cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25376/hra.7801058
title: JCI Insight97918.pdf

description: Alterations in ectopic lipid deposition and circulating lipids are major risk factors for developing cardiometabolic diseases. Angiopoietin-like protein 4 (ANGPTL4), a protein that inhibits lipoprotein lipase (LPL), controls fatty acid (FA) uptake in adipose and oxidative tissues and regulates circulating triacylglycerol-rich (TAG-rich) lipoproteins. Unfortunately, global depletion of ANGPTL4 results in severe metabolic abnormalities, inflammation, and fibrosis when mice are fed a high-fat diet (HFD), limiting our understanding of the contribution of ANGPTL4 in metabolic disorders. Here, we demonstrate that genetic ablationof ANGPTL4 in adipose tissue (AT) results in enhanced LPL activity, rapid clearance of circulating TAGs, increased AT lipolysis and FA oxidation, and decreased FA synthesis in AT. Most importantly, we found that absence of ANGPTL4 in AT prevents excessive ectopic lipid deposition in the liver and muscle, reducing novel PKC (nPKC) membrane translocation and enhancing insulin signaling. As a result, we observed a remarkable improvement in glucose tolerance in short-term HFD-fed AT-specific Angptl4-KO mice. Finally, lack of ANGPTL4 in AT enhances the clearance of proatherogenic lipoproteins, attenuates inflammation, and reduces atherosclerosis. Together, these findings uncovered an essential role of AT ANGPTL4 in regulating peripheral lipid deposition, influencing whole-body lipid and glucose metabolism and the progression of atherosclerosis
DOI: 10.25376/hra.7801058.v1
title: JCI Insight97918.pdf

description: Alterations in ectopic lipid deposition and circulating lipids are major risk factors for developing cardiometabolic diseases. Angiopoietin-like protein 4 (ANGPTL4), a protein that inhibits lipoprotein lipase (LPL), controls fatty acid (FA) uptake in adipose and oxidative tissues and regulates circulating triacylglycerol-rich (TAG-rich) lipoproteins. Unfortunately, global depletion of ANGPTL4 results in severe metabolic abnormalities, inflammation, and fibrosis when mice are fed a high-fat diet (HFD), limiting our understanding of the contribution of ANGPTL4 in metabolic disorders. Here, we demonstrate that genetic ablationof ANGPTL4 in adipose tissue (AT) results in enhanced LPL activity, rapid clearance of circulating TAGs, increased AT lipolysis and FA oxidation, and decreased FA synthesis in AT. Most importantly, we found that absence of ANGPTL4 in AT prevents excessive ectopic lipid deposition in the liver and muscle, reducing novel PKC (nPKC) membrane translocation and enhancing insulin signaling. As a result, we observed a remarkable improvement in glucose tolerance in short-term HFD-fed AT-specific Angptl4-KO mice. Finally, lack of ANGPTL4 in AT enhances the clearance of proatherogenic lipoproteins, attenuates inflammation, and reduces atherosclerosis. Together, these findings uncovered an essential role of AT ANGPTL4 in regulating peripheral lipid deposition, influencing whole-body lipid and glucose metabolism and the progression of atherosclerosis
DOI: 10.6084/m9.figshare.7801046
title: The supplemental information for RNA-Seq workflow benchmark by CWL-metrics

description: The tables of the samples retrieved from the Sequence Read Archive and the Amazon Web Service Elastic Computing Cloud instance types used for RNA-Seq workflow benchmark by CWL-metrics, a system to collect runtime metrics of workflows described in Common Workflow Language (CWL).
DOI: 10.6084/m9.figshare.7801154.v4
title: Predictive Coding Deep Neural Network in Chainer (ver.tb8b)

