cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19769230.v1
title: one-to-one orthologs

description: Manakins represent a family of small suboscine passerine birds characterized by their elaborate courtship displays, non-monogamous mating system, and sexual dimorphism. This family thus serves as a good model for the study of sexual selection. Here we present the genome assemblies of four manakin species (<em>Cryptopipo holochlora, Dixiphia pipra, Machaeropterus deliciosus</em> and <em>Masius chrysopterus</em>) generated by Single-tube Long Fragment Read (stLFR) technology. The assembled genome sizes ranged from 1.10 Gb to 1.19 Gb, with average scaffold N50 of 28 Mb and contig N50 of 169 Kb. On average, 9.82% genome region was annotated as repetitive elements, and 12,059 protein-coding genes were annotated in the genomes. We further identified about 75 Mb Z-linked sequences in manakins, containing 585 to 751 genes, and 600 Kb pseudoautosomal region (PAR). One interesting finding of these Z-linked sequences is that Z-to-autosome/PAR reversal could happen in <em>Masius chrysopterus</em>. These manakin genomes will contribute to a deeper understanding of evolutionary history and sexual selection in these species.
DOI: 10.6084/m9.figshare.19769230
title: one-to-one orthologs

description: Manakins represent a family of small suboscine passerine birds characterized by their elaborate courtship displays, non-monogamous mating system, and sexual dimorphism. This family thus serves as a good model for the study of sexual selection. Here we present the genome assemblies of four manakin species (<em>Cryptopipo holochlora, Dixiphia pipra, Machaeropterus deliciosus</em> and <em>Masius chrysopterus</em>) generated by Single-tube Long Fragment Read (stLFR) technology. The assembled genome sizes ranged from 1.10 Gb to 1.19 Gb, with average scaffold N50 of 28 Mb and contig N50 of 169 Kb. On average, 9.82% genome region was annotated as repetitive elements, and 12,059 protein-coding genes were annotated in the genomes. We further identified about 75 Mb Z-linked sequences in manakins, containing 585 to 751 genes, and 600 Kb pseudoautosomal region (PAR). One interesting finding of these Z-linked sequences is that Z-to-autosome/PAR reversal could happen in <em>Masius chrysopterus</em>. These manakin genomes will contribute to a deeper understanding of evolutionary history and sexual selection in these species.
DOI: 10.6084/m9.figshare.19769149
title: Phylogenetic tree

description: Manakins represent a family of small suboscine passerine birds characterized by their elaborate courtship displays, non-monogamous mating system, and sexual dimorphism. This family thus serves as a good model for the study of sexual selection. Here we present the genome assemblies of four manakin species (<em>Cryptopipo holochlora, Dixiphia pipra, Machaeropterus deliciosus</em> and <em>Masius chrysopterus</em>) generated by Single-tube Long Fragment Read (stLFR) technology. The assembled genome sizes ranged from 1.10 Gb to 1.19 Gb, with average scaffold N50 of 28 Mb and contig N50 of 169 Kb. On average, 9.82% genome region was annotated as repetitive elements, and 12,059 protein-coding genes were annotated in the genomes. We further identified about 75 Mb Z-linked sequences in manakins, containing 585 to 751 genes, and 600 Kb pseudoautosomal region (PAR). One interesting finding of these Z-linked sequences is that Z-to-autosome/PAR reversal could happen in <em>Masius chrysopterus</em>. These manakin genomes will contribute to a deeper understanding of evolutionary history and sexual selection in these species.
DOI: 10.6084/m9.figshare.19769149.v1
title: Phylogenetic tree

