cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12204143
title: Supplementary Material for: Therapeutic Plasma Exchange in Refractory Hyperthyroidism

description: <b><i>Introduction:</i></b> Hyperthyroid patients who are unresponsive to medical treatment remain a challenging clinical problem. <b><i>Objective:</i></b> The goal of our study was to evaluate the use of therapeutic plasma exchange (TPE) in hyperthyroid patients and their outcome after TPE. <b><i>Method:</i></b> We retrospectively reviewed 22 patients who underwent TPE for refractory thyrotoxicosis in our institution: 13 with Graves’ disease, 7 with amiodarone-induced thyrotoxicosis (AIT), 1 with toxic goiter, and 1 pregnant patient with familial nonautoimmune thyrotoxicosis. <b><i>Results:</i></b> Before TPE, all patients had severe hyperthyroidism, and antithyroid drugs were either contraindicated or not sufficiently effective to restore euthyroidism promptly. After all the TPEs, free T<sub>4</sub> (fT4) decreased significantly by 48% (<i>p</i> = 0.001) and fT3 by 52% (<i>p</i> = 0.0001). The median number of TPE sessions per patient was 4 (range: 1–10). There were no complications during the 91 TPE sessions. Total thyroidectomy with no severe side effects was performed on 16/22 patients and 1 other patient was treated with radioactive iodine. One patient died from severe thyrotoxicosis during medical care. The remaining 4 patients were followed up without any radical treatment. For all 7 patients with AIT, iterative TPE led to a significant clinical improvement, and amiodarone was continued for 1 patient. Available treatments were continued between TPE sessions (cholestyramine for 13 patients [60%] and glucocorticoids for 16 patients [73%]). <b><i>Conclusion:</i></b> TPE allowed a safe decrease of 50% in thyroid hormone levels, and it should be considered for refractory hyperthyroid patients when medical treatments are contraindicated or have failed to restore euthyroidism, irrespective of the etiology of the thyrotoxicosis.
DOI: 10.6084/m9.figshare.12203858
title: penA nucleotide sequence alignment (penA 5, X, XXXIV)

description: penA nucleotide sequence alignment (penA 5, X, and XXXIV) used for a figure in the following manuscript:<br>Emergence and evolution of antimicrobial resistance genes and mutations spreading worldwide in Neisseria gonorrhoeae<br>authored by<br>Koji Yahara, Kevin C. Ma, Tatum D. Mortimer, Ken Shimuta,, Shu-ichi Nakayama, Aki Hirabayashi, Masato Suzuki, Michio Jinnai, Hitomi Ohya, Toshiro Kuroki,# Yuko Watanabe, Mitsuru Yasuda, Takashi Deguchi, Vegard Eldholm, Odile B. Harrison, Martin C. J. Maiden, Yonatan H. Grad, Makoto Ohnishi
DOI: 10.6084/m9.figshare.12203690
title: Suppl Figure Legneds

description: Figure Legends
DOI: 10.6084/m9.figshare.12203690.v1
title: Suppl Figure Legneds

description: Figure Legends
DOI: 10.6084/m9.figshare.12203858.v2
title: penA nucleotide sequence alignment (penA 5, X, XXXIV)

description: penA nucleotide sequence alignment (penA 5, X, and XXXIV) used for a figure in the following manuscript:<br>Emergence and evolution of antimicrobial resistance genes and mutations spreading worldwide in Neisseria gonorrhoeae<br>authored by<br>Koji Yahara, Kevin C. Ma, Tatum D. Mortimer, Ken Shimuta,, Shu-ichi Nakayama, Aki Hirabayashi, Masato Suzuki, Michio Jinnai, Hitomi Ohya, Toshiro Kuroki,# Yuko Watanabe, Mitsuru Yasuda, Takashi Deguchi, Vegard Eldholm, Odile B. Harrison, Martin C. J. Maiden, Yonatan H. Grad, Makoto Ohnishi
DOI: 10.6084/m9.figshare.12203708
title: Supplementary information.zip

