cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5890867
title: Supplementary Material for: Lycorine Suppresses Endplate-Chondrocyte Degeneration and Prevents Intervertebral Disc Degeneration by Inhibiting NF-κB Signalling Pathway

description: <b><i>Background/Aims:</i></b> Cartilaginous endplate (CEP) degeneration is an important cause for intervertebral disc (IVD) degeneration that leads to low-back pain. The identification of compounds that may prevent CEP degeneration is of interest for the prevention of IVD degeneration. <b><i>Methods:</i></b> Catabolic protease expression in the CEP of disc degeneration patients was first assessed. The toxicity, function and underlying mechanism of lycorine (LY) on CEP-derived chondrocytes degeneration were assessed <i>in vitro</i> by flow cytometry analysis and western blotting. The concentration and function of LY in rat-tail disc-degeneration models were also assessed by HPLC (High Performance Liquid Chromatography) quantification and histological analysis. <b><i>Results:</i></b> In CEP cells, Interleukin (IL)-1β upregulated the expression of matrix metalloproteinase (MMP)-3, MMP-13, a disintegrin and metalloproteinase with thrombospondin motifs (ADAMTS)-4 and ADAMTS-5 that is critical for the degradation of cartilage extracellular matrix. Interestingly, LY suppressed the expression of these enzymes via the inhibition of nuclear factor-κB (NFκB) signalling and thus prevented IL-1β-induced endplate cell degeneration <i>in vitro</i>. More importantly, LY also reduced the expression of MMP-3, MMP-13, ADAMTS-4 and ADAMTS-5 in CEP and exerted a protective effect on both CEP and nucleus pulposus (NP) degeneration. In addition to its inhibitory effect on matrix-degrading protease expression, LY treatment also reduced positive regulators of proinflammatory cytokines, such as MIF, which can be secreted by CEP cells and subsequently target NP cells. <b><i>Conclusion:</i></b> LY could serve as a potential drug for treating IVD disease.
DOI: 10.6084/m9.figshare.5890837
title: Supplementary Material for: The Placental Secretome: Identifying Potential Cross-Talk Between Placenta and Islet β-Cells

description: <b><i>Background/Aims:</i></b> Insulin-secreting islet β-cells adapt to the insulin resistance associated with pregnancy by increasing functional β-cell mass, but the placental signals involved in this process are not well defined. In the current study, we analysed expression of G-protein coupled receptor (GPCR) mRNAs in mouse islets and islet GPCR ligand mRNAs in placenta during pregnancy to generate an atlas of potential interactions between the placenta and β-cells to inform future functional studies of islet adaptive responses to pregnancy. <b><i>Methods:</i></b> Quantative RT-PCR arrays were used to measure mRNA expression levels of: (i) 342 GPCRs in islets from non-pregnant mice, and in islets isolated from mice on gestational days 12 and 18; (ii) 126 islet GPCR ligands in mouse placenta at gestational days 12 and 18. <b><i>Results:</i></b> At gestational day 12, a time of rapid expansion of the β-cell mass, 189 islet GPCR mRNAs were quantifiable, while 79 of the 126 known islet GPCR ligand mRNAs were detectable in placental extracts. Approximately half of the quantifiable placental GPCR ligand genes were of unknown function in β-cells. The expression of some islet GPCR and placental ligand mRNAs varied during pregnancy, with altered expression of both GPCR and ligand mRNAs by gestational day 18. <b><i>Conclusion:</i></b> The current study has revealed numerous potential routes for interaction between the placenta and islets, and offers an atlas to inform further functional studies of their roles in adaptive responses to pregnancy, and in the regulation of the β-cell mass.
DOI: 10.6084/m9.figshare.5890822
title: Thermal structure of the Dabie eclogite-bearing terrane revealed from the results of Ti-in-zircon thermometry

description: Table S1. Results of the zircon nano-SIMS analytical results and Th/U ratios
DOI: 10.6084/m9.figshare.5890822.v1
title: Thermal structure of the Dabie eclogite-bearing terrane revealed from the results of Ti-in-zircon thermometry

description: Table S1. Results of the zircon nano-SIMS analytical results and Th/U ratios
DOI: 10.6084/m9.figshare.5890807
title: Dataset for: Random-effects meta-analysis of the clinical utility of tests and prediction models