description: The PredNet*, written in Keras, was ported to Chainer and reconstructed for convenience.Visualization of internal images in the network models was performed using a self-made converter program and Tesorboard in Tensorflow.<br><br>*Lotter, W., Kreiman, G., & Cox, D., Deep predictive coding networks for video prediction and unsupervised learning, arXiv 1605.08104.<br>This program is new version used inWatanabe E, Kitaoka A, Sakamoto K, Yasugi M and Tanaka K, Illusory Motion Reproduced by Deep Neural Networks Trained for Prediction. Frontiers in Psychology 9:345. doi: 10.3389/fpsyg.2018.00345 (2018)
DOI: 10.6084/m9.figshare.7801154.v5
title: Predictive Coding Deep Neural Network in Chainer (ver.tb8c)

description: The PredNet*, written in Keras, was ported to Chainer and reconstructed for convenience.Visualization of internal images in the network models was performed using a self-made converter program and Tesorboard in Tensorflow.<br><br>*Lotter, W., Kreiman, G., & Cox, D., Deep predictive coding networks for video prediction and unsupervised learning, arXiv 1605.08104.<br>This program is new version used inWatanabe E, Kitaoka A, Sakamoto K, Yasugi M and Tanaka K, Illusory Motion Reproduced by Deep Neural Networks Trained for Prediction. Frontiers in Psychology 9:345. doi: 10.3389/fpsyg.2018.00345 (2018)
DOI: 10.6084/m9.figshare.7801010
title: Dataset for: Partial characteristics for marked spatial point processes

description: This paper introduces a new class of partial summary characteristics for two types of marked planar point processes. We consider purely qualitatively marked spatial point processes and multitype spatial point processes with quantitative marks. After a survey of classical functional summary characteristics for qualitatively and quantitatively marked point processes, the class of partial characteristics is presented. These characteristics are defined through the periodogram, which makes the computations efficient. We demonstrate the application of our method in the analysis of a multi-species tree data recorded in the City of Melbourne.
DOI: 10.6084/m9.figshare.7801010.v1
title: Dataset for: Partial characteristics for marked spatial point processes

description: This paper introduces a new class of partial summary characteristics for two types of marked planar point processes. We consider purely qualitatively marked spatial point processes and multitype spatial point processes with quantitative marks. After a survey of classical functional summary characteristics for qualitatively and quantitatively marked point processes, the class of partial characteristics is presented. These characteristics are defined through the periodogram, which makes the computations efficient. We demonstrate the application of our method in the analysis of a multi-species tree data recorded in the City of Melbourne.
DOI: 10.6084/m9.figshare.7801154.v6
title: Predictive Coding Deep Neural Network in Chainer (ver.tb8c)

description: The PredNet*, written in Keras, was ported to Chainer and reconstructed for convenience.Visualization of internal images in the network models was performed using a self-made converter program and Tesorboard in Tensorflow.<br><br>*Lotter, W., Kreiman, G., & Cox, D., Deep predictive coding networks for video prediction and unsupervised learning, arXiv 1605.08104.<br>This program is new version used inWatanabe E, Kitaoka A, Sakamoto K, Yasugi M and Tanaka K, Illusory Motion Reproduced by Deep Neural Networks Trained for Prediction. Frontiers in Psychology 9:345. doi: 10.3389/fpsyg.2018.00345 (2018)
DOI: 10.6084/m9.figshare.7801154.v7
title: Predictive Coding Deep Neural Network in Chainer (ver.tb8d)

description: The PredNet*, written in Keras, was ported to Chainer and reconstructed for convenience.Visualization of internal images in the network models was performed using a self-made converter program and Tesorboard in Tensorflow.<br><br>*Lotter, W., Kreiman, G., & Cox, D., Deep predictive coding networks for video prediction and unsupervised learning, arXiv 1605.08104.<br>This program is new version used inWatanabe E, Kitaoka A, Sakamoto K, Yasugi M and Tanaka K, Illusory Motion Reproduced by Deep Neural Networks Trained for Prediction. Frontiers in Psychology 9:345. doi: 10.3389/fpsyg.2018.00345 (2018)
DOI: 10.6084/m9.figshare.7801154.v8
title: Predictive Coding Deep Neural Network in Chainer (ver.tb8e)

