cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5339962.v1
title: PDTCM: a systems pharmacology platform of traditional Chinese medicine for psoriasis

description: <b>Introduction:</b> Psoriasis is a refractory skin disorder, and usually requires a lifetime control. Traditional Chinese medicine (TCM) is effective and safe for this disease. However, the cellular and molecular mechanisms of TCM remedies for psoriasis are still not fully understood. TCM contains numerous natural products. Natural products have historically been invaluable as a resource of therapeutic agents. Yet, there is no integrated information about active compounds of TCM for psoriasis. <b>Method:</b> We use systems pharmacology methods to develop the Psoriasis Database of Traditional Chinese Medicine (PDTCM). The database covered a number of psoriasis-related information (formulas, TCM, compounds, target proteins, diseases and biomarkers). With these data information, an online platform was constructed <b>Results:</b> PDTCM comprises 38 empirical therapeutic formulas, 34373 compounds from 1424 medicinal plants, 44 psoriasis-related proteins and 76 biomarkers from 111 related diseases. On this platform, users can screen active compounds for a psoriasis-related target and explore molecular mechanisms of TCM. Accordingly, users can also download the retrieved structures and data information with a defined value set. In addition, it helps to get a better understanding of Chinese prescriptions in disease treatment. <b>Conclusion:</b> With the systems pharmacology-based data, PDTCM would become a valuable resource for TCM in psoriasis-related research.Key messagesPDTCM platform comprises a great deal of data on TCM and psoriasis.On this platform, users can retrieve and get needed information with systems pharmacology methods, such as active compounds screening, target prediction and molecular mechanisms exploration.It is a tool for psoriasis-related research on natural drugs systematically. PDTCM platform comprises a great deal of data on TCM and psoriasis. On this platform, users can retrieve and get needed information with systems pharmacology methods, such as active compounds screening, target prediction and molecular mechanisms exploration. It is a tool for psoriasis-related research on natural drugs systematically.
DOI: 10.6084/m9.figshare.5341255
title: Genome-wide gene expression analysis of amphioxus (<i>Branchiostoma belcheri</i>) following lipopolysaccharide challenge using strand-specific RNA-seq

description: Amphioxus is the closest living proxy for exploring the evolutionary origin of the immune system in vertebrates. To understand the immune responses of amphioxus to lipopolysaccharide (LPS), 5 ribosomal RNA (rRNA)-depleted libraries of amphioxus were constructed, including one control (0 h) library and 4 treatment libraries at 6, 12, 24, and 48 h post-injection (hpi) with LPS. The transcriptome of <i>Branchiostoma belcheri</i> was analyzed using strand-specific RNA sequencing technology (RNA-seq). A total of 6161, 6665, 7969, and 6447 differentially expressed genes (DEGs) were detected at 6, 12, 24, and 48 hpi, respectively, compared with expression levels at 0 h. We identified amphioxus genes active during the acute-phase response to LPS at different time points after stimulation. Moreover, to better visualize the resolution phase of the immune process during immune response, we identified 6057 and 5235 DEGs at 48 hpi by comparing with 6 and 24 hpi, respectively. Through real-time quantitative PCR (qRT-PCR) analysis of 12 selected DEGs, we demonstrated the accuracy of the RNA-seq data in this study. Functional enrichment analysis of DEGs demonstrated that most terms were related to defense and immune responses, disease and infection, cell apoptosis, and metabolism and catalysis. Subsequently, we identified 1330, 485, 670, 911, and 1624 time-specific genes (TSGs) at 0, 6, 12, 24, and 48 hpi. Time-specific terms at each of 5 time points were primarily involved in development, immune signaling, signal transduction, DNA repair and stability, and metabolism and catalysis, respectively. As this is the first study to report the transcriptome of an organism with primitive immunity following LPS challenge at multiple time points, it provides gene expression information for further research into the evolution of immunity in vertebrates.
DOI: 10.6084/m9.figshare.5341255.v1
title: Genome-wide gene expression analysis of amphioxus (<i>Branchiostoma belcheri</i>) following lipopolysaccharide challenge using strand-specific RNA-seq

