cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7782766
title: Quantification of Giant Unilamellar Vesicle Fusion Products by High-Throughput Image Analysis - Imaging Flow Citometry Data

description: Imaging flow citometry (IFC) datasets analysed in "Quantification of Giant Unilamellar Vesicle Fusion Products by High-Throughput Image Analysis" (under revision). The folders contain acquisitions of giant unilamellar vesicles (GUVs) for lipid exchange and content exchange controls, with file naming convention DATE_SAMPLE_REPLICATE.rif, content exchange is indicated by CE samples in the 20230228_CE.zip folder, lipid exchange by LE samples in the 20221222_LE.zip folder. 24 samples per set are included, triplicates of isolated P1 (DOPE Af488 0.6% in LE; Dex-Af488 40 uM for CE), P2 (DOPE Cy50.6% in LE; Dex-Af647 10 uM for CE), NC (P1 + P2 1:1), PC (DOPE Af488 0.3% + DOPE Cy5 0.3 in LE; Dex-Af488 20 uM + Dex-Af647 5 uM for CE), and M samples numbered 1 to 4, prepared by mixing P1, P2 and PC in different ratios (M1= 1:1:1; M2= 1:1:0.5; M3= 1:1:0.1; M4= 1:1:0.05). Only .rif files are provided, they have to be elaborated via compensation and application of an analysis template using the Amnis IDEAS software. Compensation matrices for lipid exchange (20230217_LEcom.ctm) and content exchange (20230217_CEcomp.ctm) are included, as well as the analysis template (Lipid_exchange_analysis_6.2.ast). Gating in the latter may have to be adjusted to analyse LE and CE experiments. 10000 objects in the GUV population or 50000 objects in total were acquired in each file. The files were elaborated in batch mode, outputting the statistic reports (Statistics report CE.txt for CE; Statistics report LE.txt for LE) that were elaborated using an R scirpt (included, IFC_analysis.R)
description: {"references": ["https://doi.org/10.3390/ijms24098241"]}
DOI: 10.15479/at:ista:12933
title: Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster

description: Datasets of the publication "Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster".
DOI: 10.5281/zenodo.7936679
title: 2-Dimensional habitat files for 47 representative marine species

description: <strong>2D marine species habitats in NetCDF format on 0.5*0.5 degree global regular grid.</strong> Based on Close et al. (2006) and converted from .CSV format. Filename is in format 'presence_speciesnumber.nc' where species numbers are listed in the README.txt file (identifier for each species). The README.txt file further contains each species' species_group which is the assigned depth group for each species (1=0-200m epipelagic, 2=200-1000m mesopelagic, 3=sea floor demersal) and species_name which is the Latin name of each species with underscore in between. The species occurs where the variable 'presence' equals 1 (in the accompanying paper we assume this to be the 1995-2014 climatological mean distribution). In the NetCDF files, the variable 'presence' has as an attribute 'species' which contains the Latin species name without underscore.
description: {"references": ["Close, C., et al. (2006). Distribution ranges of commercial fishes and invertebrates. Fishes in Databases and Ecosystems. Fisheries Centre Research Reports. Vancouver, Fisheries Centre, Univ. British Columbia. 14(4).", "Mor\u00e9e, A. L., Clarke, T. M., Cheung, W. W. L., and Fr\u00f6licher, T. L.: Impact of deoxygenation and warming on global marine species in the 21st century, EGUsphere [preprint], https://doi.org/10.5194/egusphere-2022-1364, 2022.", "Mor\u00e9e, A. L., Clarke, T. M., Cheung, W. W. L., and Fr\u00f6licher, T. L.: Impact of deoxygenation and warming on global marine species in the 21st century, Biogeosciences [accepted], 2023"]}
DOI: 10.5281/zenodo.7936678
title: 2-Dimensional habitat files for 47 representative marine species