description: Manakins represent a family of small suboscine passerine birds characterized by their elaborate courtship displays, non-monogamous mating system, and sexual dimorphism. This family thus serves as a good model for the study of sexual selection. Here we present the genome assemblies of four manakin species (<em>Cryptopipo holochlora, Dixiphia pipra, Machaeropterus deliciosus</em> and <em>Masius chrysopterus</em>) generated by Single-tube Long Fragment Read (stLFR) technology. The assembled genome sizes ranged from 1.10 Gb to 1.19 Gb, with average scaffold N50 of 28 Mb and contig N50 of 169 Kb. On average, 9.82% genome region was annotated as repetitive elements, and 12,059 protein-coding genes were annotated in the genomes. We further identified about 75 Mb Z-linked sequences in manakins, containing 585 to 751 genes, and 600 Kb pseudoautosomal region (PAR). One interesting finding of these Z-linked sequences is that Z-to-autosome/PAR reversal could happen in <em>Masius chrysopterus</em>. These manakin genomes will contribute to a deeper understanding of evolutionary history and sexual selection in these species.
DOI: 10.6084/m9.figshare.19769140
title: Functional annotation

description: Manakins represent a family of small suboscine passerine birds characterized by their elaborate courtship displays, non-monogamous mating system, and sexual dimorphism. This family thus serves as a good model for the study of sexual selection. Here we present the genome assemblies of four manakin species (<em>Cryptopipo holochlora, Dixiphia pipra, Machaeropterus deliciosus</em> and <em>Masius chrysopterus</em>) generated by Single-tube Long Fragment Read (stLFR) technology. The assembled genome sizes ranged from 1.10 Gb to 1.19 Gb, with average scaffold N50 of 28 Mb and contig N50 of 169 Kb. On average, 9.82% genome region was annotated as repetitive elements, and 12,059 protein-coding genes were annotated in the genomes. We further identified about 75 Mb Z-linked sequences in manakins, containing 585 to 751 genes, and 600 Kb pseudoautosomal region (PAR). One interesting finding of these Z-linked sequences is that Z-to-autosome/PAR reversal could happen in <em>Masius chrysopterus</em>. These manakin genomes will contribute to a deeper understanding of evolutionary history and sexual selection in these species.
DOI: 10.6084/m9.figshare.19769140.v1
title: Functional annotation

description: Manakins represent a family of small suboscine passerine birds characterized by their elaborate courtship displays, non-monogamous mating system, and sexual dimorphism. This family thus serves as a good model for the study of sexual selection. Here we present the genome assemblies of four manakin species (<em>Cryptopipo holochlora, Dixiphia pipra, Machaeropterus deliciosus</em> and <em>Masius chrysopterus</em>) generated by Single-tube Long Fragment Read (stLFR) technology. The assembled genome sizes ranged from 1.10 Gb to 1.19 Gb, with average scaffold N50 of 28 Mb and contig N50 of 169 Kb. On average, 9.82% genome region was annotated as repetitive elements, and 12,059 protein-coding genes were annotated in the genomes. We further identified about 75 Mb Z-linked sequences in manakins, containing 585 to 751 genes, and 600 Kb pseudoautosomal region (PAR). One interesting finding of these Z-linked sequences is that Z-to-autosome/PAR reversal could happen in <em>Masius chrysopterus</em>. These manakin genomes will contribute to a deeper understanding of evolutionary history and sexual selection in these species.
DOI: 10.6084/m9.figshare.19771225
title: The Crawled API Documents for Building the FET Lattice

description: The crawled API documents for building the ubiquitous FET lattice of Leif's.
DOI: 10.6084/m9.figshare.19771225.v1
title: The Crawled API Documents for Building the FET Lattice

description: The crawled API documents for building the ubiquitous FET lattice of Leif's.
DOI: 10.5281/zenodo.6430412
title: HDF5 datasets and python scripts to generate figures in "Butterfly distribution of relativistic electrons driven by parallel propagating lower band whistler chorus waves"

