cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5092171.v1
title: Hepatotoxicity evaluation of traditional Chinese medicines using a computational molecular model

description: <b>Background:</b> Liver injury caused by traditional Chinese medicines (TCMs) is reported from many countries around the world. TCM hepatotoxicity has attracted worldwide concerns. <b>Objective:</b> This study aims to develop a more applicable and optimal tool to evaluate TCM hepatotoxicity. <b>Methods:</b> A quantitative structure-activity relationship (QSAR) analysis was performed based on published data and U.S. Food and Drug Administration’s Liver Toxicity Knowledge Base (LTKB). <b>Results:</b> Eleven herbal ingredients with proven liver toxicity in the literature were added into the dataset besides chemicals from LTKB. The finally generated QSAR model yielded a sensitivity of 83.8%, a specificity of 70.1%, and an accuracy of 80.2%. Among the externally tested 20 ingredients from TCMs, 14 hepatotoxic ingredients were all accurately identified by the QSAR model derived from the dataset containing natural hepatotoxins. <b>Conclusions:</b> Adding natural hepatotoxins into the dataset makes the QSAR model more applicable for TCM hepatotoxicity assessment, which provides a right direction in the methodology study for TCM safety evaluation. The generated QSAR model has the practical value to prioritize the hepatotoxicity risk of TCM compounds. Furthermore, an open-access international specialized database on TCM hepatotoxicity should be quickly established.
DOI: 10.6084/m9.figshare.5092435
title: Detrital provenance, depositional environment, and palaeogeographic implications of Lower Triassic marine sediments in central Tibet

description: We present our new investigation into the depositional environment and provenance of the Yingshuiquan Formation in the central Qiangtang region of northern Tibet, in order to further our understanding of the environment of the Longmu Co–Shuanghu Palaeo–Tethys during the Early Triassic. The Yingshuiquan Formation is composed of oolitic limestone, calcareous sandstone, calcarenite, thin-bedded ribbon limestone, bioclastic limestone, and coarse oolite limestone that were deposited in a shallow-marine basin and contain abundant Lower Triassic conodont fossils (e.g. <i>Hadrodontina anceps, Pachycladina</i> sp., <i>gen. et</i> sp, <i>Pachyclaina oblique, Hibbardelloides</i> sp). We selected detrital zircons from four calcareous sandstone samples for U–Pb dating, yielding minimum age peaks of 263, 269, 275, and 280 Ma, respectively, and a minimum age of 249 Ma, based on several zircons around the same age. Analysis of the conodont biofacies and zircon LA-ICP-MS dating of calcareous sandstone indicates that the data is consistent with deposition in the Early Triassic. The Yingshuiquan Formation records Early Triassic shallow-water sediment in the Longmu Co–Shuanghu Palaeo–Tethys, and has a Southern Qiangtang and Northern Qiangtang terranes provenance. During the Early Triassic, the carbonate sediments of the Yingshuiquan Formation were deposited in an active environment around the Longmu Co–Shuanghu Palaeo–Tethys, which has became a residual sea basin.
DOI: 10.6084/m9.figshare.5092435.v1
title: Detrital provenance, depositional environment, and palaeogeographic implications of Lower Triassic marine sediments in central Tibet