description: <strong>2D marine species habitats in NetCDF format on 0.5*0.5 degree global regular grid.</strong> Based on Close et al. (2006) and converted from .CSV format. Filename is in format 'presence_speciesnumber.nc' where species numbers are listed in the README.txt file (identifier for each species). The README.txt file further contains each species' species_group which is the assigned depth group for each species (1=0-200m epipelagic, 2=200-1000m mesopelagic, 3=sea floor demersal) and species_name which is the Latin name of each species with underscore in between. The species occurs where the variable 'presence' equals 1 (in the accompanying paper we assume this to be the 1995-2014 climatological mean distribution). In the NetCDF files, the variable 'presence' has as an attribute 'species' which contains the Latin species name without underscore.
description: {"references": ["Close, C., et al. (2006). Distribution ranges of commercial fishes and invertebrates. Fishes in Databases and Ecosystems. Fisheries Centre Research Reports. Vancouver, Fisheries Centre, Univ. British Columbia. 14(4).", "Mor\u00e9e, A. L., Clarke, T. M., Cheung, W. W. L., and Fr\u00f6licher, T. L.: Impact of deoxygenation and warming on global marine species in the 21st century, EGUsphere [preprint], https://doi.org/10.5194/egusphere-2022-1364, 2022.", "Mor\u00e9e, A. L., Clarke, T. M., Cheung, W. W. L., and Fr\u00f6licher, T. L.: Impact of deoxygenation and warming on global marine species in the 21st century, Biogeosciences [accepted], 2023"]}
DOI: 10.22008/fk2/yg9vbm/w7xxqv
title: Karrat_Zinc_data_package.zip

description: :unav
DOI: 10.22008/fk2/yg9vbm
title: Zinc exploration data package - Karrat Group, central West Greenland

description: This data package contains much of the current data available the Karrat area of central West Greenland. Size: 964 MB. Contents 1) Mineral occurrences list 2) Geochemistry (excel files containing tables of geochemistry) a) Rock samples (GEUS and mineral exploration companies) b) Stream sediment samples (GEUS and mineral exploration companies) c) Heavy Mineral Concentrates (GEUS and mineral exploration companies) 3) Selection of reports (GEUS and mineral exploration companies) 4) ArcGIS data presentation with digital data
DOI: 10.5281/zenodo.7321684
title: A comparison of the climate and carbon cycle effects of carbon removal by Afforestation and Reduction of Fossil fuel emissions

description: This dataset is for the journal article titled "A comparison of the climate and carbon cycle effects of carbon removal by Afforestation and Reduction of Fossil fuel emissions".
DOI: 10.5281/zenodo.7321683
title: A comparison of the climate and carbon cycle effects of carbon removal by Afforestation and Reduction of Fossil fuel emissions

description: This dataset is for the journal article titled "A comparison of the climate and carbon cycle effects of carbon removal by Afforestation and Reduction of Fossil fuel emissions".
DOI: 10.6084/m9.figshare.22787519.v3
title: Supplemental Table S1: Descriptive statistics of production, loss, and variability traits included in the analyses.

description: Investigating the relationship between fluctuations in daily milk yield as resilience indicators and health traits in Holstein cattle
DOI: 10.6084/m9.figshare.22787519.v4
title: Supplemental Table S2: Descriptive statistics of production, loss, and variability traits included in the analyses.

description: Investigating the relationship between fluctuations in daily milk yield as resilience indicators and health traits in Holstein cattle
DOI: 10.6084/m9.figshare.22820741
title: Supplemental Table S1: Data editing steps for the phenotypes for daily milk yield data and numbers of cows, lactations, and records preserved after each data editing step.

description: Investigating the relationship between fluctuations in daily milk yield as resilience indicators and health traits in Holstein cattle
DOI: 10.5281/zenodo.7811021
title: Data and code for "Tuning the lattice thermal conductivity in van-der-Waals structures through rotational (dis)ordering"

description: This record contains neuroevolution potential (NEP) models for C, BN, and MoS<sub>2</sub> that have been constructed to model the potential energy surfaces of these materials in the presence of interlayer rotations. It also contains databases with the results from density functional theory calculations that were used for constructing the NEP models. <strong>Databases</strong><br> The <code>*.db</code> files are databases with the results from density functional theory (DFT) calculations. These are sqlite databases in ase format, see here for more information. The <code>demo-database-access.py</code> script illustrates the most basic access. <strong>Models</strong><br> The neuroevolution potential (NEP) models described in the publication can be found in the <code>nep-*.txt</code> files. They can be used in conjunction with the GPUMD package. The calorine package provides a Python interface to GPUMD. <strong>Primitive structures</strong><br> Several primitive structures in extended xyz format can be found in the <code>*.xyz</code> files. These structures have been relaxed using the NEP models included here. The <code>demo-for-using-structures-and-models.py</code> script illustrates how to access the structures and models.
DOI: 10.5281/zenodo.7811020
title: Data and code for "Tuning the lattice thermal conductivity in van-der-Waals structures through rotational (dis)ordering"

