cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4977815.v1
title: New draft item

description: Forty-four young adults (18-23 years) were divided in two groups as a function of the level of aerobic fitness (high-fit and low-fit). Participants completed the Psychomotor Vigilance Task (PVT) and an oddball task whereby they had to detect infrequent targets presented among frequent non-targets. Twenty-two participants (11 females) with a low level of aerobic fitness were allocated to the low-fit group and twenty-two (11 females) participants with a high level of aerobic fitness were allocated to the high-fit group. The participants in the high and low-fit group met the inclusion criteria of reporting at least 8 hours of training per week or less than 2 hours, respectively. Participants completed, in this order, the PVT (5 minutes), a visual oddball task (27 minutes) and the PVT (5 minutes). The tasks are detailed in the following section.
DOI: 10.6084/m9.figshare.4977788
title: InvertFractalLorenz 170505.xlsx

description: This spreadsheet model is to complement my work on the Lorenz Curve as an aspect of fractal geometry.
DOI: 10.6084/m9.figshare.4977815.v3
title: SAAF2: Sustain Attention and Aerobic Fitness

description: Forty-four young adults (18-23 years) were divided in two groups as a function of the level of aerobic fitness (high-fit and low-fit). Participants completed the Psychomotor Vigilance Task (PVT) and an oddball task whereby they had to detect infrequent targets presented among frequent non-targets. Twenty-two participants (11 females) with a low level of aerobic fitness were allocated to the low-fit group and twenty-two (11 females) participants with a high level of aerobic fitness were allocated to the high-fit group. The participants in the high and low-fit group met the inclusion criteria of reporting at least 8 hours of training per week or less than 2 hours, respectively. Participants completed, in this order, the PVT (5 minutes), a visual oddball task (27 minutes) and the PVT (5 minutes). The tasks are detailed in the following section.
DOI: 10.6084/m9.figshare.4977788.v1
title: InvertFractalLorenz 170505.xlsx

description: This spreadsheet model is to complement my work on the Lorenz Curve as an aspect of fractal geometry.
DOI: 10.6084/m9.figshare.4977746
title: Supplementary Material for: Precision Genetic and Genomic Medicine in the Middle East and North Africa Region: Are We There Yet?

description: <b><i>Purpose:</i></b> As precision medicine continues its expansion into clinical practice and research settings, it is time to investigate genetic and genomic research in the Middle East and North Africa (MENA) region to identify the strengths and deficits and to provide suggestions for future development. <b><i>Methods:</i></b> We performed a literature review of any genetic or genomic publications on breast cancer and type 2 diabetes for the years 2000-2015 and evaluated the translational value of the research using multiple evaluation metrics, including the “continuum of translation” and the Health Impact Pyramid. <b><i>Results:</i></b> A total of 138 type 2 diabetes and 231 breast cancer publications were included. There were few cohort studies or randomized controlled trials, and there was a distinct lack of pharmacogenetic or pharmacogenomic papers. Most studies were not interventional but instead evaluated susceptibility, and when placed on the continuum of translation, more than 90% of the studies were T1. <b><i>Conclusion:</i></b> This study suggests that the translational value of genetic and genomic research in the MENA region is currently suboptimal. Moving forward requires international cooperation and a collaborative cohort program in order to implement precision medicine in this area of the world.
DOI: 10.6084/m9.figshare.4977683
title: Supplementary Material for: Impact of Mild-to-Moderate Chronic Kidney Disease on One Year Outcomes after Percutaneous Coronary Intervention

