cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6384164.v1
title: Score-P measurement system code and event logs for Euro-Par 2018 paper: A Methodology for Performance Analysis of Applications Using Multi-layer I/O

description: This artifact contains the prototype implementation of a novel approach for recording I/O operations across multi-layer I/O interfaces and a case study using that approach, as described in the accompanying paper, "A Methodology for Performance Analysis of Applications Using Multi-layer I/O".<br>In order to fully utilise the high bandwidth offered by modern high-performance computing storage systems, and to handle increasingly large volumes of data, parallel I/O operations are often implemented through libraries such as HDF5, NetCDF and MPI I/O. In many cases, multiple libraries may operate concurrently within a given software stack. This concurrency and operations between libraries can impact upon each other. Given this, it is essential to be able to effectively monitor I/O operations across all libraries utilised by a given application.<br>Here, a prototype methodology for recording calls to I/O libraries on multiple layers of the software stack is presented. This methodology is implemented as an extension of Open Trace Format Version 2 (OTF2) and the Score-P measurement infrasctructure. The implementation is provided here in the tarball <b>scorep-4.0-io.tar.gz</b><b><br></b>In addition to the implementation, event logs generated by its test evaluation of the Met Office NERC Cloud model (MONC) simulator are provided. Therein, the I/O behavior of MONC using the Score-P implementation are provided. These logs, provided in the directory <b>monc_112n_14N_10T_small</b>, can be visualized in a tool such as Vampir.<br>Further instructions on recreating the analyses presented in the accompanying paper are provided in <b>artifact.pdf</b>.
DOI: 10.6084/m9.figshare.6384095
title: Unexpected bird–feather mite associations revealed by DNA metabarcoding uncovers a dynamic ecoevolutionary scenario

description: HiSeq raw data, and processed representative sequences files.
DOI: 10.6084/m9.figshare.6384095.v1
title: Unexpected bird–feather mite associations revealed by DNA metabarcoding uncovers a dynamic ecoevolutionary scenario

description: HiSeq raw data, and processed representative sequences files.
DOI: 10.6084/m9.figshare.6384092
title: Supplementary Material for: Predictors of Utilization of an Addiction-Specific Behavioural Couple Therapy in Alcohol Dependence

description: <b><i>Purpose:</i></b> The aim of this study was to examine predictors that lead to the utilization of Behavioural Couple Therapy (BCT) for patients with alcohol dependence (AD) in a ­European health care system and to identify groups that have a low probability of utilizing BCT. <b><i>Methods:</i></b> Using routinely collected data from a German rehabilitation clinic, a sample of 1,843 inpatients with AD living in a couple relationship was examined. Each patient could freely choose to participate in an addiction-specific BCT as a voluntary additional intervention during an inpatient treatment program. <b><i>Results:</i></b> The logistic regression analysis indicated that female gender, older age and a higher number of comorbid disorders were associated with a decreased probability of utilizing BCT. The decision tree found that for men, the lowest utilization rate was in the age range of 51–54 and from the age of 58 years; women with higher pressure by their partner in combination with more than 1 comorbid mental disorder and women with lower pressure by their partner (regardless of comorbid disorders) showed the lowest utilization rate. <b><i>Conclusions:</i></b> Certain subgroups of patients with AD are less likely to participate in BCT during inpatient treatment.
DOI: 10.6084/m9.figshare.6384086
title: Raw data for Peer J .rar

description: The dataset show the numeric value of texture and shape features.
DOI: 10.6084/m9.figshare.6384086.v1
title: Raw data for Peer J .rar

description: The dataset show the numeric value of texture and shape features.
DOI: 10.6084/m9.figshare.6384035
title: Stereo Digital Terrain Model - Cerberus Fossae, Mars

description: Stereo Digital Terrain Model (DTM) - Cerberus Fossae, Mars<br>To accompany:<br>Grindrod, P.M., J. Hollingsworth, F. Ayoub, and S. Hunt, (2018) The Search for Active Marsquakes Using Subpixel Coregistration and Correlation: First Results and Best Practices, Journal of Geophysical Research.<br>DTM is provided in geotiff format, for use with most GIS packages.<br>Made from the following HiRISE stereo pair:PSP_003650_1900 https://www.uahirise.org/PSP_003650_1900PSP_004283_1900 https://www.uahirise.org/PSP_004283_1900
DOI: 10.6084/m9.figshare.6384035.v1
title: Stereo Digital Terrain Model - Cerberus Fossae, Mars

