cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5873703.v2
title: Pax6 functions in development and evolution of amniote brains

description: This is the datasets to produce the main text figures and supplementary figures in the study of Yamashita et al.(2018).<br>The evolution of unique organ structures is associated with changes in conserved developmental programs. However, functional conservation and variation of homologous transcription factors (TFs) that dictate species-specific cellular dynamics have remained elusive. Here, we dissect shared and divergent functions of Pax6 during amniote brain development. Comparative functional analyses revealed that neurogenic function of Pax6 is highly conserved in the developing mouse and chick pallium, while stage-specific binary functions of Pax6 in neurogenesis are unique to mouse neuronal progenitors, which are consistent with temporal regulation of Notch signaling. Furthermore, we identified that Pax6-dependent enhancer activity of Dbx1 is extensively conserved between mammals and chick, although Dbx1 expression in the developing pallium are highly divergent in these species. Our results suggest that spatio-temporal changes in Pax6-dependent regulatory programs contributed to species-specific neurogenic patterns in mammalian and avian lineages, which underlie morphological divergence of amniote pallial architectures.<br>
DOI: 10.6084/m9.figshare.5873703.v1
title: Pax6 functions in development and evolution of amniote brains

description: This is the datasets to produce the main text figures and supplementary figures in the study of Yamashita et al.(2018).<br>The evolution of unique organ structures is associated with changes in conserved developmental programs. However, functional conservation and variation of homologous transcription factors (TFs) that dictate species-specific cellular dynamics have remained elusive. Here, we dissect shared and divergent functions of Pax6 during amniote brain development. Comparative functional analyses revealed that neurogenic function of Pax6 is highly conserved in the developing mouse and chick pallium, while stage-specific binary functions of Pax6 in neurogenesis are unique to mouse neuronal progenitors, which are consistent with temporal regulation of Notch signaling. Furthermore, we identified that Pax6-dependent enhancer activity of Dbx1 is extensively conserved between mammals and chick, although Dbx1 expression in the developing pallium are highly divergent in these species. Our results suggest that spatio-temporal changes in Pax6-dependent regulatory programs contributed to species-specific neurogenic patterns in mammalian and avian lineages, which underlie morphological divergence of amniote pallial architectures.<br>
DOI: 10.6084/m9.figshare.5873697
title: Testing reticulate versus coalescent origins of Erica lusitanica using a species phylogeny of the northern heathers (Ericeae, Ericaceae)

description: Accepted version of:<br><br>Mugrabi de Kuppler AL, Fagúndez J, Bellstedt DU, Oliver EGH, Léon J, Pirie MD (2015) Testing reticulate versus coalescent origins of Erica lusitanica using a species phylogeny of the northern heathers (Ericeae, Ericaceae). Molecular Phylogenetics and Evolution 88:121–131. http://dx.doi.org/10.1016/j.ympev.2015.04.005<br>
DOI: 10.6084/m9.figshare.5873697.v1
title: Testing reticulate versus coalescent origins of Erica lusitanica using a species phylogeny of the northern heathers (Ericeae, Ericaceae)

description: Accepted version of:<br><br>Mugrabi de Kuppler AL, Fagúndez J, Bellstedt DU, Oliver EGH, Léon J, Pirie MD (2015) Testing reticulate versus coalescent origins of Erica lusitanica using a species phylogeny of the northern heathers (Ericeae, Ericaceae). Molecular Phylogenetics and Evolution 88:121–131. http://dx.doi.org/10.1016/j.ympev.2015.04.005<br>
DOI: 10.6084/m9.figshare.5873685
title: The Effect of Pharmacological Inhibition of Serine Proteases on Neuronal Networks in vitro

description: Data-set related to the publication
DOI: 10.6084/m9.figshare.5873685.v1
title: The Effect of Pharmacological Inhibition of Serine Proteases

description: Data-set related to the publication
DOI: 10.6084/m9.figshare.5873685.v3
title: The Effect of Pharmacological Inhibition of Serine Proteases on Neuronal Networks in vitro

description: Data-set related to the publication
DOI: 10.6084/m9.figshare.5873685.v2
title: The Effect of Pharmacological Inhibition of Serine Proteases on Neuronal Networks in vitro

description: Data-set related to the publication
DOI: 10.6084/m9.figshare.5873649
title: Geomedia_extract_AGENDA_titre&desc.zip