description: HDF5 datasets and python scripts to generate figures in "Butterfly distribution of relativistic electrons driven by parallel propagating lower band whistler chorus waves" RBW simulation datasets in HDF5 format: 300pT.h5 The particle dataset to generate the figures. Python scripts to generate figures in the manuscript. - Environment: Python 3.6.7 :: Anaconda 4.4.0 (64-bit) - Required modules: matplotlib, numpy, h5py Figure1.py Generate figure 1. Figure2.py Generate figure 2. Figure3.py Generate figure 3. Figure4.py Generate figure 4. QLDe.py Calculate bounce averaged diffusion coefficients according to Shprits et al. (2006) (doi: https://doi.org/10.1029/ 2006JA011725).
DOI: 10.5281/zenodo.5507227
title: HDF5 datasets and python scripts to generate figures in "Butterfly distribution of relativistic electrons driven by parallel propagating lower band whistler chorus waves"

description: HDF5 datasets and python scripts to generate figures in "Butterfly distribution of relativistic electrons driven by parallel propagating lower band whistler chorus waves" RBW simulation datasets in HDF5 format: 300pT.h5 The particle dataset to generate the figures. Python scripts to generate figures in the manuscript. - Environment: Python 3.6.7 :: Anaconda 4.4.0 (64-bit) - Required modules: matplotlib, numpy, h5py Figure1.py Generate figure 1. Figure2.py Generate figure 2. Figure3.py Generate figure 3. Figure4.py Generate figure 4. QLDe.py Calculate bounce averaged diffusion coefficients according to Shprits et al. (2006) (doi: https://doi.org/10.1029/ 2006JA011725).
DOI: 10.6084/m9.figshare.19771306.v1
title: Repeat annotation

description: Manakins represent a family of small suboscine passerine birds characterized by their elaborate courtship displays, non-monogamous mating system, and sexual dimorphism. This family thus serves as a good model for the study of sexual selection. Here we present the genome assemblies of four manakin species (<em>Cryptopipo holochlora, Dixiphia pipra, Machaeropterus deliciosus</em> and <em>Masius chrysopterus</em>) generated by Single-tube Long Fragment Read (stLFR) technology. The assembled genome sizes ranged from 1.10 Gb to 1.19 Gb, with average scaffold N50 of 28 Mb and contig N50 of 169 Kb. On average, 9.82% genome region was annotated as repetitive elements, and 12,059 protein-coding genes were annotated in the genomes. We further identified about 75 Mb Z-linked sequences in manakins, containing 585 to 751 genes, and 600 Kb pseudoautosomal region (PAR). One interesting finding of these Z-linked sequences is that Z-to-autosome/PAR reversal could happen in <em>Masius chrysopterus</em>. These manakin genomes will contribute to a deeper understanding of evolutionary history and sexual selection in these species.
DOI: 10.6084/m9.figshare.19771306
title: Repeat annotation

description: Manakins represent a family of small suboscine passerine birds characterized by their elaborate courtship displays, non-monogamous mating system, and sexual dimorphism. This family thus serves as a good model for the study of sexual selection. Here we present the genome assemblies of four manakin species (<em>Cryptopipo holochlora, Dixiphia pipra, Machaeropterus deliciosus</em> and <em>Masius chrysopterus</em>) generated by Single-tube Long Fragment Read (stLFR) technology. The assembled genome sizes ranged from 1.10 Gb to 1.19 Gb, with average scaffold N50 of 28 Mb and contig N50 of 169 Kb. On average, 9.82% genome region was annotated as repetitive elements, and 12,059 protein-coding genes were annotated in the genomes. We further identified about 75 Mb Z-linked sequences in manakins, containing 585 to 751 genes, and 600 Kb pseudoautosomal region (PAR). One interesting finding of these Z-linked sequences is that Z-to-autosome/PAR reversal could happen in <em>Masius chrysopterus</em>. These manakin genomes will contribute to a deeper understanding of evolutionary history and sexual selection in these species.
DOI: 10.6084/m9.figshare.19771234
title: Table S3..xlsx

description: Table S3. Dataset used in this study containing values for A) phenotypic traits and B) Above-ground dry biomass (Biomass; TP1 Only) and C) Summary of sample for each maternal line, population and ecotype for the two transplant experiments.
DOI: 10.6084/m9.figshare.19771234.v1
title: Table S3..xlsx

