cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7381550.v1
title: Central Composite Experimental Designs for Multiple Responses with Different Models

description: Central Composite Designs (CCDs) [Box and Wilson [1951]] are widely accepted and used experimental designs for fitting second order polynomial models in response surface methods. However, these designs are based only on the number of explanatory variables being investigated. In a multi-response problem where prior information is available in the form of a screening experiment or previous process knowledge, investigators often know which factors will be used in the estimation of each response. This work presents an alternative design based on CCDs that allows main effects to be aliased for factors that are not related to the same response. This results in fewer required runs than current designs, saving investigators both time and money, by taking this prior information into account. R-package “DoE.multi.response” is included as a supplement for constructing these designs.
DOI: 10.7284/124081
title: Fluorometer data collected during research cruise OC1603B using a WET Labs WETStar instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7381541.v1
title: Bone changes in the lower limbs from participation in an FES rowing exercise program implemented within two years after traumatic spinal cord injury

description: <b>Objective</b>: To determine the effect of a functional electrical stimulation (FES) rowing program on bone mineral density (BMD) when implemented within two years after SCI. <b>Design</b>: Prospective. <b>Setting</b>: Health Care Facility. <b>Participants</b>: Convenience sample; four adults with recent (&lt;2 years) traumatic, motor complete SCI (C7-T12 AIS A-B). <b>Intervention</b>: A 90-session FES rowing exercise program; participants attended 30-minute FES training sessions approximately three times each week for the duration of their participation. <b>Outcome Measures</b>: BMD in the distal femur and tibia were measured using peripheral Quantitative Computed Tomography (pQCT) at enrollment (T<sub>0</sub>) and after 30 (T<sub>1</sub>), 60 (T<sub>2</sub>), and 90 (T<sub>3</sub>) sessions. Bone stimulus was calculated for each rower at each time point using the average number of weekly loading cycles, peak foot reaction force, and bone mineral content from the previous time point. A regression analysis was used to determine the relationship between calculated bone stimulus and change in femoral trabecular BMD between time points. <b>Results</b>: Trabecular BMD in the femur and tibia decreased for all participants in T<sub>0-1</sub>, but the rate of loss slowed or reversed between T<sub>1-2</sub>, with little-to-no bone loss for most participants during T<sub>2-3</sub>. The calculated bone stimulus was significantly correlated with change in femoral trabecular BMD (P = 0.016; R<sup>2 </sup>= 0.458). <b>Conclusion</b>: Consistent participation in an FES rowing program provides sufficient forces and loading cycles to reduce or reverse expected bone loss at the distal femur and tibia, at least temporarily, in some individuals within two years after SCI. <b>Trial Registration</b>: NCT02008149.
DOI: 10.7284/124077
title: GNSS (Global Navigation Satellite System) data collected during research cruise OC1603B using a Ashtech ADU5 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/124082
title: Gyrocompass data collected during research cruise OC1603B using a Sperry MK-37 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/124083
title: PTU (Pressure, Temperature, Humidity) data collected during research cruise OC1603B using a Vaisala PTU300 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/124084
title: Radiometer data collected during research cruise OC1603B using a RMR Co. PRP instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/124085
title: Water Temperature data collected during research cruise OC1603B using a Sea-Bird SBE-38 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7381400
title: Metabolite BridgeDb ID Mapping Database (20181126)

description: BridgeDb ID mapping database for metabolites, using HMDB 4.0 (Release of 29-09-2018), ChEBI 169 (Release of 01 Nov. 2018), and Wikidata (26 Nov. 2018) as data sources.<br>Several updated mappings, with additional test to eliminate double mappings in WikiPathways (from Wikidata to any other type of included database).<br><i>This work was funded by ELIXIR, the research infrastructure for life-science data.</i>
DOI: 10.7284/124086
title: Transmissometer data collected during research cruise OC1603B using a WET Labs C-Star instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7381400.v1
title: Metabolite BridgeDb ID Mapping Database (20181126)

description: BridgeDb ID mapping database for metabolites, using HMDB 4.0 (Release of 29-09-2018), ChEBI 169 (Release of 01 Nov. 2018), and Wikidata (26 Nov. 2018) as data sources.<br>Several updated mappings, with additional test to eliminate double mappings in WikiPathways (from Wikidata to any other type of included database).<br><i>This work was funded by ELIXIR, the research infrastructure for life-science data.</i>
DOI: 10.7284/124087
title: TSG (Thermosalinograph) data collected during research cruise OC1603B using a Sea-Bird SBE-45 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/124100
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise OC1603C using a Hawaii UHDAS instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7381358.v1
title: Beyond density: municipal expenditures and the shape and location of development