description: <b><i>Background/Aim:</i></b> Patients with severe chronic kidney disease (CKD) have a higher risk of adverse events after percutaneous coronary intervention (PCI). There is conflicting evidence regarding the benefit of drug-eluting stents (DES) in patients with CKD. This study is aimed at assessing the effect of mild-to-moderate CKD on PCI outcomes, and determining if DES reduce adverse events amongst these patients. <b><i>Method:</i></b> We used our PCI database to determine demographic, procedural and outcome variables for 1960 consecutive patients (October 2009-October 2012). Kidney function was measured by the estimated glomerular filtration rate (eGFR - CKD-Epidemiology Collaboration creatinine based). Multivariate analysis was performed to determine independent variables associated with mortality and major adverse cardiovascular events (MACE). <b><i>Results:</i></b> The independent variables, predictive of 12-month mortality in PCI patients, were: age &gt;64 years (hazard ratio [HR] 3.10 [95% CI 1.73-5.55], <i>p</i> &lt; 0.001), 3-vessel disease (HR 1.72 [95% CI 1.10-2.68], <i>p</i> = 0.016) and CKD stage. Compared to stage 1 CKD (eGFR &gt;89), HR of death increased in a progressive pattern below eGFR &lt;75: eGFR 60-74, HR 2.40 (95% CI 1.2-4.78), <i>p</i> = 0.013, eGFR 45-59, HR 3.27 (95% CI 1.55-6.9), <i>p</i> = 0.002, eGFR 30-44, HR 4.10 (95% CI 1.82-9.24), <i>p</i> = 0.001, eGFR &lt;30, HR 7.97 (95% CI 3.65-17.40), <i>p</i> &lt; 0.001. In patients with eGFR &lt;75, multivariate analysis demonstrated that DES use was an independent predictor of lower MACE (HR BMS vs. DES 1.8, <i>p</i> = 0.0044). <b><i>Conclusion:</i></b> Age, severity of CKD and 3-vessel disease were independent predictors of mortality following PCI. The mortality risk in CKD patients increased progressively with eGFR &lt;75. The use of DES was associated with a lower rate of MACE in CKD patients with eGFR &lt;75.
DOI: 10.6084/m9.figshare.4977683.v1
title: Supplementary Material for: Impact of Mild-to-Moderate Chronic Kidney Disease on One Year Outcomes after Percutaneous Coronary Intervention

description: <b><i>Background/Aim:</i></b> Patients with severe chronic kidney disease (CKD) have a higher risk of adverse events after percutaneous coronary intervention (PCI). There is conflicting evidence regarding the benefit of drug-eluting stents (DES) in patients with CKD. This study is aimed at assessing the effect of mild-to-moderate CKD on PCI outcomes, and determining if DES reduce adverse events amongst these patients. <b><i>Method:</i></b> We used our PCI database to determine demographic, procedural and outcome variables for 1960 consecutive patients (October 2009-October 2012). Kidney function was measured by the estimated glomerular filtration rate (eGFR - CKD-Epidemiology Collaboration creatinine based). Multivariate analysis was performed to determine independent variables associated with mortality and major adverse cardiovascular events (MACE). <b><i>Results:</i></b> The independent variables, predictive of 12-month mortality in PCI patients, were: age &gt;64 years (hazard ratio [HR] 3.10 [95% CI 1.73-5.55], <i>p</i> &lt; 0.001), 3-vessel disease (HR 1.72 [95% CI 1.10-2.68], <i>p</i> = 0.016) and CKD stage. Compared to stage 1 CKD (eGFR &gt;89), HR of death increased in a progressive pattern below eGFR &lt;75: eGFR 60-74, HR 2.40 (95% CI 1.2-4.78), <i>p</i> = 0.013, eGFR 45-59, HR 3.27 (95% CI 1.55-6.9), <i>p</i> = 0.002, eGFR 30-44, HR 4.10 (95% CI 1.82-9.24), <i>p</i> = 0.001, eGFR &lt;30, HR 7.97 (95% CI 3.65-17.40), <i>p</i> &lt; 0.001. In patients with eGFR &lt;75, multivariate analysis demonstrated that DES use was an independent predictor of lower MACE (HR BMS vs. DES 1.8, <i>p</i> = 0.0044). <b><i>Conclusion:</i></b> Age, severity of CKD and 3-vessel disease were independent predictors of mortality following PCI. The mortality risk in CKD patients increased progressively with eGFR &lt;75. The use of DES was associated with a lower rate of MACE in CKD patients with eGFR &lt;75.
DOI: 10.6084/m9.figshare.4977635
title: TWH HENAN DATA

description: The data involve about 1400 peasant family heads in Shenqiu County, Henan province, China. The data were collected in 2016.
DOI: 10.6084/m9.figshare.4977635.v1
title: TWH HENAN DATA

description: The data involve about 1400 peasant family heads in Shenqiu County, Henan province, China. The data were collected in 2016.
DOI: 10.6084/m9.figshare.4977632
title: Mckernan_etal._2017_GSL_SP_454-1930