description: Table S3. Dataset used in this study containing values for A) phenotypic traits and B) Above-ground dry biomass (Biomass; TP1 Only) and C) Summary of sample for each maternal line, population and ecotype for the two transplant experiments.
DOI: 10.17864/1947.000380
title: Data used in the PhD thesis 'SeaCoat - Marine based edible coatings for minimally processed fruit'

description: This dataset contains data obtained from experimental work on the physical and chemical properties and bioactivities of fresh-cut apples and pears coated with an edible coating containing extract of the seaweed Codium tomentosum. The data was obtained using a spectrophotometer microplate reader, a homogenizer, a Chroma Meter, a centrifuge, a gas analyser (Oxybaby), a digital refractometer, a texture analyser (TA.XTplus), and a thermocycling CFX ConnectTM Real-Time PCR System (Bio-Rad).
DOI: 10.6084/m9.figshare.19769212
title: DataCode.zip

description: These data are original data and code from "A SALT-ENSEMBLE LEARNING FRAMEWORK FOR URBAN FUNCTIONAL ZONES MAPPING USING REMOTE SENSING AND VGI DATA", including study area data, impervious surface data, OSM data, Google image after process of PCA and code used for classification.
DOI: 10.6084/m9.figshare.19769212.v1
title: DataCode.zip

description: These data are original data and code from "A SALT-ENSEMBLE LEARNING FRAMEWORK FOR URBAN FUNCTIONAL ZONES MAPPING USING REMOTE SENSING AND VGI DATA", including study area data, impervious surface data, OSM data, Google image after process of PCA and code used for classification.
DOI: 10.5281/zenodo.6546165
title: Epigenetic clock estimations in patients with isolated REM Sleep Behavior Disorder

description: Isolated REM Sleep Behavior Disorder (iRBD) is the strongest prodromal marker for conversion to α-synucleinopathies. A continuum between aging and neurodegeneration has been proposed, but this hypothesis has not been tested in iRBD so far. Here we used epigenetic clocks, estimated from DNA methylation arrays using the DNA Methylation Age Calculator available at https://dnamage.genetics.ucla.edu/home, to measure biological aging in videopolysomnography-confirmed iRBD patients (iRBDs, n=28), videopolysomnography-negative controls (CTR_neg; n=57), and controls from the general population (CTR_pop; n=31)<strong>.</strong>
description: Funding: Italian Ministry of Health (Ricerca Corrente)
DOI: 10.5281/zenodo.6546164
title: Epigenetic clock estimations in patients with isolated REM Sleep Behavior Disorder

description: Isolated REM Sleep Behavior Disorder (iRBD) is the strongest prodromal marker for conversion to α-synucleinopathies. A continuum between aging and neurodegeneration has been proposed, but this hypothesis has not been tested in iRBD so far. Here we used epigenetic clocks, estimated from DNA methylation arrays using the DNA Methylation Age Calculator available at https://dnamage.genetics.ucla.edu/home, to measure biological aging in videopolysomnography-confirmed iRBD patients (iRBDs, n=28), videopolysomnography-negative controls (CTR_neg; n=57), and controls from the general population (CTR_pop; n=31)<strong>.</strong>
description: Funding: Italian Ministry of Health (Ricerca Corrente)
DOI: 10.6084/m9.figshare.19307903
title: Supplementary Material for: Risk of Immune-Related Pneumonitis with PD-1/PD-L1 Inhibitors in Different Cancer Types and Treatment Regimens: A Systematic Review and Meta-analysis of 22 randomized controlled trials