description: The use of data from multiple studies or centers for the validation of a clinical test or a multivariable prediction model allows researchers to investigate the test’s/model’s performance in multiple settings and populations. Recently, meta-analytic techniques have been proposed to summarize discrimination and calibration across study populations. Here, we rather consider performance in terms of Net Benefit, which is a measure of clinical utility that weighs the benefits of true positive classifications against the harms of false positives. We posit that it is important to examine clinical utility across multiple settings of interest. This requires a suitable meta-analysis method, and we propose a Bayesian trivariate random-effects meta-analysis of sensitivity, specificity, and prevalence. Across a range of chosen harm-to-benefit ratios, this provides a summary measure of Net Benefit, a prediction interval, and an estimate of the probability that the test/model is clinically useful in a new setting. In addition, the prediction interval and probability of usefulness can be calculated conditional on the known prevalence in a new setting. The proposed methods are illustrated by two case studies: one on the meta-analysis of published studies on ear thermometry to diagnose fever in children, and one on the validation of a multivariable clinical risk prediction model for the diagnosis of ovarian cancer in a multicenter dataset. Crucially, in both case studies the clinical utility of the test/model was heterogeneous across settings, limiting its usefulness in practice. This emphasizes that heterogeneity in clinical utility should be assessed before a test/model is routinely implemented.
DOI: 10.6084/m9.figshare.5890807.v1
title: Dataset for: Random-effects meta-analysis of the clinical utility of tests and prediction models

description: The use of data from multiple studies or centers for the validation of a clinical test or a multivariable prediction model allows researchers to investigate the test’s/model’s performance in multiple settings and populations. Recently, meta-analytic techniques have been proposed to summarize discrimination and calibration across study populations. Here, we rather consider performance in terms of Net Benefit, which is a measure of clinical utility that weighs the benefits of true positive classifications against the harms of false positives. We posit that it is important to examine clinical utility across multiple settings of interest. This requires a suitable meta-analysis method, and we propose a Bayesian trivariate random-effects meta-analysis of sensitivity, specificity, and prevalence. Across a range of chosen harm-to-benefit ratios, this provides a summary measure of Net Benefit, a prediction interval, and an estimate of the probability that the test/model is clinically useful in a new setting. In addition, the prediction interval and probability of usefulness can be calculated conditional on the known prevalence in a new setting. The proposed methods are illustrated by two case studies: one on the meta-analysis of published studies on ear thermometry to diagnose fever in children, and one on the validation of a multivariable clinical risk prediction model for the diagnosis of ovarian cancer in a multicenter dataset. Crucially, in both case studies the clinical utility of the test/model was heterogeneous across settings, limiting its usefulness in practice. This emphasizes that heterogeneity in clinical utility should be assessed before a test/model is routinely implemented.
DOI: 10.6084/m9.figshare.5890777
title: Dataset for: Sex matters: Females in proestrus show greater diazepam anxiolysis and BDNF- and parvalbumin-positive neurons than males

description: In humans and animal models, sex differences are reported for anxiety-like behavior and response to anxiogenic stimuli. In the current work, we studied anxiety-like behavior and response to the prototypical anti-anxiety drug, diazepam. We used 6th generation outbred lines of adult Long Evans rats with high and low anxiety-like behavior phenotypes to investigate the impact of proestrus on the baseline and diazepam-induced behavior. At three doses of diazepam (0, 0.1 and 1.0 mg/kg, i.p.), we measured anxiogenic responses on the elevated plus maze of adult male and female rats. We assessed parvalbumin and brain-derived neurotrophin protein levels in forebrain and limbic structures implicated in anxiety/stress using immunohistochemistry. At baseline, we saw significant differences between anxiety lines, with high anxiety lines displaying less time on the open arms of the elevated plus maze, and less open arm entries, regardless of sex. During proestrus, high anxiety females showed less anxiety-like behavior at 0.1 mg/kg while low anxiety females displayed less anxiety-like behavior at 0.1 and 1.0 doses, relative to males. Brain-derived neurotrophin protein was elevated in females in the medial prefrontal cortex and central amygdala while parvalbumin-immunoreactive cells were greater in males in the medial prefrontal cortex. Parvalbumin-positive cells in high anxiety females were higher in CA2 and dentate gyrus relative to males from the same line. In sum, when tested in proestrus, females showed greater anxiolytic effects of diazepam relative to males, and this correlated with increases in neurotrophin and parvalbumin neuron density in corticolimbic structures.
DOI: 10.6084/m9.figshare.5890777.v1
title: Dataset for: Sex matters: Females in proestrus show greater diazepam anxiolysis and BDNF- and parvalbumin-positive neurons than males

