cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5568391.v1
title: Causes of blood methylomic variation for middle-aged women measured by the HumanMethylation450 array

description: To address the limitations in current classic twin/family research on the genetic and/or environmental causes of human methylomic variation, we measured blood DNA methylation for 479 women (mean age 56 years) including 66 monozygotic (MZ), 66 dizygotic (DZ) twin pairs and 215 sisters of twins, and 11 random technical duplicates using the HumanMethylation450 array. For each methylation site, we estimated the correlation for pairs of duplicates, MZ twins, DZ twins, and siblings, fitted variance component models by assuming the variation is explained by genetic factors, by shared and individual environmental factors, and by independent measurement error, and assessed the best fitting model. We found that the average (standard deviation) correlations for duplicate, MZ, DZ, and sibling pairs were 0.10 (0.35), 0.07 (0.21), -0.01 (0.14) and -0.04 (0.07). At the genome-wide significance level of 10<sup>−7</sup>, 93.3% of sites had no familial correlation, and 5.6%, 0.1%, and 0.2% of sites were correlated for MZ, DZ, and sibling pairs. For 86.4%, 6.9%, and 7.1% of sites, the best fitting model included measurement error only, a genetic component, and at least one environmental component. For the 13.6% of sites influenced by genetic and/or environmental factors, the average proportion of variance explained by environmental factors was greater than that explained by genetic factors (0.41 vs. 0.37, <i>P</i> value &lt;10<sup>−15</sup>). Our results are consistent with, for middle-aged woman, blood methylomic variation measured by the HumanMethylation450 array being largely explained by measurement error, and more influenced by environmental factors than by genetic factors.
DOI: 10.6084/m9.figshare.5568394
title: Variant Histone H2afv reprograms DNA methylation during early zebrafish development

description: The DNA methylome is re-patterned during discrete phases of vertebrate development. In zebrafish, there are 2 waves of global DNA demethylation and re-methylation: the first occurs before gastrulation when the parental methylome is changed to the zygotic pattern and the second occurs after formation of the embryonic body axis, during organ specification. The occupancy of the histone variant H2A.Z and regions of DNA methylation are generally anti-correlated, and it has been proposed that H2A.Z restricts the boundaries of highly methylated regions. While many studies have described the dynamics of methylome changes during early zebrafish development, the factors involved in establishing the DNA methylation landscape in zebrafish embryos have not been identified. We test the hypothesis that the zebrafish ortholog of H2A.Z (H2afv) restricts DNA methylation during development. We find that, in control embryos, bulk genome methylation decreases after gastrulation, with a nadir at the bud stage, and peaks during mid-somitogenesis; by 24 hours post -fertilization, total DNA methylation levels return to those detected in gastrula. Early zebrafish embryos depleted of H2afv have significantly more bulk DNA methylation during somitogenesis, suggesting that H2afv limits methylation during this stage of development. H2afv deficient embryos are small, with multisystemic abnormalities. Genetic interaction experiments demonstrate that these phenotypes are suppressed by depletion of DNA methyltransferase 1 (Dnmt1). This work demonstrates that H2afv is essential for global DNA methylation reprogramming during early vertebrate development and that embryonic development requires crosstalk between H2afv and Dnmt1.
DOI: 10.6084/m9.figshare.5568394.v1
title: Variant Histone H2afv Reprograms DNA Methylation During Early Zebrafish Development

description: The DNA methylome is re-patterned during discrete phases of vertebrate development. In zebrafish, there are two waves of global DNA demethylation and re-methylation: the first occurs prior to gastrulation when the parental methylome is changed to the zygotic pattern and the second occurs after formation of the embryonic body axis, during organ specification. The occupancy of the histone variant H2A.Z and regions of DNA methylation are generally anti-correlated, and it has been proposed that H2A.Z restricts the boundaries of highly methylated regions. While many studies have described the dynamics of methylome changes during early zebrafish development, the factors involved in establishing the DNA methylation landscape in zebrafish embryos have not been identified. We test the hypothesis that the zebrafish ortholog of H2A.Z (H2afv) restricts DNA methylation during development. We find that in control embryos, bulk genome methylation decreases after gastrulation, with a nadir at the bud stage and peaks during mid-somitogenesis and by 24 hours post-fertilization, total DNA methylation levels return to that detected in gastrula. Early zebrafish embryos depleted of H2afv have significantly more bulk DNA methylation during somitogenesis, suggesting that H2afv limits methylation during this stage of development. H2afv deficient embryos are small, with multisystemic abnormalities. Genetic interaction experiments demonstrate that these phenotypes are suppressed by depletion of DNA methyltransferase 1 (Dnmt1). This work demonstrates that H2afv is essential for global DNA methylation reprogramming during early vertebrate development and that embryonic development requires crosstalk between H2afv and Dnmt1.
DOI: 10.6084/m9.figshare.5568394.v2
title: Variant Histone H2afv reprograms DNA methylation during early zebrafish development