description: A clear understanding of the relationship between development patterns and municipal expenditures is complicated by how one chooses to quantify these patterns. Extant literature often employs a single density measure to capture the low-density nature of sprawl. While density provides an intuitive link to economies of scale and congestion costs, it fails to capture other spatial characteristics of sprawl related to centrality, connectedness, and mixed use that may influence municipal expenditures according to Smart Growth and New Urbanism advocates. This study uses Massachusetts orthoimagery data to construct multidimensional measures of residential and commercial land use patterns. Municipal expenditures associated with public works, fire, and police are regressed on multidimensional measures of land use as well as a number of demand controls. Findings indicate that economies and diseconomies do exist with respect to the multidimensional metrics considered. Support is mixed for development patterns emphasized by Smart Growth and New Urbanism advocates.
DOI: 10.7284/124090
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise OC1603C using a Sea-Bird SBE-911+ instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7381304
title: The role of DNA methylation in human trophoblast differentiation

description: The placenta is a vital fetal exchange organ connecting mother and baby. Specialised placental epithelial cells, called trophoblasts, are essential for adequate placental function. Trophoblasts transform the maternal vasculature to allow efficient blood flow to the placenta and facilitate adequate nutrient uptake. Placental development is in part regulated by epigenetic mechanisms. However, our understanding of how DNA methylation contributes to human trophoblast differentiation is limited. To better understand how genome-wide methylation differences affect trophoblast differentiation, reduced representation bisulfite sequencing (RRBS) was conducted on four matched sets of trophoblasts; side-population trophoblasts (a candidate human trophoblast stem cell population), cytotrophoblasts (an intermediate progenitor population), and extravillous trophoblasts (EVT, a terminally differentiated population) each isolated from the same first trimester placenta. Each trophoblast population had a distinct methylome. In line with their close differentiation relationship, the methylation profile of side-population trophoblasts was most similar to cytotrophoblasts, whilst EVT had the most distinct methylome. In comparison to mature trophoblast populations, side-population trophoblasts exhibited differential methylation of genes and miRNAs involved in cell cycle regulation, differentiation, and regulation of pluripotency. A combined methylomic and transcriptomic approach was taken to better understand cytotrophoblast differentiation to EVT. This revealed methylation of 41 genes involved in epithelial to mesenchymal transition and metastatic cancer pathways, which likely contributes to the acquisition of an invasive EVT phenotype. However, the methylation status of a gene did not always predict gene expression. Therefore, while CpG methylation plays a role in trophoblast differentiation, it is likely not the only regulatory mechanism involved in this process.
DOI: 10.6084/m9.figshare.7381301
title: Dataset for: Baicalin targets the AKT-PH domain, activates AKT/GSK3β phosphorylation and improves glucose metabolism

description: Baicalin is one of the main flavonoids of the dried root of Scutellaria baicalensis Georgi and is reported to exert beneficial effects on the regulation of glucose/lipid metabolism. However, understanding the specific target and unique mechanism of improving glucose utilization is a challenge. In this paper, target fishing via with baicalin probe revealed that baicalin was bound with AKT. An immunofluorescence assay further demonstrated the colocalization of baicalin with AKT in the cytoplasm. A competitive test and virtual docking showed that baicalin might bind to the pleckstrin homology (PH) domain of AKT. The specific binding hampered AKT membrane translocation, activated the phosphorylation of AKT on Ser473, induced the downstream glycogen synthase kinase 3β (GSK3β) activation, and affected glycogen synthesis.
DOI: 10.6084/m9.figshare.7381301.v1
title: Dataset for: Baicalin targets the AKT-PH domain, activates AKT/GSK3β phosphorylation and improves glucose metabolism

description: Baicalin is one of the main flavonoids of the dried root of Scutellaria baicalensis Georgi and is reported to exert beneficial effects on the regulation of glucose/lipid metabolism. However, understanding the specific target and unique mechanism of improving glucose utilization is a challenge. In this paper, target fishing via with baicalin probe revealed that baicalin was bound with AKT. An immunofluorescence assay further demonstrated the colocalization of baicalin with AKT in the cytoplasm. A competitive test and virtual docking showed that baicalin might bind to the pleckstrin homology (PH) domain of AKT. The specific binding hampered AKT membrane translocation, activated the phosphorylation of AKT on Ser473, induced the downstream glycogen synthase kinase 3β (GSK3β) activation, and affected glycogen synthesis.
DOI: 10.7284/124093
title: Fluorometer data collected during research cruise OC1603C using a WET Labs WETStar instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7381304.v2
title: The role of DNA methylation in human trophoblast differentiation