description: RSS feeds of 36 daily newspapers (in french, english, spanish) of 23 countries, RSS feeds international, 1 January 2014-30 June 2015 – UPD (collected during French research project ANR Geomedia : free access for scientific use only)
DOI: 10.6084/m9.figshare.5873649.v2
title: Geomedia_extract_AGENDA_titre&desc.zip

description: RSS feeds of 36 daily newspapers (in french, english, spanish) of 23 countries, RSS feeds international, 1 January 2014-30 June 2015 – UPD (collected during French research project ANR Geomedia : free access for scientific use only)
DOI: 10.6084/m9.figshare.5873649.v1
title: Geomedia_extract_AGENDA_titre&desc.zip

description: RSS feeds of 36 daily newspapers (in french, english, spanish) of 23 countries, RSS feeds international, 1 January 2014-30 June 2015 – UPD (collected during French research project ANR Geomedia : free access for scientific use only)
DOI: 10.6084/m9.figshare.5873640
title: Screening of biomarkers for liver adenoma in low-dose-rate γ-ray-irradiated mice

description: <b>Purpose:</b> Chronic low-dose-rate (20 mGy/day) γ-irradiation increases the incidence of hepatocellular adenomas (HCA) in female B6C3F1 mice. The purpose of this study is to identify potential serum biomarkers for these HCAs by a new approach. <b>Material and methods:</b> Microarray analysis were performed to compare the gene expression profiles of HCAs from mice exposed to low-dose-rate γ-rays with those of normal livers from non-irradiated mice. From the differentially expressed genes, those for possibly secretory proteins were selected. Then, the levels of the proteins in sera were analysed by ELISA. <b>Results:</b> Microarray analysis identified 4181 genes differentially expressed in HCAs (&gt;2.0-fold). From these genes, those for α-fetoprotein (Afp), α-1B-glycoprotein (A1bg) and serine peptidase inhibitor Kazal type-3 (Spink3) were selected as the genes for candidate proteins. ELISA revealed that the levels of Afp and A1bg proteins in sera significantly increased and decreased, respectively, in low-dose-rate irradiated mice with HCAs and also same tendency was observed in human patients with hepatocellular carcinomas. <b>Conclusion:</b> These results indicate that A1bg could be a new serum biomarker for liver tumor. This new approach of using microarray to select genes for secretory proteins is useful for prediction of novel tumor markers in sera.
DOI: 10.6084/m9.figshare.5873640.v2
title: Screening of biomarkers for liver adenoma in low-dose-rate γ-ray-irradiated mice

description: <b>Purpose:</b> Chronic low-dose-rate (20 mGy/day) γ-irradiation increases the incidence of hepatocellular adenomas (HCA) in female B6C3F1 mice. The purpose of this study is to identify potential serum biomarkers for these HCAs by a new approach. <b>Material and methods:</b> Microarray analysis were performed to compare the gene expression profiles of HCAs from mice exposed to low-dose-rate γ-rays with those of normal livers from non-irradiated mice. From the differentially expressed genes, those for possibly secretory proteins were selected. Then, the levels of the proteins in sera were analysed by ELISA. <b>Results:</b> Microarray analysis identified 4181 genes differentially expressed in HCAs (&gt;2.0-fold). From these genes, those for α-fetoprotein (Afp), α-1B-glycoprotein (A1bg) and serine peptidase inhibitor Kazal type-3 (Spink3) were selected as the genes for candidate proteins. ELISA revealed that the levels of Afp and A1bg proteins in sera significantly increased and decreased, respectively, in low-dose-rate irradiated mice with HCAs and also same tendency was observed in human patients with hepatocellular carcinomas. <b>Conclusion:</b> These results indicate that A1bg could be a new serum biomarker for liver tumor. This new approach of using microarray to select genes for secretory proteins is useful for prediction of novel tumor markers in sera.
DOI: 10.6084/m9.figshare.5873640.v1
title: Screening of biomarkers for liver adenoma in low-dose-rate gamma-ray-irradiated mice.

