cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.23515965.v1
title: data.zip

description: The following are data used within the repository https://github.com/BIOGOAT/organoid_leukemia_analysis.git
DOI: 10.6084/m9.figshare.23515890.v1
title: Damián et al. 2023 <em>Turnera velutina</em> database to estimate phenotypic integration plasticity

description: Database used to estimate the phenotypic integration of maternal families of <em>Turnera velutina</em> plants under two light environments. <br> The database contains information for 12 maternal families and 260 individuals in which functional traits were measured while exposed to two light treatments: T65, in which plants received 65% of total sunlight, and T50 in which the light availability was 50%. T50 is considered the light environment in which plants typically grow in their natural environment. <br> <strong>The database contains the following traits:</strong> <br> ID: Consecutive number for plants in the database, unique for each plant. LOCATION: Number 1 to 5, indicates the experimental plot wich the plants were stablished at the beggining of the experiment. TREATMENT: Light availability treatment. T65 indicates availability of 65% of sun light while T50 indicates that light was reduced at 50%. The treatments were obtained using an exclosure of shade mesh. FAMILY: Maternal family. All plants were obteined throughtout self-pollination of plants of maternal families in which levels of phenotypic integration were estimated and reported previously (Damián et al. 2019) INDIVIDUAL: Individual plant for each maternal family. There were between 40-50 plants per family, asigned between both light treatments. N_LEAVES: The total numer of leaves sampled on each plant. We only selected apical leaves, fully developed. <br> <strong>Functional traits</strong> LMA: Leaf mass per area HCN_content: Hydrogen cyanide content. The average value obtained in the sampled leaves. TRICHOME_DENSITY: The number of trichomes per milimeter square estimated in two fields of 14 mm<sup>2</sup> CHLOROPHYLL_CONTENT: Chlorophyll content estimated in four points in the leaf with the CCM-200 (Opti-Sciences), and then expressed as g/cm<sup>2</sup> of chlorophyll using the equation in Damián et al. (2018) NITROGEN_CONTENT: Average value of leaf nitrogen content measured in two samples analyzed by mass spectrometry. CN_RATIO: The ratio between carbon and nitrogen, measured in two samples analyzed by mass spectrometry. C13_CONTENT: δ13C content measured in two samples analyzed by mass spectrometry. HEIGHT: Length of the longest branch of each plant. It was used as covariable in the estimation of phenotypic integration in the Package PHENIX (Torices & Muñoz-Pajares) <br> Two samples were analyzed by mass spectrometry <br>
DOI: 10.6084/m9.figshare.23515752.v1
title: Real data results

description: The processed data used for the real application section of the paper: <em>Relaxing parametric assumptions for non-linear Mendelian randomization using a doubly-ranked stratification method.</em> real_data_results_Residual_Strata10: real data results using the residual stratification with 10 strata real_data_results_DoublyRanked_Strata10: real data results using the doubly-ranked stratification with 10 strata real_data_results_Residual_Strata77: real data results using the residual stratification with 77 strata real_data_results_DoublyRanked_Strata77: real data results using the doubly-ranked stratification with 77 strata <br>
DOI: 10.6084/m9.figshare.22699402.v2
title: 16S rDNA sequencing and mass spectrometry-based metabolite profiling of offspring in mice at 24 weeks old

description: Maternal overnutrition can dramatically increase the susceptibility of offspring to metabolic diseases,whereas maternal exercise may improve glucose metabolism in offspring. C57BL/6 female mice were randomly assigned to four subgroups according to a diet and exercise paradigm before and during pregnancy as follows:NC(fed with normal chow diet and sedentary),NCEx(fed with normal chow diet and running),HF (fed with high-fat diet and sedentary),and HFEx(fed with high-fat diet and running).Integrative 16S rDNA sequencing and mass spectrometry-based metabolite profiling were synchronously performed to characterize the effects of maternal exercise on the gut microbiota composition and metabolite alterations in offspring.
DOI: 10.6084/m9.figshare.22699402.v1
title: 2023-16S rDNA sequencing and mass spectrometry-based metabolite profiling of offspring at 24 weeks old