description: Data file of experimental conditions and results for the pressure dependent permeability of Whitby Mudstone. From:<br>Rosanne McKernan, Julian Mecklenburgh, Ernie Rutter & Kevin Taylor [2017]. Microstructural controls on the pressure-dependent permeability of Whitby mudstone. In: Rutter, E. H., Mecklenburgh, J. & Taylor, K. G. (eds) Geomechanical and Petrophysical Properties of Mudrocks. Geological Society, London, Special Publications, 454. https://doi.org/10.1144/SP454.15<br>
DOI: 10.6084/m9.figshare.4977626
title: Systematic Search of Outcome-Driven Predictive Process Monitoring v1.0

description: Listing of papers retrieved during a Systematic Literature Search of publications in the field of predictive process monitoring conducted in May 2017.<br>
DOI: 10.6084/m9.figshare.4977632.v1
title: Mckernan_etal._2017_GSL_SP_454-1930

description: Data file of experimental conditions and results for the pressure dependent permeability of Whitby Mudstone. From:<br>Rosanne McKernan, Julian Mecklenburgh, Ernie Rutter & Kevin Taylor [2017]. Microstructural controls on the pressure-dependent permeability of Whitby mudstone. In: Rutter, E. H., Mecklenburgh, J. & Taylor, K. G. (eds) Geomechanical and Petrophysical Properties of Mudrocks. Geological Society, London, Special Publications, 454. https://doi.org/10.1144/SP454.15<br>
DOI: 10.6084/m9.figshare.4977560
title: Malus domestica illustrations

description: Illustrations of Malus sylvestris made for the Technical guidelines for genetic conservation and use by European Forest Genetic Resources Programme (EUFORGEN)
DOI: 10.6084/m9.figshare.4977584.v1
title: Pinus leucodermis syn P. heldreichii

description: Illustration of Pinus leucodermis syn P. heldreichii
DOI: 10.17632/538krtt5hy.3
title: Data for: Reliability and applicability of the revised Cochrane risk-of-bias tool for randomised trials (RoB 2): low inter-rater reliability and challenges in application

description: database underlying the findings of the study "Reliability and applicability of the revised Cochrane risk-of-bias tool for randomised trials (RoB 2): low inter-rater reliability and challenges in application" submitte to the Journal of Clinical Epidemiology
DOI: 10.6084/m9.figshare.4977497
title: Automated classification of tropical shrub species: a hybrid of leaf shape approach

description: Databaset name: myDAUN datasetPassword: myDAUN2017
DOI: 10.6084/m9.figshare.4977494
title: Supplementary Material for: Overexpression of Toll-Like Receptors 2, 3, 4, and 8 Is Correlated to the Vascular Atherosclerotic Process in the Hyperlipidemic Rabbit Model: The Effect of Statin Treatment

description: <b><i>Background:</i></b> Atherosclerosis is the major cause of cardiovascular disease; hypercholesterolemia is a major risk factor. We hypothesized that specific TLR members (TLR2, TLR3, TLR4, TLR8) may play a role in atherosclerosis progression and its accompanying inflammatory response. We determined the association of atherosclerotic lesions and TLR mRNA expression in different aortic sites. We also assessed the effects of fluvastatin (Flu) treatment on TLR expression and plaque characteristics. <b><i>Methods:</i></b> Male rabbits, fed with an atherogenic diet for a duration of 3 months, were screened for advanced atherosclerotic lesions in the aorta. Additional animals received normal diet or normal diet plus Flu for 1 additional month. TLR mRNA expression in various thoracic and abdominal aortic segments was assessed, together with atherosclerotic changes. <b><i>Results:</i></b> After high lipid diet, the atherosclerotic burden increased more in the abdominal than in the thoracic aorta; TLR2, 3, 4, and 8 also increased significantly. Flu decreased atherosclerotic plaque, calcium deposition, lipid cores, intraplaque hemorrhage, erythrocyte membranes, endothelial cells, and macrophage infiltration, while increasing smooth muscle cells in plaques of both aortic segments; it also lowered TLR2, 3, 4, and 8 expression in all aortic segments to a stronger degree than resumption of normal diet. There was a strong association between blood and tissue parameters during experimental period and finally a strong correlation found between these parameters with mRNA of TLR2, 3, 4, and 8 in various stages. <b><i>Conclusion:</i></b> For the first time TLR2, 3, 4, and 8 mRNA expression is prospectively explored after hypercholesterolemic diet in the rabbit model. TLR2, 3, 4, and 8 mRNA expression is strongly upregulated and correlates with the progression of atherosclerosis in the aorta. Flu significantly inhibited this progress and reduced inflammation via TLR downregulation which was strongly associated with regression of plaque morphology and atherosclerosis promoting factors.
DOI: 10.6084/m9.figshare.4977497.v1
title: Automated classification of tropical shrub species: a hybrid of leaf shape approach