description: Purpose: Chronic low-dose-rate (20 mGy/d) gamma-irradiation increases the incidence of hepatocellular adenomas (HCA) in female B6C3F1 mice. The purpose of this study is to identify potential serum biomarkers for these HCAs by a new approach. Material and methods: Microarray analysis were performed to compare the gene expression profiles of HCAs from mice exposed to low-dose-rate gamma rays with those of normal livers from non-irradiated mice. From the differentially expressed genes, those for possibly secretory proteins were selected. Then the levels of the proteins in sera were analysed by ELISA. Results: Microarray analysis identified 4,181 genes differentially expressed in HCAs (&gt;2.0-fold). From these genes, those for Alpha-fetoprotein (Afp), Alpha-1B- glycoprotein (A1bg) and Serine peptidase inhibitor Kazal type 3 (Spink3) were selected as the genes for candidate proteins. ELISA revealed that the levels of Afp and A1bg proteins in sera significantly increased and decreased, respectively, in low dose-rate irradiated mice with HCAs and also same tendency was observed in human patients with hepatocellular carcinomas. Conclusion: These results indicate that A1bg could be a new serum biomarker for liver tumor. This new approach of using microarray to select genes for secretory proteins is useful for prediction of novel tumor markers in sera.
DOI: 10.6084/m9.figshare.5873616
title: Statistical optimization for lipase production from solid waste of vegetable oil industry

description: The production of biofuel using thermostable bacterial lipase from hot spring bacteria out of low-cost agricultural residue olive oil cake is reported in the present paper. Using a lipase enzyme from <i>Bacillus licheniformis</i>, a 66.5% yield of methyl esters was obtained. Optimum parameters were determined, with maximum production of lipase at a pH of 8.2, temperature 50.8°C, moisture content of 55.7%, and biosurfactant content of 1.693 mg. The contour plots and 3D surface responses depict the significant interaction of pH and moisture content with biosurfactant during lipase production. Chromatographic analysis of the lipase transesterification product was methyl esters, from kitchen waste oil under optimized conditions, generated methyl palmitate, methyl stearate, methyl oleate, and methyl linoleate.
DOI: 10.6084/m9.figshare.5873616.v1
title: Statistical optimization for lipase production from solid waste of vegetable oil industry

description: The production of biofuel using thermostable bacterial lipase from hot spring bacteria out of low-cost agricultural residue olive oil cake is reported in the present paper. Using a lipase enzyme from <i>Bacillus licheniformis</i>, a 66.5% yield of methyl esters was obtained. Optimum parameters were determined, with maximum production of lipase at a pH of 8.2, temperature 50.8°C, moisture content of 55.7%, and biosurfactant content of 1.693 mg. The contour plots and 3D surface responses depict the significant interaction of pH and moisture content with biosurfactant during lipase production. Chromatographic analysis of the lipase transesterification product was methyl esters, from kitchen waste oil under optimized conditions, generated methyl palmitate, methyl stearate, methyl oleate, and methyl linoleate.
DOI: 10.17028/rd.lboro.5873586
title: Supplementary information files for Macroinvertebrate taxonomic and functional trait compositions within lotic habitats affected by river restoration practices

description: Supplementary files for article Macroinvertebrate taxonomic and functional trait compositions within lotic habitats affected by river restoration practices. <br>The widespread degradation of lotic ecosystems has prompted extensive river restoration efforts globally, but many studies have reported modest ecological responses to rehabilitation practices. The functional properties of biotic communities are rarely examined within post-project appraisals, which would provide more ecological information underpinning ecosystem responses to restoration practices and potentially pinpoint project limitations. This study examines macroinvertebrate community responses to three projects which aimed to physically restore channel morphologies. Taxonomic and functional trait compositions supported by widely occurring lotic habitats (biotopes) were examined across paired restored and non-restored (control) reaches. The multivariate location (average community composition) of taxonomic and functional trait compositions differed marginally between control and restored reaches. However, changes in the amount of multivariate dispersion were more robust and indicated greater ecological heterogeneity within restored reaches, particularly when considering functional trait compositions. Organic biotopes (macrophyte stands and macroalgae) occurred widely across all study sites and supported a high alpha (within-habitat) taxonomic diversity compared to mineralogical biotopes (sand and gravel patches), which were characteristic of restored reaches. However, mineralogical biotopes possessed a higher beta (between-habitat) functional diversity, although this was less pronounced for taxonomic compositions. This study demonstrates that examining the functional and structural properties of taxa across distinct biotopes can provide a greater understanding of biotic responses to river restoration works. Such information could be used to better understand the ecological implications of rehabilitation practices and guide more effective management strategies.<br>
DOI: 10.17028/rd.lboro.5873586.v1
title: Supplementary information files for Macroinvertebrate taxonomic and functional trait compositions within lotic habitats affected by river restoration practices

