cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4737538
title: Supplementary Material for: Asymptomatic Carotid Artery Stenosis Treated with Medical Therapy Alone: Temporal Trends and Implications for Risk Assessment and the Design of Future Studies

description: <b><i>Background:</i></b> The rate of adverse clinical outcomes among patients with asymptomatic carotid stenosis receiving medical therapy alone can be used to guide clinical decision-making and to inform future research. We aimed to investigate temporal changes in the incidence rate of clinical outcomes among patients with asymptomatic carotid stenosis receiving medical therapy alone and to explore the implications of these changes for the design of future comparative studies. <b><i>Summary:</i></b> We searched MEDLINE, the Cochrane Central Register of Controlled Trials, US Food and Drug Administration documents, and reference lists of included studies (last search: December 31, 2012). We selected prospective cohort studies of medical therapy for asymptomatic carotid artery stenosis and we extracted information on study characteristics, risk of bias, and outcomes. We performed meta-analyses to estimate summary incidence rates, meta-regressions to assess trends over time, and simulations to explore sample size requirements for the design of future studies comparing new treatments against medical therapy. The main outcomes of interest were ipsilateral stroke, any stroke, cardiovascular death, death, and myocardial infarction. We identified 41 studies of medical therapy for patients with asymptomatic carotid stenosis (last recruitment year: 1978-2009). The summary incidence rate of ipsilateral carotid territory stroke (25 studies) was 1.7 per 100 person-years. This incidence rate was significantly lower in recent studies (last recruitment year from 2000 onwards) as compared to studies that ended recruitment earlier (1.0 vs. 2.3 events per 100 person-years; p &lt; 0.001). The incidence rates of any territory stroke (17 studies), cardiovascular death (6 studies), death (13 studies), and myocardial infarction (5 studies) were 2.7, 4.1, 4.6, and 1.8 per 100 person-years, respectively. Simulations showed that future studies would need to enroll large numbers of patients with a relatively high incidence rate under medical therapy, and evaluate interventions with large effect sizes, to have adequate power to reliably detect treatment effects. <b><i>Key Messages:</i></b> Improved prognosis under medical therapy alone has narrowed the potential range of risk reduction attainable with new treatments for asymptomatic carotid stenosis. Future comparative studies will need to enroll large numbers of patients to assess treatment effectiveness.
DOI: 10.6084/m9.figshare.4737511
title: LICOR output.zip

description: LICOR output from measurements of metabolic rates of male and female Osmia bicornis exposed to neonicotinoids as larvae.
DOI: 10.6084/m9.figshare.4737535.v1
title: Subeng vertebrate tracks: digital archive of a historic Upper Triassic palaeosurface (lower Elliot Formation), Leribe, Lesotho

description: Here we present the results of our sedimentological, stratigraphic and ichnological investigations at a historic ichnosite in NE Lesotho that is among the first documented vertebrate track-bearing palaeosurfaces in southern Gondwana. <br><br>Contains the Subeng Agisoft 3D model (and associated photographs) in addition to the CloudCompare model and rendered palaeosurface figure.
DOI: 10.6084/m9.figshare.4737538.v1
title: Supplementary Material for: Asymptomatic Carotid Artery Stenosis Treated with Medical Therapy Alone: Temporal Trends and Implications for Risk Assessment and the Design of Future Studies

description: <b><i>Background:</i></b> The rate of adverse clinical outcomes among patients with asymptomatic carotid stenosis receiving medical therapy alone can be used to guide clinical decision-making and to inform future research. We aimed to investigate temporal changes in the incidence rate of clinical outcomes among patients with asymptomatic carotid stenosis receiving medical therapy alone and to explore the implications of these changes for the design of future comparative studies. <b><i>Summary:</i></b> We searched MEDLINE, the Cochrane Central Register of Controlled Trials, US Food and Drug Administration documents, and reference lists of included studies (last search: December 31, 2012). We selected prospective cohort studies of medical therapy for asymptomatic carotid artery stenosis and we extracted information on study characteristics, risk of bias, and outcomes. We performed meta-analyses to estimate summary incidence rates, meta-regressions to assess trends over time, and simulations to explore sample size requirements for the design of future studies comparing new treatments against medical therapy. The main outcomes of interest were ipsilateral stroke, any stroke, cardiovascular death, death, and myocardial infarction. We identified 41 studies of medical therapy for patients with asymptomatic carotid stenosis (last recruitment year: 1978-2009). The summary incidence rate of ipsilateral carotid territory stroke (25 studies) was 1.7 per 100 person-years. This incidence rate was significantly lower in recent studies (last recruitment year from 2000 onwards) as compared to studies that ended recruitment earlier (1.0 vs. 2.3 events per 100 person-years; p &lt; 0.001). The incidence rates of any territory stroke (17 studies), cardiovascular death (6 studies), death (13 studies), and myocardial infarction (5 studies) were 2.7, 4.1, 4.6, and 1.8 per 100 person-years, respectively. Simulations showed that future studies would need to enroll large numbers of patients with a relatively high incidence rate under medical therapy, and evaluate interventions with large effect sizes, to have adequate power to reliably detect treatment effects. <b><i>Key Messages:</i></b> Improved prognosis under medical therapy alone has narrowed the potential range of risk reduction attainable with new treatments for asymptomatic carotid stenosis. Future comparative studies will need to enroll large numbers of patients to assess treatment effectiveness.
DOI: 10.6084/m9.figshare.4737478
title: Supplementary Material for: NOX2-Derived ROS-Mediated Surface Translocation of BLT1 Is Essential for Exocytosis in Human Eosinophils Induced by LTB4

description: <b><i>Background:</i></b> Leukotriene B<sub>4</sub> (LTB<sub>4</sub>) is a proinflammatory lipid mediator that elicits eosinophil exocytosis, leading to allergic inflammation. However, the detailed intracellular signaling mechanisms of eosinophil exocytosis induced by LTB<sub>4</sub> are poorly understood. Herein, we report that NADPH oxidase (NOX)2-derived reactive oxygen species (ROS)-mediated BLT1 migration to the cell surface is required for exocytosis in human eosinophils induced by LTB<sub>4</sub>. <b><i>Methods:</i></b> Peripheral blood eosinophils were purified and stimulated for up to 60 min with LTB<sub>4</sub>. The signaling role of NOX2-derived ROS in BLT1-dependent exocytosis in LTB<sub>4</sub>-stimulated eosinophils was investigated. <b><i>Results:</i></b> Stimulating eosinophils with LTB<sub>4</sub> induced intracellular ROS production and surface upregulation of the exocytosis marker protein CD63 via BLT1-mediated signaling. LTB<sub>4</sub> induced p47<sup>phox</sup> phosphorylation and 91<sup>phox</sup> expression required for NOX2 activation in a BLT1-dependent manner. Pretreatment with NOX2 inhibitors, but not mitochondria inhibitor, prevented LTB<sub>4</sub>-induced ROS generation and exocytosis. At 30 min after stimulation with LTB<sub>4</sub>, BLT1 expression at the cell surface was upregulated. LTB<sub>4</sub>-triggered surface upregulation of BLT1 was also blocked by inhibition of ROS generation with NOX2 inhibitors. Moreover, stimulation for 30 min with LTB<sub>4</sub> resulted in the interaction of BLT1 with NOX2 by immunoprecipitation. LTB<sub>4</sub>-induced ROS generation, surface upregulation of BLT1 and exocytosis was also inhibited by pretreatment with a lipid raft disruptor, protein kinase C inhibitor, or Src kinase inhibitor. <b><i>Conclusion:</i></b> These results suggest that NOX2-derived ROS-mediated BLT1 trafficking to the cell surface plays a key role in the exocytosis of human eosinophils induced by LTB<sub>4</sub>.
DOI: 10.6084/m9.figshare.4737481
title: Dataset for the SIDER R package

description: Dataset corresponding to the SIDER R package<br>
DOI: 10.6084/m9.figshare.4737511.v1
title: LICOR output.zip

description: LICOR output from measurements of metabolic rates of male and female Osmia bicornis exposed to neonicotinoids as larvae.
DOI: 10.6084/m9.figshare.4737478.v1
title: Supplementary Material for: NOX2-Derived ROS-Mediated Surface Translocation of BLT1 Is Essential for Exocytosis in Human Eosinophils Induced by LTB4

description: <b><i>Background:</i></b> Leukotriene B<sub>4</sub> (LTB<sub>4</sub>) is a proinflammatory lipid mediator that elicits eosinophil exocytosis, leading to allergic inflammation. However, the detailed intracellular signaling mechanisms of eosinophil exocytosis induced by LTB<sub>4</sub> are poorly understood. Herein, we report that NADPH oxidase (NOX)2-derived reactive oxygen species (ROS)-mediated BLT1 migration to the cell surface is required for exocytosis in human eosinophils induced by LTB<sub>4</sub>. <b><i>Methods:</i></b> Peripheral blood eosinophils were purified and stimulated for up to 60 min with LTB<sub>4</sub>. The signaling role of NOX2-derived ROS in BLT1-dependent exocytosis in LTB<sub>4</sub>-stimulated eosinophils was investigated. <b><i>Results:</i></b> Stimulating eosinophils with LTB<sub>4</sub> induced intracellular ROS production and surface upregulation of the exocytosis marker protein CD63 via BLT1-mediated signaling. LTB<sub>4</sub> induced p47<sup>phox</sup> phosphorylation and 91<sup>phox</sup> expression required for NOX2 activation in a BLT1-dependent manner. Pretreatment with NOX2 inhibitors, but not mitochondria inhibitor, prevented LTB<sub>4</sub>-induced ROS generation and exocytosis. At 30 min after stimulation with LTB<sub>4</sub>, BLT1 expression at the cell surface was upregulated. LTB<sub>4</sub>-triggered surface upregulation of BLT1 was also blocked by inhibition of ROS generation with NOX2 inhibitors. Moreover, stimulation for 30 min with LTB<sub>4</sub> resulted in the interaction of BLT1 with NOX2 by immunoprecipitation. LTB<sub>4</sub>-induced ROS generation, surface upregulation of BLT1 and exocytosis was also inhibited by pretreatment with a lipid raft disruptor, protein kinase C inhibitor, or Src kinase inhibitor. <b><i>Conclusion:</i></b> These results suggest that NOX2-derived ROS-mediated BLT1 trafficking to the cell surface plays a key role in the exocytosis of human eosinophils induced by LTB<sub>4</sub>.
DOI: 10.6084/m9.figshare.4737481.v1
title: Dataset for the SIDER R package

description: Dataset corresponding to the SIDER R package<br>
DOI: 10.6084/m9.figshare.4737358
title: Slingsby_TaylorPlots

description: Supplementary Data and R Markdown workflows for Slingsby et al. "Intensifying post-fire weather and biological invasion drive species loss in a Mediterranean-type biodiversity hotspot"<br>All data and repeatable R code workflows (R Markdown) used in the study are available here or as SI Datasets. Code and data are provided under the MIT license, but where possible we would appreciate users acknowledging "the South African Environmental Observation Network (SAEON) and partners" and citing this paper and/or the original data source outlined in the paper. We would also see it as a courtesy to inform the lead author of your intended use of the data. Co-authorship is not a prerequisite, but we would like to minimize duplication of effort and/or warn users where their plans for the data do not seem appropriate.
DOI: 10.6084/m9.figshare.4737337
title: Stacking faults and the -surface on first-order pyramidal planes in -titanium

description: Using first principles methods, we calculated the entire -surface of the first-order pyramidal planes in -titanium. Slip on these planes involving dislocations with -type Burgers vectors is one means by which -titanium polycrystals may supplement slip on prism planes with -type Burgers vectors to maintain ductility. We find one low energy and one high energy stacking fault with energies of 163 and 681 , respectively. Contrary to previous suggestions, we do not find a stable stable stacking fault at .
DOI: 10.6084/m9.figshare.4737352
title: Evolution of pollen morphology in Loranthaceae

description: Earlier studies indicate a strong correlation of pollen morphology and ultrastructure with taxonomy in Loranthaceae. Using high-resolution light microscopy and scanning electron microscopy imaging of the same pollen grains, we document pollen types of 35 genera including 15 studied for the first time. Using a molecular phylogenetic framework based on currently available sequence data with good genus-coverage, we reconstruct trends in the evolution of Loranthaceae pollen and pinpoint traits of high diagnostic value, partly confirming earlier intuitive hypotheses based on morphological observations. We find that pollen morphology in Loranthaceae is strongly linked to phylogenetic relationships. Some pollen types are diagnostic for discrete genera or evolutionary lineages, opening the avenue to recruit dispersed fossil pollen as age constraints for dated phylogenies and as independent data for testing biogeographic scenarios; so far based exclusively on modern-day data. Correspondences and discrepancies between palynological and molecular data and current taxonomic/systematic concepts are identified and suggestions made for future palynological and molecular investigations of Loranthaceae.
DOI: 10.6084/m9.figshare.4737352.v1
title: Evolution of pollen morphology in Loranthaceae