description: Stereo Digital Terrain Model (DTM) - Cerberus Fossae, Mars<br>To accompany:<br>Grindrod, P.M., J. Hollingsworth, F. Ayoub, and S. Hunt, (2018) The Search for Active Marsquakes Using Subpixel Coregistration and Correlation: First Results and Best Practices, Journal of Geophysical Research.<br>DTM is provided in geotiff format, for use with most GIS packages.<br>Made from the following HiRISE stereo pair:PSP_003650_1900 https://www.uahirise.org/PSP_003650_1900PSP_004283_1900 https://www.uahirise.org/PSP_004283_1900
DOI: 10.6084/m9.figshare.6383864
title: Figure data for "Time-Resolved Nonlinear Ghost Imaging"

description: Data for the figures in the article "Time-Resolved Nonlinear Ghost Imaging".<br>Article DOI : https://doi.org/10.1021/acsphotonics.8b00653
DOI: 10.6084/m9.figshare.6383837
title: Impact of a quiz in video data files

description: Two SPSS datasets evaluating the impact of a quiz in an educational video. Students were exposed to three variations of video and subsequent MCQ scores are captured
DOI: 10.6084/m9.figshare.6383837.v1
title: Impact of a quiz in video data files

description: Two SPSS datasets evaluating the impact of a quiz in an educational video. Students were exposed to three variations of video and subsequent MCQ scores are captured
DOI: 10.6084/m9.figshare.6383834
title: HiPRECISION HiRISE Image Products - Cerberus Fossae, Mars.

description: HiPRECISION HiRISE Image Products - Cerberus Fossae, Mars.<br>To accompany:<br>Grindrod, P.M., J. Hollingsworth, F. Ayoub, and S. Hunt, (2018) The Search for Active Marsquakes Using Subpixel Coregistration and Correlation: First Results and Best Practices, Journal of Geophysical Research.<br><br><br>Images are provided in .cub format, for use in the freely-available USGS ISIS software (https://isis.astrogeology.usgs.gov/).
DOI: 10.6084/m9.figshare.6383834.v1
title: HiPRECISION HiRISE Image Products - Cerberus Fossae, Mars.

description: HiPRECISION HiRISE Image Products - Cerberus Fossae, Mars.<br>To accompany:<br>Grindrod, P.M., J. Hollingsworth, F. Ayoub, and S. Hunt, (2018) The Search for Active Marsquakes Using Subpixel Coregistration and Correlation: First Results and Best Practices, Journal of Geophysical Research.<br><br><br>Images are provided in .cub format, for use in the freely-available USGS ISIS software (https://isis.astrogeology.usgs.gov/).
DOI: 10.17028/rd.lboro.6383804
title: Initial testing of strip detector

description: Data obtained whilst testing control software.<br>Please contact the researcher if you wish to request access to this deposit.<br>
DOI: 10.17028/rd.lboro.6383804.v1
title: Initial testing of strip detector

description: Data obtained whilst testing control software.<br>Please contact the researcher if you wish to request access to this deposit.<br>
DOI: 10.6084/m9.figshare.6383525
title: Master Data

description: Data and R scripts used for Binning during my master thesis<br>
DOI: 10.6084/m9.figshare.6383525.v1
title: Master Data

description: Data and R scripts used for Binning during my master thesis<br>
DOI: 10.6084/m9.figshare.6383516
title: Data for "The 2015 International Aneurysm CFD Challenge"

description: Here you can find supplementary material to the journal publication "Real-World Variability in the Prediction of Intracranial Aneurysm Wall Shear Stress: The 2015 International Aneurysm CFD Challenge"- The surface of the computational domain from each team for each case with wall shear stress (WSS) and normalized WSS fields.- The time-averaged velocity data- The Segmented surfaces (processed and "raw")- Information sent out to the participants.- An empty questionnaire which participants were asked to fill out- A de-identified spreadsheet with computed and reported hemodynamic parameters- A presentation showing figures of the entire computational model, the WSS pattern, and the normalized WSS for each case.
DOI: 10.6084/m9.figshare.6383516.v1
title: Data for "The 2015 International Aneurysm CFD Challenge"

description: Here you can find supplementary material to the journal publication "Real-World Variability in the Prediction of Intracranial Aneurysm Wall Shear Stress: The 2015 International Aneurysm CFD Challenge"- The surface of the computational domain from each team for each case with wall shear stress (WSS) and normalized WSS fields.- The time-averaged velocity data- The Segmented surfaces (processed and "raw")- Information sent out to the participants.- An empty questionnaire which participants were asked to fill out- A de-identified spreadsheet with computed and reported hemodynamic parameters- A presentation showing figures of the entire computational model, the WSS pattern, and the normalized WSS for each case.
DOI: 10.6084/m9.figshare.6383360
title: Gender inequity during the Ph.D.: females in the life sciences benefit less from their scientific contacts

description: Analysis of Gender Differences in the Life Sciences among Ph.D. graduates. <br>
DOI: 10.6084/m9.figshare.6383360.v2
title: Gender inequity during the Ph.D.: females in the life sciences benefit less from their scientific contacts

description: Analysis of Gender Differences in the Life Sciences among Ph.D. graduates. <br>
DOI: 10.6084/m9.figshare.6383360.v1
title: Gender inequity during the Ph.D.: females in the life sciences benefit less from their scientific contacts

description: Analysis of Gender Differences in the Life Sciences among Ph.D. graduates. <br>
DOI: 10.6084/m9.figshare.6383288
title: RNA sequencing to predict response to TNF-α inhibitors reveals possible mechanism for nonresponse in smokers

description: <b>Background</b>: Several studies have employed microarray-based profiling to predict response to tumor necrosis factor-alpha inhibitors (TNFi) in rheumatoid arthritis (RA); yet efforts to validate these targets have failed to show predictive abilities acceptable for clinical practice. <b>Methods</b>: The eighty most extreme responders and nonresponders to TNFi therapy were selected from the observational BiOCURA cohort. RNA sequencing was performed on mRNA from peripheral blood mononuclear cells (PBMCs) collected before initiation of treatment. The expression of pathways as well as individual gene transcripts between responders and nonresponders was investigated. Promising targets were technically replicated and validated in <i>n</i> = 40 new patients using qPCR assays. <b>Results</b>: Before therapy initiation, nonresponders had lower expression of pathways related to interferon and cytokine signaling, while also showing higher levels of two genes, GPR15 and SEMA6B (<i>p</i> = 0.02). The two targets could be validated, however, additional analyses revealed that GPR15 and SEMA6B did not independently predict response, but were rather dose-dependent markers of smoking (<i>p</i> <b>Conclusions</b>: The study did not identify new transcripts ready to use in clinical practice, yet GPR15 and SEMA6B were recognized as candidate explanatory markers for the reduced treatment success in RA smokers.
DOI: 10.6084/m9.figshare.6383288.v2
title: RNA sequencing to predict response to TNF-α inhibitors reveals possible mechanism for nonresponse in smokers

description: <b>Background</b>: Several studies have employed microarray-based profiling to predict response to tumor necrosis factor-alpha inhibitors (TNFi) in rheumatoid arthritis (RA); yet efforts to validate these targets have failed to show predictive abilities acceptable for clinical practice. <b>Methods</b>: The eighty most extreme responders and nonresponders to TNFi therapy were selected from the observational BiOCURA cohort. RNA sequencing was performed on mRNA from peripheral blood mononuclear cells (PBMCs) collected before initiation of treatment. The expression of pathways as well as individual gene transcripts between responders and nonresponders was investigated. Promising targets were technically replicated and validated in <i>n</i> = 40 new patients using qPCR assays. <b>Results</b>: Before therapy initiation, nonresponders had lower expression of pathways related to interferon and cytokine signaling, while also showing higher levels of two genes, GPR15 and SEMA6B (<i>p</i> = 0.02). The two targets could be validated, however, additional analyses revealed that GPR15 and SEMA6B did not independently predict response, but were rather dose-dependent markers of smoking (<i>p</i> <b>Conclusions</b>: The study did not identify new transcripts ready to use in clinical practice, yet GPR15 and SEMA6B were recognized as candidate explanatory markers for the reduced treatment success in RA smokers.
DOI: 10.6084/m9.figshare.6383288.v1
title: RNA-Sequencing to Predict Response to TNF-α inhibitors Reveals Possible Mechanism for Non-response in Smokers

description: <b>Background</b>: Several studies have employed microarray-based profiling to predict response to tumor necrosis factor-alpha inhibitors (TNFi) in rheumatoid arthritis (RA); yet efforts to validate these targets have failed to show predictive abilities acceptable for clinical practice. <b>Methods</b>: The eighty most extreme responders and non-responders to TNFi therapy were selected from the observational BiOCURA cohort. RNA-sequencing was performed on mRNA from peripheral blood mononuclear cells (PBMCs) collected before initiation of treatment. The expression of pathways as well as individual gene transcripts between responders and non-responders was investigated. Promising targets were technically replicated and validated in n=40 new patients using qPCR-assays. <b>Results</b>: Before therapy-initiation, non-responders had lower expression of pathways related to interferon and cytokine signaling, while also showing higher levels of two genes, GPR15 and SEMA6B (p=0.02). The two targets could be validated, however, additional analyses revealed that GPR15 and SEMA6B did not independently predict response, but were rather dose-dependent markers of smoking (p&lt;0.0001). <b>Conclusions</b>: The study did not identify new transcripts ready to use in clinical practice, yet GPR15 and SEMA6B were recognized as candidate explanatory markers for the reduced treatment success in RA smokers.
DOI: 10.6084/m9.figshare.6383276
title: Habitat and ecological diversity influences the species-area relationship and the biogeography of the Sicilian archipelago’s isopods

description: Terrestrial isopods are a well-studied invertebrate taxon in Sicily and in the surrounding islands (Maltese archipelago included). During the last 30 years their systematics, ecology and biogeography have been analysed by many authors. The size and the diverse geological origin of the Sicilian archipelago represents an ideal open laboratory in which to study some biogeographical patterns, such as the species-area relationship (SAR). Since many species show limited adaptation to broad physiological conditions and low mobility, and, therefore, their active dispersion is very slow, SAR can be a useful means to examine biogeographical patterns of isopods. Here we analyse their biogeography and whether there is a relationship between the area and the habitat variability of the island surveyed, and whether these factors have an either direct or coupled influence on species richness and ecology. Moreover, we evaluate a potential relationship between Isopoda species richness and the distance from the centre of dispersion (Sicily). Finally, we test for a difference in species and habitat richness between volcanic and non-volcanic islands. Our results show a positive correlation between the area and the habitat, more significant than that between the area and the species, leading us to speculate that habitat diversity has an influence on the SAR of isopods. We find a significantly higher richness of both species and habitats on non-volcanic islands. Finally, our analysis confutes the hypothesis that the number of isopod species on the archipelago’s islets declines with the distance from Sicily. We suggest some potential explanations.
DOI: 10.6084/m9.figshare.6383276.v1
title: Habitat and ecological diversity influences the species-area relationship and the biogeography of the Sicilian archipelago’s isopods

description: Terrestrial isopods are a well-studied invertebrate taxon in Sicily and in the surrounding islands (Maltese archipelago included). During the last 30 years their systematics, ecology and biogeography have been analysed by many authors. The size and the diverse geological origin of the Sicilian archipelago represents an ideal open laboratory in which to study some biogeographical patterns, such as the species-area relationship (SAR). Since many species show limited adaptation to broad physiological conditions and low mobility, and, therefore, their active dispersion is very slow, SAR can be a useful means to examine biogeographical patterns of isopods. Here we analyse their biogeography and whether there is a relationship between the area and the habitat variability of the island surveyed, and whether these factors have an either direct or coupled influence on species richness and ecology. Moreover, we evaluate a potential relationship between Isopoda species richness and the distance from the centre of dispersion (Sicily). Finally, we test for a difference in species and habitat richness between volcanic and non-volcanic islands. Our results show a positive correlation between the area and the habitat, more significant than that between the area and the species, leading us to speculate that habitat diversity has an influence on the SAR of isopods. We find a significantly higher richness of both species and habitats on non-volcanic islands. Finally, our analysis confutes the hypothesis that the number of isopod species on the archipelago’s islets declines with the distance from Sicily. We suggest some potential explanations.
DOI: 10.6084/m9.figshare.6383225
title: Supplementary Material for: Comprehensive and Integrative Analysis Reveals the Diagnostic, Clinicopathological and Prognostic Significance of Polo-Like Kinase 1 in Hepatocellular Carcinoma