description: BACKGROUND: Pneumonitis, the specific toxicity associated with PD-1/PD-L1 inhibitors, is severe and potentially life-threatening, and its incidence and severity are poorly understood among different tumor types or treatment methods. This meta-analysis was performed to compare the incidence and severity of pneumonitis among different tumor types and treatment regimens. METHODS: MEDLINE and EMBASE were retrieved until September 2021. Meta-analysis of the risk of pneumonitis was calculated using a fixed effect model. Pooled analysis of the incidence of pneumonitis in different tumor types was performed using mataprop function. RESULTS: Twenty two randomized controlled trials (RCTs) (n=10700) were included for pool-analysis, and eighteen RCTs (n=8852) were eligible for meta-analysis. For all-grade pneumonitis, the risk of the combination therapy (PD-1/PD-L1 plus CTLA-4 inhibitor) was 3.62 times significantly higher than that of monotherapy, and 4.06 and 1.78 times significantly higher than that of chemotherapy and placebo compared with monotherapy. The incidence of pneumonitis was not significantly different between PD-1/PD-L1 inhibitor versus ipilimumab or between low-doses versus high-doses. For high-grade (grade ≥ 3) pneumonitis, the risk in PD-1/PD-L1 inhibitors alone was 3.62 times significantly higher than chemotherapy. No significant difference was found in the incidence of pneumonitis between combination versus monotherapy, monotherapy versus placebo, combination versus ipilimumab alone, monotherapy versus ipilimumab alone or low-doses versus high-doses. CONCLUSIONS: Compared with chemotherapy, PD-1/PD-L1 inhibitor monotherapy may cause more treatment-related pneumonitis. Increasing the dose of PD-1/PD-L1 inhibitor does not significantly increase the incidence of pneumonitis. Compared with the monotherapy, combination therapy does not increase the incidence of pneumonitis significantly.
DOI: 10.6084/m9.figshare.19307903.v1
title: Supplementary Material for: Risk of Immune-Related Pneumonitis with PD-1/PD-L1 Inhibitors in Different Cancer Types and Treatment Regimens: A Systematic Review and Meta-analysis of 22 randomized controlled trials

description: BACKGROUND: Pneumonitis, the specific toxicity associated with PD-1/PD-L1 inhibitors, is severe and potentially life-threatening, and its incidence and severity are poorly understood among different tumor types or treatment methods. This meta-analysis was performed to compare the incidence and severity of pneumonitis among different tumor types and treatment regimens. METHODS: MEDLINE and EMBASE were retrieved until September 2021. Meta-analysis of the risk of pneumonitis was calculated using a fixed effect model. Pooled analysis of the incidence of pneumonitis in different tumor types was performed using mataprop function. RESULTS: Twenty two randomized controlled trials (RCTs) (n=10700) were included for pool-analysis, and eighteen RCTs (n=8852) were eligible for meta-analysis. For all-grade pneumonitis, the risk of the combination therapy (PD-1/PD-L1 plus CTLA-4 inhibitor) was 3.62 times significantly higher than that of monotherapy, and 4.06 and 1.78 times significantly higher than that of chemotherapy and placebo compared with monotherapy. The incidence of pneumonitis was not significantly different between PD-1/PD-L1 inhibitor versus ipilimumab or between low-doses versus high-doses. For high-grade (grade ≥ 3) pneumonitis, the risk in PD-1/PD-L1 inhibitors alone was 3.62 times significantly higher than chemotherapy. No significant difference was found in the incidence of pneumonitis between combination versus monotherapy, monotherapy versus placebo, combination versus ipilimumab alone, monotherapy versus ipilimumab alone or low-doses versus high-doses. CONCLUSIONS: Compared with chemotherapy, PD-1/PD-L1 inhibitor monotherapy may cause more treatment-related pneumonitis. Increasing the dose of PD-1/PD-L1 inhibitor does not significantly increase the incidence of pneumonitis. Compared with the monotherapy, combination therapy does not increase the incidence of pneumonitis significantly.
DOI: 10.6084/m9.figshare.19771339
title: Impact Paper Underlying Data set Wheel of Life.xlsx