description: The placenta is a vital fetal exchange organ connecting mother and baby. Specialised placental epithelial cells, called trophoblasts, are essential for adequate placental function. Trophoblasts transform the maternal vasculature to allow efficient blood flow to the placenta and facilitate adequate nutrient uptake. Placental development is in part regulated by epigenetic mechanisms. However, our understanding of how DNA methylation contributes to human trophoblast differentiation is limited. To better understand how genome-wide methylation differences affect trophoblast differentiation, reduced representation bisulfite sequencing (RRBS) was conducted on four matched sets of trophoblasts; side-population trophoblasts (a candidate human trophoblast stem cell population), cytotrophoblasts (an intermediate progenitor population), and extravillous trophoblasts (EVT, a terminally differentiated population) each isolated from the same first trimester placenta. Each trophoblast population had a distinct methylome. In line with their close differentiation relationship, the methylation profile of side-population trophoblasts was most similar to cytotrophoblasts, whilst EVT had the most distinct methylome. In comparison to mature trophoblast populations, side-population trophoblasts exhibited differential methylation of genes and miRNAs involved in cell cycle regulation, differentiation, and regulation of pluripotency. A combined methylomic and transcriptomic approach was taken to better understand cytotrophoblast differentiation to EVT. This revealed methylation of 41 genes involved in epithelial to mesenchymal transition and metastatic cancer pathways, which likely contributes to the acquisition of an invasive EVT phenotype. However, the methylation status of a gene did not always predict gene expression. Therefore, while CpG methylation plays a role in trophoblast differentiation, it is likely not the only regulatory mechanism involved in this process.
DOI: 10.7284/124089
title: GNSS (Global Navigation Satellite System) data collected during research cruise OC1603C using a Ashtech ADU5 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7381304.v1
title: The role of DNA methylation in human trophoblast differentiation

description: The placenta is a vital fetal exchange organ connecting mother and baby. Specialised placental epithelial cells, called trophoblasts, are essential for adequate placental function. Trophoblasts transform the maternal vasculature to allow efficient blood flow to the placenta and facilitate adequate nutrient uptake. Placental development is in part regulated by epigenetic mechanisms. However, our understanding of how DNA methylation contributes to human trophoblast differentiation is limited. To better understand how genome-wide methylation differences affect trophoblast differentiation, reduced representation bisulfite sequencing (RRBS) was conducted on four matched sets of trophoblasts (a candidate human trophoblast stem cell population), cytotrophoblasts (an intermediate progenitor population) and extravillous trophoblasts (EVT, a terminally differentiated population) each isolated from the same first trimester placenta. Each trophoblast population had a distinct methylome. In line with their close differentiation relationship, the methylation profile of side-population trophoblasts was most similar to cytotrophoblasts, whilst EVT had the most distinct methylome. In comparison to mature trophoblast populations, side-population trophoblasts exhibited differential methylation of genes and miRNAs involved in cell cycle regulation, differentiation, and regulation of pluripotency. A combined methylomic and transcriptomic approach was taken to better understand cytotrophoblast differentiation to EVT. This revealed methylation of 41 genes involved in epithelial to mesenchymal transition and metastatic cancer pathways, which likely contributes to the acquisition of an invasive EVT phenotype. However, the methylation status of a gene did not always predict gene expression. Therefore, while CpG methylation plays a role in trophoblast differentiation, it is likely not the only regulatory mechanism involved in this process.
DOI: 10.7284/124094
title: Gyrocompass data collected during research cruise OC1603C using a Sperry MK-37 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/124095
title: PTU (Pressure, Temperature, Humidity) data collected during research cruise OC1603C using a Vaisala PTU300 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/124096
title: Radiometer data collected during research cruise OC1603C using a RMR Co. PRP instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/124097
title: Water Temperature data collected during research cruise OC1603C using a Sea-Bird SBE-38 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7381145
title: Supplementary Files for Bourke et al (2019) in G3

description: <br>Supplementary Files for Bourke et al (2019) in G3
DOI: 10.7284/124098
title: Transmissometer data collected during research cruise OC1603C using a WET Labs C-Star instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7381145.v1
title: Supplementary Files for Bourke et al (2019) in G3

description: <br>Supplementary Files for Bourke et al (2019) in G3
DOI: 10.6084/m9.figshare.7381130
title: DNA alignments for 15 bryophyte species

description: DNA alignments for 15 bryophyte species from A. Ledent et al. 'No borders during the post-glacial assembly of European bryophytes'
DOI: 10.7284/124099
title: TSG (Thermosalinograph) data collected during research cruise OC1603C using a Sea-Bird SBE-45 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7381121
title: The effect of microRNA-129 on the migration and invasion in NSCLC cells and its mechanism