description: We present our new investigation into the depositional environment and provenance of the Yingshuiquan Formation in the central Qiangtang region of northern Tibet, in order to further our understanding of the environment of the Longmu Co–Shuanghu Palaeo–Tethys during the Early Triassic. The Yingshuiquan Formation is composed of oolitic limestone, calcareous sandstone, calcarenite, thin-bedded ribbon limestone, bioclastic limestone, and coarse oolite limestone that were deposited in a shallow-marine basin and contain abundant Lower Triassic conodont fossils (e.g. <i>Hadrodontina anceps, Pachycladina</i> sp., <i>gen. et</i> sp, <i>Pachyclaina oblique, Hibbardelloides</i> sp). We selected detrital zircons from four calcareous sandstone samples for U–Pb dating, yielding minimum age peaks of 263, 269, 275, and 280 Ma, respectively, and a minimum age of 249 Ma, based on several zircons around the same age. Analysis of the conodont biofacies and zircon LA-ICP-MS dating of calcareous sandstone indicates that the data is consistent with deposition in the Early Triassic. The Yingshuiquan Formation records Early Triassic shallow-water sediment in the Longmu Co–Shuanghu Palaeo–Tethys, and has a Southern Qiangtang and Northern Qiangtang terranes provenance. During the Early Triassic, the carbonate sediments of the Yingshuiquan Formation were deposited in an active environment around the Longmu Co–Shuanghu Palaeo–Tethys, which has became a residual sea basin.
DOI: 10.6084/m9.figshare.5097205
title: Table S1 from Model-based analysis of an outbreak of bubonic plague in Cairo in 1801

description: Data used in this study
DOI: 10.6084/m9.figshare.5097205.v1
title: Table S1 from Model-based analysis of an outbreak of bubonic plague in Cairo in 1801

description: Data used in this study
DOI: 10.6084/m9.figshare.5097304
title: Supplementary Data Sets from 3-hydroxyisobutyryl-CoA hydrolase involved in isoleucine catabolism regulates triacylglycerol accumulation in <i>Phaeodactylum tricornutum</i>

description: Supplemental Data S1: MCEE gene distribution in different organisms. Supplemental Data S2: Primers used in this study for qPCR and the construction of RNAi expression vector, overexpression vector and GFP fusion vector. Supplemental Data S3: Metabolite contents (mg g-1 dry biomass) in wild-type, two overexpression lines (hibch-OE1 and hibch-OE3) and one silenced strain (pcc1p). Values are presented as the mean of three biological replicates. Supplemental Data S4: The values of fold change in transcript levels of genes encoding componens involved in BCAA degradation.
DOI: 10.6084/m9.figshare.5097304.v1
title: Supplementary Data Sets from 3-hydroxyisobutyryl-CoA hydrolase involved in isoleucine catabolism regulates triacylglycerol accumulation in <i>Phaeodactylum tricornutum</i>

description: Supplemental Data S1: MCEE gene distribution in different organisms. Supplemental Data S2: Primers used in this study for qPCR and the construction of RNAi expression vector, overexpression vector and GFP fusion vector. Supplemental Data S3: Metabolite contents (mg g-1 dry biomass) in wild-type, two overexpression lines (hibch-OE1 and hibch-OE3) and one silenced strain (pcc1p). Values are presented as the mean of three biological replicates. Supplemental Data S4: The values of fold change in transcript levels of genes encoding componens involved in BCAA degradation.
DOI: 10.6084/m9.figshare.5097400
title: Supplementary videos S1 to S4: high-speed videos of a hovering hummingbird

description: Electronic supplementary videos S1 to S4 for <i>Quantifying the dynamic wing morphing of hovering hummingbird</i> in <i>Royal Society Open Science</i>.<br>High-speed videos of a hovering hummingbird (<i>Amazilia amazilia</i>), filmed at 2000 frames per second using four synchronised high-speed cameras.<br>
DOI: 10.6084/m9.figshare.5097400.v2
title: Supplementary videos S1 to S4: high-speed videos of a hovering hummingbird

description: Electronic supplementary videos S1 to S4 for <i>Quantifying the dynamic wing morphing of hovering hummingbird</i> in <i>Royal Society Open Science</i>.<br>High-speed videos of a hovering hummingbird (<i>Amazilia amazilia</i>), filmed at 2000 frames per second using four synchronised high-speed cameras.<br>
DOI: 10.6084/m9.figshare.5097400.v1
title: Supplementary videos S1 to S4: high-speed videos of a hovering hummingbird

