculosis infection (Nâ =â 1072). (XLS 31 kb)
DOI: 10.6084/m9.figshare.6389330
title: Additional file 10 of Identification and analysis of ribosome-associated lncRNAs using ribosome profiling data

description: Table S7. Analysis of ribosomal associations of mRNAs and lncRNAs. (XLSX 46.7 kb)
DOI: 10.6084/m9.figshare.6389330.v1
title: Additional file 10 of Identification and analysis of ribosome-associated lncRNAs using ribosome profiling data

description: Table S7. Analysis of ribosomal associations of mRNAs and lncRNAs. (XLSX 46.7 kb)
DOI: 10.5517/ccdc.csd.cc25bz2l
title: CCDC 2006539: Experimental Crystal Structure Determination

description: Related Article: Chiara Domestici, Leonardo Tensi, Francesco Zaccaria, Nade Kissimina, Massimiliano Valentini, Roberto D'Amato, Ferdinando Costantino, Cristiano Zuccaccia, Alceo Macchioni|2020|Sci.Bull.|65|1614|doi:10.1016/j.scib.2020.06.015
DOI: 10.5517/ccdc.csd.cc25bz3m
title: CCDC 2006540: Experimental Crystal Structure Determination

description: Related Article: Chiara Domestici, Leonardo Tensi, Francesco Zaccaria, Nade Kissimina, Massimiliano Valentini, Roberto D'Amato, Ferdinando Costantino, Cristiano Zuccaccia, Alceo Macchioni|2020|Sci.Bull.|65|1614|doi:10.1016/j.scib.2020.06.015
DOI: 10.6084/m9.figshare.6389318
title: Additional file 2: of Predictors of latent tuberculosis infection treatment completion in the US private sector: an analysis of administrative claims data

description: Results of a logistic regression model which examines associations between patient characteristics and the completion of ≥6 months of daily-dose isoniazid treatment for latent tuberculosis infection (N = 1072). (XLSX 11 kb)
DOI: 10.6084/m9.figshare.6389318.v1
title: Additional file 2: of Predictors of latent tuberculosis infection treatment completion in the US private sector: an analysis of administrative claims data

description: Results of a logistic regression model which examines associations between patient characteristics and the completion of ≥6 months of daily-dose isoniazid treatment for latent tuberculosis infection (N = 1072). (XLSX 11 kb)
DOI: 10.6084/m9.figshare.6389303
title: Additional file 1: of Predictors of latent tuberculosis infection treatment completion in the US private sector: an analysis of administrative claims data

description: Excel file detailing the billing codes used in the analyses. Each tab provides information about a different variable.Â (XLS 385 kb)
DOI: 10.6084/m9.figshare.6389303.v1
title: Additional file 1: of Predictors of latent tuberculosis infection treatment completion in the US private sector: an analysis of administrative claims data

description: Excel file detailing the billing codes used in the analyses. Each tab provides information about a different variable.Â (XLS 385 kb)
DOI: 10.6084/m9.figshare.6389207
title: Outcomes of protocolised analgesia and sedation in a neurocritical care unit

description: <i>Objectives</i>: Providing analgesia and sedation while allowing for neurological assessment is important in the neurocritical care unit (NCCU), yet data are limited about the effects of protocolised analgesia and sedation. We developed an analgesia-based sedation protocol and evaluated its effect on medication utilisation and costs in the NCCU. <i>Methods</i>: We conducted a retrospective cohort study of patients who are mechanically ventilated and admitted to a 12-bed NCCU over four years. To compare outcomes, we used gamma and negative binomial regression models, and interrupted time-series sensitivity analyses. <i>Results</i>: The study cohort consisted of 1197 patients: 576 pre-protocol and 621 post-protocol. The protocol resulted in an increase in fentanyl use [incidence rate ratio (IRR) = 2.8, (95% confidence limits (CLs) 1.9, 4.2)] and a decrease in propofol use (IRR = 0.8, CLs 0.6, 1.0). There was a decrease in fentanyl (cost ratio = 0.8, CLs 0.5, 1.1) and propofol costs (cost ratio = 0.6, CLs 0.5, 0.8). The sensitivity analyses results were similar. There was no effect on healthcare utilisation, healthcare costs, and in-hospital mortality. <i>Conclusion</i>: Protocolised analgesia and sedation increased analgesia use, decreased sedative use, and reduced medication-associated costs in the NCCU. Our results suggest that similar NCCUs should consider use of population-specific protocols to manage analgesia and sedation.
DOI: 10.6084/m9.figshare.6389207.v1
title: Outcomes of protocolised analgesia and sedation in a neurocritical care unit