description: The DNA methylome is re-patterned during discrete phases of vertebrate development. In zebrafish, there are 2 waves of global DNA demethylation and re-methylation: the first occurs before gastrulation when the parental methylome is changed to the zygotic pattern and the second occurs after formation of the embryonic body axis, during organ specification. The occupancy of the histone variant H2A.Z and regions of DNA methylation are generally anti-correlated, and it has been proposed that H2A.Z restricts the boundaries of highly methylated regions. While many studies have described the dynamics of methylome changes during early zebrafish development, the factors involved in establishing the DNA methylation landscape in zebrafish embryos have not been identified. We test the hypothesis that the zebrafish ortholog of H2A.Z (H2afv) restricts DNA methylation during development. We find that, in control embryos, bulk genome methylation decreases after gastrulation, with a nadir at the bud stage, and peaks during mid-somitogenesis; by 24 hours post -fertilization, total DNA methylation levels return to those detected in gastrula. Early zebrafish embryos depleted of H2afv have significantly more bulk DNA methylation during somitogenesis, suggesting that H2afv limits methylation during this stage of development. H2afv deficient embryos are small, with multisystemic abnormalities. Genetic interaction experiments demonstrate that these phenotypes are suppressed by depletion of DNA methyltransferase 1 (Dnmt1). This work demonstrates that H2afv is essential for global DNA methylation reprogramming during early vertebrate development and that embryonic development requires crosstalk between H2afv and Dnmt1.
DOI: 10.6084/m9.figshare.5584228.v2
title: Notch1 regulates tongue cancer cells proliferation, apoptosis and invasion

description: <b>Objectives:</b> Notch1 regulates tumor biology in a complex, context-dependent manner. The roles of Notch1 in tongue cancer are still controversial. The aim of this study is to investigate the roles of Notch1 in tongue cancer. <b>Materials and Methods:</b> The expression of Notch1 was tested between tongue cancer and normal samples by using immunohistochemistry. Tongue cancer cells were transfected with siRNA or plasmid, respectively. Cell proliferation, apoptosis, migration and invasion ability were tested in appropriate ways. The subcutaneous tumor model was established to observe the tumor growth. <b>Results:</b> Notch1 was upregulated in tongue carcinoma tissues and the expression of Notch1 was related with tumor stage and differentiation. Overexpression of Notch1 could increase tongue cancer cells proliferation, invasion and migration. But inhibited the expression of Notch1 could decrease cells proliferation, invasion and migration and promote cell apoptosis <i>in vitro</i> and <i>in vivo</i>. <b>Conclusion:</b> Our results prove that the oncogenic role of Notch1 in tongue cancer and provide the direction of targeted therapy of tongue cancer.
DOI: 10.6084/m9.figshare.5584258
title: Aflatoxin B<sub>1</sub> and sterigmatocystin in wheat and wheat products from supermarkets in China

description: Wheat is an important cereal but it is often contaminated with mycotoxins. The natural occurrence of aflatoxin B<sub>1</sub> (AFB<sub>1</sub>) and sterigmatocystin (STC) was determined in 178 food samples (32 wheat samples and 146 wheat products) purchased from Chinese supermarkets. The methodology was validated, the wheat and wheat products samples were treated with a modified QuEChERS (quick, easy, cheap, effective, rugged, and safe) and quantified by liquid chromatography-tandem mass spectrometry (LC-MS/MS). From these samples 18.8% of wheat and 8.2% of cracker samples were contaminated with AFB<sub>1</sub>. Mean levels were 0.06 µg/kg and 0.05µg/kg, respectively. There was no AFB<sub>1</sub> contamination in white bread or whole meal bread. Meanwhile 53.1% of wheat, 59.2% of crackers, 20.8% of white bread and 16% of whole meal bread samples were contaminated with STC. The mean levels were 0.07, 0.79, 0.12 and 0.12 µg/kg respectively. Although the levels were low, this demonstrates the need for more comprehensive surveys for these two mycotoxins in wheat and wheat products from China.
DOI: 10.6084/m9.figshare.5584258.v1
title: Aflatoxin B<sub>1</sub> and sterigmatocystin in wheat and wheat products from supermarkets in China

description: Wheat is an important cereal but it is often contaminated with mycotoxins. The natural occurrence of aflatoxin B<sub>1</sub> (AFB<sub>1</sub>) and sterigmatocystin (STC) was determined in 178 food samples (32 wheat samples and 146 wheat products) purchased from Chinese supermarkets. The methodology was validated, the wheat and wheat products samples were treated with a modified QuEChERS (quick, easy, cheap, effective, rugged, and safe) and quantified by liquid chromatography-tandem mass spectrometry (LC-MS/MS). From these samples 18.8% of wheat and 8.2% of cracker samples were contaminated with AFB<sub>1</sub>. Mean levels were 0.06 µg/kg and 0.05µg/kg, respectively. There was no AFB<sub>1</sub> contamination in white bread or whole meal bread. Meanwhile 53.1% of wheat, 59.2% of crackers, 20.8% of white bread and 16% of whole meal bread samples were contaminated with STC. The mean levels were 0.07, 0.79, 0.12 and 0.12 µg/kg respectively. Although the levels were low, this demonstrates the need for more comprehensive surveys for these two mycotoxins in wheat and wheat products from China.
DOI: 10.6084/m9.figshare.5589862
title: Resurrection of genus Nidirana (Anura: Ranidae) and synonymizing N. caldwelli with N. adenopleura, with description of a new species from China. Supplementary Table S1

description: The taxonomy of <i>Babina </i>sensu lato was
controversial in the past decades. In this study, the phylogeny of genus <i>Babina </i>sensu lato was
re-constructed based on genetic analysis, morphological comparison and
advertisement call analysis. We found that <i>Babina </i>sensu stricto and previous
subgenus <i>Nidirana </i>should be two distinct genera in the family Ranidae. <i>N. caldwelli </i>is confirmed to be a
synonym of <i>N. adenopleura </i>because of the small genetic divergence and the lack of distinct morphological
differences. A new species, <i>Nidirana
nankunensis </i>sp. nov. is described
based on a series of specimens collected from Mt. Nankun, Guangdong Province,
China, which can be distinguished from other known congeners by having a
behavior of nest construction, distinctive advertisement calls, significant
divergence in the mitochondrial genes, and a combination of morphological
characters. Currently, the genus <i>Babina
</i>contains two species and
the genus <i>Nidirana </i>contains eight species.
DOI: 10.6084/m9.figshare.5589862.v1
title: Resurrection of genus Nidirana (Anura: Ranidae) and synonymizing N. caldwelli with N. adenopleura, with description of a new species from China. Supplementary Table S1

description: The taxonomy of <i>Babina </i>sensu lato was
controversial in the past decades. In this study, the phylogeny of genus <i>Babina </i>sensu lato was
re-constructed based on genetic analysis, morphological comparison and
advertisement call analysis. We found that <i>Babina </i>sensu stricto and previous
subgenus <i>Nidirana </i>should be two distinct genera in the family Ranidae. <i>N. caldwelli </i>is confirmed to be a
synonym of <i>N. adenopleura </i>because of the small genetic divergence and the lack of distinct morphological
differences. A new species, <i>Nidirana
nankunensis </i>sp. nov. is described
based on a series of specimens collected from Mt. Nankun, Guangdong Province,
China, which can be distinguished from other known congeners by having a
behavior of nest construction, distinctive advertisement calls, significant
divergence in the mitochondrial genes, and a combination of morphological
characters. Currently, the genus <i>Babina
</i>contains two species and
the genus <i>Nidirana </i>contains eight species.
DOI: 10.6084/m9.figshare.5594230
title: Genome-wide Association Study of Piglet Uniformity and Farrowing Interval

description: This "genotype_and_phenotype.zip" file contains the genotypes of 884 individuals (884-individual.map and 884-individual.ped ) and the phenotypic data of piglet university and farrowing interval (phenotype1_Piglet uniformity.xlsx and phenotype2_Farrowing interval.xlsx).
DOI: 10.6084/m9.figshare.5598883
title: Table S3 from Long-term archives reveal shifting extinction selectivity in China's postglacial mammal fauna