description: Amphioxus is the closest living proxy for exploring the evolutionary origin of the immune system in vertebrates. To understand the immune responses of amphioxus to lipopolysaccharide (LPS), five ribosomal RNA (rRNA)-depleted libraries of amphioxus were constructed, including one control (0 h) library and four treatment libraries at 6, 12, 24, and 48 h post-injection (hpi) with LPS. The transcriptome of <i>Branchiostoma belcheri</i> was analyzed using strand-specific RNA sequencing technology (RNA-seq). A total of 6161, 6665, 7969, and 6447 differentially expressed genes (DEGs) were detected at 6, 12, 24, and 48 hpi, respectively, compared to expression levels at 0 h. We identified amphioxus genes active during the acute-phase response to LPS at different time points after stimulation. Moreover, in order to better visualize the resolution phase of the immune process during immune response, we identified 6057 and 5235 DEGs at 48 hpi by comparing with 6 and 24 hpi, respectively. Through real-time quantitative PCR (qRT-PCR) analysis of 12 selected DEGs, we demonstrated the accuracy of the RNA-seq data in this study. Functional enrichment analysis of DEGs demonstrated that most terms were related to defense and immune responses, disease and infection, cell apoptosis, and metabolism and catalysis. Subsequently, we identified 1330, 485, 670, 911, and 1624 time-specific genes (TSGs) at 0, 6, 12, 24, and 48 hpi. Time-specific terms at each of five time points were primarily involved in development, immune signaling, signal transduction, DNA repair and stability, and metabolism and catalysis, respectively. As this is the first study to report the transcriptome of an organism with primitive immunity following LPS challenge at multiple time points, it provides gene expression information for further research into the evolution of immunity in vertebrates.
DOI: 10.6084/m9.figshare.5341255.v3
title: Genome-wide gene expression analysis of amphioxus (<i>Branchiostoma belcheri</i>) following lipopolysaccharide challenge using strand-specific RNA-seq

description: Amphioxus is the closest living proxy for exploring the evolutionary origin of the immune system in vertebrates. To understand the immune responses of amphioxus to lipopolysaccharide (LPS), 5 ribosomal RNA (rRNA)-depleted libraries of amphioxus were constructed, including one control (0 h) library and 4 treatment libraries at 6, 12, 24, and 48 h post-injection (hpi) with LPS. The transcriptome of <i>Branchiostoma belcheri</i> was analyzed using strand-specific RNA sequencing technology (RNA-seq). A total of 6161, 6665, 7969, and 6447 differentially expressed genes (DEGs) were detected at 6, 12, 24, and 48 hpi, respectively, compared with expression levels at 0 h. We identified amphioxus genes active during the acute-phase response to LPS at different time points after stimulation. Moreover, to better visualize the resolution phase of the immune process during immune response, we identified 6057 and 5235 DEGs at 48 hpi by comparing with 6 and 24 hpi, respectively. Through real-time quantitative PCR (qRT-PCR) analysis of 12 selected DEGs, we demonstrated the accuracy of the RNA-seq data in this study. Functional enrichment analysis of DEGs demonstrated that most terms were related to defense and immune responses, disease and infection, cell apoptosis, and metabolism and catalysis. Subsequently, we identified 1330, 485, 670, 911, and 1624 time-specific genes (TSGs) at 0, 6, 12, 24, and 48 hpi. Time-specific terms at each of 5 time points were primarily involved in development, immune signaling, signal transduction, DNA repair and stability, and metabolism and catalysis, respectively. As this is the first study to report the transcriptome of an organism with primitive immunity following LPS challenge at multiple time points, it provides gene expression information for further research into the evolution of immunity in vertebrates.
DOI: 10.6084/m9.figshare.5341255.v2
title: Genome-wide gene expression analysis of amphioxus (Branchiostoma belcheri) following lipopolysaccharide challenge using strand-specific RNA-seq

description: Amphioxus is the closest living proxy for exploring the evolutionary origin of the immune system in vertebrates. To understand the immune responses of amphioxus to lipopolysaccharide (LPS), five ribosomal RNA (rRNA)-depleted libraries of amphioxus were constructed, including one control (0 h) library and four treatment libraries at 6, 12, 24, and 48 h post-injection (hpi) with LPS. The transcriptome of <i>Branchiostoma belcheri</i> was analyzed using strand-specific RNA sequencing technology (RNA-seq). A total of 6161, 6665, 7969, and 6447 differentially expressed genes (DEGs) were detected at 6, 12, 24, and 48 hpi, respectively, compared to expression levels at 0 h. We identified amphioxus genes active during the acute-phase response to LPS at different time points after stimulation. Moreover, in order to better visualize the resolution phase of the immune process during immune response, we identified 6057 and 5235 DEGs at 48 hpi by comparing with 6 and 24 hpi, respectively. Through real-time quantitative PCR (qRT-PCR) analysis of 12 selected DEGs, we demonstrated the accuracy of the RNA-seq data in this study. Functional enrichment analysis of DEGs demonstrated that most terms were related to defense and immune responses, disease and infection, cell apoptosis, and metabolism and catalysis. Subsequently, we identified 1330, 485, 670, 911, and 1624 time-specific genes (TSGs) at 0, 6, 12, 24, and 48 hpi. Time-specific terms at each of five time points were primarily involved in development, immune signaling, signal transduction, DNA repair and stability, and metabolism and catalysis, respectively. As this is the first study to report the transcriptome of an organism with primitive immunity following LPS challenge at multiple time points, it provides gene expression information for further research into the evolution of immunity in vertebrates.
DOI: 10.6084/m9.figshare.5349100
title: X-ray Absorption Spectroscopy and Magnetism of Synthetic Greigite and Greigite Magnetosomes in Magnetotactic Bacteria