description: Databaset name: myDAUN datasetPassword: myDAUN2017
DOI: 10.6084/m9.figshare.4977464
title: Extended GenoCAD plant grammar for Plant X-tender

description: Extension of the plant grammar previously implemented in GenoCAD (Coll et al. Plos One, 2015). It inlcudes new regualtory sequences (i.e.n<em>opaline synthase promoter </em> and cauliflower mosaic virus CaMV 35S terminator) and a new rule to facilitate virtual assembly of the selected biological parts into the expression cassette. The new rule allows the design of a simple expression cassette segment without the whole vector.
DOI: 10.6084/m9.figshare.4977464.v1
title: Extended GenoCAD plant grammar for Plant X-tender

description: Extension of the plant grammar previously implemented in GenoCAD (Coll et al. Plos One, 2015). It inlcudes new regualtory sequences (i.e.n<em>opaline synthase promoter </em> and cauliflower mosaic virus CaMV 35S terminator) and a new rule to facilitate virtual assembly of the selected biological parts into the expression cassette. The new rule allows the design of a simple expression cassette segment without the whole vector.
DOI: 10.21421/d2/0rdmfq
title: Stability and adaptability of valencia Groundnut genotypes (Arachis hypogeae) across different environments in eastern and southern Africa

description: This database includes the research work carried out on regional groundnut varieties focusing on the identification of stable Valencia genotypes and stratification of environments in the region for targeted breeding. The experiments were conducted in Malawi in 2013 to 2016 cropping seasons. Groundnut is a very important food and cash crop in Eastern and Southern Africa with varying multiple uses. Groundnut (Arachis hypogaea L., AABB, 2n=4x=40) is a self-pollinated crop and is an annual crop distinguished from most other legume crop species by producing aerial flowers and fruiting below ground. The groundnut breeding program in Malawi is the regional hub that supplies Eastern and Southern Africa Region with improved resilient varieties. The program makes over 150 new crosses per year targeting different market niches which are then advanced culminating in adaptability trials across the region. Based on their agronomic performance in advanced and regional yield trials for yield and other traits such as disease resistance, the superior genotypes will be selected and advanced further in National performance trials and farmer participatory variety selection in preparation for release and commercialization and or wider use by farmers. The environmental stratification achieved from this study will help in reduction of phenotyping cost by conducting experiments in fewer representative environments.The agronomic data (grain yield) of the Valencia genotypes evaluated is hereby presented, that helped in dissecting the stability status of the genotypes across environments and at the same time stratification of environments into mega-environments. The most adapted and stable genotypes identified can be advanced for release in the respective country regions and or use in breeding programs for further genetic enhancement. The mega-environments identified can be used for early generation screening and at the same time to acquire data for release in the region as a measure to save resources
DOI: 10.6084/m9.figshare.4975835
title: TPLakes_Temperature

description: The first comprehensive data set of 15-year (2001–2015) nighttime and daytime lake surface water temperature (LSWT) of 374 lakes (≥10 km2 each) over the Tibetan Plateau, using MODIS (Moderate Resolution Imaging Spectroradiometer) Land Surface Temperature (LST) products as well as four lake boundary shapefiles (i.e. 2002, 2005, 2009, and 2014) derived from Landsat/CBERS/GaoFen-1 satellite images.
DOI: 10.6084/m9.figshare.4975829
title: The anticancer effect of mebendazole may be due to M1 monocyte/macrophage activation via ERK1/2 and TLR8-dependent inflammasome activation