description: Maternal overnutrition can dramatically increase the susceptibility of offspring to metabolic diseases,whereas maternal exercise may improve glucose metabolism in offspring. C57BL/6 female mice were randomly assigned to four subgroups according to a diet and exercise paradigm before and during pregnancy as follows:NC(fed with normal chow diet and sedentary),NCEx(fed with normal chow diet and running),HF (fed with high-fat diet and sedentary),and HFEx(fed with high-fat diet and running).Integrative 16S rDNA sequencing and mass spectrometry-based metabolite profiling were synchronously performed to characterize the effects of maternal exercise on the gut microbiota composition and metabolite alterations in offspring.
DOI: 10.6084/m9.figshare.23516187
title: Understanding and optimizing fish counting techniques based on electrical impedance measurements: dataset

description: A complete dataset for the manuscript "Understanding and optimizing fish counting techniques based on electrical impedance measurements"
DOI: 10.6084/m9.figshare.23515965
title: data.zip

description: The following are data used within the repository https://github.com/BIOGOAT/organoid_leukemia_analysis.git
DOI: 10.6084/m9.figshare.23513307
title: Establishment of SLC7A11‐knockout mouse and its functional investigation in melanoma

description: Establishment of SLC7A11‐knockout mouse and its functional investigation in melanoma
DOI: 10.48758/ufz.12624
title: Eddy covariance rawdata from grassland site 'Am Grossen Bruch' (DE-GsB) in Central Germany for August 2015 (201508)

description: eddy covariance raw data (20Hz) from Am Grossen Bruch (Grosses Bruch) in 2.3m height, acquisition of CSAT3, LI7500 and LI7700 with eddymeas, converted from slt- and dia-files to ascii-format (u, v, w, T_Sonic, CO2, H2O, p_75, CH4, P_77, T_77, SA_DIAG, GA75_DIAG, GA77_DIAG_a, GA77_DIA_b), no time column, individual file names are indicating the starting time of the data acquisition period (according to RFlux-requirements)

sonic alignment: 280 deg
IRGA: LI75H-1600

Am Grossen Bruch DoY 213-243 (Aug 2015)

file: DE-GsB_201508_eddy-raw_csv.zip

more files available in the same repository
DOI: 10.34740/kaggle/dsv/5937193
title: AutoXGB
DOI: 10.5258/soton/d1809
title: Dataset : Port cities of the future database 1

description: This dataset supports the article ' Love thy neighbour: social benefits and port-city relationships' published in the journal Sustainability The data consists of responses to an Online questionnaire and is presented in .csv file format.
DOI: 10.5281/zenodo.6980009
title: Single-cell analysis of megakaryopoiesis in peripheral CD34+ cells: insights into ETV6-related thrombocytopenia

description: This repository contains necessary files for reproducing the analysis in Bigot et al, 2023. The instructions for reproducing the analysis are given in github (https://github.com/poggiteam/ETV6_2020).
DOI: 10.5281/zenodo.6980008
title: Single-cell analysis of megakaryopoiesis in peripheral CD34+ cells: insights into ETV6-related thrombocytopenia

description: This repository contains necessary files for reproducing the analysis in Bigot et al, 2023. The instructions for reproducing the analysis are given in github (https://github.com/poggiteam/ETV6_2020).
DOI: 10.5281/zenodo.4431628
title: Supplement: Functional strain redundancy and persistent phage infection in a Swiss hard cheese starter culture

description: Undefined starter cultures are bacterial communities used in cheese making. They are phenotypically stable and propagated under constant conditions in milk. This makes them interesting to understand the eco-evolutionary dynamics of microbial communities. While cheese starter cultures are known to be dominated by a few bacterial species, little is known about the composition, functional relevance, and temporal dynamics of strain-level diversity. Here, we applied shotgun metagenomics to analyze historical samples spanning 22 years and continuous propagation for 123 generations of an important Swiss cheese starter culture. We found that the bacterial community is highly stable and dominated by two species, Streptococcus thermophilus and Lactobacillus delbrueckii subsp. lactis. Each species is represented by a few coexisting strains. Genome sequencing, metabolomics analysis, and co-culturing experiments show that these strains are functionally redundant, but differ tremendously in their phage resistance potential. Moreover, we identified two highly abundant Streptococcus phages that seem to stably coexist in the community without any negative impact on bacterial growth or strain persistence, and despite the presence of a large diversity of matching CRISPR spacers. Our findings provide novel insights into strain-level diversity in domesticated microbial communities and highlight an important role of bacteria-phage interactions in cheese starter cultures.
DOI: 10.5281/zenodo.4431629
title: Supplement: Functional strain redundancy and persistent phage infection in a Swiss hard cheese starter culture