description: In humans and animal models, sex differences are reported for anxiety-like behavior and response to anxiogenic stimuli. In the current work, we studied anxiety-like behavior and response to the prototypical anti-anxiety drug, diazepam. We used 6th generation outbred lines of adult Long Evans rats with high and low anxiety-like behavior phenotypes to investigate the impact of proestrus on the baseline and diazepam-induced behavior. At three doses of diazepam (0, 0.1 and 1.0 mg/kg, i.p.), we measured anxiogenic responses on the elevated plus maze of adult male and female rats. We assessed parvalbumin and brain-derived neurotrophin protein levels in forebrain and limbic structures implicated in anxiety/stress using immunohistochemistry. At baseline, we saw significant differences between anxiety lines, with high anxiety lines displaying less time on the open arms of the elevated plus maze, and less open arm entries, regardless of sex. During proestrus, high anxiety females showed less anxiety-like behavior at 0.1 mg/kg while low anxiety females displayed less anxiety-like behavior at 0.1 and 1.0 doses, relative to males. Brain-derived neurotrophin protein was elevated in females in the medial prefrontal cortex and central amygdala while parvalbumin-immunoreactive cells were greater in males in the medial prefrontal cortex. Parvalbumin-positive cells in high anxiety females were higher in CA2 and dentate gyrus relative to males from the same line. In sum, when tested in proestrus, females showed greater anxiolytic effects of diazepam relative to males, and this correlated with increases in neurotrophin and parvalbumin neuron density in corticolimbic structures.
DOI: 10.6084/m9.figshare.5890735
title: WRR_climatechange_ag_CRB.zip

description: These set of files include the code, input files, and processed output referenced in our article submisson to Water Resources Research titled "IMPACTS OF NEAR-TERM CLIMATE CHANGE ON IRRIGATION DEMANDS AND<br>CROP YIELDS IN THE COLUMBIA RIVER BASIN". Details of the methodology can be accessed in the journal article.
DOI: 10.6084/m9.figshare.5890735.v1
title: WRR_climatechange_ag_CRB.zip

description: These set of files include the code, input files, and processed output referenced in our article submisson to Water Resources Research titled "IMPACTS OF NEAR-TERM CLIMATE CHANGE ON IRRIGATION DEMANDS AND<br>CROP YIELDS IN THE COLUMBIA RIVER BASIN". Details of the methodology can be accessed in the journal article.
DOI: 10.6084/m9.figshare.5890606
title: Silique length and seed number

description: The data set containing the silique length and corresponding seed number within silique.
DOI: 10.6084/m9.figshare.5890579
title: Matlab Code - calculation of sea level (PRSL)

description: Code: calculation of P<sub>RSL</sub> for both ‘coral’ and ‘range’ type vertical uncertainties, as well as U-series and radiocarbon ages [pdf of Matlab code file]<br>Supplement to Hibbert et al., 2018 (Scientific Data)<br>
DOI: 10.6084/m9.figshare.5890579.v1
title: Matlab Code - calculation of sea level

description: Code: calculation of P<sub>RSL</sub> for both ‘coral’ and ‘range’ type vertical uncertainties, as well as U-series and radiocarbon ages [pdf of Matlab code file]<br>Supplement to Hibbert et al., 2018 (Scientific Data)<br>
DOI: 10.6084/m9.figshare.5890579.v2
title: Matlab Code - calculation of sea level (PRSL)

description: Code: calculation of P<sub>RSL</sub> for both ‘coral’ and ‘range’ type vertical uncertainties, as well as U-series and radiocarbon ages [pdf of Matlab code file]<br>Supplement to Hibbert et al., 2018 (Scientific Data)<br>
DOI: 10.6084/m9.figshare.5890573
title: Partitioning of soil phosphorus among arbuscular and ectomycorrhizal trees in tropical and subtropical forests

description: Partitioning of soil phosphorus (P) pools has been proposed as a key mechanism maintaining plant diversity, but experimental support is lacking. Here, we provided different chemical forms of P to 15 tree species with contrasting root symbiotic relationships to investigate plant P acquisition in both tropical and subtropical forests. Both ectomycorrhizal (ECM) and arbuscular mycorrhizal (AM) trees responded positively to addition of inorganic P, but strikingly, ECM trees acquired more P from a complex organic form (phytic acid). Most ECM tree species and all AM tree species also showed some capacity to take up simple organic P (monophosphate). Mycorrhizal colonization was negatively correlated with soil extractable P concentration, suggesting that mycorrhizal fungi may regulate organic P acquisition among tree species. Our results support the hypothesis that ECM and AM plants partition soil P sources, which may play an ecologically important role in promoting species coexistence in tropical and subtropical forests.
DOI: 10.6084/m9.figshare.5890567
title: Modern coral depth distributions used to calculate past sea levels (Hibbert et al., 2018, Scientific Data)