description: Scanning transmission X-ray microscopy at the Fe 2p (L<sub>2,3</sub>), O1s, C1s, and S2p edges was used to study greigite magnetosomes and other cellular content of a magnetotactic bacterium known as a multicellular magnetotactic prokaryote (MMP). X-ray absorption spectrum (XAS) and X-ray magnetic circular dichroism (XMCD) spectra of greigite (Fe<sub>3</sub>S<sub>4</sub>) nanoparticles, synthesized via a hydrothermal method, were measured. Although XAS of the synthetic greigite nanoparticles and biotic magnetosome crystals in MMPs are slightly different due to partial oxidation of the MMP greigite, the XMCD spectra of the two materials are in good agreement. The Fe 2p XAS and XMCD spectra of Fe<sub>3</sub>S<sub>4</sub> are quite different from those of its oxygen analog, magnetite (Fe<sub>3</sub>O<sub>4</sub>), suggesting Fe<sub>3</sub>S<sub>4</sub> has a different electronic and magnetic structure than Fe<sub>3</sub>O<sub>4</sub> despite having the same crystal structure. Sulfate and sulfide species were also identified in MMPs, both of which are likely involved in sulfur metabolism.
DOI: 10.6084/m9.figshare.5349100.v2
title: X-ray Absorption Spectroscopy and Magnetism of Synthetic Greigite and Greigite Magnetosomes in Magnetotactic Bacteria

description: Scanning transmission X-ray microscopy at the Fe 2p (L<sub>2,3</sub>), O1s, C1s, and S2p edges was used to study greigite magnetosomes and other cellular content of a magnetotactic bacterium known as a multicellular magnetotactic prokaryote (MMP). X-ray absorption spectrum (XAS) and X-ray magnetic circular dichroism (XMCD) spectra of greigite (Fe<sub>3</sub>S<sub>4</sub>) nanoparticles, synthesized via a hydrothermal method, were measured. Although XAS of the synthetic greigite nanoparticles and biotic magnetosome crystals in MMPs are slightly different due to partial oxidation of the MMP greigite, the XMCD spectra of the two materials are in good agreement. The Fe 2p XAS and XMCD spectra of Fe<sub>3</sub>S<sub>4</sub> are quite different from those of its oxygen analog, magnetite (Fe<sub>3</sub>O<sub>4</sub>), suggesting Fe<sub>3</sub>S<sub>4</sub> has a different electronic and magnetic structure than Fe<sub>3</sub>O<sub>4</sub> despite having the same crystal structure. Sulfate and sulfide species were also identified in MMPs, both of which are likely involved in sulfur metabolism.
DOI: 10.6073/pasta/9f4f43b8bf95c28896fcb1d8ef5f020b
title: Sediment, crab, and vegetation data from Sapelo Island, Georgia: 2017 - 2019

description: Sediment samples, Sesarma reticulatum gut and tissue samples, Spartina alterniflora leaves, and benthic diatoms were analyzed for a suite of biogeochemical parameters, including total carbon, total nitrogen, stable isotopes of carbon and nitrogen, and a subset of samples were analyzed for total hydrolyzable amino acids. Samples were collected between 2017 and 2019 on Sapelo Island, Georgia, USA. Samples were collected from Sesarma-grazed and un-grazed creeks. Analyses were conducted at the University of Florida and are associated with the manuscript by Morrison et al. entitled Influence of the keystone grazer, Sesarma reticulatum, on the hydrology and organic matter cycling of salt marshes in the southeastern United States.
DOI: 10.6084/m9.figshare.5357746
title: Data uploading

description: data
DOI: 10.6084/m9.figshare.5357746.v2
title: Data uploading

description: data
DOI: 10.6084/m9.figshare.5357746.v1
title: Data of subsurface moorings