description: The excel sheet presents a data set collected through a qualitative, online survey investigating the impact of hypoglycaemia on the quality of life of parents of children, adolescents and young adults with type 1 diabetes. The data set includes participants' original nominations of areas of life and their related written reponses. The translations of the nonimations and responses are also presented in the sheet. The data set was analysed using thematic analyses.
DOI: 10.5281/zenodo.6482119
title: Data and code for "High-speed 3D imaging flow cytometry with optofluidic spatial transformation"

description: Data and codes used in Ugawa & Ota, "High-speed 3D imaging flow cytometry with optofluidic spatial transformation".
DOI: 10.5281/zenodo.6482118
title: Data and code for "High-speed 3D imaging flow cytometry with optofluidic spatial transformation"

description: Data and codes used in Ugawa & Ota, "High-speed 3D imaging flow cytometry with optofluidic spatial transformation".
DOI: 10.6084/m9.figshare.11786238
title: Tubuloid kidney organoid - single cell RNA-seq

description: It is included data derived from the processing of single-cell and single-nuclei RNA-seq from several samples (see below). This data corresponds to the input and intermediate output files from https://github.com/saezlab/Xu_tubuloid . Data The data include: Binary sparse matrices for the UMI gene expression quantification from cellranger (filtered feature-barcode matrices). These are TAR archive files named with the name of the sample. Seurat Objects with normalized data, embeddings of dimensionality reduction, clustering and cell cluster annotation. These are TAR archive files including final objects, grouped by sample type: SeuratObjects_[SortedCells | Organoids | Human Kidney Tissue]. The HumanKidneyTissue also includes the SeuratObject after Harmony integration. Exported barcode idents from unsupervised clustering and manual annotation ("barcodeIdents*.csv" files). Label transfer via Symphony mapping to tubuloid cells from each organoid to a integrated reference atlas of human kidney tissue (SymphonyMapped*.csv). Samples The data corresponds to the following samples, which were profiled at the single-cell resolution: CK5 early organoid (Healthy). Organoid generated from CD24+ sorted cells from human adult kidney tissue at an early stage. CK119 late organoid (Healthy). Organoid generated from CD24+ sorted cells from human adult kidney tissue at a late stage.<br> JX1 late organoid (Healthy). Organoid generated following Hans Clever's protocol for kidney organoids. JX2 PKD1-KO organoid (PKD). Organoid generated from CD24+ sorted cells from human adult kidney tissue, for which PKD1 was gene-edited to reproduce PKD phenotype, developed at a late stage. JX3 PKD2-KO organoid (PKD). Organoid generated from CD24+ sorted cells from human adult kidney tissue, for which PKD2 was gene-edited to reproduce PKD phenotype, developed at a late stage. CK120 CD13. CD13+ sorted cells from human adult kidney tissue. CK121 CD24. CD24+ sorted cells from human adult kidney tissue.<br> In addition, human adult kidney tissue were profiled in the context of ADPKD:<br> CK224 : human specimen with ADPKD (PKD2- genotype).<br> CK225 : human specimen with ADPKD (PKD1- genotype). ADPKD3: human specimen with ADPKD (ND genotype).<br> Control1 : human specimen with healthy tissue. Control2 : human specimen with healthy tissue.
DOI: 10.5258/soton/d2215
title: Contact Resistivity and Epoxy Thermal Degradation

description: This dataset supports the Southampton doctoral thesis entitled "Numerical Modelling of Lightning Strikes to Wind Turbine Blades: Analysis of Equipotential Bonding for CFRP Spars" it contains the experimental activity performed in the PhD project. It provides the experimental values and mathematical calculations done to estimate the contact resistivity of equipotential bonding joints and the thermal degradation of epoxy resin. The softwares employed for mathematical calculations were Excel and OriginLab. These data were published in my papers entitled "Estimation of Contact Resistivity in Lightning Protection Equipotential Bonding Joints of Wind Turbine Blades" and "Numerical simulation of lightning strike damage to wind turbine blades and validation against conducted current test data".