description: <b>Purpose:</b> To investigate the effect of microRNA-129 on the migration and invasion in (Non small cell lung cancer) NSCLC cells and involved mechanism. <b>Materials and Methods:</b> A549 cells were cultured and transfected with microRNA-129 (miR-129) mimic. Wound-healing assay and transwell assay were used to analyses the migration and invasion of A549 cells, respectively. The SOX4 expression changes were detected by qRT-PCR and Western blot. Dual-luciferase reporter assay was used to determine the binding site between miR-129 and the 3’-UTR of SOX4. A549 cells, miR-129 up-regulated A549 cells and miR-129 + SOX4 up-regulated A549 cells were treated with TGF-β in order to induce the epithelial-mesenchymal transition (EMT). The miR-129 and SOX4 after TGF-β treatment were measured. The EMT markers level changes were detected by western blot. <b>Results:</b> Up-regulation of miR-129 significantly inhibited the migration and invasion of A549 cells. miR-129 mimic transfection could reduce the mRNA and protein level of SOX4. Dual-luciferase reporter assay showed that miR-129 could bind to the 3’-UTR of SOX4. TGF-β induced EMT accompanied by the reduction of miR-129 and elevating of SOX4. Up-regulation of miR-129 could reverse the EMT marker changes caused by TGF-β, however, the SOX4 overexpression antagonized this effect of miR-129. <b>Conclusions:</b> miR-129 could suppress the migration and invasion of A549 cells. The potential mechanism may be that miR-129 inhibit EMT via targeting SOX4.
DOI: 10.6084/m9.figshare.7381121.v1
title: The effect of microRNA-129 on the migration and invasion in NSCLC cells and its mechanism

description: <b>Purpose:</b> To investigate the effect of microRNA-129 on the migration and invasion in (Non small cell lung cancer) NSCLC cells and involved mechanism. <b>Materials and Methods:</b> A549 cells were cultured and transfected with microRNA-129 (miR-129) mimic. Wound-healing assay and transwell assay were used to analyses the migration and invasion of A549 cells, respectively. The SOX4 expression changes were detected by qRT-PCR and Western blot. Dual-luciferase reporter assay was used to determine the binding site between miR-129 and the 3’-UTR of SOX4. A549 cells, miR-129 up-regulated A549 cells and miR-129 + SOX4 up-regulated A549 cells were treated with TGF-β in order to induce the epithelial-mesenchymal transition (EMT). The miR-129 and SOX4 after TGF-β treatment were measured. The EMT markers level changes were detected by western blot. <b>Results:</b> Up-regulation of miR-129 significantly inhibited the migration and invasion of A549 cells. miR-129 mimic transfection could reduce the mRNA and protein level of SOX4. Dual-luciferase reporter assay showed that miR-129 could bind to the 3’-UTR of SOX4. TGF-β induced EMT accompanied by the reduction of miR-129 and elevating of SOX4. Up-regulation of miR-129 could reverse the EMT marker changes caused by TGF-β, however, the SOX4 overexpression antagonized this effect of miR-129. <b>Conclusions:</b> miR-129 could suppress the migration and invasion of A549 cells. The potential mechanism may be that miR-129 inhibit EMT via targeting SOX4.
DOI: 10.7284/124113
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise OC1604B using a Hawaii UHDAS instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.25388/nwu.7381082
title: Data sharing among researchers in South Africa

description: <i>This data depicts the data sharing practices of researchers in South African universities. It further highlights the level of collaboration of researchers in sharing data in the country. <br></i>
DOI: 10.6084/m9.figshare.7381130.v1
title: DNA alignments for 15 bryophyte species

description: DNA alignments for 15 bryophyte species from A. Ledent et al. 'No borders during the post-glacial assembly of European bryophytes'
DOI: 10.7284/124105
title: Fluorometer data collected during research cruise OC1604B using a WET Labs WETStar instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/124101
title: GNSS (Global Navigation Satellite System) data collected during research cruise OC1604B using a Ashtech ADU5 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/124106
title: Gyrocompass data collected during research cruise OC1604B using a Sperry MK-37 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.25388/nwu.7381082.v4
title: Data sharing among researchers in South Africa

description: <i>This data depicts the data sharing practices of researchers in South African universities. It further highlights the level of collaboration of researchers in sharing data in the country. <br></i>
DOI: 10.7284/124107
title: PTU (Pressure, Temperature, Humidity) data collected during research cruise OC1604B using a Vaisala PTU300 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/124108
title: Radiometer data collected during research cruise OC1604B using a RMR Co. PRP instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/124109
title: Radiometer data collected during research cruise OC1604B using a Biospherical QSR-2200 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition