cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3443969
title: The electronic trade in endemic plants of Cyprus through the Internet

description: This study assesses the current situation regarding the electronic trade of the Cypriot endemic plants. We examine the plant material sold over the Internet, prices and vendors, and we explore to what extent this activity complies with national laws and international treaties. Overall, 48 taxa (34% of the Cypriot endemic flora) are traded by 21 nurseries of Europe and North America, belonging mostly to Lamiaceae, Brassicaceae, Iridaceae, Asparagaceae, Fabaceae and Asteraceae. Seeds are the commonest form of sale; prices range from €0.12 to 0.79 per seed and from €0.31 to 2.56 per gram. The price range for live plants is €5.67–30.22 (highest for <i>Quercus alnifolia</i>). Among the traded taxa, two are designated critically endangered, another two endangered, four vulnerable, 12 are globally rare and threatened and 12 are protected at the international level. None of the nurseries surveyed seem to have been granted a permit by the authorities of Cyprus to harvest and sell its wild flora, at least during the last decade. State authorities should extend the current legislative framework so as to cover all endemic and nationally threatened taxa, monitor their wild populations, engage in routine surveillance of their e-trade and regulate access to the country’s genetic resources.
DOI: 10.6084/m9.figshare.3443969.v2
title: The electronic trade in endemic plants of Cyprus through the Internet

description: This study assesses the current situation regarding the electronic trade of the Cypriot endemic plants. We examine the plant material sold over the Internet, prices and vendors, and we explore to what extent this activity complies with national laws and international treaties. Overall, 48 taxa (34% of the Cypriot endemic flora) are traded by 21 nurseries of Europe and North America, belonging mostly to Lamiaceae, Brassicaceae, Iridaceae, Asparagaceae, Fabaceae and Asteraceae. Seeds are the commonest form of sale; prices range from €0.12 to 0.79 per seed and from €0.31 to 2.56 per gram. The price range for live plants is €5.67–30.22 (highest for <i>Quercus alnifolia</i>). Among the traded taxa, two are designated critically endangered, another two endangered, four vulnerable, 12 are globally rare and threatened and 12 are protected at the international level. None of the nurseries surveyed seem to have been granted a permit by the authorities of Cyprus to harvest and sell its wild flora, at least during the last decade. State authorities should extend the current legislative framework so as to cover all endemic and nationally threatened taxa, monitor their wild populations, engage in routine surveillance of their e-trade and regulate access to the country’s genetic resources.
DOI: 10.6084/m9.figshare.3443969.v1
title: The electronic trade in endemic plants of Cyprus through the Internet

description: This study assesses the current situation regarding the electronic trade of the Cypriot endemic plants. We examine the plant material sold over the Internet, prices and vendors, and we explore to what extent this activity complies with national laws and international treaties. Overall, 48 taxa (34% of the Cypriot endemic flora) are traded by 21 nurseries of Europe and North America, belonging mostly to Lamiaceae, Brassicaceae, Iridaceae, Asparagaceae, Fabaceae and Asteraceae. Seeds are the commonest form of sale; prices range from €0.12 to 0.79 per seed and from €0.31 to 2.56 per gram. The price range for live plants is €5.67–30.22 (highest for <i>Quercus alnifolia</i>). Among the traded taxa, two are designated critically endangered, another two endangered, four vulnerable, 12 are globally rare and threatened and 12 are protected at the international level. None of the nurseries surveyed seem to have been granted a permit by the authorities of Cyprus to harvest and sell its wild flora, at least during the last decade. State authorities should extend the current legislative framework so as to cover all endemic and nationally threatened taxa, monitor their wild populations, engage in routine surveillance of their e-trade and regulate access to the country’s genetic resources.
DOI: 10.6084/m9.figshare.3443963
title: DICOMs Parasuchus.zip

description: CT data set for the phytosaurian taxon <i>Parasuchus angustifrons<br></i>CT data sets are also deposited with the specimens in the BSPG (Bayerische Staatssammlung für Paläontologie und Geologie, Munich, Germany) collections, where the physical specimen is housed. <br>NOTE! If you use the data for publication, please inform the curator at BSPG, Dr. Oliver Rauhut (o.rauhut@lrz.uni-muenchen.de).
DOI: 10.6084/m9.figshare.3443960
title: DICOMs Ebrachosuchus.zip

description: CT dataset for the phytosaurian taxon <i>Ebrachosuchus neukami.</i> CT data sets are also deposited with the specimens in the BSPG (Bayerische Staatssammlung für Paläontologie und Geologie, Munich, Germany) collections, where the physical specimen is housed. <br>NOTE! If you use the data for publication, please inform the curator at BSPG, Dr. Oliver Rauhut (o.rauhut@lrz.uni-muenchen.de).<br>
DOI: 10.6084/m9.figshare.3443936
title: Supplementary Material for: Risk of Ischemic Stroke in High Risk Atrial Fibrillation Patients during Periods of Warfarin Discontinuation for Surgical Procedures

description: <i>Importance:</i> The risk of ischemic stroke during periods of warfarin discontinuation for surgical procedures is recognized but not well characterized. <i>Objective:</i> The study aimed to quantitate the risk of ischemic stroke associated with high risk atrial fibrillation during periods of warfarin discontinuation. <i>Design, Setting and Participants:</i> A cohort of 4,060 patients (mean follow-up period of 3.5 ± 1.3 years) were randomized into the Atrial Fibrillation Follow-Up Investigation of Rhythm Management study. Patients enrolled in the study had atrial fibrillation plus at least one other risk factor for stroke or death: age ≥65 years', systemic hypertension, diabetes mellitus, congestive heart failure, transient ischemic attack, prior stroke, left atrium &gt;50 mm, left ventricular fractional shortening &lt;25% or left ventricular ejection fraction &lt;40%. <i>Exposure:</i> Warfarin discontinuation for procedure. <i>Main Outcome and Measures:</i> The association of warfarin discontinuation with the incidence of ischemic stroke using pooled repeated measures and Cox proportional hazards analyses during follow-up after adjusting for age, gender, obesity, diabetes mellitus, hypercholesterolemia, cigarette smoking and study period. <i>Results:</i> Warfarin discontinuation for procedure occurred in 265 (0.4%) of the 71,355 person observations. Compared with those without warfarin discontinuation, the rate of ischemic stroke was higher among participants with surgery-related warfarin discontinuation (1.1% of 265 person observations vs. 0.2% of 71,090 person observations, p = 0.001). Warfarin discontinuation was associated with an increased risk for ischemic stroke (relative risk 5.8; 95% CI 1.8-18.4) after adjusting for potential confounders. The population-attributable risk associated with surgery-related warfarin discontinuation was estimated to be 23.1% (95% CI 15.2-30.9%) for ischemic stroke. <i>Conclusions and Relevance:</i> The 6-fold higher risk of ischemic stroke associated with discontinuation of warfarin for surgical procedures must be recognized in high risk atrial fibrillation patients and considered in the risk-benefit analysis of any procedure.
DOI: 10.6084/m9.figshare.3443936.v1
title: Supplementary Material for: Risk of Ischemic Stroke in High Risk Atrial Fibrillation Patients during Periods of Warfarin Discontinuation for Surgical Procedures

description: <i>Importance:</i> The risk of ischemic stroke during periods of warfarin discontinuation for surgical procedures is recognized but not well characterized. <i>Objective:</i> The study aimed to quantitate the risk of ischemic stroke associated with high risk atrial fibrillation during periods of warfarin discontinuation. <i>Design, Setting and Participants:</i> A cohort of 4,060 patients (mean follow-up period of 3.5 ± 1.3 years) were randomized into the Atrial Fibrillation Follow-Up Investigation of Rhythm Management study. Patients enrolled in the study had atrial fibrillation plus at least one other risk factor for stroke or death: age ≥65 years', systemic hypertension, diabetes mellitus, congestive heart failure, transient ischemic attack, prior stroke, left atrium &gt;50 mm, left ventricular fractional shortening &lt;25% or left ventricular ejection fraction &lt;40%. <i>Exposure:</i> Warfarin discontinuation for procedure. <i>Main Outcome and Measures:</i> The association of warfarin discontinuation with the incidence of ischemic stroke using pooled repeated measures and Cox proportional hazards analyses during follow-up after adjusting for age, gender, obesity, diabetes mellitus, hypercholesterolemia, cigarette smoking and study period. <i>Results:</i> Warfarin discontinuation for procedure occurred in 265 (0.4%) of the 71,355 person observations. Compared with those without warfarin discontinuation, the rate of ischemic stroke was higher among participants with surgery-related warfarin discontinuation (1.1% of 265 person observations vs. 0.2% of 71,090 person observations, p = 0.001). Warfarin discontinuation was associated with an increased risk for ischemic stroke (relative risk 5.8; 95% CI 1.8-18.4) after adjusting for potential confounders. The population-attributable risk associated with surgery-related warfarin discontinuation was estimated to be 23.1% (95% CI 15.2-30.9%) for ischemic stroke. <i>Conclusions and Relevance:</i> The 6-fold higher risk of ischemic stroke associated with discontinuation of warfarin for surgical procedures must be recognized in high risk atrial fibrillation patients and considered in the risk-benefit analysis of any procedure.
DOI: 10.6084/m9.figshare.3443933
title: S1.docx