description: Supplementary files for article Macroinvertebrate taxonomic and functional trait compositions within lotic habitats affected by river restoration practices. <br>The widespread degradation of lotic ecosystems has prompted extensive river restoration efforts globally, but many studies have reported modest ecological responses to rehabilitation practices. The functional properties of biotic communities are rarely examined within post-project appraisals, which would provide more ecological information underpinning ecosystem responses to restoration practices and potentially pinpoint project limitations. This study examines macroinvertebrate community responses to three projects which aimed to physically restore channel morphologies. Taxonomic and functional trait compositions supported by widely occurring lotic habitats (biotopes) were examined across paired restored and non-restored (control) reaches. The multivariate location (average community composition) of taxonomic and functional trait compositions differed marginally between control and restored reaches. However, changes in the amount of multivariate dispersion were more robust and indicated greater ecological heterogeneity within restored reaches, particularly when considering functional trait compositions. Organic biotopes (macrophyte stands and macroalgae) occurred widely across all study sites and supported a high alpha (within-habitat) taxonomic diversity compared to mineralogical biotopes (sand and gravel patches), which were characteristic of restored reaches. However, mineralogical biotopes possessed a higher beta (between-habitat) functional diversity, although this was less pronounced for taxonomic compositions. This study demonstrates that examining the functional and structural properties of taxa across distinct biotopes can provide a greater understanding of biotic responses to river restoration works. Such information could be used to better understand the ecological implications of rehabilitation practices and guide more effective management strategies.<br>
DOI: 10.6084/m9.figshare.5873568
title: High-throughput image-based monitoring of cell aggregation and microspheroid formation

description: The Aggregation_data contains the time-lapse images and the results obtained using the proposed methodology.<br>The Validation contains the raw data (manual and automatic segmentation) to compute the relative error, sensitivity and precision as described in the paper.
DOI: 10.6084/m9.figshare.5873568.v1
title: High-throughput image-based monitoring of cell aggregation and microspheroid formation

description: The Aggregation_data contains the time-lapse images and the results obtained using the proposed methodology.<br>The Validation contains the raw data (manual and automatic segmentation) to compute the relative error, sensitivity and precision as described in the paper.
DOI: 10.6084/m9.figshare.5873559
title: MAP_data.xlsx

description: This dataset contains the results of a bleeding-resuscitation animal experiment. After anesthesia and instrumentation (t<sub>bsl</sub>) animals were bled till the initial stroke volume index dropped by 50% (t<sub>0</sub>). Fluid replacement was performed in 4 equivalent steps (t<sub>1-4</sub>) with balanced crystalloid solution to reach the baseline values of MAP. Invasive hemodynamic measurements and blood gas analyses were performed after each step.<br>
DOI: 10.6084/m9.figshare.5873550
title: Dataset on co-occurence of Parvulastra parvivipara and oysters in intertidal boulder-field habitat

description: Percentage cover of oysters and densities of Parvulastra parvivipara sea stars underneath haphazardly selected boulders at two intertidal boulder-field sites (Cape Vivonne and Point Brown) on Western Eyre peninsula, South Australia. Percentage cover and boulder areas were measured by importing photographs (including a ruler for scale) of the underside of boulders into SketchUp v8 and using the programme to make the calculations.
DOI: 10.6084/m9.figshare.5873550.v1
title: Dataset on invasion of Parvulastra parvivipara intertidal boulder-field habitat by Pacific oysters

description: Percentage cover of Pacific oysters (Crassostrea gigas) and densities of Parvulastra parvivipara sea stars underneath haphazardly selected boulders at two intertidal boulder-field sites (Cape Vivonne and Point Brown) on Western Eyre peninsula, South Australia. Percentage cover and boulder areas were measured by importing photographs (including a ruler for scale) of the underside of boulders into SketchUp v8 and using the programme to make the calculations.
DOI: 10.6084/m9.figshare.5873475
title: simu.m from Self-organization across scales: from molecules to organisms

description: Matlab code of Monostable and Bistable 1-component case
DOI: 10.6084/m9.figshare.5873475.v1
title: simu.m from Self-organization across scales: from molecules to organisms

description: Matlab code of Monostable and Bistable 1-component case
DOI: 10.6084/m9.figshare.5873469
title: simu2comp.m from Self-organization across scales: from molecules to organisms

description: Matlab code for 2-component case
DOI: 10.6084/m9.figshare.5873469.v1
title: simu2comp.m from Self-organization across scales: from molecules to organisms

