cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6008927
title: Additional file 16: of Global analysis of primary mesenchyme cell cis-regulatory modules by chromatin accessibility profiling

description: Table S11. Coordinates for the set of ATAC-seq differential peaks that overlapped DNase-seq differential peaks by at least 75% merged with the set of DNase-seq peaks that overlapped ATAC-seq differential peaks by at least 75%. Column 1: Scaffold: S. purpuratus genome version 3.1 scaffold containing the peak. Column 2: Start: Start coordinate of the peak. Column 3: End: End coordinate of the peak. (XLSX 48 kb)
DOI: 10.6084/m9.figshare.6008927.v1
title: Additional file 16: of Global analysis of primary mesenchyme cell cis-regulatory modules by chromatin accessibility profiling

description: Table S11. Coordinates for the set of ATAC-seq differential peaks that overlapped DNase-seq differential peaks by at least 75% merged with the set of DNase-seq peaks that overlapped ATAC-seq differential peaks by at least 75%. Column 1: Scaffold: S. purpuratus genome version 3.1 scaffold containing the peak. Column 2: Start: Start coordinate of the peak. Column 3: End: End coordinate of the peak. (XLSX 48 kb)
DOI: 10.6084/m9.figshare.6008900
title: Additional file 3: of BALDR: a computational pipeline for paired heavy and light chain immunoglobulin reconstruction in single-cell RNA-seq data

description: Clonal assignments for human single-cell datasets. The single cells were assigned to clonal families based on the V, J and CDR length for paired IGH and IgL chains. (XLSX 46 kb)
DOI: 10.6084/m9.figshare.6008900.v1
title: Additional file 3: of BALDR: a computational pipeline for paired heavy and light chain immunoglobulin reconstruction in single-cell RNA-seq data

description: Clonal assignments for human single-cell datasets. The single cells were assigned to clonal families based on the V, J and CDR length for paired IGH and IgL chains. (XLSX 46 kb)
DOI: 10.6084/m9.figshare.6008879
title: Additional file 13: of Global analysis of primary mesenchyme cell cis-regulatory modules by chromatin accessibility profiling

description: Table S8. Peaks cloned into EpGFPII and injected into S. purpuratus eggs. Column 1: ATAC Peak Name: Peak number obtained from ATAC-seq RPS peak names. These are the peaks cloned into the EpGFPII plasmid. Column 2: Scaffold: S. purpuratus genome version 3.1 scaffold containing the peak. Column 3: Start: Start coordinate of the peak. Column 4: End: End coordinate of the peak. Column 5: Name of closest gene. Column 6: PMC DE gene?: "Yes" if the closest gene is a PMC DE gene. Column 7: DNase-seq Diff Peak?: "Yes" if this peak is also differential in the DNase-seq dataset. Column 8: GFP Expression?: "Yes, PMC-specific" if the construct drives PMC-specific GFP expression in 48-hour embryos. Column 9: Region Cloned: The coordinates of the region (containing the peak plus flanking regions) cloned into the EpGFPII plasmid. Column 10: Orientation wrt Closest Gene: "Normal" orientation indicates that the peak was cloned in its normal orientation relative to the coding strand of the closest gene. "Reversed" means that the orientation was reversed relative to the coding strand of the closest gene. Column 11: Notes: Additional information, if applicable, regarding additional peaks cloned into the same construct. (XLSX 52 kb)
DOI: 10.6084/m9.figshare.6008879.v1
title: Additional file 13: of Global analysis of primary mesenchyme cell cis-regulatory modules by chromatin accessibility profiling