description: The gtf and fasta files from the newly identified MSTRG lncRNAs and miRNAs
DOI: 10.6084/m9.figshare.12203858.v1
title: penA nucleotide sequence alignment (penA 5, X, XXXIV, and 1)

description: penA nucleotide sequence alignment (penA 5, X, XXXIV, and 1) used for a figure in the following manuscript:<br>Emergence and evolution of antimicrobial resistance genes and mutations spreading worldwide in Neisseria gonorrhoeae<br>authored by<br>Koji Yahara, Kevin C. Ma, Tatum D. Mortimer, Ken Shimuta,, Shu-ichi Nakayama, Aki Hirabayashi, Masato Suzuki, Michio Jinnai, Hitomi Ohya, Toshiro Kuroki,# Yuko Watanabe, Mitsuru Yasuda, Takashi Deguchi, Vegard Eldholm, Odile B. Harrison, Martin C. J. Maiden, Yonatan H. Grad, Makoto Ohnishi
DOI: 10.6084/m9.figshare.12203708.v3
title: Supplementary information.zip

description: The gtf and fasta files from the newly identified MSTRG lncRNAs and miRNAs
DOI: 10.6084/m9.figshare.12203708.v2
title: Supplementary information.zip

description: The gtf and fasta files from the newly identified MSTRG lncRNAs and miRNAs
DOI: 10.25345/c58759
title: MassIVE MSV000086009 - mTORC1 couples cyst(e)ine availability with GPX4 protein synthesis and ferroptosis regulation
title: Glutathione peroxidase 4 (GPX4) utilizes glutathione (GSH) to detoxify lipid peroxidation and plays an essential role in inhibiting ferroptosis. As a selenoprotein, GPX4 protein synthesis is highly inefficient and energetically costly. How cells coordinate GPX4 synthesis with nutrient availability remains unclear. In this study, integrated proteomic and functional analyses reveal that SLC7A11-mediated cystine uptake promotes not only GSH synthesis but also GPX4 protein synthesis. Mechanistically, cyst(e)ine activates mechanistic/mammalian target of rapamycin complex 1 (mTORC1) and promotes GPX4 protein synthesis at least partly through the mTORC1-4E-BP signaling axis. Pharmacologic inhibition of mTORC1 decreases GPX4 protein levels, sensitizes cancer cells to ferroptosis, and synergizes with ferroptosis inducers (FINs) to suppress patient-derived xenograft tumor growth in vivo. Together, our results reveal a hitherto unrecognized regulatory mechanism to coordinate GPX4 protein synthesis with cyst(e)ine availability and suggest to use the combination of mTORC1 inhibitors and FINs in cancer treatment.
DOI: 10.6084/m9.figshare.12203567
title: Additional file 1 of CD3+T-lymphocyte infiltration is an independent prognostic factor for advanced nasopharyngeal carcinoma

description: Additional file 1: Supplementary Figure 1. Expression of immune-related markers in LA and MET nasopharyngeal tumors. Difference in CD3+ TIL, CD8+ TIL infiltration, subsets of TIL infiltration and Tumoral PD-L1 expression (membranous or cytoplasmic) between (A) locally advanced (LA, n = 63) versus metastatic (MET, n = 20) nasopharyngeal carcinoma cases or (B) primary tumor (1ry) and metastatic sites (MT sites) in available paired tissues from some of the LA patients before and after relapse and development of metastasis (n = 6). * Numbers indicate the median.
DOI: 10.6084/m9.figshare.12203567.v1
title: Additional file 1 of CD3+T-lymphocyte infiltration is an independent prognostic factor for advanced nasopharyngeal carcinoma

description: Additional file 1: Supplementary Figure 1. Expression of immune-related markers in LA and MET nasopharyngeal tumors. Difference in CD3+ TIL, CD8+ TIL infiltration, subsets of TIL infiltration and Tumoral PD-L1 expression (membranous or cytoplasmic) between (A) locally advanced (LA, n = 63) versus metastatic (MET, n = 20) nasopharyngeal carcinoma cases or (B) primary tumor (1ry) and metastatic sites (MT sites) in available paired tissues from some of the LA patients before and after relapse and development of metastasis (n = 6). * Numbers indicate the median.
DOI: 10.6084/m9.figshare.12203525
title: Gut and intestinal biometrics of the giant trevally, Caranx ignobilis, fed an experimental diet with difference sources of activated charcoal