description: Matlab code for 2-component case
DOI: 10.6084/m9.figshare.5873436
title: Groundwater extraction-induced land subsidence: a geodetic strain rate study in Kelantan, Malaysia

description: Kelantan is one of the highest groundwater-consumption states in Malaysia. The groundwater extraction provides an alternative solution for accessing a fresh water supply. However, over-exploitation of groundwater can lead to harmful geomorphological effects. We investigate the deformation rate due to land subsidence in Kelantan, Malaysia, using 17 years of GPS time-series (1999.0 – 2016.0) recorded at 11 GPS sites. Our results agree with a previous study, suggesting that northern Kelantan is subsiding at a maximum rate of 4.22 ± 0.17 mm/yr (1σ confidence level). The region also shows higher ground deformation rates than the other parts of Peninsular Malaysia (0.22 ppm/yr). In addition to the observed vertical subsidence, there is a corresponding horizontal deformation signal that manifests as strain accumulation. The dilatation strain rate shows a clear contractional pattern along the SW-NE trend of the Kelantan River, which is associated with the extensional signal in the surrounding regions.
DOI: 10.6084/m9.figshare.5873436.v1
title: Groundwater extraction-induced land subsidence: a geodetic strain rate study in Kelantan, Malaysia

description: Kelantan is one of the highest groundwater-consumption states in Malaysia. The groundwater extraction provides an alternative solution for accessing a fresh water supply. However, over-exploitation of groundwater can lead to harmful geomorphological effects. We investigate the deformation rate due to land subsidence in Kelantan, Malaysia, using 17 years of GPS time-series (1999.0 – 2016.0) recorded at 11 GPS sites. Our results agree with a previous study, suggesting that northern Kelantan is subsiding at a maximum rate of 4.22 ± 0.17 mm/yr (1σ confidence level). The region also shows higher ground deformation rates than the other parts of Peninsular Malaysia (0.22 ppm/yr). In addition to the observed vertical subsidence, there is a corresponding horizontal deformation signal that manifests as strain accumulation. The dilatation strain rate shows a clear contractional pattern along the SW-NE trend of the Kelantan River, which is associated with the extensional signal in the surrounding regions.
DOI: 10.6084/m9.figshare.5873394
title: cb and ls

description: chinese participnats' cb and ls
DOI: 10.6084/m9.figshare.5873394.v1
title: cb and ls

description: chinese participnats' cb and ls
DOI: 10.6084/m9.figshare.5873370
title: Supplementary Material for: Correlation between B-Type Natriuretic Peptide and N-Terminal pro-B-Type Natriuretic Peptide in a Large Japanese Population at Risk of Stage A Heart Failure

description: <b><i>Background:</i></b> The measurements of B-type natriuretic peptide (BNP) and N-terminal pro-B-type natriuretic peptide (NT-proBNP) are useful for ruling out heart failure and as prognostic markers in not only heart failure populations but also general populations. It is not clear whether these two biomarkers are elevated in parallel or associated with demographic characteristics in large populations at risk of stage A heart failure. Here we investigated the relationship between BNP and NT-proBNP and extended the evaluation of this association to known demographic disparities in stage A heart failure. <b><i>Methods:</i></b> Of 4,310 ambulatory patients, we analyzed the cases of the 3,643 (mean age 65 ± 11 years, 46% male, and 79% on antihypertensive medication) patients whose serum BNP and NT-proBNP levels were both measured and who had a history of and/or risk factors for cardiovascular disease from the Japan Morning Surge-Home Blood Pressure (J-HOP) Study dataset. <b><i>Results:</i></b> The median (25th–75th percentiles) BNP and NT-proBNP values were 18.7 (9.3–38.5) pg/mL and 50.3 (25.5–97.4) pg/mL. There was a significant association between log-transformed BNP and log-transformed NT-proBNP (<i>r</i> = 818, <i>p</i> &lt; 0.001). A multiple linear regression analysis showed that log-transformed NT-proBNP was significantly associated with log-transformed BNP (beta coefficient = 0.774, <i>p</i> &lt; 0.001). When stratified by demographic characteristics, these associations remained (all <i>p</i> &lt; 0.001). <b><i>Conclusion:</i></b> In a large Japanese population at risk of stage A heart failure, there was a significant association between BNP and NT-proBNP after adjustment and stratification by demographics.