description: Empirically derived modern coral depth distributions used as a modern analogue to reconstruct sea level (Hibbert et al., 2018, <i>Scientific Data</i>, accepted). <br><br>This is the latest iteration of these taxon-specific depth distributions, derived from the 2017 update to the Ocean Biogeographical Information System (OBIS, 2017). We use this data to define taxon-specific depth distributions that are then used to reconstruct sea level from fossil corals using the methodology in Hibbert et al., 2016 (<i>Quaternary Science Reviews</i> 145, 1-56).<br>
DOI: 10.6084/m9.figshare.5890555
title: Vaisar et al, Type 2 Diabetes is Associated with Loss of HDL Endothelium Protective Functions

description: Targeted proteomics analysis of HDL from people with and without T2D. Attached files contain Skyline documents with relevant SRM-LCMS data. Data is directly accessible at PanoramaWeb Public, https://panoramaweb.org/labkey/VaisarHDL_T2D.url.<br>Original publication - Vaisar et al, PlosOne 2018.<br>
DOI: 10.6084/m9.figshare.5890555.v1
title: Vaisar et al, Type 2 Diabetes is Associated with Loss of HDL Endothelium Protective Functions

description: Targeted proteomics analysis of HDL from people with and without T2D. Attached files contain Skyline documents with relevant SRM-LCMS data. Data is directly accessible at PanoramaWeb Public, https://panoramaweb.org/labkey/VaisarHDL_T2D.url.<br>Original publication - Vaisar et al, PlosOne 2018.<br>
DOI: 10.6084/m9.figshare.5890552
title: eliza_ant_data.xlsx

description: Decision of the first 20 ants crossing the decision line when choosing to follow either the pheromone or personal memory.
DOI: 10.6084/m9.figshare.5890552.v1
title: eliza_ant_data.xlsx

description: Decision of the first 20 ants crossing the decision line when choosing to follow either the pheromone or personal memory.
DOI: 10.6084/m9.figshare.5890474
title: savedrecs.bib

description: This file contains the metadata for all of the articles retrieved from Web of Science.<br>
DOI: 10.6084/m9.figshare.5890471
title: map.txt

description: This file contains information related to the structure of the co-authorship network.<br>
DOI: 10.6084/m9.figshare.5890468
title: partition.clu

description: This file contains the group identifiers for all of the authors in the dataset.<br>
DOI: 10.6084/m9.figshare.5890468.v1
title: partition.clu

description: This file contains the group identifiers for all of the authors in the dataset.<br>
DOI: 10.6084/m9.figshare.5890462
title: analysis.R

description: This file contains all of the R code used in the bibliometric analysis.<br>
DOI: 10.6084/m9.figshare.5890456
title: network.net

description: This file contains information related to the structure of the co-authorship network.
DOI: 10.6084/m9.figshare.5890447
title: Effects of native biodiversity on grape loss of four castes: testing the biotic resistance hypothesis

description: The agricultural practices strongly influence the biodiversity of agricultural areas, and the ecological services that these ecosystems provide. One of the services that have been most affected is the biological resistance to pests.Wine production is a common type of agriculture throughout the world, and it has a strong historical and economic importance for certain countries such as Portugal. But this type of agriculture is subject a high number of pests that affect the production, and farmers use pesticides to combat these pests, thus affecting the biodiversity that inhabits and uses the vineyards for food. This study took place in the Bairrada region in Central Portugal. We used six vineyards to assess the losses caused by fungi, birds and insects in four castes (Touriga, Baga, Arinto and Chardonnay), and evaluated whether pests have a preference for any caste or color (white and red). Bird and insect communities were studied and divided into functional guilds (pest, neutral or auxiliary), to compare with grape losses and assess if these natural communities hold a potential to naturally control wine pests (biotic resistance hypothesis). The edge effect in grape losses was also evaluated. We recorded a small proportion of grape losses, but we verified that insects had a preference for the Baga and Chardonnay castes. We observed that color did not influence the birds and insect's losses. In relation to the fungi losses, we registered a preference for the caste Baga. Most insects and birds observed in vineyards were pests, which entails a low level of biological control in this agricultural ecosystem. Although the relation between the edge and grape losses was not significant, there were more losses in the first 100 meters from the edge.Further studies will be necessaries to fully evaluate the role of local biodiversity in vineyards. To better evaluate the biotic resistance hypothesis it would be necessary to sample an organic vineyard, i.e. without the use of the pesticides.<br>
DOI: 10.6084/m9.figshare.5890447.v1
title: Effects of native biodiversity on grape loss of four castes: testing the biotic resistance hypothesis