description: The supplementary materials for "Weight and prognosis for influenza A(H1N1)pdm09 infection during the pandemic period between 2009 and 2011: a systematic review of observational studies with meta-analysis".
DOI: 10.6084/m9.figshare.3443933.v1
title: S1.docx

description: The supplementary materials for "Weight and prognosis for influenza A(H1N1)pdm09 infection during the pandemic period between 2009 and 2011: a systematic review of observational studies with meta-analysis".
DOI: 10.6084/m9.figshare.3443930
title: All Database annotation

description: Transcriptome annotations of <em>Coptotermes formosanus</em>
DOI: 10.6084/m9.figshare.3443921
title: Molecular findings from 537 individuals with inherited retinal disease.

description: Abstract <strong>Background</strong> Inherited retinal diseases (IRDs) are a clinically and genetically heterogeneous set of disorders, for which diagnostic second-generation sequencing (next-generation sequencing, NGS) services have been developed worldwide. <strong>Methods</strong> We present the molecular findings of 537 individuals referred to a 105-gene diagnostic NGS test for IRDs. We assess the diagnostic yield, the spectrum of clinical referrals, the variant analysis burden and the genetic heterogeneity of IRD. We retrospectively analyse disease-causing variants, including an assessment of variant frequency in Exome Aggregation Consortium (ExAC). <strong>Results</strong> Individuals were referred from 10 clinically distinct classifications of IRD. Of the 4542 variants clinically analysed, we have reported 402 mutations as a cause or a potential cause of disease in 62 of the 105 genes surveyed. These variants account or likely account for the clinical diagnosis of IRD in 51% of the 537 referred individuals. 144 potentially disease-causing mutations were identified as novel at the time of clinical analysis, and we further demonstrate the segregation of known disease-causing variants among individuals with IRD. We show that clinically analysed variants indicated as rare in dbSNP and the Exome Variant Server remain rare in ExAC, and that genes discovered as a cause of IRD in the post-NGS era are rare causes of IRD in a population of clinically surveyed individuals. <strong>Conclusions</strong> Our findings illustrate the continued powerful utility of custom-gene panel diagnostic NGS tests for IRD in the clinic, but suggest clear future avenues for increasing diagnostic yields.
DOI: 10.6084/m9.figshare.3443921.v1
title: Molecular findings from 537 individuals with inherited retinal disease.

description: Abstract <strong>Background</strong> Inherited retinal diseases (IRDs) are a clinically and genetically heterogeneous set of disorders, for which diagnostic second-generation sequencing (next-generation sequencing, NGS) services have been developed worldwide. <strong>Methods</strong> We present the molecular findings of 537 individuals referred to a 105-gene diagnostic NGS test for IRDs. We assess the diagnostic yield, the spectrum of clinical referrals, the variant analysis burden and the genetic heterogeneity of IRD. We retrospectively analyse disease-causing variants, including an assessment of variant frequency in Exome Aggregation Consortium (ExAC). <strong>Results</strong> Individuals were referred from 10 clinically distinct classifications of IRD. Of the 4542 variants clinically analysed, we have reported 402 mutations as a cause or a potential cause of disease in 62 of the 105 genes surveyed. These variants account or likely account for the clinical diagnosis of IRD in 51% of the 537 referred individuals. 144 potentially disease-causing mutations were identified as novel at the time of clinical analysis, and we further demonstrate the segregation of known disease-causing variants among individuals with IRD. We show that clinically analysed variants indicated as rare in dbSNP and the Exome Variant Server remain rare in ExAC, and that genes discovered as a cause of IRD in the post-NGS era are rare causes of IRD in a population of clinically surveyed individuals. <strong>Conclusions</strong> Our findings illustrate the continued powerful utility of custom-gene panel diagnostic NGS tests for IRD in the clinic, but suggest clear future avenues for increasing diagnostic yields.
DOI: 10.6084/m9.figshare.3443918
title: Supplementary Material for: Awareness of Chronic Kidney Disease and Depressive Symptoms: National Health and Nutrition Examination Surveys 2005-2010