description: Subsurface
moorings have been deployed since 2014 by the Institute of Oceanology, Chinese
Academy of Sciences (IOCAS).
DOI: 10.6084/m9.figshare.5363980
title: Bleeding risk of apixaban, dabigatran, and low-dose rivaroxaban compared with warfarin in Japanese patients with non-valvular atrial fibrillation: a propensity matched analysis of administrative claims data

description: <b>Objectives:</b> There is scarce evidence comparing novel oral anticoagulants (NOACs) with warfarin in real-world settings in Japan. This study compared the risk of bleeding events among patients with non-valvular atrial fibrillation (NVAF) initiating treatment with NOACs versus warfarin. <b>Methods:</b> A retrospective cohort study was conducted using a de-identified electronic health record based database of health claims and Diagnosis Procedure Combination data from 275 consenting hospitals in Japan. NVAF patients newly initiated on oral anticoagulants were eligible. Based on the first prescription, patients were assigned to 5/2.5 mg BID apixaban, 150/110 mg BID dabigatran, 15/10 mg QD rivaroxaban (approved dose lower in Japan compared to Western countries [20/15 mg QD]) or warfarin groups. One-to-one propensity score matching (PSM) was used to balance patient characteristics between warfarin and each NOAC. Patients were followed up to 1 year post-first prescription. <b>Results:</b> Among 38,662 eligible patients, a total of 5977, 5090, and 6726 matched pairs were identified for warfarin versus apixaban, warfarin versus dabigatran, and warfarin versus rivaroxaban, respectively after PSM. Compared to warfarin, apixaban (hazard ratio [HR] 0.586; 95% CI 0.421–0.815), dabigatran (HR 0.617; 0.425–0.895) and rivaroxaban (HR 0.693; 0.514–0.933) were associated with a significantly lower risk of major bleeding. The risk of any bleeding was significantly lower for apixaban (HR 0.782; 0.682–0.896), but not for dabigatran (HR 0.988; 0.860–1.135) or rivaroxaban (HR 0.938; 0.832–1.057) when comparing to warfarin. <b>Conclusions:</b> Among Japanese patients with NVAF, treatment with apixaban 5/2.5 mg BID was associated with a significantly lower risk of major bleeding and any bleeding when compared to warfarin. Treatment with dabigatran 150/110 mg BID or rivaroxaban 15/10 mg QD was associated with a significantly lower risk of major bleeding, but not any bleeding, than warfarin. The potential benefit of individual NOACs in real-world practice needs to be assessed further.
DOI: 10.6084/m9.figshare.5363980.v1
title: Bleeding risk of apixaban, dabigatran, and low-dose rivaroxaban compared with warfarin in Japanese patients with non-valvular atrial fibrillation: a propensity matched analysis of administrative claims data

description: <b>Objectives:</b> There is scarce evidence comparing novel oral anticoagulants (NOACs) with warfarin in real-world settings in Japan. This study compared the risk of bleeding events among patients with non-valvular atrial fibrillation (NVAF) initiating treatment with NOACs versus warfarin. <b>Methods:</b> A retrospective cohort study was conducted using a de-identified electronic health record based database of health claims and Diagnosis Procedure Combination data from 275 consenting hospitals in Japan. NVAF patients newly initiated on oral anticoagulants were eligible. Based on the first prescription, patients were assigned to 5/2.5 mg BID apixaban, 150/110 mg BID dabigatran, 15/10 mg QD rivaroxaban (approved dose lower in Japan compared to Western countries [20/15 mg QD]) or warfarin groups. One-to-one propensity score matching (PSM) was used to balance patient characteristics between warfarin and each NOAC. Patients were followed up to 1 year post-first prescription. <b>Results:</b> Among 38,662 eligible patients, a total of 5977, 5090, and 6726 matched pairs were identified for warfarin versus apixaban, warfarin versus dabigatran, and warfarin versus rivaroxaban, respectively after PSM. Compared to warfarin, apixaban (hazard ratio [HR] 0.586; 95% CI 0.421–0.815), dabigatran (HR 0.617; 0.425–0.895) and rivaroxaban (HR 0.693; 0.514–0.933) were associated with a significantly lower risk of major bleeding. The risk of any bleeding was significantly lower for apixaban (HR 0.782; 0.682–0.896), but not for dabigatran (HR 0.988; 0.860–1.135) or rivaroxaban (HR 0.938; 0.832–1.057) when comparing to warfarin. <b>Conclusions:</b> Among Japanese patients with NVAF, treatment with apixaban 5/2.5 mg BID was associated with a significantly lower risk of major bleeding and any bleeding when compared to warfarin. Treatment with dabigatran 150/110 mg BID or rivaroxaban 15/10 mg QD was associated with a significantly lower risk of major bleeding, but not any bleeding, than warfarin. The potential benefit of individual NOACs in real-world practice needs to be assessed further.
DOI: 10.34740/kaggle/dsv/7932764
title: Public Opinion Russia Ukraine War (Updated Daily)
DOI: 10.17633/rd.brunel.5371525
title: Analysis of the impact of exhaust valve profile on the scavenging and combustion process in a 2-stroke Boosted Uniflow Scavenged Gasoline (BUSDIG) engine