description: Table S8. Peaks cloned into EpGFPII and injected into S. purpuratus eggs. Column 1: ATAC Peak Name: Peak number obtained from ATAC-seq RPS peak names. These are the peaks cloned into the EpGFPII plasmid. Column 2: Scaffold: S. purpuratus genome version 3.1 scaffold containing the peak. Column 3: Start: Start coordinate of the peak. Column 4: End: End coordinate of the peak. Column 5: Name of closest gene. Column 6: PMC DE gene?: "Yes" if the closest gene is a PMC DE gene. Column 7: DNase-seq Diff Peak?: "Yes" if this peak is also differential in the DNase-seq dataset. Column 8: GFP Expression?: "Yes, PMC-specific" if the construct drives PMC-specific GFP expression in 48-hour embryos. Column 9: Region Cloned: The coordinates of the region (containing the peak plus flanking regions) cloned into the EpGFPII plasmid. Column 10: Orientation wrt Closest Gene: "Normal" orientation indicates that the peak was cloned in its normal orientation relative to the coding strand of the closest gene. "Reversed" means that the orientation was reversed relative to the coding strand of the closest gene. Column 11: Notes: Additional information, if applicable, regarding additional peaks cloned into the same construct. (XLSX 52 kb)
DOI: 10.6084/m9.figshare.6008876
title: Additional file 2: of BALDR: a computational pipeline for paired heavy and light chain immunoglobulin reconstruction in single-cell RNA-seq data

description: Results of Ig reconstruction using BALDR. The V(D)J gene annotations, CDR3 sequences, the number of reads mapping to the Ig chain using bowtie2, whether the chain is productive, and the complete sequences are shown for the Ig chains reconstructed using BALDR pipeline for all the human datasets (AW2-AW3 (SE151) plasmablast dataset with and without in silico read normalization, plasmablast AW1 (PE101, PE75, PE50, SE101, SE75, and SE50), the VH (PE76) CD19+ Linâ B cell dataset, and the AW2-AW3 (SE50) for IG_mapped+Unmapped method) and the rhesus macaque datasets (BL8, BL6.1, and BL6.2). When the RT-PCR sequence is available, the V(D)J genes and the CDR3 sequence are also shown for the corresponding chains, and concordance between the BALDR reconstructed chains and the RT-PCR sequence is indicated. The results for Ig reconstruction using the BASIC method are also shown along with matching RT-PCR for AW2-AW3 (SE101 and SE50), VH (PE76), and AW1 (PE101, PE75, PE50, SE101, SE75, and SE50) datasets. (XLSX 2190 kb)
DOI: 10.6084/m9.figshare.6008876.v1
title: Additional file 2: of BALDR: a computational pipeline for paired heavy and light chain immunoglobulin reconstruction in single-cell RNA-seq data

description: Results of Ig reconstruction using BALDR. The V(D)J gene annotations, CDR3 sequences, the number of reads mapping to the Ig chain using bowtie2, whether the chain is productive, and the complete sequences are shown for the Ig chains reconstructed using BALDR pipeline for all the human datasets (AW2-AW3 (SE151) plasmablast dataset with and without in silico read normalization, plasmablast AW1 (PE101, PE75, PE50, SE101, SE75, and SE50), the VH (PE76) CD19+ Linâ B cell dataset, and the AW2-AW3 (SE50) for IG_mapped+Unmapped method) and the rhesus macaque datasets (BL8, BL6.1, and BL6.2). When the RT-PCR sequence is available, the V(D)J genes and the CDR3 sequence are also shown for the corresponding chains, and concordance between the BALDR reconstructed chains and the RT-PCR sequence is indicated. The results for Ig reconstruction using the BASIC method are also shown along with matching RT-PCR for AW2-AW3 (SE101 and SE50), VH (PE76), and AW1 (PE101, PE75, PE50, SE101, SE75, and SE50) datasets. (XLSX 2190 kb)
DOI: 10.6084/m9.figshare.6008861
title: MOESM2 of The impact of Rhodiola rosea on the gut microbial community of Drosophila melanogaster

description: Additional file 2: Table S1. OTU table provided by 16S rRNA amplicon sequencing of female D. melanogaster at early and late stages of the fly lifespan.
DOI: 10.6084/m9.figshare.6008861.v1
title: MOESM2 of The impact of Rhodiola rosea on the gut microbial community of Drosophila melanogaster

description: Additional file 2: Table S1. OTU table provided by 16S rRNA amplicon sequencing of female D. melanogaster at early and late stages of the fly lifespan.
DOI: 10.6084/m9.figshare.6008855
title: Additional file 12: of Global analysis of primary mesenchyme cell cis-regulatory modules by chromatin accessibility profiling

description: Table S21. DNase-seq peaks significantly differentially enriched (DESeq2 nominal p &lt; 0.1) in PMC-minus embryos compared to control embryos. Column definitions as in Additional file 10, Table S7. (XLSX 144 kb)
DOI: 10.6084/m9.figshare.6008855.v1
title: Additional file 12: of Global analysis of primary mesenchyme cell cis-regulatory modules by chromatin accessibility profiling

description: Table S21. DNase-seq peaks significantly differentially enriched (DESeq2 nominal p &lt; 0.1) in PMC-minus embryos compared to control embryos. Column definitions as in Additional file 10, Table S7. (XLSX 144 kb)
DOI: 10.6084/m9.figshare.6008834
title: Additional file 11: of Global analysis of primary mesenchyme cell cis-regulatory modules by chromatin accessibility profiling

description: Table S20. DNase-seq peaks identified in PMC-minus embryos at 28 hpf (mesenchyme blastula stage). Column 1: Scaffold: S. purpuratus genome version 3.1 scaffold containing the peak. Column 2: Peak Start: Start coordinate of the peak. Column 3: Peak end: End coordinate of the peak. (XLSX 2969 kb)
DOI: 10.6084/m9.figshare.6008834.v1
title: Additional file 11: of Global analysis of primary mesenchyme cell cis-regulatory modules by chromatin accessibility profiling

description: Table S20. DNase-seq peaks identified in PMC-minus embryos at 28 hpf (mesenchyme blastula stage). Column 1: Scaffold: S. purpuratus genome version 3.1 scaffold containing the peak. Column 2: Peak Start: Start coordinate of the peak. Column 3: Peak end: End coordinate of the peak. (XLSX 2969 kb)
DOI: 10.6084/m9.figshare.6008831
title: Additional file 1: of Amenable epigenetic traits of dental pulp stem cells underlie high capability of xeno-free episomal reprogramming

description: Table S1. List of commercial and patient-derived dental stem cell samples used. Table S2. DiPS colony counts of dental pulp stem cell samples used for reprogramming under different culture conditions. Figure S1. Transduction efficiencies for reprogramming DPSCs. Figure S2. Generation of iPS cells from DPSCs in the presence of enhancer compounds. Figure S3. Time course during episomal-based reprogramming of DPSCs. Figure S4. Characterisation of DPSCs cultured in xeno-free media. Figure S5. Cytogenetics and in vivo characterisation of DiPS lines generated under xeno-free culture conditions. Table S3. List of differentially methylated regions of selected genes in DPSCs versus ASCs with respect to iPS (DiPS and AiPS) and H1 hES cell lines. Table S4. DNA methylation raw data analysed with multiple probe sets of PAX9 gene that exhibit significant differences between DPSCs and ASCs. Table S5. Top networks by ingenuity pathway analysis (IPA) for differentially methylated genes in ASCs versus AiPS cells that do not exhibit such differences in DPSCs versus DiPS cells. Figure S6. Pluripotent and self-renewal supporting characteristics of DPSCs. (ZIP 8876 kb)
DOI: 10.6084/m9.figshare.6008831.v1
title: Additional file 1: of Amenable epigenetic traits of dental pulp stem cells underlie high capability of xeno-free episomal reprogramming

description: Table S1. List of commercial and patient-derived dental stem cell samples used. Table S2. DiPS colony counts of dental pulp stem cell samples used for reprogramming under different culture conditions. Figure S1. Transduction efficiencies for reprogramming DPSCs. Figure S2. Generation of iPS cells from DPSCs in the presence of enhancer compounds. Figure S3. Time course during episomal-based reprogramming of DPSCs. Figure S4. Characterisation of DPSCs cultured in xeno-free media. Figure S5. Cytogenetics and in vivo characterisation of DiPS lines generated under xeno-free culture conditions. Table S3. List of differentially methylated regions of selected genes in DPSCs versus ASCs with respect to iPS (DiPS and AiPS) and H1 hES cell lines. Table S4. DNA methylation raw data analysed with multiple probe sets of PAX9 gene that exhibit significant differences between DPSCs and ASCs. Table S5. Top networks by ingenuity pathway analysis (IPA) for differentially methylated genes in ASCs versus AiPS cells that do not exhibit such differences in DPSCs versus DiPS cells. Figure S6. Pluripotent and self-renewal supporting characteristics of DPSCs. (ZIP 8876 kb)
DOI: 10.6084/m9.figshare.6008828
title: Additional file 1 of Why are some groups physically active and others not? A contrast group analysis in leisure settings

description: Observation-Data-File. (SAV 25 kb)
DOI: 10.6084/m9.figshare.6008828.v1
title: Additional file 1 of Why are some groups physically active and others not? A contrast group analysis in leisure settings

description: Observation-Data-File. (SAV 25 kb)
DOI: 10.6084/m9.figshare.6008825
title: Additional file 10: of Global analysis of primary mesenchyme cell cis-regulatory modules by chromatin accessibility profiling

description: Table S7. Peaks significantly differentially enriched (DESeq2 nominal p &lt; 0.1) in control, whole embryos compared to U0126-treated, PMC-minus embryos. Column 1: DNase-seq Peak Name: peak number, obtained from DNase-seq RPS peak names. Column 2-9: as described for Additional file 6: Table S5. (XLSX 227 kb)
DOI: 10.6084/m9.figshare.6008825.v1
title: Additional file 10: of Global analysis of primary mesenchyme cell cis-regulatory modules by chromatin accessibility profiling

description: Table S7. Peaks significantly differentially enriched (DESeq2 nominal p &lt; 0.1) in control, whole embryos compared to U0126-treated, PMC-minus embryos. Column 1: DNase-seq Peak Name: peak number, obtained from DNase-seq RPS peak names. Column 2-9: as described for Additional file 6: Table S5. (XLSX 227 kb)
DOI: 10.6084/m9.figshare.6008687
title: Additional file 5: of FusorSV: an algorithm for optimally combining data from multiple structural variation detection methods

description: This file contains Table S5. (XLSX 145 kb)
DOI: 10.6084/m9.figshare.6008687.v1
title: Additional file 5: of FusorSV: an algorithm for optimally combining data from multiple structural variation detection methods

description: This file contains Table S5. (XLSX 145 kb)
DOI: 10.6084/m9.figshare.6008666
title: Additional file 4: of Downregulation of the NLRP3 inflammasome by adiponectin rescues Duchenne muscular dystrophy

description: Individual data values for all experiments are available in an Excel file. Data sets are sorted by figure, and an additional section is provided in order to recap n &lt; 6 experiments. (XLSX 45 kb)
DOI: 10.6084/m9.figshare.6008666.v1
title: Additional file 4: of Downregulation of the NLRP3 inflammasome by adiponectin rescues Duchenne muscular dystrophy

description: Individual data values for all experiments are available in an Excel file. Data sets are sorted by figure, and an additional section is provided in order to recap n &lt; 6 experiments. (XLSX 45 kb)
DOI: 10.6084/m9.figshare.6008657
title: Additional file 3: of Endemic, exotic and novel apicomplexan parasites detected during a national study of ticks from companion animals in Australia