description: The agricultural practices strongly influence the biodiversity of agricultural areas, and the ecological services that these ecosystems provide. One of the services that have been most affected is the biological resistance to pests.Wine production is a common type of agriculture throughout the world, and it has a strong historical and economic importance for certain countries such as Portugal. But this type of agriculture is subject a high number of pests that affect the production, and farmers use pesticides to combat these pests, thus affecting the biodiversity that inhabits and uses the vineyards for food. This study took place in the Bairrada region in Central Portugal. We used six vineyards to assess the losses caused by fungi, birds and insects in four castes (Touriga, Baga, Arinto and Chardonnay), and evaluated whether pests have a preference for any caste or color (white and red). Bird and insect communities were studied and divided into functional guilds (pest, neutral or auxiliary), to compare with grape losses and assess if these natural communities hold a potential to naturally control wine pests (biotic resistance hypothesis). The edge effect in grape losses was also evaluated. We recorded a small proportion of grape losses, but we verified that insects had a preference for the Baga and Chardonnay castes. We observed that color did not influence the birds and insect's losses. In relation to the fungi losses, we registered a preference for the caste Baga. Most insects and birds observed in vineyards were pests, which entails a low level of biological control in this agricultural ecosystem. Although the relation between the edge and grape losses was not significant, there were more losses in the first 100 meters from the edge.Further studies will be necessaries to fully evaluate the role of local biodiversity in vineyards. To better evaluate the biotic resistance hypothesis it would be necessary to sample an organic vineyard, i.e. without the use of the pesticides.<br>
DOI: 10.6084/m9.figshare.5887141
title: coordinates_for_supmat.zip

description: Supplementary Material for "Thioamide substitution to probe the hydroxyproline recognition of VHL ligand"<br><br>Coordinates of (DFT) PBF (water) MN15-L/aug-cc-pVTZ(-F) optimized geometries in xyz format.<br><br>Publication to be added upon acceptance.<br>
DOI: 10.6084/m9.figshare.5887141.v1
title: coordinates_for_supmat.zip

description: Supplementary Material for "Thioamide substitution to probe the hydroxyproline recognition of VHL ligand"<br><br>Coordinates of (DFT) PBF (water) MN15-L/aug-cc-pVTZ(-F) optimized geometries in xyz format.<br><br>Publication to be added upon acceptance.<br>
DOI: 10.6084/m9.figshare.5887003
title: Supplemental_Figures_S1-S20.pdf

description: Supplemental Figures S1-S20.
DOI: 10.6084/m9.figshare.5887003.v1
title: Supplemental_Figures_S1-S20.pdf

description: Supplemental Figures S1-S20.
DOI: 10.6084/m9.figshare.5886994
title: Supplemental_Tables_S1-S9.xlsx

description: Supplemental Tables S1-S9.
DOI: 10.6084/m9.figshare.5886955
title: Water Surface Elevation Rasters

description: Model results as shown in Figure 2 of the manuscript.<br><br>Simulated water surface elevation (m, NAVD88) for R (rainfall excess), S (hurricane storm surge), and R (rainfall excess and hurricane storm surge) at 0 days (hurricane located well offshore and surface water flood initialized), respectively; +1.5 days (center of hurricane is located southwest of New Orleans); +1.75 days (center of hurricane located southeast of Baton Rouge), respectively; Simulated peak water levels (m, NAVD88) obtained for R, S, and RS, respectively.
DOI: 10.6084/m9.figshare.5886955.v1
title: Water Surface Elevation Rasters

description: Model results as shown in Figure 2 of the manuscript.<br><br>Simulated water surface elevation (m, NAVD88) for R (rainfall excess), S (hurricane storm surge), and R (rainfall excess and hurricane storm surge) at 0 days (hurricane located well offshore and surface water flood initialized), respectively; +1.5 days (center of hurricane is located southwest of New Orleans); +1.75 days (center of hurricane located southeast of Baton Rouge), respectively; Simulated peak water levels (m, NAVD88) obtained for R, S, and RS, respectively.