description: Mebendazole (MBZ), a drug commonly used for helminitic infections, has recently gained substantial attention as a repositioning candidate for cancer treatment. However, the mechanism of action behind its anticancer activity remains unclear. To address this problem, we took advantage of the curated MBZ-induced gene expression signatures in the LINCS Connectivity Map (CMap) database. The analysis revealed strong negative correlation with MEK/ERK1/2 inhibitors. Moreover, several of the most upregulated genes in response to MBZ exposure were related to monocyte/macrophage activation. The MBZ-induced gene expression signature in the promyeloblastic HL-60 cell line was strongly enriched in genes involved in monocyte/macrophage pro-inflammatory (M1) activation. This was subsequently validated using MBZ-treated THP-1 monocytoid cells that demonstrated gene expression, surface markers and cytokine release characteristic of the M1 phenotype. At high concentrations MBZ substantially induced the release of IL-1β and this was further potentiated by lipopolysaccharide (LPS). At low MBZ concentrations, cotreatment with LPS was required for MBZ-stimulated IL-1β secretion to occur. Furthermore, we show that the activation of protein kinase C, ERK1/2 and NF-kappaB were required for MBZ-induced IL-1β release. MBZ-induced IL-1β release was found to be dependent on NLRP3 inflammasome activation and to involve TLR8 stimulation. Finally, MBZ induced tumor-suppressive effects in a coculture model with differentiated THP-1 macrophages and HT29 colon cancer cells. In summary, we report that MBZ induced a pro-inflammatory (M1) phenotype of monocytoid cells, which may, at least partly, explain MBZ’s anticancer activity observed in animal tumor models and in the clinic.
DOI: 10.6084/m9.figshare.4975829.v1
title: The anticancer effect of mebendazole may be due to M1 monocyte/macrophage activation via ERK1/2 and TLR8-dependent inflammasome activation

description: Mebendazole (MBZ), a drug commonly used for helminitic infections, has recently gained substantial attention as a repositioning candidate for cancer treatment. However, the mechanism of action behind its anticancer activity remains unclear. To address this problem, we took advantage of the curated MBZ-induced gene expression signatures in the LINCS Connectivity Map (CMap) database. The analysis revealed strong negative correlation with MEK/ERK1/2 inhibitors. Moreover, several of the most upregulated genes in response to MBZ exposure were related to monocyte/macrophage activation. The MBZ-induced gene expression signature in the promyeloblastic HL-60 cell line was strongly enriched in genes involved in monocyte/macrophage pro-inflammatory (M1) activation. This was subsequently validated using MBZ-treated THP-1 monocytoid cells that demonstrated gene expression, surface markers and cytokine release characteristic of the M1 phenotype. At high concentrations MBZ substantially induced the release of IL-1β and this was further potentiated by lipopolysaccharide (LPS). At low MBZ concentrations, cotreatment with LPS was required for MBZ-stimulated IL-1β secretion to occur. Furthermore, we show that the activation of protein kinase C, ERK1/2 and NF-kappaB were required for MBZ-induced IL-1β release. MBZ-induced IL-1β release was found to be dependent on NLRP3 inflammasome activation and to involve TLR8 stimulation. Finally, MBZ induced tumor-suppressive effects in a coculture model with differentiated THP-1 macrophages and HT29 colon cancer cells. In summary, we report that MBZ induced a pro-inflammatory (M1) phenotype of monocytoid cells, which may, at least partly, explain MBZ’s anticancer activity observed in animal tumor models and in the clinic.
DOI: 10.6084/m9.figshare.4975787
title: ORCID: Connecting research and researchers

description: Presentation created for the Roundtable on Data and Publishing in the Social Sciences, 5 May 2017
DOI: 10.6084/m9.figshare.4975229
title: Reproducible results for: Self-reported dietary adherence, disease-specific symptoms, and quality of life are associated with healthcare provider follow-up in celiac disease

description: This fileset contains survey data collected by Beyond Celiac and described in the manuscript. This fileset also contains all figures and tables from the paper and all code necessary to reproduce them.<br>## Description of survey data files (in the zip file)<br>beyond celiac survey questions.tsvThe first row contains the names of each column. Each subsequent row corresponds to one question in the survey. The ans_type column can be used to join the "beyond celiac survey answers.tsv" table and indicates the possible answers to each question.<br>beyond celiac survey answers.tsvThe first row contains the names of each column. Each subsequent row corresponds to one possible answer for at least one question in the survey. For a given ans_type, each possible answer has a corresponding ans_num.<br>beyond celiac survey responses.tsvThese are the actual survey responses. The first row indicates the ques_id from "beyond celiac survey questions.tsv" and each subsequent row corresponds to one survey participant. If a given ques_id was a free text question (ans_type = 12), the response is simply the free text response. Otherwise, the response is coded as the corresponding ans_num for that ques_id and ans_type.<br>Here we have included all survey responses from individuals who reported (1) having celiac disease themselves (2) being at least 19 years old. However, due to an error in data collection, several questions were skipped for individuals who reported being over 65 years old, which is why we did not use this age group in the paper.