description: These are the raw data of gut and intestinal biometrics of giant trivially fish Caranx ignobilis fed an experimental diet with different type of charcoal
DOI: 10.6084/m9.figshare.12203375
title: Soil fungal networks maintain local dominance of ectomycorrhizal trees - Experimental Data

description: Please refer to the NERC Environmental Information Data Centre at https://doi.org/10.5285/f1d17e61-bb6c-47a9-a648-062c63ea7f16.This data-set is the experimental data for the paper Liang et al. 2020 Nature Communications, entitled "Soil fungal networks maintain local dominance of ectomycorrhizal trees". It contains results on seedling growth and survival for two hyphal exclusion experiments in a subtropical forest. The data-set include four data files, entitled “Tree_Seedling_Survival.csv”, “Tree_Seedling_Growth.csv”, “Tree_Seedling_Root_Colonization.csv”, and “In-growth_Core_Enviroment.csv”, with metrics including survival status, height, total biomass and the biomass of component plant parts, percentage root colonisation by mycorrhizas, for tree seedlings of ten common species including five ectomycorrhizal (ECM) and five arbuscular mycorrhizal (AM) species, which were transplanted in the in-growth cores with windows covering different sizes of nylon meshes (35 vs. 0.5 µm). The aim of the experiments was to test the prediction that differential access to root-associated fungal networks regulates plant-soil feedbacks, and quantify how access to root-associated fungal connections affects growth, fitness and pathogen loads of seedlings in patches of subtropical forest dominated by adult trees that associate with either ECM or AM fungi.
DOI: 10.6084/m9.figshare.12203375.v2
title: Soil fungal networks maintain local dominance of ectomycorrhizal trees - Experimental Data

description: Please refer to the NERC Environmental Information Data Centre at https://doi.org/10.5285/f1d17e61-bb6c-47a9-a648-062c63ea7f16.This data-set is the experimental data for the paper Liang et al. 2020 Nature Communications, entitled "Soil fungal networks maintain local dominance of ectomycorrhizal trees". It contains results on seedling growth and survival for two hyphal exclusion experiments in a subtropical forest. The data-set include four data files, entitled “Tree_Seedling_Survival.csv”, “Tree_Seedling_Growth.csv”, “Tree_Seedling_Root_Colonization.csv”, and “In-growth_Core_Enviroment.csv”, with metrics including survival status, height, total biomass and the biomass of component plant parts, percentage root colonisation by mycorrhizas, for tree seedlings of ten common species including five ectomycorrhizal (ECM) and five arbuscular mycorrhizal (AM) species, which were transplanted in the in-growth cores with windows covering different sizes of nylon meshes (35 vs. 0.5 µm). The aim of the experiments was to test the prediction that differential access to root-associated fungal networks regulates plant-soil feedbacks, and quantify how access to root-associated fungal connections affects growth, fitness and pathogen loads of seedlings in patches of subtropical forest dominated by adult trees that associate with either ECM or AM fungi.
DOI: 10.6084/m9.figshare.12203525.v1
title: Gut and intestinal biometrics of the giant trevally, Caranx ignobilis, fed an experimental diet with difference sources of activated charcoal

description: These are the raw data of gut and intestinal biometrics of giant trivially fish Caranx ignobilis fed an experimental diet with different type of charcoal
DOI: 10.6084/m9.figshare.12203375.v1
title: Soil fungal networks maintain local dominance of ectomycorrhizal trees - Experimental Data