description: Historical wild mammal database
DOI: 10.6084/m9.figshare.5598883.v1
title: Table S3 from Long-term archives reveal shifting extinction selectivity in China's postglacial mammal fauna

description: Historical wild mammal database
DOI: 10.6084/m9.figshare.5598886
title: Table S1 from Long-term archives reveal shifting extinction selectivity in China's postglacial mammal fauna

description: Holocene wild mammal database
DOI: 10.6084/m9.figshare.5598886.v1
title: Table S1 from Long-term archives reveal shifting extinction selectivity in China's postglacial mammal fauna

description: Holocene wild mammal database
DOI: 10.6084/m9.figshare.5605456
title: Experimental_Data_arxiv_1611.03511

description: ## Supplementary raw data to## https://arxiv.org/abs/1611.03511## and following versions of the preprint## further details&explanations in the main text<br>"Characterisation"contains data related to preliminary characterisation of the photonic chip<br>"GroundSearch"contains all raw data related to the ground state search for the 1qubit Hamiltonian as in Fig, 3 of the main paper<br>"ExcitedSearch"contains all raw data related to the excited state search for the 1qubit Hamiltonian as in Fig, 3 of the main paper<br>"ExcitedSearch"contains all raw data related to the IPEA algorithm performed for both the ground and excited eigenstate found, as in Fig, 3 of the main paper
DOI: 10.6084/m9.figshare.5605456.v1
title: Experimental_Data_arxiv_1611.03511

description: ## Supplementary raw data to## https://arxiv.org/abs/1611.03511## and following versions of the preprint## further details&explanations in the main text<br>"Characterisation"contains data related to preliminary characterisation of the photonic chip<br>"GroundSearch"contains all raw data related to the ground state search for the 1qubit Hamiltonian as in Fig, 3 of the main paper<br>"ExcitedSearch"contains all raw data related to the excited state search for the 1qubit Hamiltonian as in Fig, 3 of the main paper<br>"ExcitedSearch"contains all raw data related to the IPEA algorithm performed for both the ground and excited eigenstate found, as in Fig, 3 of the main paper
DOI: 10.6084/m9.figshare.5605465
title: Simulations_Data_arxiv_1611.03511

description: ## Supplementary raw data to## https://arxiv.org/abs/1611.03511 ## and following versions of the preprint## further details&explanations in the main text<br>The Folder tree structure is the following (in {} brackets variable syntax, in [] options):<br>- "{Number of qubits for the simulation}qbit" (if ambiguous, followed by "_Hstructureanalysed")<br>-- "{Typeof}States[_{number of operators in the truncated ansatz}] "OR -- "{Typeof}States[ _FS]" for runs adopting the FoldedSpectrum method<br>---"NMeas {number of simulated photon counts for each algorithm step, adopted to investigate the role of Poissonian noise}"<br>---- "FullData_NMeas{Poissonian counts}_Excite#_{identifier fo the excited state}_NParticles#{number of parricles used}"## main file where for each step of each iteration of the WAVES algorithm we record:[iteration step, final best guess for the eigenstate, fidelity of the best guess with the whole spectrum of eigenstates of the Hamiltonian analysed, fidelity with the targeted eigenstate, average energy for the particle swarm, average purity for the particle swarm, [set of particles used for the iteration, objective function for each of the particles, fidelity of each particle with the whole spectrum of eigenstates of the Hamiltonian analysed] ]<br>---- "STREAM_NMeas{Poissonian counts}_Excite#_{identifier fo the excited state}_NParticles#{number of parricles used}"## txt summary of main performances per each attempted iteration of the WAVES algorithm
DOI: 10.6084/m9.figshare.5605465.v1
title: Simulations_Data_arxiv_1611.03511