description: The PredNet*, written in Keras, was ported to Chainer and reconstructed for convenience.Visualization of internal images in the network models was performed using a self-made converter program and Tesorboard in Tensorflow.<br><br>*Lotter, W., Kreiman, G., & Cox, D., Deep predictive coding networks for video prediction and unsupervised learning, arXiv 1605.08104.<br>This program is new version used inWatanabe E, Kitaoka A, Sakamoto K, Yasugi M and Tanaka K, Illusory Motion Reproduced by Deep Neural Networks Trained for Prediction. Frontiers in Psychology 9:345. doi: 10.3389/fpsyg.2018.00345 (2018)
DOI: 10.6084/m9.figshare.7801154.v9
title: Predictive Coding Deep Neural Network in Chainer (ver.tb8f)

description: The PredNet*, written in Keras, was ported to Chainer and reconstructed for convenience.Visualization of internal images in the network models was performed using a self-made converter program and Tesorboard in Tensorflow.<br><br>*Lotter, W., Kreiman, G., & Cox, D., Deep predictive coding networks for video prediction and unsupervised learning, arXiv 1605.08104.<br>This program is new version used inWatanabe E, Kitaoka A, Sakamoto K, Yasugi M and Tanaka K, Illusory Motion Reproduced by Deep Neural Networks Trained for Prediction. Frontiers in Psychology 9:345. doi: 10.3389/fpsyg.2018.00345 (2018)
DOI: 10.6084/m9.figshare.7800989.v1
title: Post-hoc analysis from phase III trials of human papillomavirus vaccines: considerations on impact on non-vaccine types

description: <b>Background</b>: Substantial heterogeneity has been reported in efficacy against high-grade cervical intraepithelial neoplasia (CIN) irrespective of HPV type in phase III results for bivalent and quadrivalent human papillomavirus virus (HPV) vaccines (AS04-HPV and qHPV). Real-world data recently confirmed a very high overall impact of AS04-HPV, supporting the validity of the observed heterogeneity. To explore the reasons for heterogeneous efficacy, we assessed vaccine impact on high-grade lesions not caused by vaccine types. <b>Research methods</b>: We extracted case counts of CIN lesions containing (1) at least one vaccine HPV type, (2) at least one vaccine HPV type and a high-risk non-vaccine type (co-infections) and (3) no vaccine types (non-vaccine or no high-risk HPV types). Based on these, Phase III cross-protective efficacies were estimated with exclusion (3) and with inclusion (2 and 3) of co-infections. <b>Results</b>: Cross-protective efficacy of AS04-HPV against CIN3 lesions ranges from 81.3% (95%CI: 34.7;96.5) (excluding co-infections) to 88.5% (95%CI:62.4;97.8) (including co-infections). For qHPV the efficacy ranges from −58.7% (95%CI: −180.5;8.5) (excluding co-infections) to 13.1% (95%CI: −39.0;45.9) (including co-infections). <b>Conclusions</b>: Heterogenous overall efficacy against CIN3 between AS04-HPV and qHPV is driven by differential efficacy against lesions that do not contain vaccine types, which may be related to the impact of different adjuvants on the immune response.
DOI: 10.6084/m9.figshare.7800965
title: Association of pazopanib-induced toxicities with outcome of patients with advanced soft tissue sarcoma; a retrospective analysis based on the European Organisation for Research and Treatment of Cancer (EORTC) 62043 and 62072 clinical trials