description: The data used in the following paper is archived here:<br>Wang, X., Ma, J., and Zhao, H., "Analysis of the impact of exhaust valve profile on the scavenging and combustion process in a 2-stroke Boosted Uniflow Scavenged Gasoline (BUSDIG) engine". IMechE Internal Combustion Engines 2017 conference. Accepted.<br>The descriptions for each data are listed in "captions.docx".
DOI: 10.17633/rd.brunel.5371525.v1
title: Analysis of the impact of exhaust valve profile on the scavenging and combustion process in a 2-stroke Boosted Uniflow Scavenged Gasoline (BUSDIG) engine

description: The data used in the following paper is archived here:<br>Wang, X., Ma, J., and Zhao, H., "Analysis of the impact of exhaust valve profile on the scavenging and combustion process in a 2-stroke Boosted Uniflow Scavenged Gasoline (BUSDIG) engine". IMechE Internal Combustion Engines 2017 conference. Accepted.<br>The descriptions for each data are listed in "captions.docx".
DOI: 10.6084/m9.figshare.5372887
title: Using time-varying quantile regression approaches to model the influence of prenatal and infant exposures on childhood growth

description: For many applications, it is valuable to assess whether the effects of exposures over time vary by quantiles of the outcome. We have previously shown that quantile methods complement the traditional mean-based analyses, and are useful for studies of body size. Here, we extended previous work to time-varying quantile associations. Using data from over 18,000 children in the U.S. Collaborative Perinatal Project, we investigated the impact of maternal pre-pregnancy body mass index (BMI), maternal pregnancy weight gain, placental weight, and birth weight on childhood body size measured 4 times between 3 months and 7 years, using both parametric and non-parametric time-varying quantile regressions. Using our proposed model assessment tool, we found that non-parametric models fit the childhood growth data better than the parametric approaches. We also observed that quantile analysis resulted in difference inferences than the conditional mean models in three of the four constructs (maternal per-pregancy BMI, maternal weight gain, and placental weight). Overall, these results suggest the utility of applying time-varying quantile models for longitudinal outcome data. They also suggest that in the studies of body size, merely modelling the conditional mean may lead to incomplete summary of the data.
DOI: 10.6084/m9.figshare.5372887.v2
title: Using time-varying quantile regression approaches to model the influence of prenatal and infant exposures on childhood growth

description: For many applications, it is valuable to assess whether the effects of exposures over time vary by quantiles of the outcome. We have previously shown that quantile methods complement the traditional mean-based analyses, and are useful for studies of body size. Here, we extended previous work to time-varying quantile associations. Using data from over 18,000 children in the U.S. Collaborative Perinatal Project, we investigated the impact of maternal pre-pregnancy body mass index (BMI), maternal pregnancy weight gain, placental weight, and birth weight on childhood body size measured 4 times between 3 months and 7 years, using both parametric and non-parametric time-varying quantile regressions. Using our proposed model assessment tool, we found that non-parametric models fit the childhood growth data better than the parametric approaches. We also observed that quantile analysis resulted in difference inferences than the conditional mean models in three of the four constructs (maternal per-pregancy BMI, maternal weight gain, and placental weight). Overall, these results suggest the utility of applying time-varying quantile models for longitudinal outcome data. They also suggest that in the studies of body size, merely modelling the conditional mean may lead to incomplete summary of the data.
DOI: 10.5281/zenodo.10866598
title: Supplementary data files of manuscript
DOI: 10.5281/zenodo.10570729
title: Supplementary data files of manuscript
DOI: 10.5281/zenodo.10570730
title: Supplementary data files of manuscript
DOI: 10.5281/zenodo.10866636
title: Supplementary data files of manuscript
DOI: 10.6084/m9.figshare.5379217
title: Supplement to NEM 3090

description: Genes analysed and their accession numbers<br><br>
DOI: 10.6084/m9.figshare.5379217.v1
title: Supplement to NEM 3090

description: Genes analysed and their accession numbers<br><br>