description: ## Supplementary raw data to## https://arxiv.org/abs/1611.03511 ## and following versions of the preprint## further details&explanations in the main text<br>The Folder tree structure is the following (in {} brackets variable syntax, in [] options):<br>- "{Number of qubits for the simulation}qbit" (if ambiguous, followed by "_Hstructureanalysed")<br>-- "{Typeof}States[_{number of operators in the truncated ansatz}] "OR -- "{Typeof}States[ _FS]" for runs adopting the FoldedSpectrum method<br>---"NMeas {number of simulated photon counts for each algorithm step, adopted to investigate the role of Poissonian noise}"<br>---- "FullData_NMeas{Poissonian counts}_Excite#_{identifier fo the excited state}_NParticles#{number of parricles used}"## main file where for each step of each iteration of the WAVES algorithm we record:[iteration step, final best guess for the eigenstate, fidelity of the best guess with the whole spectrum of eigenstates of the Hamiltonian analysed, fidelity with the targeted eigenstate, average energy for the particle swarm, average purity for the particle swarm, [set of particles used for the iteration, objective function for each of the particles, fidelity of each particle with the whole spectrum of eigenstates of the Hamiltonian analysed] ]<br>---- "STREAM_NMeas{Poissonian counts}_Excite#_{identifier fo the excited state}_NParticles#{number of parricles used}"## txt summary of main performances per each attempted iteration of the WAVES algorithm
DOI: 10.5281/zenodo.10866499
title: Supplementary data: Predicting grid frequency short-term dynamics with Gaussian processes and sequence modeling

description: This repository contains data and result files for the paper "Predicting grid frequency short-term dynamics with Gaussian processes and sequence modelling".  The code to generate the models and reproduce the results of the comparative study in the above paper is available on this  github repository

Supplementary data:

- The trained_models folder contains the results of the trained models.

- The folder data contains data needed for for the comparative study for the year 2019 in the paper above.  This data set (except knn_point_predictions.npy) is generated with the code in this github repository. knn_point_predictions.npy is generated with the code in this github repository .
DOI: 10.5281/zenodo.10866500
title: Supplementary data: Predicting grid frequency short-term dynamics with Gaussian processes and sequence modeling

description: This repository contains data and result files for the paper "Predicting grid frequency short-term dynamics with Gaussian processes and sequence modelling".  The code to generate the models and reproduce the results of the comparative study in the above paper is available on this  github repository

Supplementary data:

- The trained_models folder contains the results of the trained models.

- The folder data contains data needed for for the comparative study for the year 2019 in the paper above.  This data set (except knn_point_predictions.npy) is generated with the code in this github repository. knn_point_predictions.npy is generated with the code in this github repository .
DOI: 10.6084/m9.figshare.5606914
title: Additional file 1

description: Additional file 1 containing Table S1 to S7 and Figure S1 to S4
DOI: 10.6084/m9.figshare.5606914.v1
title: Additional file 1

description: Additional file 1 containing Table S1 to S7 and Figure S1 to S4
DOI: 10.6084/m9.figshare.5607730
title: X-ray micro-tomography of intermittency in multiphase flow at steady state using a differential imaging method

description: For further information please contact corresponding author: q.lin11@imperial.ac.uk
DOI: 10.6084/m9.figshare.5607730.v1
title: X-ray micro-tomography of intermittency in multiphase flow at steady state using a differential imaging method

description: For further information please contact corresponding author: q.lin11@imperial.ac.uk
DOI: 10.6084/m9.figshare.5612818
title: Supplementary File 1 Li et al

description: RNA-seq comparisons of all data sets<br>
DOI: 10.6084/m9.figshare.5612818.v1
title: Supplementary File 1 Li et al

description: RNA-seq comparisons of all data sets<br>
DOI: 10.25378/janelia.5613169
title: ShuTu: Rat dentate gyrus granule cell 63X

description: Here we provide images of a rat dentate gyrus granule cell (63X) for practicing reconstruction using the ShuTu software platform. The cell was filled and imaged by Ching-Lung Hsu in the Spruston Lab. Two resolutions are provided, 63X and 100X. For quick evaluation, use this file 63X. <br>ShuTu (Chinese for "dendrite") is a software platform for semi-automated reconstruction of neuronal morphology. It is designed for neurons stained following patch-clamp recording and biocytin filling/staining. With an additional preprocessing step, it can also handle fluorescence images from confocal stacks.Even when there is only a single neuron in the imaged volume, automated reconstruction is tricky, because of background. Thus, ShuTu was developed to facilitate a two-step process: automated reconstruction, followed by manual correction. The software uses sophisticated algorithms to perform the automated reconstruction, as well as a convenient user interface to facilitate efficient completion of the reconstruction via manual annotation.<br><br>