description: This record contains neuroevolution potential (NEP) models for C, BN, and MoS<sub>2</sub> that have been constructed to model the potential energy surfaces of these materials in the presence of interlayer rotations. It also contains databases with the results from density functional theory calculations that were used for constructing the NEP models. <strong>Databases</strong><br> The <code>*.db</code> files are databases with the results from density functional theory (DFT) calculations. These are sqlite databases in ase format, see here for more information. The <code>demo-database-access.py</code> script illustrates the most basic access. <strong>Models</strong><br> The neuroevolution potential (NEP) models described in the publication can be found in the <code>nep-*.txt</code> files. They can be used in conjunction with the GPUMD package. The calorine package provides a Python interface to GPUMD. <strong>Primitive structures</strong><br> Several primitive structures in extended xyz format can be found in the <code>*.xyz</code> files. These structures have been relaxed using the NEP models included here. The <code>demo-for-using-structures-and-models.py</code> script illustrates how to access the structures and models.
DOI: 10.7488/ds/3858
title: Isolating the effects of forest regrowth and functional adjustments upon global change impacts on Yucatán's forest biomass
title: Model-data fusion based analysis of climate response of semi-dry tropical forests in the Yucatan, Mexico

description: Tropical forests hold large stocks of carbon in biomass and face pressures from changing climate and anthropogenic disturbance. Understanding the impact of these pressures on biomass is vital for effective forest management and conservation over the next century. Forests' capacity to store biomass under future conditions and accumulate biomass during regrowth after clearance are major knowledge gaps. Here we use chronosequence data, satellite observations and a C-cycle process model to diagnose woody C dynamics in two major dry forest ecotypes (semi-deciduous and semi-evergreen) in Yucatán, Mexico. Woody biomass differences between mature semi-deciduous (90 MgC/ha) and semi-evergreen (175 MgC/ha) forest landscapes are mostly explained by differences in climate (c. 60%), particularly temperature, humidity and soil moisture effects on production. Functional variation in foliar phenology, woody allocation, and wood turnover rate explained c. 40% of biomass differences between ecotypes. Modelling experiments explored varied forest clearance and regrowth cycles, under a range of climate and CO2 change scenarios up to 2100. Climate scenario projections indicate that production and steady state biomass in both ecotypes were reduced by forecast warming and drying (mean biomass 2021-2100 reduced 16-19% compared to 2001-2020), but compensated by fertilisation from rising CO2. Functional analysis indicates that trait adjustments could amplify biomass losses by c. 70%. Experiments with disturbance and recovery across historically reported levels for the Yucatán indicate reductions to mean forest biomass stocks over 2021-2100 similar in magnitude to climate change impacts (10-19% reductions for disturbance with recovery). Forest disturbance without regrowth amplifies biomass loss by three- or four-fold. Our results identify the potential for functional adjustments, hypothesised to limit climate risks, to magnify biomass reductions over the coming century. However, the range of impacts of land use and land use change are as, or more, substantive than the totality of direct and indirect climate impacts. The dataset is related to the upcoming publication "Isolating the effects of regrowth and functional adjustments on climate and land use impacts on Yucatán's forest biomass in the twenty-first century" (in review).
description: All dataset description are provided within the associated readme.txt
DOI: 10.6084/m9.figshare.22787744.v2
title: Supplemental Table S5: Number of specific disease cases included in each disease category and each disease-fluctuation relationship groups (DFR).

description: Investigating the relationship between fluctuations in daily milk yield as resilience indicators and health traits in Holstein cattle
DOI: 10.6084/m9.figshare.22787750.v1
title: Supplemental Table S6: Estimates of parity and lactation stage fixed effect on milk fluctuation traits.

description: Investigating the relationship between fluctuations in daily milk yield as resilience indicators and health traits in Holstein cattle
DOI: 10.6084/m9.figshare.22820804
title: Supplementary Material for: Intrauterine Blood Transfusion for Parvo B19 Induced Fetal Anemia: Neuroimaging Findings and Long-Term Neurological Outcomes