description: Undefined starter cultures are bacterial communities used in cheese making. They are phenotypically stable and propagated under constant conditions in milk. This makes them interesting to understand the eco-evolutionary dynamics of microbial communities. While cheese starter cultures are known to be dominated by a few bacterial species, little is known about the composition, functional relevance, and temporal dynamics of strain-level diversity. Here, we applied shotgun metagenomics to analyze historical samples spanning 22 years and continuous propagation for 123 generations of an important Swiss cheese starter culture. We found that the bacterial community is highly stable and dominated by two species, Streptococcus thermophilus and Lactobacillus delbrueckii subsp. lactis. Each species is represented by a few coexisting strains. Genome sequencing, metabolomics analysis, and co-culturing experiments show that these strains are functionally redundant, but differ tremendously in their phage resistance potential. Moreover, we identified two highly abundant Streptococcus phages that seem to stably coexist in the community without any negative impact on bacterial growth or strain persistence, and despite the presence of a large diversity of matching CRISPR spacers. Our findings provide novel insights into strain-level diversity in domesticated microbial communities and highlight an important role of bacteria-phage interactions in cheese starter cultures.
DOI: 10.5281/zenodo.8041951
title: Dataset: Relation of pest insect-killing and soilborne pathogen-inhibition abilities to species diversification in environmental Pseudomonas protegens

description: This dataset is related to "<em>Relation of pest insect-killing and soilborne pathogen-inhibition abilities to species diversification in environmental Pseudomonas protegens</em>" and contains all the data obtained from insect experiments and plant-pathogen inhibition assays.
DOI: 10.18112/openneuro.ds004606.v1.0.2
title: A Polish Electroencephalography, Alzheimer’s Risk-genes, Lifestyle and Neuroimaging (PEARL-Neuro) Database
DOI: 10.5517/ccdc.csd.cc2dhvd5
title: CCDC 2219767: Experimental Crystal Structure Determination

description: Related Article: Zhengguo Zhang, Hongxiao Lv, Kun Yang, Xiutang Zhang|2023|Dalton Trans.|52|7119|doi:10.1039/D3DT00554B
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.6084/m9.figshare.23522286
title: Supplementary file 2.zip

description: Fasta file
DOI: 10.6084/m9.figshare.23522286.v1
title: Supplementary file 2.zip

description: Fasta file
DOI: 10.6084/m9.figshare.23522339
title: Supplementary Material 4 from The effect of placentation type, litter size, lactation and gestation length on cancer risk in mammals

description: Raw dataset used in the analyses
DOI: 10.6084/m9.figshare.23522339.v1
title: Supplementary Material 4 from The effect of placentation type, litter size, lactation and gestation length on cancer risk in mammals

description: Raw dataset used in the analyses
DOI: 10.48480/2c10-kp95
title: Parametervergleich der Biomethanbildungs-Kinetiken ausgewählter landwirtschaftlicher Reststoffe
DOI: 10.48758/ufz.12629
title: Eddy covariance rawdata from grassland site 'Am Grossen Bruch' (DE-GsB) in Central Germany for June 2015 (201506)

description: eddy covariance raw data (20Hz) from Am Grossen Bruch (Grosses Bruch) in 2.3m height, acquisition of CSAT3, LI7500 and LI7700 with eddymeas, converted from slt- and dia-files to ascii-format (u, v, w, T_Sonic, CO2, H2O, p_75, CH4, P_77, T_77, SA_DIAG, GA75_DIAG, GA77_DIAG_a, GA77_DIA_b), no time column, individual file names are indicating the starting time of the data acquisition period (according to RFlux-requirements)

sonic alignment: 280 deg
IRGA: LI75H-1600

Am Grossen Bruch DoY 152-181 (Jun 2015)

file: DE-GsB_201506_eddy-raw_csv.zip
DOI: 10.5281/zenodo.8041997
title: OA_Data_DB002

description: The data contains a limited set of CFD and icing conditions, including input geometry and mesh, and post-processed data for collection efficiencies and water catch rates.
DOI: 10.5281/zenodo.8041996
title: OA_Data_DB002