description: Earlier studies indicate a strong correlation of pollen morphology and ultrastructure with taxonomy in Loranthaceae. Using high-resolution light microscopy and scanning electron microscopy imaging of the same pollen grains, we document pollen types of 35 genera including 15 studied for the first time. Using a molecular phylogenetic framework based on currently available sequence data with good genus-coverage, we reconstruct trends in the evolution of Loranthaceae pollen and pinpoint traits of high diagnostic value, partly confirming earlier intuitive hypotheses based on morphological observations. We find that pollen morphology in Loranthaceae is strongly linked to phylogenetic relationships. Some pollen types are diagnostic for discrete genera or evolutionary lineages, opening the avenue to recruit dispersed fossil pollen as age constraints for dated phylogenies and as independent data for testing biogeographic scenarios; so far based exclusively on modern-day data. Correspondences and discrepancies between palynological and molecular data and current taxonomic/systematic concepts are identified and suggestions made for future palynological and molecular investigations of Loranthaceae.
DOI: 10.6084/m9.figshare.4737481.v2
title: Dataset for the SIDER R package

description: Dataset corresponding to the SIDER R package<br>
DOI: 10.6084/m9.figshare.4737316
title: Supplementary Material for: Thrombosis in Inherited Fibrinogen Disorders

description: Although inherited fibrinogen disorders (IFD) are primarily considered to be bleeding disorders, they are associated with a higher thrombotic complication risk than defects in other clotting factors. Managing IFD patients with thrombosis is challenging as anticoagulant treatment may exacerbate the underlying bleeding risk which can be life-threatening. Due to the low prevalence of IFD, there is little information on pathophysiology or optimal treatment of thrombosis in these patients. We searched the literature for cases of thrombosis among IFD patients and identified a total of 128 patient reports. In approximately half of the cases, thromboses were spontaneous, while in the others trauma, surgery, and parturition contributed to the risk. The true mechanism(s) of thrombosis in IFD patients remain to be elucidated. A variety of anticoagulant treatments have been used in the treatment or prevention of thrombosis, sometimes with concurrent fibrinogen replacement therapy. There is no definite evidence that fibrinogen supplementation increases the risk of thrombosis, and it may potentially be effective in the treatment and prevention of both thrombosis and hemorrhage in IFD patients.
DOI: 10.6084/m9.figshare.4737307
title: Hydrogeology of the Sabatini Volcanic District (Central Italy)

description: This paper supports the ‘Hydrogeological map of the Sabatini Volcanic District’. The map provides an overview of the hydrogeological setting of the Sabatini Volcanic District, using experimental water level data integrated with former volcanological and hydrogeological studies. The 1:50,000 scale map was produced in order to provide support to local authorities and professionals working on groundwater management. Fifteen hydrogeological complexes were defined based on volcanological properties and hydrogeological conditions.
DOI: 10.6084/m9.figshare.4737307.v1
title: Hydrogeology of the Sabatini Volcanic District (Central Italy)

description: This paper supports the ‘Hydrogeological map of the Sabatini Volcanic District’. The map provides an overview of the hydrogeological setting of the Sabatini Volcanic District, using experimental water level data integrated with former volcanological and hydrogeological studies. The 1:50,000 scale map was produced in order to provide support to local authorities and professionals working on groundwater management. Fifteen hydrogeological complexes were defined based on volcanological properties and hydrogeological conditions.
DOI: 10.6084/m9.figshare.4737316.v1
title: Supplementary Material for: Thrombosis in Inherited Fibrinogen Disorders