description: Electronic supplementary videos S1 to S4 for <i>Quantifying the dynamic wing morphing of hovering hummingbird</i> in <i>Royal Society Open Science</i>.<br>High-speed videos of a hovering hummingbird (<i>Amazilia amazilia</i>), filmed at 2000 frames per second using four synchronised high-speed cameras.<br>
DOI: 10.6084/m9.figshare.5097808
title: Angiogenic profile and smoking in the Finnish Genetics of Pre-Eclampsia Consortium (FINNPEC) cohort

description: <b>Objectives:</b> The biological mechanism by which smoking reduces the risk of pre-eclampsia (PE) is unresolved. We studied serum levels of soluble fms-like tyrosine kinase 1 (sFlt-1), placental growth factor (PlGF) and their ratio, in addition to soluble endoglin (sEng) in early and late pregnancy to ascertain whether these factors are altered in women who smoke. <b>Subjects and methods:</b> First trimester serum samples were available from 217 women who later developed PE and 238 women who did not develop PE. Second/third trimester serum samples were available from 174 PE and 54 non-PE women. <b>Results:</b> PE women who smoked during pregnancy had elevated first trimester concentrations of serum PlGF [geometric mean (95% CI): 39.8 (32.6–48.5) pg/ml, <i>p</i> = .001] and reduced sEng concentration [5.0 (4.6–5.6) ng/ml, <i>p</i> = .047] compared to PE non-smokers [30.0 (28.1–32.1) pg/ml and 6.1 (5.9–6.4) ng/ml, respectively]. Non-smoking women in the PE group had the highest sFlt-1/PlGF ratio in early and late pregnancy. <b>Conclusions</b>: The protective effect of smoking in reducing the risk of PE may be due to the early pregnancy change towards pro-angiogenic marker profile. Also, in late pregnancy, smoking exerted effect in sFlt-1/PlGF ratio in PE pregnancies, and may complicate its use as a prognostic and diagnostic marker.Key messagesSmoking appears to have angiogenic effects in early pregnancy with reduced sEng concentrations and elevated PlGF concentrations in both normal and PE pregnancies.Throughout pregnancy, smoking exerted effect in PlGF concentration and sFlt-1/PlGF ratio in PE pregnancies, and thus may complicate its use as a prognostic and diagnostic marker. Smoking appears to have angiogenic effects in early pregnancy with reduced sEng concentrations and elevated PlGF concentrations in both normal and PE pregnancies. Throughout pregnancy, smoking exerted effect in PlGF concentration and sFlt-1/PlGF ratio in PE pregnancies, and thus may complicate its use as a prognostic and diagnostic marker.
DOI: 10.6084/m9.figshare.5097808.v1
title: Angiogenic profile and smoking in the Finnish Genetics of Pre-Eclampsia Consortium (FINNPEC) cohort

description: <b>Objectives:</b> The biological mechanism by which smoking reduces the risk of pre-eclampsia (PE) is unresolved. We studied serum levels of soluble fms-like tyrosine kinase 1 (sFlt-1), placental growth factor (PlGF) and their ratio, in addition to soluble endoglin (sEng) in early and late pregnancy to ascertain whether these factors are altered in women who smoke. <b>Subjects and methods:</b> First trimester serum samples were available from 217 women who later developed PE and 238 women who did not develop PE. Second/third trimester serum samples were available from 174 PE and 54 non-PE women. <b>Results:</b> PE women who smoked during pregnancy had elevated first trimester concentrations of serum PlGF [geometric mean (95% CI): 39.8 (32.6–48.5) pg/ml, <i>p</i> = .001] and reduced sEng concentration [5.0 (4.6–5.6) ng/ml, <i>p</i> = .047] compared to PE non-smokers [30.0 (28.1–32.1) pg/ml and 6.1 (5.9–6.4) ng/ml, respectively]. Non-smoking women in the PE group had the highest sFlt-1/PlGF ratio in early and late pregnancy. <b>Conclusions</b>: The protective effect of smoking in reducing the risk of PE may be due to the early pregnancy change towards pro-angiogenic marker profile. Also, in late pregnancy, smoking exerted effect in sFlt-1/PlGF ratio in PE pregnancies, and may complicate its use as a prognostic and diagnostic marker.Key messagesSmoking appears to have angiogenic effects in early pregnancy with reduced sEng concentrations and elevated PlGF concentrations in both normal and PE pregnancies.Throughout pregnancy, smoking exerted effect in PlGF concentration and sFlt-1/PlGF ratio in PE pregnancies, and thus may complicate its use as a prognostic and diagnostic marker. Smoking appears to have angiogenic effects in early pregnancy with reduced sEng concentrations and elevated PlGF concentrations in both normal and PE pregnancies. Throughout pregnancy, smoking exerted effect in PlGF concentration and sFlt-1/PlGF ratio in PE pregnancies, and thus may complicate its use as a prognostic and diagnostic marker.
DOI: 10.6084/m9.figshare.5102941
title: Homeobox C10 inhibits the osteogenic differentiation potential of mesenchymal stem cells