description: <b>Background:</b> There is an unmet need for markers predicting the outcome of patients with advanced soft tissue sarcoma (STS) treated with pazopanib. Since toxicity might be related to the anti-tumor activity of the drug, the aim of this study was to determine whether pazopanib-induced proteinuria, hypothyroidism and cardiotoxicity grade 3-4 were associated with outcome. <b>Methods:</b> The combined results of the EORTC 62043 and 62072 trials were retrospectively assessed and used in a landmark analysis to evaluate the effect of the toxicities on progression-free survival (PFS) and overall survival (OS), using the Kaplan-Meier method and Cox regression models. <b>Results:</b> Of the 333 eligible patients, 259 patients were included in the analyses, for which a landmark time point of 60 days after randomization/registration was selected. Proteinuria occurred in 25.1%, hypothyroidism in 22.0% and cardiotoxicity grade 3–4 in 5.8% of the patients (any grade in 41.7%). There was no effect of the occurrence of proteinuria (6-months PFS 35.4% for patients with vs. 38.3% for patients without proteinuria, HR 1.01, <i>p</i> = .953), hypothyroidism (41.2% vs. 36.5%, HR 0.82, <i>p</i> = .210) or cardiotoxicity grade 3–4 (26.7% vs. 38.2%, HR 0.97, <i>p</i> = .897) on PFS. Nor was there an effect of proteinuria (6-months OS 63.2% for patients with vs. 74.4% for patients without proteinuria, HR 1.22, <i>p</i> = .196), hypothyroidism (76.2% vs. 70.5%, HR 0.75, <i>p</i> = .093) or cardiotoxicity grade 3–4 (80.0% vs. 77.2%, HR 0.93, <i>p</i> = .801) on OS. <b>Conclusion:</b> There was no association between the occurrence of pazopanib-induced proteinuria, hypothyroidism and cardiotoxicity and outcome. Therefore, these toxicities cannot be used as predictors for pazopanib activity in patients with advanced STS.
DOI: 10.6084/m9.figshare.7800965.v1
title: Association of pazopanib-induced toxicities with outcome of patients with advanced soft tissue sarcoma; a retrospective analysis based on the European Organisation for Research and Treatment of Cancer (EORTC) 62043 and 62072 clinical trials

description: <b>Background:</b> There is an unmet need for markers predicting the outcome of patients with advanced soft tissue sarcoma (STS) treated with pazopanib. Since toxicity might be related to the anti-tumor activity of the drug, the aim of this study was to determine whether pazopanib-induced proteinuria, hypothyroidism and cardiotoxicity grade 3-4 were associated with outcome. <b>Methods:</b> The combined results of the EORTC 62043 and 62072 trials were retrospectively assessed and used in a landmark analysis to evaluate the effect of the toxicities on progression-free survival (PFS) and overall survival (OS), using the Kaplan-Meier method and Cox regression models. <b>Results:</b> Of the 333 eligible patients, 259 patients were included in the analyses, for which a landmark time point of 60 days after randomization/registration was selected. Proteinuria occurred in 25.1%, hypothyroidism in 22.0% and cardiotoxicity grade 3–4 in 5.8% of the patients (any grade in 41.7%). There was no effect of the occurrence of proteinuria (6-months PFS 35.4% for patients with vs. 38.3% for patients without proteinuria, HR 1.01, <i>p</i> = .953), hypothyroidism (41.2% vs. 36.5%, HR 0.82, <i>p</i> = .210) or cardiotoxicity grade 3–4 (26.7% vs. 38.2%, HR 0.97, <i>p</i> = .897) on PFS. Nor was there an effect of proteinuria (6-months OS 63.2% for patients with vs. 74.4% for patients without proteinuria, HR 1.22, <i>p</i> = .196), hypothyroidism (76.2% vs. 70.5%, HR 0.75, <i>p</i> = .093) or cardiotoxicity grade 3–4 (80.0% vs. 77.2%, HR 0.93, <i>p</i> = .801) on OS. <b>Conclusion:</b> There was no association between the occurrence of pazopanib-induced proteinuria, hypothyroidism and cardiotoxicity and outcome. Therefore, these toxicities cannot be used as predictors for pazopanib activity in patients with advanced STS.
DOI: 10.25376/hra.7800959
title: The effect of age, sex and strains on the performance and outcome in animal models of stroke.pdf