description: This data-set is the experimental data for the paper Liang et al. 2020 Nature Communications, entitled "Soil fungal networks maintain local dominance of ectomycorrhizal trees". It contains results on seedling growth and survival for two hyphal exclusion experiments in a subtropical forest. The data-set include four data files, entitled “Tree_Seedling_Survival.csv”, “Tree_Seedling_Growth.csv”, “Tree_Seedling_Root_Colonization.csv”, and “In-growth_Core_Enviroment.csv”, with metrics including survival status, height, total biomass and the biomass of component plant parts, percentage root colonisation by mycorrhizas, for tree seedlings of ten common species including five ectomycorrhizal (ECM) and five arbuscular mycorrhizal (AM) species, which were transplanted in the in-growth cores with windows covering different sizes of nylon meshes (35 vs. 0.5 µm). The aim of the experiments was to test the prediction that differential access to root-associated fungal networks regulates plant-soil feedbacks, and quantify how access to root-associated fungal connections affects growth, fitness and pathogen loads of seedlings in patches of subtropical forest dominated by adult trees that associate with either ECM or AM fungi.
DOI: 10.6084/m9.figshare.12203339
title: DataAssimilation_0.56deg_ens64_o3_Modellevel_2hourly_20080629-20080721.nc

description: Data assimilation analysis of ozone concentrations derived from multi-constituent satellite data assimilation at 0.56-degree resolution
DOI: 10.6084/m9.figshare.12203342
title: Simulation Model Script from Disruption of cross-feeding interactions by invading taxa can cause invasional meltdown in microbial communities

description: Code for generating model simulations
DOI: 10.6084/m9.figshare.12203336
title: Supplemental information on moth pollen transport networks in agro-ecosystems from Nocturnal pollinators strongly contribute to pollen transport of wild flowers in an agricultural landscape

description: A file containing 4 descriptive data tables and 2 figures associated with recorded data.
DOI: 10.6084/m9.figshare.12203339.v1
title: DataAssimilation_0.56deg_ens64_o3_Modellevel_2hourly_20080629-20080721.nc

description: Data assimilation analysis of ozone concentrations derived from multi-constituent satellite data assimilation at 0.56-degree resolution
DOI: 10.6084/m9.figshare.12203336.v1
title: Supplemental information on moth pollen transport networks in agro-ecosystems from Nocturnal pollinators strongly contribute to pollen transport of wild flowers in an agricultural landscape

description: A file containing 4 descriptive data tables and 2 figures associated with recorded data.
DOI: 10.6084/m9.figshare.12203321
title: Data for Fig 1 from Force networks, torque balance and Airy stress in the planar vertex model of a confluent epithelium. 30 October 2019 2 April 2020

description: The vertex model is a popular framework for modelling tightly packed biological cells, such as confluent epithelia. Cells are described by convex polygons tiling the plane and their equilibrium is found by minimizing a global mechanical energy, with vertex locations treated as degrees of freedom. Drawing on analogies with granular materials, we describe the force network for a localized monolayer and derive the corresponding discrete Airy stress function, expressed for each N-sided cell as N scalars defined over kites covering the cell. We show how a torque balance (commonly overlooked in implementations of the vertex model) requires each internal vertex to lie at the orthocentre of the triangle formed by neighbouring edge centroids. Torque balance also places a geometric constraint on the stress in the neighbourhood of cellular trijunctions, and requires cell edges to be orthogonal to the links of a dual network that connect neighbouring cell centres and thereby triangulate the monolayer. We show how the Airy stress function depends on cell shape when a standard energy functional is adopted, and discuss implications for computational implementations of the model.
DOI: 10.6084/m9.figshare.12203324
title: DataAssimilation_0.56deg_ens64_eminox_Surface_Mean_20080629-20080721.nc

description: Data assimilation analysis of surface NOx emissions derived from multi-constituent satellite data assimilation at 0.56-degree resolution
DOI: 10.6084/m9.figshare.12203321.v1
title: Data for Fig 1 from Force networks, torque balance and Airy stress in the planar vertex model of a confluent epithelium. 30 October 2019 2 April 2020