description: <b><i>Purpose:</i></b> Mesenchymal stem cells (MSCs) are a reliable cell source for tissue regeneration. However, the molecular mechanisms underlying the directed differentiation of MSCs remain unclear which impedes potential clinical applications. Recent studies have discovered that Homeobox (HOX) genes are involved in the differentiation regulation of MSCs and bone formation. In this study, we investigate the <i>HOXC10</i> function in the osteogenic differentiation potential of MSCs. <b><i>Materials and Methods:</i></b> Stem cells from apical papilla (SCAPs) and adipose-derived stem cells (ADSCs) were used in this study. Alkaline phosphatase (ALP) activity assays, ALP staining, Alizarin red staining, quantitative calcium analysis, osteogenesis-associated gene expression, and <i>in vivo</i> transplantation experiments were used to study osteogenic differentiation potential. <b><i>Results:</i></b> Our results showed that overexpression of <i>HOXC10</i> in SCAPs inhibited ALP activity and mineralization <i>in vitro</i> and decreased the mRNA expression of collagen alpha-1 (I) chain, bone sialoprotein, osteocalcin, and a key transcription factor, runt-related transcription factor 2, in SCAPs. Depletion of <i>HOXC10</i> promoted osteogenic differentiation in SCAPs <i>in vitro</i>. In addition, <i>in vivo</i> transplantation experiments in nude mice confirmed that SCAPs osteogenesis was triggered when <i>HOXC10</i> was downregulated. Furthermore, depletion of <i>HOXC10</i> also enhanced osteogenic differentiation in ADSCs. <b><i>Conclusions:</i></b> Taken together, these results indicated that <i>HOXC10</i> decreased the MSC osteogenic differentiation potential. Thus, inhibition of <i>HOXC10</i> in MSCs might have the potential to improve tissue regeneration and provide insight into the mechanism underlying the directed differentiation of MSCs.
DOI: 10.6084/m9.figshare.5102941.v1
title: Homeobox C10 inhibits the osteogenic differentiation potential of mesenchymal stem cells

description: <b><i>Purpose:</i></b> Mesenchymal stem cells (MSCs) are a reliable cell source for tissue regeneration. However, the molecular mechanisms underlying the directed differentiation of MSCs remain unclear which impedes potential clinical applications. Recent studies have discovered that Homeobox (HOX) genes are involved in the differentiation regulation of MSCs and bone formation. In this study, we investigate the <i>HOXC10</i> function in the osteogenic differentiation potential of MSCs. <b><i>Materials and Methods:</i></b> Stem cells from apical papilla (SCAPs) and adipose-derived stem cells (ADSCs) were used in this study. Alkaline phosphatase (ALP) activity assays, ALP staining, Alizarin red staining, quantitative calcium analysis, osteogenesis-associated gene expression, and <i>in vivo</i> transplantation experiments were used to study osteogenic differentiation potential. <b><i>Results:</i></b> Our results showed that overexpression of <i>HOXC10</i> in SCAPs inhibited ALP activity and mineralization <i>in vitro</i> and decreased the mRNA expression of collagen alpha-1 (I) chain, bone sialoprotein, osteocalcin, and a key transcription factor, runt-related transcription factor 2, in SCAPs. Depletion of <i>HOXC10</i> promoted osteogenic differentiation in SCAPs <i>in vitro</i>. In addition, <i>in vivo</i> transplantation experiments in nude mice confirmed that SCAPs osteogenesis was triggered when <i>HOXC10</i> was downregulated. Furthermore, depletion of <i>HOXC10</i> also enhanced osteogenic differentiation in ADSCs. <b><i>Conclusions:</i></b> Taken together, these results indicated that <i>HOXC10</i> decreased the MSC osteogenic differentiation potential. Thus, inhibition of <i>HOXC10</i> in MSCs might have the potential to improve tissue regeneration and provide insight into the mechanism underlying the directed differentiation of MSCs.
DOI: 10.6084/m9.figshare.5103712
title: SI Table 1 from Uncovering the underlying mechanism of cancer tumorigenesis and development under immune microenvironment from global quantification of the landscape

description: The interactions among cells and cytokines.
DOI: 10.6084/m9.figshare.5103712.v1
title: SI Table 1 from Uncovering the underlying mechanism of cancer tumorigenesis and development under immune microenvironment from global quantification of the landscape

description: The interactions among cells and cytokines.
DOI: 10.34740/kaggle/dsv/7932529
title: Empower Women Now
DOI: 10.6084/m9.figshare.5106580
title: Evaluated data

description: This data contains the evaluated results from the 5 experiments as defined by the guideline document from CPTAC Assay Portal.Worksheet a: Experiment 1Worksheet b: Experiment 2<br>Worksheet c: Experiment 3<br>Worksheet d: Experiment 4<br>Worksheet e: Experiment 5<br>
DOI: 10.6084/m9.figshare.5106580.v1
title: Evaluated Data from 5 experiments.xlsx

description: Mass spectrometry (MS) based targeted
proteomic methods such as selected reaction monitoring (SRM) are emerging as a
promising tool for verification of candidate proteins in biological and
biomedical applications. The Clinical Proteomic Tumor Analysis Consortium
(CPTAC) of the National Cancer Institute has investigated the standardization
and analytical validation of the SRM assays and demonstrated robust analytical
performance on different instruments across different laboratories. An Assay
Portal has also been established by CPTAC to provide the research community a
resource consisting of large sets of targeted MS-based assays, and a depository
to share assays publicly. Herein, we report the development of 98 SRM assays
that have been thoroughly characterized according to the CPTAC Assay
Characterization Guidance Document; 37 of these passed all five experimental
tests. The assays cover 70 proteins previously identified at the protein level
in ovarian tumors. The experiments, methods and results for characterizing these
SRM assays for their MS response, repeatability, selectivity, stability, and endogenous
detection are described in detail. Data are available via PeptideAtlas,
Panorama and the CPTAC Assay Portal.
DOI: 10.6084/m9.figshare.5106580.v2
title: Evaluated Data from 5 experiments.xlsx

description: This data contains the evaluated results from the 5 experiments as defined by the guideline document from CPTAC Assay Portal.Worksheet a: Experiment 1Worksheet b: Experiment 2<br>Worksheet c: Experiment 3<br>Worksheet d: Experiment 4<br>Worksheet e: Experiment 5<br>
DOI: 10.6084/m9.figshare.5106580.v3
title: Evaluated Data from 5 experiments.xlsx

description: This data contains the evaluated results from the 5 experiments as defined by the guideline document from CPTAC Assay Portal.Worksheet a: Experiment 1Worksheet b: Experiment 2<br>Worksheet c: Experiment 3<br>Worksheet d: Experiment 4<br>Worksheet e: Experiment 5<br>
DOI: 10.6084/m9.figshare.5106580.v4
title: Evaluated Data

description: This data contains the evaluated results from the 5 experiments as defined by the guideline document from CPTAC Assay Portal.Worksheet a: Experiment 1Worksheet b: Experiment 2<br>Worksheet c: Experiment 3<br>Worksheet d: Experiment 4<br>Worksheet e: Experiment 5<br>
DOI: 10.6084/m9.figshare.5106829
title: Experimental information

description: This data includes the experimental information including the list of selected peptides for the experiments and final reports (a), TSQ parameters (b), on column peptide amounts for Batch 1 assays (c) and for Batch 2 assays (d) used for the experiment 1, and on column peptide amounts of all the assays used for the experiment 2 (e).
DOI: 10.6084/m9.figshare.5106829.v1
title: Experimental information

description: This data includes the experimental information including the list of selected peptides for the experiments and final reports (a), TSQ parameters (b), on column peptide amounts for Batch 1 assays (c) and for Batch 2 assays (d) used for the experiment 1, and on column peptide amounts of all the assays used for the experiment 2 (e).
DOI: 10.6084/m9.figshare.5106829.v2
title: Experimental information

description: This data includes the experimental information including the list of selected peptides for the experiments and final reports (a), TSQ parameters (b), on column peptide amounts for Batch 1 assays (c) and for Batch 2 assays (d) used for the experiment 1, and on column peptide amounts of all the assays used for the experiment 2 (e).
DOI: 10.6084/m9.figshare.5106829.v3
title: Experimental information

description: This data includes the experimental information including the list of selected peptides for the experiments and final reports (a), TSQ parameters (b), on column peptide amounts for Batch 1 assays (c) and for Batch 2 assays (d) used for the experiment 1, and on column peptide amounts of all the assays used for the experiment 2 (e).
DOI: 10.6084/m9.figshare.5106829.v4
title: Experimental information

description: This data includes the experimental information including the list of selected peptides for the experiments and final reports (a), TSQ parameters (b), on column peptide amounts for Batch 1 assays (c) and for Batch 2 assays (d) used for the experiment 1, and on column peptide amounts of all the assays used for the experiment 2 (e).
DOI: 10.6084/m9.figshare.5106829.v5
title: Experimental information

description: This data includes the experimental information including the list of selected peptides for the experiments and final reports (a), TSQ parameters (b), on column peptide amounts for Batch 1 assays (c) and for Batch 2 assays (d) used for the experiment 1, and on column peptide amounts of all the assays used for the experiment 2 (e).
DOI: 10.6084/m9.figshare.5106838
title: Peak areas of individual measurements

description: This data contains peak areas of individual measurements of the light (or endogenous) and heavy peptides from the 5 experiments.a: Experiment 1_Batch 1b: Experiment 1_Batch 2c: Experiment 2<br>d: Experiment 3<br>e: Experiment 4<br>f: Experiment 5<br>
DOI: 10.6084/m9.figshare.5106838.v1
title: Peak areas of individual measurements from 5 experiments

description: This data contains peak areas of individual measurements of the light (or endogenous) and heavy peptides from the 5 experiments.a: Experiment 1_Batch 1b: Experiment 1_Batch 2c: Experiment 2<br>d: Experiment 3<br>e: Experiment 4<br>f: Experiment 5<br>
DOI: 10.6084/m9.figshare.5106838.v3
title: Peak areas of individual measurements from 5 experiments

description: This data contains peak areas of individual measurements of the light (or endogenous) and heavy peptides from the 5 experiments.a: Experiment 1_Batch 1b: Experiment 1_Batch 2c: Experiment 2<br>d: Experiment 3<br>e: Experiment 4<br>f: Experiment 5<br>
DOI: 10.6084/m9.figshare.5107303
title: Raw data of Victoria West cores from The Victoria West: earliest prepared core technology in the Acheulean at Canteen Kopje and implications for the cognitive evolution of early hominids

description: Raw data for the Victoria West cores excavated from the Canteen Kopje site.
DOI: 10.6084/m9.figshare.5107303.v1
title: Raw data of Victoria West cores from The Victoria West: earliest prepared core technology in the Acheulean at Canteen Kopje and implications for the cognitive evolution of early hominids

description: Raw data for the Victoria West cores excavated from the Canteen Kopje site.