description: Stroke is one of the leading causes of death worldwide, and the majority of cerebral stroke is caused by occlusionof cerebral circulation, which eventually leads to brain infarction. Although stroke occurs mainly in the agedpopulation, most animal models for experimental stroke in vivo almost universally rely on young-adult rodentsfor the evaluation of neuropathological, neurological, or behavioral outcomes after stroke due to their greateravailability, lower cost, and fewer health problems. However, it is well established that aged animals differ fromyoung animals in terms of physiology, neurochemistry, and behavior. Stroke-induced changes are more pronouncedwith advancing age. Therefore, the overlooked role of age in animal models of stroke could have animpact on data quality and hinder the translation of rodent models to humans. In addition to aging, other factorsalso influence functional performance after ischemic stroke. In this article, we summarize the differences betweenyoung and aged animals, the impact of age, sex and animal strains on performance and outcome in animalmodels of stroke and emphasize age as a key factor in preclinical stroke studies.
DOI: 10.25380/iastate.7800956
title: Imaging of Unstained DNA Origami Triangles with Electron Microscopy

description: Imaging of scaffolded DNA and DNA origami nanostructures has been dominated by atomic force microscopy of samples immobilized on bulk substrates. Less commonly used for DNA imaging are electron microscopy techniques, which are typically carried out either after negative staining of DNA or by direct imaging using a bright field cryo-TEM. Here, direct imaging of unstained DNA origami nanostructures on thin electron-transparent substrates utilizing high angular annular dark field scanning transmission electron microscopy )(HAADFSTEM) is reported. This approach establishes a simple method for depositing and imaging intact DNA triangles with mass-thickness contrast, sufficient to measure the scaffold-to-scaffold distances and the length of the triangle’s seam. The signal-to-noise ratio (SNR) of the DNA supported on amorphous carbon as a function of the carbon thickness is measured on three types of commercially available TEM grids to analyze the image resolution. This allows for an edge detection of ~1 nm height DNA triangles on carbon substrates as thick as ~25 nm. Additional observations on the effect on SNR with the imaging modes are discussed. The effect of cation concentration used for pre-treating the grid surface on the image resolution is also explored. Our work presents proof-of-concept results demonstrating that electron microscopy can be utilized to resolve key elements of the DNA origami triangle, without staining or employing exceedingly complicated preparation protocols.<br>
DOI: 10.25376/hra.7800959.v1
title: The effect of age, sex and strains on the performance and outcome in animal models of stroke.pdf

description: Stroke is one of the leading causes of death worldwide, and the majority of cerebral stroke is caused by occlusionof cerebral circulation, which eventually leads to brain infarction. Although stroke occurs mainly in the agedpopulation, most animal models for experimental stroke in vivo almost universally rely on young-adult rodentsfor the evaluation of neuropathological, neurological, or behavioral outcomes after stroke due to their greateravailability, lower cost, and fewer health problems. However, it is well established that aged animals differ fromyoung animals in terms of physiology, neurochemistry, and behavior. Stroke-induced changes are more pronouncedwith advancing age. Therefore, the overlooked role of age in animal models of stroke could have animpact on data quality and hinder the translation of rodent models to humans. In addition to aging, other factorsalso influence functional performance after ischemic stroke. In this article, we summarize the differences betweenyoung and aged animals, the impact of age, sex and animal strains on performance and outcome in animalmodels of stroke and emphasize age as a key factor in preclinical stroke studies.
DOI: 10.25380/iastate.7800956.v1
title: Imaging of Unstained DNA Origami Triangles with Electron Microscopy