description: The data contains a limited set of CFD and icing conditions, including input geometry and mesh, and post-processed data for collection efficiencies and water catch rates.
DOI: 10.48480/ybe2-3806
title: Parameter comparison of biomethane formation kinetics of selected agricultural residues
DOI: 10.5281/zenodo.8041959
title: Language List

description: Langauge List
DOI: 10.5281/zenodo.8041960
title: Language List

description: Langauge List
DOI: 10.5281/zenodo.8042083
title: Language List

description: Langauge List
DOI: 10.3886/icpsr25622.v1
title: Consumer Expenditure Survey, 2007: Diary Survey
title: Version 1

description: The ongoing Consumer Expenditure Survey (CES) provides a continuous flow of information on the buying habits of American consumers and also furnishes data to support periodic revisions of the Consumer Price Index.
description: National probability sample of households designed to represent the total noninstitutionalized civilian population.
description: Datasets: DS1: Consumer Expenditure Survey, 2007: Diary Survey
description: Noninstitutionalized civilian population of the United States.
description: computer-assisted personal interview (CAPI); face-to-face interviewThese data are distributed exactly as they arrived from the data depositor. ICPSR has not checked or processed this material. Users should consult the investigators if further information is desired.
DOI: 10.6084/m9.figshare.22093037
title: A draft genome assembly of reef-building octocoral <em>Heliopora coerulea</em>

description: <strong>Abstract</strong> Coral reefs are under existential threat from climate change and anthropogenic impacts. Genomic studies have enhanced our knowledge of resilience and responses of some coral species to environmental stress, but reference genomes are lacking for many coral species. The blue coral <em>Heliopora</em> is the only reef-building octocoral genus and exhibits optimal growth at a temperature close to the bleaching threshold of scleractinian corals. Local and high-latitude expansions of <em>Heliopora coerulea</em> were reported in the last decade, but little is known about the molecular mechanisms underlying its thermal resistance. We generated a draft genome of <em>H. coerulea</em> with an assembled size of 429.9 Mb, scaffold N50 of 1.42 Mb and BUSCO completeness of 94.9%. The genome contains 239.1 Mb repetitive sequences, 27,108 protein coding genes, 6,225 lncRNAs, and 79 miRNAs. This reference genome provides a valuable resource for in-depth studies on the adaptive mechanisms of corals under climate change and the evolution of skeleton in cnidarian. <br> <strong>Data Records</strong> The Illumina, PacBio HiFi, and RNAseq data have been deposited in NCBI Sequence Read Archive with accession number SRR23530023, SRR23530024, SRR23530025, SRR23530026, SRR23530027, SRR23530028, SRR23530029, SRR23530030, and SRR23530031, under Bioproject accession number PRJNA936655. The genome assembly has been deposited at GenBank with accession number JASJOG000000000. The genome annotation (“Hco_maker_PASA_Final.gff”) and predicted genes (“Hco_v1.transcript.fasta” and “Hco_v1.protein.fasta”), lncRNA (“Hco_lncRNA.fasta”), and miRNA (“Hco_miRNA_mature.fasta”) has been deposited in the Figshare database. <br> #Genome paper published in <strong>Scientific Data</strong> in 2023.
DOI: 10.6084/m9.figshare.22586110
title: Supplementary Material for: TLR7 activation in M-CSF-dependent monocyte-derived human macrophages potentiates inflammatory responses and prompts neutrophil recruitment

description: Toll-like receptor 7 (TLR7) is an endosomal Pathogen-Associated Molecular Pattern (PAMP) receptor that senses single-stranded RNA (ssRNA) and whose engagement results in the production of type I IFN and pro-inflammatory cytokines upon viral exposure. Recent genetic studies have established that a dysfunctional TLR7-initiated signaling is directly linked to the development of inflammatory responses. We present evidences that TLR7 is preferentially expressed by monocyte-derived macrophages generated in the presence of M-CSF (M-MØ). We now show that TLR7 activation in M-MØ triggers a weak MAPK, NFκB and STAT1 activation and results in low production of type I IFN. Of note, TLR7 engagement re-programs MAFB+ M-MØ towards a pro-inflammatory transcriptional profile characterized by the expression of neutrophil-attracting chemokines (CXCL1-3, CXCL5, CXCL8), whose expression is dependent on the transcription factors MAFB and AhR. Moreover, TLR7-activated M-MØ display enhanced pro-inflammatory responses and a stronger production of neutrophil-attracting chemokines upon secondary stimulation. As aberrant TLR7 signaling and enhanced pulmonary neutrophil/lymphocyte ratio associate with impaired resolution of virus-induced inflammatory responses, these results suggest that targeting macrophage TLR7 might be a therapeutic strategy for viral infections where monocyte-derived macrophages exhibit a pathogenic role.
DOI: 10.6084/m9.figshare.23501031
title: Supplementary Material for: Clinical Significance of Serum Iron Metabolism-Related Markers in Patients with Nasopharyngeal Carcinoma