description: The vertex model is a popular framework for modelling tightly packed biological cells, such as confluent epithelia. Cells are described by convex polygons tiling the plane and their equilibrium is found by minimizing a global mechanical energy, with vertex locations treated as degrees of freedom. Drawing on analogies with granular materials, we describe the force network for a localized monolayer and derive the corresponding discrete Airy stress function, expressed for each N-sided cell as N scalars defined over kites covering the cell. We show how a torque balance (commonly overlooked in implementations of the vertex model) requires each internal vertex to lie at the orthocentre of the triangle formed by neighbouring edge centroids. Torque balance also places a geometric constraint on the stress in the neighbourhood of cellular trijunctions, and requires cell edges to be orthogonal to the links of a dual network that connect neighbouring cell centres and thereby triangulate the monolayer. We show how the Airy stress function depends on cell shape when a standard energy functional is adopted, and discuss implications for computational implementations of the model.
DOI: 10.6084/m9.figshare.12203324.v1
title: DataAssimilation_0.56deg_ens64_eminox_Surface_Mean_20080629-20080721.nc

description: Data assimilation analysis of surface NOx emissions derived from multi-constituent satellite data assimilation at 0.56-degree resolution
DOI: 10.6084/m9.figshare.12203306
title: DataAssimilation_0.56deg_ens32_o3_Modellevel_2hourly_20080629-20080721.nc

description: Data assimilation analysis of ozone concentrations derived from multi-constituent satellite data assimilation at 0.56-degree resolution
DOI: 10.6084/m9.figshare.12203297
title: DataAssimilation_0.56deg_ens32_eminox_Surface_Mean_20080629-20080721.nc

description: Data assimilation analysis of surface NOx emissions derived from multi-constituent satellite data assimilation at 0.56-degree resolution
DOI: 10.6084/m9.figshare.12203306.v1
title: DataAssimilation_0.56deg_ens32_o3_Modellevel_2hourly_20080629-20080721.nc

description: Data assimilation analysis of ozone concentrations derived from multi-constituent satellite data assimilation at 0.56-degree resolution
DOI: 10.6084/m9.figshare.12203294
title: DataAssimilation_2.8deg_ens32_o3_Modellevel_2hourly_20080629-20080721.nc

description: Data assimilation analysis of ozone concentrations derived from multi-constituent satellite data assimilation at 2.8-degree resolution
DOI: 10.6084/m9.figshare.12203291
title: DataAssimilation_2.8deg_ens32_no2_Modellevel_2hourly_20080629-20080721.nc

description: Data assimilation analysis of NO2 concentration derived from multi-constituent satellite data assimilation at 2.8-degree resolution
DOI: 10.6084/m9.figshare.12203297.v1
title: DataAssimilation_0.56deg_ens32_eminox_Surface_Mean_20080629-20080721.nc

description: Data assimilation analysis of surface NOx emissions derived from multi-constituent satellite data assimilation at 0.56-degree resolution
DOI: 10.6084/m9.figshare.12203288
title: DataAssimilation_2.8deg_ens32_eminox_Surface_Mean_20080629-20080721.nc

description: Data assimilation analysis of surface NOx emission derived from multi-constituent satellite data assimilation at 2.8-degree resolution
DOI: 10.6084/m9.figshare.12203291.v1
title: DataAssimilation_2.8deg_ens32_no2_Modellevel_2hourly_20080629-20080721.nc

description: Data assimilation analysis of NO2 concentration derived from multi-constituent satellite data assimilation at 2.8-degree resolution
DOI: 10.6084/m9.figshare.12203294.v1
title: DataAssimilation_2.8deg_ens32_o3_Modellevel_2hourly_20080629-20080721.nc

description: Data assimilation analysis of ozone concentrations derived from multi-constituent satellite data assimilation at 2.8-degree resolution
DOI: 10.6084/m9.figshare.12203288.v1
title: DataAssimilation_2.8deg_ens32_eminox_Surface_Mean_20080629-20080721.nc

description: Data assimilation analysis of surface NOx emission derived from multi-constituent satellite data assimilation at 2.8-degree resolution
DOI: 10.6084/m9.figshare.12203309.v4
title: original data of LC-qqqMS.zip