description: Table S3. Prevalence of Apicomplexa species Australia-wide and in each state and territory summarised for all tick species from all hosts, individual tick species from all hosts, and individual tick species from dogs, cats and horses. (XLSX 35 kb)
DOI: 10.6084/m9.figshare.6008657.v1
title: Additional file 3: of Endemic, exotic and novel apicomplexan parasites detected during a national study of ticks from companion animals in Australia

description: Table S3. Prevalence of Apicomplexa species Australia-wide and in each state and territory summarised for all tick species from all hosts, individual tick species from all hosts, and individual tick species from dogs, cats and horses. (XLSX 35 kb)
DOI: 10.6084/m9.figshare.6008648
title: MOESM1 of Estimation of leaf traits from reflectance measurements: comparison between methods based on vegetation indices and several versions of the PROSPECT model

description: Additional file 1. Contains the experimental dataset used in this study e.g. the measured wheat leaf reflectance over the white background and the corresponding chlorophyll a and b, carotenoid, dry matter and water contents. The EXCEL file includes 4 sheets. The first sheet is the description of the dataset. The sheet ‘reflectance_Chl’ includes the leaf reflectance over the white background measured from 400 mm to 2200 mm for 186 wheat leaves and the corresponding chlorophyll a and b and carotenoid content measured destructively. The sheet ‘reflectance_Cw_Cm’ is the leaf reflectance over the white background measured from 350 mm to 2500 mm for 186 wheat leaves and the corresponding water and dry matter contents from destructive measurements. Sheet ‘reflectance of white background’ describes the reflectance of the white background.
DOI: 10.6084/m9.figshare.6008648.v1
title: MOESM1 of Estimation of leaf traits from reflectance measurements: comparison between methods based on vegetation indices and several versions of the PROSPECT model

description: Additional file 1. Contains the experimental dataset used in this study e.g. the measured wheat leaf reflectance over the white background and the corresponding chlorophyll a and b, carotenoid, dry matter and water contents. The EXCEL file includes 4 sheets. The first sheet is the description of the dataset. The sheet ‘reflectance_Chl’ includes the leaf reflectance over the white background measured from 400 mm to 2200 mm for 186 wheat leaves and the corresponding chlorophyll a and b and carotenoid content measured destructively. The sheet ‘reflectance_Cw_Cm’ is the leaf reflectance over the white background measured from 350 mm to 2500 mm for 186 wheat leaves and the corresponding water and dry matter contents from destructive measurements. Sheet ‘reflectance of white background’ describes the reflectance of the white background.
DOI: 10.6084/m9.figshare.6008639
title: Additional file 2: of FusorSV: an algorithm for optimally combining data from multiple structural variation detection methods

description: Shell script used for population SV calling using GenomeSTRiP. (SH 10 kb)
DOI: 10.6084/m9.figshare.6008639.v1
title: Additional file 2: of FusorSV: an algorithm for optimally combining data from multiple structural variation detection methods

description: Shell script used for population SV calling using GenomeSTRiP. (SH 10 kb)
DOI: 10.6084/m9.figshare.6008279
title: EVALUATION OF ASPHALTENE PRECIPITATION IN DIFFERENT CONDITIONS OF COMPOSITION, TEMPERATURE, AND PRESSION

description: Asphaltenes are a heavy fraction of petroleum with the ability for self-association, a phenomenon that can occur spontaneously in the reservoirs or in any of the various stages of production and processing, depending on variations in pressure, temperature, composition and shearing, among others. In this work, it was evaluated the precipitation of asphaltenes in two oils (P01 and P02) in different conditions of temperature and pressure and in the absence or presence of CO2. Under high pressure and temperature conditions, the precipitation of asphaltenes was observed in the presence of CO2 in mixtures with methane, while the addition of propane induced precipitation in the absence of CO2. The results of analyses elemental (CHNO), SEM, FTIR and LDI-MS were consistent with the structure assigned to samples of this nature (oils, maltenes and fractions of asphaltenes insoluble in n-pentane, C5I, and n-heptane, C7I).
DOI: 10.6084/m9.figshare.6008279.v1
title: EVALUATION OF ASPHALTENE PRECIPITATION IN DIFFERENT CONDITIONS OF COMPOSITION, TEMPERATURE, AND PRESSION