description: INTRODUCTION: We aimed to evaluate neuroimaging findings and long-term neurodevelopment of fetuses and children following intrauterine blood transfusion [IUT] for parvo B19 infection induced anemia compared to those with RBC alloimmunization. METHODS: We conducted a retrospective cohort study including women who underwent an IUT due to fetal anemia between 2006 to 2019 in a tertiary, university-affiliated medical center. The cohort was divided into two: a study group - fetuses affected by congenital parvo-B19 infection; and a control group - fetuses affected by RBC alloimmunization. Retrospective data such as antenatal sonographic evaluations, fetal brain MRI results and short-term fetal and neonatal outcomes were collected. All children underwent a neurodevelopmental evaluation after birth using a Vineland questionnaire. Primary outcome was defined as the presence or absence of neurodevelopmental delay. Secondary outcome was defined as the presence of abnormal fetal neuroimaging findings such as cerebellar hypoplasia, polymicrogyria, intracranial hemorrhage or severe ventriculomegaly. RESULTS: Overall, 71 fetuses requiring at least one IUT were included in the study. Of these, 18 were affected by parvo B19 infection and 53 by RBC alloimmunization with various associated antibodies. Fetuses in the parvo B19 group presented at an earlier gestational age [22.91 ± 3.36 weeks vs. 27.37 ± 4.67 weeks, p=0.002] and were more affected by hydrops [93.33% vs. 16.98%, p&lt;0.001]. Three fetuses out of the 18[16.67%] fetuses in the parvo B19 group died in utero following the IUT. Abnormal neuro-imaging findings were detected in 4/15 [26.7%] of the parvo B19 survivors vs. 2/ 53 [3.8%] of fetuses affected by RBC alloimmunization [p=0.005]. There was no difference in long-term neurodevelopmental delay rates between the children in the study and control groups, as assessed at the average age of 3.65 and 6.53 years, accordingly. CONCLUSION: Fetal anemia due to parvo B19, treated with IUT, might be associated with increased rates of abnormal neuro-sonographic findings. The correlation between those findings and long-term adverse neuro-developmental outcomes requires further investigation
DOI: 10.34740/kaggle/dsv/5689497
title: YouTube Daily
DOI: 10.6084/m9.figshare.22820807
title: Supplementary Material for: Intrauterine Blood Transfusion for Parvo B19 Induced Fetal Anemia: Neuroimaging Findings and Long-Term Neurological Outcomes

description: INTRODUCTION: We aimed to evaluate neuroimaging findings and long-term neurodevelopment of fetuses and children following intrauterine blood transfusion [IUT] for parvo B19 infection induced anemia compared to those with RBC alloimmunization. METHODS: We conducted a retrospective cohort study including women who underwent an IUT due to fetal anemia between 2006 to 2019 in a tertiary, university-affiliated medical center. The cohort was divided into two: a study group - fetuses affected by congenital parvo-B19 infection; and a control group - fetuses affected by RBC alloimmunization. Retrospective data such as antenatal sonographic evaluations, fetal brain MRI results and short-term fetal and neonatal outcomes were collected. All children underwent a neurodevelopmental evaluation after birth using a Vineland questionnaire. Primary outcome was defined as the presence or absence of neurodevelopmental delay. Secondary outcome was defined as the presence of abnormal fetal neuroimaging findings such as cerebellar hypoplasia, polymicrogyria, intracranial hemorrhage or severe ventriculomegaly. RESULTS: Overall, 71 fetuses requiring at least one IUT were included in the study. Of these, 18 were affected by parvo B19 infection and 53 by RBC alloimmunization with various associated antibodies. Fetuses in the parvo B19 group presented at an earlier gestational age [22.91 ± 3.36 weeks vs. 27.37 ± 4.67 weeks, p=0.002] and were more affected by hydrops [93.33% vs. 16.98%, p&lt;0.001]. Three fetuses out of the 18[16.67%] fetuses in the parvo B19 group died in utero following the IUT. Abnormal neuro-imaging findings were detected in 4/15 [26.7%] of the parvo B19 survivors vs. 2/ 53 [3.8%] of fetuses affected by RBC alloimmunization [p=0.005]. There was no difference in long-term neurodevelopmental delay rates between the children in the study and control groups, as assessed at the average age of 3.65 and 6.53 years, accordingly. CONCLUSION: Fetal anemia due to parvo B19, treated with IUT, might be associated with increased rates of abnormal neuro-sonographic findings. The correlation between those findings and long-term adverse neuro-developmental outcomes requires further investigation
DOI: 10.6084/m9.figshare.22820807.v1
title: Supplementary Material for: Intrauterine Blood Transfusion for Parvo B19 Induced Fetal Anemia: Neuroimaging Findings and Long-Term Neurological Outcomes