description: “Terahertz spectroscopy for the accurate identification of <i>Panax quinquefolium</i> based on non-conjugated 24(R)-pseudoginsenoside F<sub>11</sub>” (manuscript ID: 545470)-data
DOI: 10.6084/m9.figshare.12203270
title: Native-invasive spatial seed aggregation competition trials

description: PurposeTo explore spatial pattern, provenance, and interactions between seeds and with a mimic exotic in a controlled context.HypothesisSpatial aggregeation of seeds shifts the net outcome of native-exotic interactions.PredictionsIncreased seed aggregated increases competitive interactions intra and inter-specifically.<br>Native seeds can outcompete an invasive species at some seed aggregations.<br>One of the key effects of the invasive species brome is physical interference (tested by a mimic plant and by measuring light levels in competition).DesignTwo species tested. Phacelia tancetifolia and Bromus rubens. Greenhouse trials, full-spectrum light, 15cm pots. A total of 8 weeks experimentation, and fixed density series with replacement at 10 seeds per pot. The aggregation of seed was clumped or dispersed in sowing for each species in mixture and monocultures.
DOI: 10.6084/m9.figshare.12203309
title: original data of LC-qqqMS.zip

description: “Terahertz spectroscopy for the accurate identification of <i>Panax quinquefolium</i> based on non-conjugated 24(R)-pseudoginsenoside F<sub>11</sub>” (manuscript ID: 545470)-data
DOI: 10.6084/m9.figshare.12203249
title: Data from: The role of herbivory in the macroevolution of vertebrate hormone dynamics

description: This data accompanies our 2020 publication in Ecology Letters titled "The role of herbivory in the macroevolution of vertebrate hormone dynamics." <br>Edwards_etal_2020_EcolLett contains 8 tabs: 4 partitions of the dataset with a tab for their corresponding metadata. The "sample_level" tab contains the individual level data on glucocorticoids measurements, species diet, species mass, and factors associated with sample collection. Column information is described in the "sample_level_meta" tab. The "species_level" tab contains the data partitioned at the species level, and column information is described in "species_level_meta". The "desantis" tab has the original data from Desantis et al. 2013 in orange text and reassignments in black text. The "hbase" tab has the original data from the HormoneBase used in Vitousek et al. 2019 in orange text and reassignments in black text. Edwards_etal_2020_phylo is the phylogeny file for the species included in the above dataset.
DOI: 10.6084/m9.figshare.12203186
title: Hauber et al IOB 2020

description: Maternal investment and egg rejection details data set.
DOI: 10.6084/m9.figshare.12203186.v1
title: Hauber et al IOB 2020

description: Maternal investment and egg rejection details data set.
DOI: 10.6084/m9.figshare.12203120
title: MD_data_GRL

description: Molecular Dynamics simulaiton data for lunar water formation induced by electric field
DOI: 10.6084/m9.figshare.12203117
title: Inverse transform of templateflow's tpl-MNI152NLin2009cAsym_from-MNI152NLin6Asym_mode-image_xfm

description: The templateflow api does not make this inverse transform available, so here it is, computed by SimpleITK's InvertDisplacementFieldImageFilter (see attached code)<br>
DOI: 10.6084/m9.figshare.12203021
title: Source_data_files

description: Data source for the figure in the article.
DOI: 10.6084/m9.figshare.12203117.v1
title: Inverse transform of templateflow's tpl-MNI152NLin2009cAsym_from-MNI152NLin6Asym_mode-image_xfm

description: The templateflow api does not make this inverse transform available, so here it is, computed by SimpleITK's InvertDisplacementFieldImageFilter (see attached code)<br>
DOI: 10.6084/m9.figshare.12203120.v2
title: MD_data_GRL

description: Molecular Dynamics simulaiton data for lunar water formation induced by electric field
DOI: 10.6084/m9.figshare.12203009
title: Graphics_Data

description: Data presented in the figures.
DOI: 10.6084/m9.figshare.12203009.v1
title: Graphics_Data

description: Data presented in the figures.