description: Asphaltenes are a heavy fraction of petroleum with the ability for self-association, a phenomenon that can occur spontaneously in the reservoirs or in any of the various stages of production and processing, depending on variations in pressure, temperature, composition and shearing, among others. In this work, it was evaluated the precipitation of asphaltenes in two oils (P01 and P02) in different conditions of temperature and pressure and in the absence or presence of CO2. Under high pressure and temperature conditions, the precipitation of asphaltenes was observed in the presence of CO2 in mixtures with methane, while the addition of propane induced precipitation in the absence of CO2. The results of analyses elemental (CHNO), SEM, FTIR and LDI-MS were consistent with the structure assigned to samples of this nature (oils, maltenes and fractions of asphaltenes insoluble in n-pentane, C5I, and n-heptane, C7I).
DOI: 10.6084/m9.figshare.6008273
title: PHENOMENOLOGICAL APPROACHES TO STUDY LEARNING IN THE TERTIARY LEVEL CHEMISTRY LABORATORY

description: Despite the widespread notion amongst chemistry educators that the laboratory is essential to learn chemistry, it is often a neglected area of teaching and, arguably, of educational research. Research has typically focused on secondary education, single institutions, and isolated interventions that are mostly assessed quantitatively. It has also honed in on compartmentalised features instead of searching understanding of broader aspects of learning through experimentation. This paper contends there is a gap in subject specific, tertiary level research that is comprehensive and learning-centred instead of fragmented and instruction-based. A shift in focus requires consideration of methodological approaches that can effectively tackle the challenges of researching complex learning environments. This paper reckons qualitative approaches, specifically phenomenology, are better suited for this purpose. To illustrate this potential, it summarises an exemplar phenomenological study that investigated students’ experience of change in instructional style from an expository (traditional) laboratory program to one that was cooperative and project-based (reformed). The study suggests the experience was characterised by a transition from a learning environment that promoted mindless behaviour to one in which students were mindfully engaged in their learning. Thus, this work puts forth the use of Mindfulness Theory to investigate and support design of laboratory experiences.
DOI: 10.6084/m9.figshare.6008267
title: PEDAGOGICAL LINK-MAKING IN HIGHER EDUCATION SCIENCE CLASSROOMS

description: The higher Education, when compared to basic Education, deals with much more specialized knowledge, usually thought in more technical terms. This specialization of the disciplinary fields that are objects of the graduate courses and the technical character present in most of these courses tend to compartmentalize the knowledge. We developed this work with the aim of analyzing the pedagogical link-making, as proposed by Scott, Mortimer and Ametller (2011), used by four professors of Higher Education, when teaching a class. We observe that the links between the content and the context depend on the area in which the professor acts. Micro and meso continuity links, in turn, do not depend on the area of knowledge, but on the performance of the professor. Macro relations, which could help build a coherent idea of the curriculum, are little present in the lessons of all the professors analysed.
DOI: 10.6084/m9.figshare.6008267.v1
title: PEDAGOGICAL LINK-MAKING IN HIGHER EDUCATION SCIENCE CLASSROOMS

description: The higher Education, when compared to basic Education, deals with much more specialized knowledge, usually thought in more technical terms. This specialization of the disciplinary fields that are objects of the graduate courses and the technical character present in most of these courses tend to compartmentalize the knowledge. We developed this work with the aim of analyzing the pedagogical link-making, as proposed by Scott, Mortimer and Ametller (2011), used by four professors of Higher Education, when teaching a class. We observe that the links between the content and the context depend on the area in which the professor acts. Micro and meso continuity links, in turn, do not depend on the area of knowledge, but on the performance of the professor. Macro relations, which could help build a coherent idea of the curriculum, are little present in the lessons of all the professors analysed.