description: INTRODUCTION: We aimed to evaluate neuroimaging findings and long-term neurodevelopment of fetuses and children following intrauterine blood transfusion [IUT] for parvo B19 infection induced anemia compared to those with RBC alloimmunization. METHODS: We conducted a retrospective cohort study including women who underwent an IUT due to fetal anemia between 2006 to 2019 in a tertiary, university-affiliated medical center. The cohort was divided into two: a study group - fetuses affected by congenital parvo-B19 infection; and a control group - fetuses affected by RBC alloimmunization. Retrospective data such as antenatal sonographic evaluations, fetal brain MRI results and short-term fetal and neonatal outcomes were collected. All children underwent a neurodevelopmental evaluation after birth using a Vineland questionnaire. Primary outcome was defined as the presence or absence of neurodevelopmental delay. Secondary outcome was defined as the presence of abnormal fetal neuroimaging findings such as cerebellar hypoplasia, polymicrogyria, intracranial hemorrhage or severe ventriculomegaly. RESULTS: Overall, 71 fetuses requiring at least one IUT were included in the study. Of these, 18 were affected by parvo B19 infection and 53 by RBC alloimmunization with various associated antibodies. Fetuses in the parvo B19 group presented at an earlier gestational age [22.91 ± 3.36 weeks vs. 27.37 ± 4.67 weeks, p=0.002] and were more affected by hydrops [93.33% vs. 16.98%, p&lt;0.001]. Three fetuses out of the 18[16.67%] fetuses in the parvo B19 group died in utero following the IUT. Abnormal neuro-imaging findings were detected in 4/15 [26.7%] of the parvo B19 survivors vs. 2/ 53 [3.8%] of fetuses affected by RBC alloimmunization [p=0.005]. There was no difference in long-term neurodevelopmental delay rates between the children in the study and control groups, as assessed at the average age of 3.65 and 6.53 years, accordingly. CONCLUSION: Fetal anemia due to parvo B19, treated with IUT, might be associated with increased rates of abnormal neuro-sonographic findings. The correlation between those findings and long-term adverse neuro-developmental outcomes requires further investigation
DOI: 10.5281/zenodo.7935632
title: Perturbations in fatty acid metabolism and collagen production infer pathogenicity of a novel MBTPS2 variant in Osteogenesis imperfecta

description: (i) PCR-sequencing: Chromatograms were generated by PCR-sequencing of a region within exon 4 of MBTPS2 using DNA extracted from a healthy control and the proband's fibroblasts (ii) Gene expression was quantified by qRT-PCR using RNA extracted from fibroblasts. Transcript levels of each gene of interest was calculated using the 2^-deltaCt method with normalization to the average Ct values of endogenous control genes GAPDH, IPO8 and TBP. (iii) Cellular fatty acid content was quantified by GC-MS/MS. Each table represents one technical replicate. Absolute values of each fatty acid are listed in the tables; relative ratios of various fatty acids are calculated at the bottom of each table. (iv) Immunocytochemistry images of ECM proteins (COL1 = collagen type I; COL4 = collagen type IV; COL5 = collagen type V; a2b1 = integrin a2b1) and binding of collagen-hybridising peptide (R-CHP).
DOI: 10.5281/zenodo.7935631
title: Perturbations in fatty acid metabolism and collagen production infer pathogenicity of a novel MBTPS2 variant in Osteogenesis imperfecta

description: (i) PCR-sequencing: Chromatograms were generated by PCR-sequencing of a region within exon 4 of MBTPS2 using DNA extracted from a healthy control and the proband's fibroblasts (ii) Gene expression was quantified by qRT-PCR using RNA extracted from fibroblasts. Transcript levels of each gene of interest was calculated using the 2^-deltaCt method with normalization to the average Ct values of endogenous control genes GAPDH, IPO8 and TBP. (iii) Cellular fatty acid content was quantified by GC-MS/MS. Each table represents one technical replicate. Absolute values of each fatty acid are listed in the tables; relative ratios of various fatty acids are calculated at the bottom of each table. (iv) Immunocytochemistry images of ECM proteins (COL1 = collagen type I; COL4 = collagen type IV; COL5 = collagen type V; a2b1 = integrin a2b1) and binding of collagen-hybridising peptide (R-CHP).
DOI: 10.6084/m9.figshare.22776242
title: Data from high-throughput sequencing analysis of soil microbial samples from Xikuang Mining area, Hunan Province

description: The northern mining area (BKQ), the old mining area (LKQ), and the southern mining area (NKQ) of Xikuang Mountain were chosen. At each mining area, 3 sampling sites were set. All samples were processed with 16S rRNA high-throughput sequencing. Samples LKQ6 and NKQ7were also tested with metagenomics analysis.