description: <b><i>Introduction:</i></b> It is known that iron metabolism is dysregulated in nasopharyngeal carcinoma (NPC). However, a meaningful assessment of the iron metabolic status in cancer patient is still under debate. This study aims to evaluate the status of iron metabolism, as well as to explore the correlation between those related serum markers and clinicopathological features of patients with NPC. <b><i>Methods:</i></b> Peripheral blood was collected from 191 pretreatment NPC patients and 191 healthy controls. The red blood cell parameters, plasma Epstein-Barr virus (EBV) DNA load, serum iron (SI), total iron-binding capacity (TIBC), transferrin, soluble transferrin receptor (sTFR), ferritin, and hepcidin were quantitatively detected. <b><i>Results:</i></b> The mean levels of hemoglobin and red blood cell count in the NPC group were significantly lower than those in the control group, while no statistical differences in mean MCV were found between the two groups. Median levels of SI, TIBC, transferrin, and hepcidin were significantly lower in the NPC group than in the control group. Compared to patients with the T1-T2 classification, patients with the T3-T4 classification exhibited significantly lower expression levels of SI and TIBC. Serum levels of ferritin and sTFR were significantly higher in patients with M1 classification than those with M0 classification. The EBV DNA load was associated with serum levels of sTFR and hepcidin. <b><i>Conclusion:</i></b> NPC patients had functional iron deficiency. The degree of iron deficiency was related to the tumor burden and metastasis of NPC. EBV might be involved in the regulation of iron metabolism in the host.
DOI: 10.15151/esrf-dc-1089719643
title: Raw data (diffraction images) for PBD entry 8CJF "AETF, A SINGLE-COMPONENT FLAVIN-DEPENDENT TRYPTOPHAN HALOGENASE, IN COMPLEX WITH 5-BROMO-L-TRYPTOPHAN "

description: Data set collected at the Br absorption edge. The publication describing the experiment can be accessed via the PDB entry.
DOI: 10.15151/esrf-dc-1089735712
title: Raw data (diffraction images) for PDB entry 8CJE "AETF, A SINGLE-COMPONENT FLAVIN-DEPENDENT TRYPTOPHAN HALOGENASE, IN COMPLEX WITH L-TRYPTOPHAN"

description: Data set exhibiting non-merohedral twinning with high twin fraction of 0.4. The point group appears to be 422 but the space group is actually P212121. The publication describing the experiment can be accessed via the PDB entry.
DOI: 10.15151/esrf-dc-1089739837
title: Raw data (diffraction images) for PDB entry 8CJG "AETF, A SINGLE-COMPONENT FLAVIN-DEPENDENT TRYPTOPHAN HALOGENASE, IN COMPLEX WITH 7-BROMO-L-TRYPTOPHAN"

description: Data collected at the Br absorption edge. The data is merohedrally twinned with a twin fraction of 0.2. The actual space group is P43. The publication describing the experiment can be accessed via the PDB entry.
DOI: 10.15785/sbgrid/100
title: X-Ray Diffraction data from Medicago truncatula glutamine synthetase, source of 4IS4 structure

description: Native dataset, low resolution pass
DOI: 10.48786/edbt.2022.17
title: RingBFT: Resilient Consensus over Sharded Ring Topology
DOI: 10.5281/zenodo.5785494
title: Administrative OpenStack Traffic

description: This is a simple dataset which groups the administrative network traffic volume from OpenStack clouds by Virtual Machine (VM) operations. This dataset considers ten different images of OS for the VMs.