description: <b><i>Background/Aims:</i></b> Liver cancer has the second highest cancer-related death rate globally and has relatively few targeted therapeutics. Polo-like kinase 1 (PLK1) is a fascinating trigger of the cell cycle; however, the still-rudimentary understanding of PLK1 at present is a significant barrier to its clinical applications. Here, we comprehensively clarified the clinicopathological value and potential functions of PLK1 in hepatocellular carcinoma (HCC). <b><i>Methods:</i></b> HCC-related microarrays, RNA-sequencing datasets and published studies were deeply mined and integrated from The Cancer Genome Atlas, Gene Expression Omnibus, ArrayExpress, Oncomine, literature databases, and immunohistochemistry experiments. Meanwhile, the associations between PLK1 expression and its clinicopathological implications and prognostic value in HCC patients were assessed. The standardized mean difference, summary receiver operating characteristic curve and the corresponding area under the curve, hazard ratios, odds ratios (ORs), and their 95% confidence intervals (CIs) were examined by STATA 12.0. Additionally, several bioinformatics methods were used to identify the potential function of PLK1 in HCC. <b><i>Results:</i></b> Comprehensive analyses revealed that PLK1 was significantly increased in HCC (standardized mean difference = 1.34, 95% CI: 1.03–1.65, P &lt; 0.001). The results of diagnostic tests specified that in the summary receiver operating characteristic curve, the area under the curve was 0.88 (95% CI: 0.85–0.90). Furthermore, an elevated PLK1 level significantly predicted unfavorable overall survival (hazard ratio = 1.78, 95% CI: 1.10–2.88, P = 0.019) and was correlated with female gender (OR = 0.73, 95% CI: 0.56–0.95, P = 0.017), tumor thrombus (OR = 3.97, 95% CI: 1.46–10.78, P &lt; 0.001), metastasis (OR = 3.46, 95% CI: 1.33–9.01, P = 0.011), pathologic stage (OR = 1.56, 95% CI: 1.17–2.07, P = 0.002), Barcelona Clinic Liver Cancer stage (OR = 5.76, 95% CI: 2.17–15.28, P &lt; 0.001) and histologic grade (OR = 2.33, 95% CI: 1.12–487, P = 0.024). Through bioinformatics methods, we determined that enhancing the proliferative effect of PLK1 in HCC was associated with a series of hub genes and the activation of the cell cycle pathway. <b><i>Conclusions:</i></b> These findings substantiated that PLK1 may be an independent prognostic biomarker in HCC and may facilitate the development of targeted precision oncology.
DOI: 10.6084/m9.figshare.6383225.v1
title: Supplementary Material for: Comprehensive and Integrative Analysis Reveals the Diagnostic, Clinicopathological and Prognostic Significance of Polo-Like Kinase 1 in Hepatocellular Carcinoma

description: <b><i>Background/Aims:</i></b> Liver cancer has the second highest cancer-related death rate globally and has relatively few targeted therapeutics. Polo-like kinase 1 (PLK1) is a fascinating trigger of the cell cycle; however, the still-rudimentary understanding of PLK1 at present is a significant barrier to its clinical applications. Here, we comprehensively clarified the clinicopathological value and potential functions of PLK1 in hepatocellular carcinoma (HCC). <b><i>Methods:</i></b> HCC-related microarrays, RNA-sequencing datasets and published studies were deeply mined and integrated from The Cancer Genome Atlas, Gene Expression Omnibus, ArrayExpress, Oncomine, literature databases, and immunohistochemistry experiments. Meanwhile, the associations between PLK1 expression and its clinicopathological implications and prognostic value in HCC patients were assessed. The standardized mean difference, summary receiver operating characteristic curve and the corresponding area under the curve, hazard ratios, odds ratios (ORs), and their 95% confidence intervals (CIs) were examined by STATA 12.0. Additionally, several bioinformatics methods were used to identify the potential function of PLK1 in HCC. <b><i>Results:</i></b> Comprehensive analyses revealed that PLK1 was significantly increased in HCC (standardized mean difference = 1.34, 95% CI: 1.03–1.65, P &lt; 0.001). The results of diagnostic tests specified that in the summary receiver operating characteristic curve, the area under the curve was 0.88 (95% CI: 0.85–0.90). Furthermore, an elevated PLK1 level significantly predicted unfavorable overall survival (hazard ratio = 1.78, 95% CI: 1.10–2.88, P = 0.019) and was correlated with female gender (OR = 0.73, 95% CI: 0.56–0.95, P = 0.017), tumor thrombus (OR = 3.97, 95% CI: 1.46–10.78, P &lt; 0.001), metastasis (OR = 3.46, 95% CI: 1.33–9.01, P = 0.011), pathologic stage (OR = 1.56, 95% CI: 1.17–2.07, P = 0.002), Barcelona Clinic Liver Cancer stage (OR = 5.76, 95% CI: 2.17–15.28, P &lt; 0.001) and histologic grade (OR = 2.33, 95% CI: 1.12–487, P = 0.024). Through bioinformatics methods, we determined that enhancing the proliferative effect of PLK1 in HCC was associated with a series of hub genes and the activation of the cell cycle pathway. <b><i>Conclusions:</i></b> These findings substantiated that PLK1 may be an independent prognostic biomarker in HCC and may facilitate the development of targeted precision oncology.