description: <i>Background:</i> Depressive symptoms are common in patients with chronic kidney disease (CKD) and may stem from distress associated with CKD awareness. So far, no studies have examined this association. The objective of this study was to evaluate the association between awareness of CKD and depressive symptoms. <i>Methods:</i> We included adults with stages 1-4 CKD (estimated glomerular filtration rate 15-60 ml/min/1.73 m2 or urine albumin-to-creatinine ratio ≥30 mg/g) using the National Health and Nutrition Examination Surveys from 2005 to 2010. Depressive symptoms were categorized as minimal (9-item Patient Health Questionnaire (PHQ-9) score 0-4), subthreshold (PHQ-9 score 5-14) and severe (PHQ-9 score ≥15). Participants were classified as aware of CKD if they answered yes to the question: ‘Have you ever been told you have weak or failing kidneys?' Multivariable logistic regression was used to identify variables independently associated with at least subthreshold depressive symptoms (PHQ-9 ≥5). <i>Results:</i> In 2,500 participants with CKD, the weighted prevalence was 21.4% for subthreshold and 3.1% for severe depressive symptoms. The weighted prevalence of CKD awareness was 6.4%. Independent predictors of depressive symptoms included younger age, female gender, never been married, less than high-school education, annual family income Conclusions: Awareness of CKD is significantly associated with depressive symptoms independent of known confounding factors. Future studies should examine mediators of this association, especially in light of national efforts to promote CKD awareness.
DOI: 10.6084/m9.figshare.3443918.v2
title: Supplementary Material for: Awareness of Chronic Kidney Disease and Depressive Symptoms: National Health and Nutrition Examination Surveys 2005-2010

description: <i>Background:</i> Depressive symptoms are common in patients with chronic kidney disease (CKD) and may stem from distress associated with CKD awareness. So far, no studies have examined this association. The objective of this study was to evaluate the association between awareness of CKD and depressive symptoms. <i>Methods:</i> We included adults with stages 1-4 CKD (estimated glomerular filtration rate 15-60 ml/min/1.73 m2 or urine albumin-to-creatinine ratio ≥30 mg/g) using the National Health and Nutrition Examination Surveys from 2005 to 2010. Depressive symptoms were categorized as minimal (9-item Patient Health Questionnaire (PHQ-9) score 0-4), subthreshold (PHQ-9 score 5-14) and severe (PHQ-9 score ≥15). Participants were classified as aware of CKD if they answered yes to the question: ‘Have you ever been told you have weak or failing kidneys?' Multivariable logistic regression was used to identify variables independently associated with at least subthreshold depressive symptoms (PHQ-9 ≥5). <i>Results:</i> In 2,500 participants with CKD, the weighted prevalence was 21.4% for subthreshold and 3.1% for severe depressive symptoms. The weighted prevalence of CKD awareness was 6.4%. Independent predictors of depressive symptoms included younger age, female gender, never been married, less than high-school education, annual family income Conclusions: Awareness of CKD is significantly associated with depressive symptoms independent of known confounding factors. Future studies should examine mediators of this association, especially in light of national efforts to promote CKD awareness.
DOI: 10.6084/m9.figshare.3443918.v1
title: Supplementary Material for: Awareness of Chronic Kidney Disease and Depressive Symptoms: National Health and Nutrition Examination Surveys 2005-2010

description: <i>Background:</i> Depressive symptoms are common in patients with chronic kidney disease (CKD) and may stem from distress associated with CKD awareness. So far, no studies have examined this association. The objective of this study was to evaluate the association between awareness of CKD and depressive symptoms. <i>Methods:</i> We included adults with stages 1-4 CKD (estimated glomerular filtration rate 15-60 ml/min/1.73 m2 or urine albumin-to-creatinine ratio ≥30 mg/g) using the National Health and Nutrition Examination Surveys from 2005 to 2010. Depressive symptoms were categorized as minimal (9-item Patient Health Questionnaire (PHQ-9) score 0-4), subthreshold (PHQ-9 score 5-14) and severe (PHQ-9 score ≥15). Participants were classified as aware of CKD if they answered yes to the question: ‘Have you ever been told you have weak or failing kidneys?' Multivariable logistic regression was used to identify variables independently associated with at least subthreshold depressive symptoms (PHQ-9 ≥5). <i>Results:</i> In 2,500 participants with CKD, the weighted prevalence was 21.4% for subthreshold and 3.1% for severe depressive symptoms. The weighted prevalence of CKD awareness was 6.4%. Independent predictors of depressive symptoms included younger age, female gender, never been married, less than high-school education, annual family income Conclusions: Awareness of CKD is significantly associated with depressive symptoms independent of known confounding factors. Future studies should examine mediators of this association, especially in light of national efforts to promote CKD awareness.
DOI: 10.6084/m9.figshare.3443897
title: Supplementary Material for: Metabolomics of Chronic Kidney Disease Progression: A Case-Control Analysis in the Chronic Renal Insufficiency Cohort Study

description: <b><i>Background:</i></b> Whereas several longitudinal metabolomics studies have been conducted in individuals with normal estimated glomerular filtration rate (eGFR) at baseline, disease progression among individuals with established chronic kidney disease (CKD) has not been rigorously examined. <b><i>Methods:</i></b> We performed a nested case-control study of rapid CKD progression in the Chronic Renal Insufficiency Cohort Study, profiling baseline plasma from 200 individuals each with eGFR slope 2/year (cases) or between -1 and +1 ml/min/1.73 m<sup>2</sup>/year (controls), matched on baseline eGFR and proteinuria. To directly assess how the kidney modulates circulating metabolites, we profiled plasma from the aorta and renal vein of 25 hospital-based individuals. <b><i>Results:</i></b> At baseline, cases and controls had a mean eGFR of 41.7 ± 13.3 and 45.0 ± 14.5 ml/min/1.73 m<sup>2</sup>, respectively. Ten plasma metabolites were nominally associated with CKD progression in logistic regression models adjusted for age, sex, race/ethnicity, hypertension, systolic and diastolic blood pressure, diabetes, eGFR and proteinuria; no metabolite achieved the Bonferroni-adjusted significance threshold (p &lt; 0.0003). In a cross-sectional analysis, all 6 of the metabolites that were higher in cases than controls were significantly associated with eGFR at baseline. By contrast, threonine, methionine and arginine were lower in cases than in controls and had no association with baseline eGFR. Furthermore, in the hospital-based cohort that underwent renal arteriovenous sampling, these 3 metabolites were net released from the kidney. Combining these metabolites into a panel of markers further strengthened their association with CKD progression. <b><i>Conclusion:</i></b> Our results motivate interest in arginine, methionine and threonine as potential indicators of renal metabolic function and markers of renal prognosis.
DOI: 10.6084/m9.figshare.3443897.v1
title: Supplementary Material for: Metabolomics of Chronic Kidney Disease Progression: A Case-Control Analysis in the Chronic Renal Insufficiency Cohort Study

description: <b><i>Background:</i></b> Whereas several longitudinal metabolomics studies have been conducted in individuals with normal estimated glomerular filtration rate (eGFR) at baseline, disease progression among individuals with established chronic kidney disease (CKD) has not been rigorously examined. <b><i>Methods:</i></b> We performed a nested case-control study of rapid CKD progression in the Chronic Renal Insufficiency Cohort Study, profiling baseline plasma from 200 individuals each with eGFR slope 2/year (cases) or between -1 and +1 ml/min/1.73 m<sup>2</sup>/year (controls), matched on baseline eGFR and proteinuria. To directly assess how the kidney modulates circulating metabolites, we profiled plasma from the aorta and renal vein of 25 hospital-based individuals. <b><i>Results:</i></b> At baseline, cases and controls had a mean eGFR of 41.7 ± 13.3 and 45.0 ± 14.5 ml/min/1.73 m<sup>2</sup>, respectively. Ten plasma metabolites were nominally associated with CKD progression in logistic regression models adjusted for age, sex, race/ethnicity, hypertension, systolic and diastolic blood pressure, diabetes, eGFR and proteinuria; no metabolite achieved the Bonferroni-adjusted significance threshold (p &lt; 0.0003). In a cross-sectional analysis, all 6 of the metabolites that were higher in cases than controls were significantly associated with eGFR at baseline. By contrast, threonine, methionine and arginine were lower in cases than in controls and had no association with baseline eGFR. Furthermore, in the hospital-based cohort that underwent renal arteriovenous sampling, these 3 metabolites were net released from the kidney. Combining these metabolites into a panel of markers further strengthened their association with CKD progression. <b><i>Conclusion:</i></b> Our results motivate interest in arginine, methionine and threonine as potential indicators of renal metabolic function and markers of renal prognosis.
DOI: 10.6084/m9.figshare.3443885
title: Emerging Infrastructure for Open Access Monitoring in Japan

description: Poster presentation at Open Repositories 2016 in Dublin