description: Imaging of scaffolded DNA and DNA origami nanostructures has been dominated by atomic force microscopy when the DNA molecules are immobilized on bulk substrates. Less commonly used for DNA imaging are electron microscopy techniques, which are normally carried out either after negative staining of DNA or by direct imaging using a bright field cryo-TEM. Here, we report direct imaging of unstained DNA origami nanostructures on thin electron-transparent substrates by utilizing high angular annular dark field scanning transmission electron microscopy (HAADF-STEM). Our approach establishes a simple method for depositing and imaging of intact DNA triangles with mass-thickness contrast, sufficient to permit identification of the scaffold-to-scaffold distances and the length of the triangle’s seam. We follow the signal-to-noise ratio (SNR) of the DNA supported on amorphous carbon as a function of the carbon thickness in three types of commercially available TEM grids to analyze the image resolution. Accurate edge detection of DNA triangles of ~1 nm height can be achieved on up to 20 nm thick carbon substrates. Additional observations on the effect on SNR with the imaging modes are discussed. The effect of cation concentration used for pre-treating the grid surface on the image resolution is also explored.
DOI: 10.6084/m9.figshare.7800929
title: Didymella tanaceti 2012 population SSR, SDHI and MAT data

description: <i>Didymella tanaceti </i>population collected in 2012 from Tasmania, Australia. Each isolate is an individual. Includes Field (12-51907, 12-63242, 12-70046 and 12-70047) and time of sampling (August 2012 or November 2012) for each isolates. Number of Microsatellite repeats are listed for 9 SSR markers. SDHI Substitution is the Succinate dehydrogenase Subunit substitution identified from HRM analysis Mating-type indicates if isolates are of MAT1-1 or MAT1-2 mating type.<br>
DOI: 10.25380/iastate.7800956.v2
title: Imaging of Unstained DNA Origami Triangles with Electron Microscopy

description: Imaging of scaffolded DNA and DNA origami nanostructures has been dominated by atomic force microscopy when the DNA molecules are immobilized on bulk substrates. Less commonly used for DNA imaging are electron microscopy techniques, which are normally carried out either after negative staining of DNA or by direct imaging using a bright field cryo-TEM. Here, we report direct imaging of unstained DNA origami nanostructures on thin electron-transparent substrates by utilizing high angular annular dark field scanning transmission electron microscopy (HAADF-STEM). Our approach establishes a simple method for depositing and imaging of intact DNA triangles with mass-thickness contrast, sufficient to permit identification of the scaffold-to-scaffold distances and the length of the triangle’s seam. We follow the signal-to-noise ratio (SNR) of the DNA supported on amorphous carbon as a function of the carbon thickness in three types of commercially available TEM grids to analyze the image resolution. Accurate edge detection of DNA triangles of ~1 nm height can be achieved on up to 20 nm thick carbon substrates. Additional observations on the effect on SNR with the imaging modes are discussed. The effect of cation concentration used for pre-treating the grid surface on the image resolution is also explored.
DOI: 10.6084/m9.figshare.7800929.v1
title: Didymella tanaceti 2012 population SSR, SDHI and MAT data

description: <i>Didymella tanaceti </i>population collected in 2012 from Tasmania, Australia. Each isolate is an individual. Includes Field (12-51907, 12-63242, 12-70046 and 12-70047) and time of sampling (August 2012 or November 2012) for each isolates. Number of Microsatellite repeats are listed for 9 SSR markers. SDHI Substitution is the Succinate dehydrogenase Subunit substitution identified from HRM analysis Mating-type indicates if isolates are of MAT1-1 or MAT1-2 mating type.<br>
DOI: 10.6084/m9.figshare.7800917
title: Clinical data for USPIO-enhanced MRI dataset

description: Clinical data for the 5 head and neck squamous cell carcinoma (HNSCC) patients, representing our cohort. Patients and disease identifiers are detailed in this *.csv file.
DOI: 10.6084/m9.figshare.7800920
title: ReadMe_Clinical data_USPIO-enhanced MRI dataset

description: Supplemental information about the variables provided in the clinical dataset file.
DOI: 10.6084/m9.figshare.7800917.v2
title: Clinical data for USPIO-enhanced MRI dataset

description: Clinical data for the 5 head and neck squamous cell carcinoma (HNSCC) patients, representing our cohort. Patients and disease identifiers are detailed in this *.csv file.