description: <i>Objectives</i>: Providing analgesia and sedation while allowing for neurological assessment is important in the neurocritical care unit (NCCU), yet data are limited about the effects of protocolised analgesia and sedation. We developed an analgesia-based sedation protocol and evaluated its effect on medication utilisation and costs in the NCCU. <i>Methods</i>: We conducted a retrospective cohort study of patients who are mechanically ventilated and admitted to a 12-bed NCCU over four years. To compare outcomes, we used gamma and negative binomial regression models, and interrupted time-series sensitivity analyses. <i>Results</i>: The study cohort consisted of 1197 patients: 576 pre-protocol and 621 post-protocol. The protocol resulted in an increase in fentanyl use [incidence rate ratio (IRR) = 2.8, (95% confidence limits (CLs) 1.9, 4.2)] and a decrease in propofol use (IRR = 0.8, CLs 0.6, 1.0). There was a decrease in fentanyl (cost ratio = 0.8, CLs 0.5, 1.1) and propofol costs (cost ratio = 0.6, CLs 0.5, 0.8). The sensitivity analyses results were similar. There was no effect on healthcare utilisation, healthcare costs, and in-hospital mortality. <i>Conclusion</i>: Protocolised analgesia and sedation increased analgesia use, decreased sedative use, and reduced medication-associated costs in the NCCU. Our results suggest that similar NCCUs should consider use of population-specific protocols to manage analgesia and sedation.
DOI: 10.6084/m9.figshare.6389108.v1
title: Sub-critical water extraction of thyreostats from bovine muscle followed by liquid chromatography-tandem mass spectrometry

description: Thyreostats can be used fraudulently to promote a rapid weight increase of breeding animals at low cost. Their severe toxicological effects impose the development of reliable analytical methods to be used in monitoring plans. This work describes an alternative approach to isolate residues of thiouracil, methyl-thiouracil, propyl-thiouracil, phenyl-thiouracil, tapazole and mercaptobenzimidazole from bovine muscle tissue. The developed procedure is based on three steps: <i>i</i>) matrix solid phase dispersion with C<sub>18</sub> for the preliminary sample preparation; <i>ii</i>) subcritical water extraction (SWE) at 160°C and 100 bar; <i>iii</i>) clean-up on an Oasis HLB cartridge. The quantitative determination was performed by liquid chromatography-electrospray-tandem mass spectrometry (LC-MS/MS) in dual polarity ionization by using internal standardization. The SWE-LC-MS/MS method was validated according to the identification criteria of the Commission decision 2002/657/EC. The relative recoveries ranged from 72% to 97%; within-lab reproducibility was less than 18%. The decision limit and the detection capability of all analytes were below the recommended concentration, set at 10 µg kg<sup>−1</sup>, but the validation results demonstrated that this method could only be applied for screening of thiouracil and methyl-thiouracil. Besides the analytical advantages related to the use of water as solvent extraction, the procedure allowed significant removal of lipids, whose detrimental effects on instrumentation and MS sensitivity are well-known.
DOI: 10.6084/m9.figshare.6388880
title: Provenance analysis of Oligocene sandstone from the Cerro Pelón area, southern Gulf of Mexico