description: Although inherited fibrinogen disorders (IFD) are primarily considered to be bleeding disorders, they are associated with a higher thrombotic complication risk than defects in other clotting factors. Managing IFD patients with thrombosis is challenging as anticoagulant treatment may exacerbate the underlying bleeding risk which can be life-threatening. Due to the low prevalence of IFD, there is little information on pathophysiology or optimal treatment of thrombosis in these patients. We searched the literature for cases of thrombosis among IFD patients and identified a total of 128 patient reports. In approximately half of the cases, thromboses were spontaneous, while in the others trauma, surgery, and parturition contributed to the risk. The true mechanism(s) of thrombosis in IFD patients remain to be elucidated. A variety of anticoagulant treatments have been used in the treatment or prevention of thrombosis, sometimes with concurrent fibrinogen replacement therapy. There is no definite evidence that fibrinogen supplementation increases the risk of thrombosis, and it may potentially be effective in the treatment and prevention of both thrombosis and hemorrhage in IFD patients.
DOI: 10.6084/m9.figshare.4737229
title: Bayesian semiparametric reproductive dispersion mixed models for non-normal longitudinal data: estimation and case influence analysis

description: Semiparametric reproductive dispersion mixed model (SPRDMM) is a natural extension of the reproductive dispersion model and the semiparametric mixed model. In this paper, we relax the normality assumption of random effects in SPRDMM and use a truncated and centred Dirichlet process prior to specify random effects, and present the Bayesian P-spline to approximate the smoothing unknown function. A hybrid algorithm combining the block Gibbs sampler and the Metropolis–Hastings algorithm is implemented to sample observations from the posterior distribution. Also, we develop Bayesian case deletion influence measure for SPRDMM based on the <i>φ</i>-divergence and present those computationally feasible formulas. Several simulation studies and a real example are presented to illustrate the proposed methodologies.
DOI: 10.6084/m9.figshare.4737232
title: Structure of resilience in Irritable Bowel Syndrome

description: Dataset from N=74 (+30 non-participants) subjects with irritable bowel syndrome (Rome III criteria). Of these, n=54 underwent gut-directed hypnotherapy. <br>Group A (n=37) was assessed pre hypnotherapy (T1) and 10 months post hypnotherapy (T2). Group B (n=37) was assessed as a control group at T2. A subset of group 2 (n=16) received also hypnotherapy, and was examined respectively after 10 months (T3). <br><br>Assessed variables comprise factors of resilience:<br>10 item CDRISC (resilience)<br>BFI-K (neuroticism scale)<br>SWE (self-efficacy)<br>STCI (trait cheerfulness scale)<br>CERQ (adaptive/dysfunctional emotion regulation strategies)<br>FSozU (social support)<br><br>and 2. symptom severity, affective status, and wellbeing<br> <br>HADS (psychological distress)<br>IBS-SSS (IBS severity)<br>quality of life visual analogue scales<br><br>All available scores (raw scores or standardized) from these questionnaires are in the file. <br><br>In Group A at T1, IBS-SSS and resilience measures were not captured. <br>Resilience factors were merged to compound scores unweighted (additional) and weighted based on regression coefficients from PCA. Scores and regression coefficients are in the file. Sensitive data such as diagnoses, socioeconomic variables or birth and examination dates were taken out of the file to safeguard anonymity and patient rights.
DOI: 10.6084/m9.figshare.4737235
title: A risk scoring system to predict coronary stent thrombosis

description: <b>Objective:</b> Stent thrombosis (ST) is a potentially life-threatening complication of percutaneous coronary intervention (PCI). We aimed to develop a scoring system to predict the risk of ST following PCI. <b>Research design and methods:</b> Odds ratios (ORs) for risk factors associated with ST were identified from a meta-analysis based on a systematic literature review, and through consensus expert opinion (Delphi–RAND method). The combined ORs were used to calculate risk scores for acute (within 24 hours), early (within 30 days) and late (31 days to 1 year) ST. Risk scores were validated against patient-level data from the TRITON-TIMI 38 study. Twenty risk factors were identified. <b>Results:</b> The most highly predictive factor for early and late ST was “incomplete duration of dual antiplatelet therapy”. Derived total risk scores ranged from 0 to 22 for acute and early ST, and from 0 to 20 for late ST. Increasing scores were associated with an increasing risk of ST when applied to trial data. Model discrimination was 0.60 (<i>p</i> = .0028), 0.67 (<i>p</i> p <b>Conclusion:</b> Our weighted scoring system may help to stratify ST risk and individualize antiplatelet therapy in patients undergoing PCI.
DOI: 10.6084/m9.figshare.4737313.v2
title: InterMine training slides

description: Slides for an InterMine training session presented at EMBL-EBI's "Introduction to Omics data integration" training course. Provides hands-on examples of querying genes and gene lists, as well as filtering, enriching, and using InterMine's data visualisations and webservices.