description: In southeastern Mexico, Jurassic and Cretaceous rocks are buried beneath voluminous Palaeogenesedimentary successions, the origin of which is still under debate. Some authors proposed that these Palaeogene successions were derived from Proterozoic, granulite-facies rocks of Oaxaquia, a microcontinental block exhumed during a Late Cretaceous–Palaeogene orogenic event driven by variations in convergence rates along the Pacific margin of North America. Alternatively, other authors suggested that these successions were mostly derived from the Guatemala suture complex, which contains eclogite- to greenschist-facies metamorphic rocks that were exhumed along the Caribbean-North America plate boundary during latest Cretaceous and Palaeogene time. In order to test these scenarios, we present new petrographic data, chemical analysis of detrital heavy minerals, and U-Pb ages of detrital zircons to clarify some aspects on the origin of Oligocene sandstones exposed in the Cerro Pelón area, southeastern Mexico. Our data indicate that the studied sandstones were mostly sourced from eclogite- to greenschist-facies metasedimentary, metaigneous, and ultramafic rocks of the Guatemala suture complex. Minor contributions from the Chiapas Massif Complex exposed directly to the south of the Cerro Pelón area are also documented. Based on these data, we conclude that the accumulation of at least part of the Palaeogene stratigraphic record in southeastern Mexico was mostly controlled by the development of the Caribbean-North America plate boundary rather than by orogenic processes at the Pacific margin of North America.
DOI: 10.6084/m9.figshare.6388880.v1
title: Provenance analysis of Oligocene sandstone from the Cerro Pelón area, southern Gulf of Mexico

description: In southeastern Mexico, Jurassic and Cretaceous rocks are buried beneath voluminous Palaeogenesedimentary successions, the origin of which is still under debate. Some authors proposed that these Palaeogene successions were derived from Proterozoic, granulite-facies rocks of Oaxaquia, a microcontinental block exhumed during a Late Cretaceous–Palaeogene orogenic event driven by variations in convergence rates along the Pacific margin of North America. Alternatively, other authors suggested that these successions were mostly derived from the Guatemala suture complex, which contains eclogite- to greenschist-facies metamorphic rocks that were exhumed along the Caribbean-North America plate boundary during latest Cretaceous and Palaeogene time. In order to test these scenarios, we present new petrographic data, chemical analysis of detrital heavy minerals, and U-Pb ages of detrital zircons to clarify some aspects on the origin of Oligocene sandstones exposed in the Cerro Pelón area, southeastern Mexico. Our data indicate that the studied sandstones were mostly sourced from eclogite- to greenschist-facies metasedimentary, metaigneous, and ultramafic rocks of the Guatemala suture complex. Minor contributions from the Chiapas Massif Complex exposed directly to the south of the Cerro Pelón area are also documented. Based on these data, we conclude that the accumulation of at least part of the Palaeogene stratigraphic record in southeastern Mexico was mostly controlled by the development of the Caribbean-North America plate boundary rather than by orogenic processes at the Pacific margin of North America.
DOI: 10.6084/m9.figshare.6388844
title: Calculus Interventions Data

description: N=123 calculus student data. Each row contains data pertaining to an individual student. Condition refers to the type of intervention(s) a student received. The student's score on the calculus exam is broken up into a conceptual score (out of 9 points), a procedural score (out of 9 points), and an overall score (out of 18 points) which is the sum of the conceptual and procedural scores. GPA indicates a student's overall grade point average.
DOI: 10.6084/m9.figshare.6388844.v2
title: Calculus Interventions Data

description: N=123 calculus student data. Each row contains data pertaining to an individual student. Condition refers to the type of intervention(s) a student received. The student's score on the calculus exam is broken up into a conceptual score (out of 9 points), a procedural score (out of 9 points), and an overall score (out of 18 points) which is the sum of the conceptual and procedural scores. GPA indicates a student's overall grade point average.
DOI: 10.6084/m9.figshare.6388844.v1
title: Calculus Interventions Data

description: N=123 calculus student data. Each row contains data pertaining to an individual student. Condition refers to the type of intervention(s) a student received. The student's score on the calculus exam is broken up into a conceptual score (out of 9 points), a procedural score (out of 9 points), and an overall score (out of 18 points) which is the sum of the conceptual and procedural scores. GPA indicates a student's overall grade point average.