cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5850051.v1
title: Relationship between disease activity and patient-reported outcomes in rheumatoid arthritis: <i>Post hoc</i> analyses of overall and Japanese results from two phase 3 clinical trials

description: <b>Objective:</b> To examine patient-reported outcomes (PROs) in patients with different rheumatoid arthritis (RA) disease activity levels and identify residual symptoms. <b>Methods:</b><i>Post hoc</i> analyses of overall and Japanese data from two randomized controlled trials including RA patients with previous inadequate responses to methotrexate (NCT01710358) or no/minimal previous disease-modifying antirheumatic drug treatment (NCT01711359) (sponsor: Eli Lilly and Company). Week 24 assessments were disease activity (Simplified Disease Activity Index, Disease Activity Score/Disease Activity Score 28 joints-erythrocyte sedimentation rate) and PROs (pain visual analog scale [VAS], morning joint stiffness [MJS], Health Assessment Questionnaire-Disability Index, Functional Assessment of Chronic Illness Therapy-Fatigue, and Medical Outcomes Study Short Form 36 Health Survey Physical and Mental Component Scores). <b>Results:</b> Patients achieving remission/low disease activity (LDA) at Week 24 had larger/significant improvements from baseline in pain, MJS, disability, fatigue, and physical and emotional quality of life versus patients with high/moderate disease activity. Some patients achieving remission and LDA, reported residual pain (pain VAS &gt;10 mm): 20.8–39.3% and 48.7–70.0% (overall study populations), 16.0–34.5% and 47.1–62.0% (Japanese patients). Residual MJS and fatigue were also reported. <b>Conclusion:</b> Remission/LDA were associated with improvements in PROs in overall and Japanese patient populations; however, some patients achieving remission had residual symptoms, including pain.
DOI: 10.6084/m9.figshare.5850042
title: Biomarkers in Recurrent Grade III Glioma Patients Treated with Bevacizumab and Irinotecan

description: Predictive biomarkers and prognostic models are required to identify recurrent grade III glioma patients who benefit from existing treatment. In this study of 62 recurrent grade III glioma patients, a range of clinical and paraclinical factors are tested for association with progression-free survival, overall survival, and response to bevacizumab and irinotecan therapy. Significant factors from univariate screening are included in multivariate analysis. Biomarkers previously advanced as predictive or prognostic in the first-line setting did not affect outcome in this patient cohort. Based on the optimized model for overall survival, comprising performance status and p53 expression, a prognostic index is established.
DOI: 10.6084/m9.figshare.5850042.v1
title: Biomarkers in Recurrent Grade III Glioma Patients Treated with Bevacizumab and Irinotecan

description: Predictive biomarkers and prognostic models are required to identify recurrent grade III glioma patients who benefit from existing treatment. In this study of 62 recurrent grade III glioma patients, a range of clinical and paraclinical factors are tested for association with progression-free survival, overall survival, and response to bevacizumab and irinotecan therapy. Significant factors from univariate screening are included in multivariate analysis. Biomarkers previously advanced as predictive or prognostic in the first-line setting did not affect outcome in this patient cohort. Based on the optimized model for overall survival, comprising performance status and p53 expression, a prognostic index is established.
DOI: 10.6084/m9.figshare.5850018
title: Full-Pulse Tomographic Reconstruction with Deep Neural Networks

description: Plasma tomography consists of reconstructing a two-dimensional radiation profile of a poloidal cross section of a fusion device based on line-integrated measurements along several lines of sight. The reconstruction process is computationally intensive, and in practice, only a few reconstructions are usually computed per pulse. In this work, we trained a deep neural network based on a large collection of sample tomograms that have been produced at JET over several years. Once trained, the network is able to reproduce those results with high accuracy. More importantly, it can compute all the tomographic reconstructions for a given pulse in just a few seconds. This makes it possible to visualize several phenomena—such as plasma heating, disruptions, and impurity transport—over the course of the entire pulse.
DOI: 10.6084/m9.figshare.5850018.v2
title: Full-Pulse Tomographic Reconstruction with Deep Neural Networks

description: Plasma tomography consists of reconstructing a two-dimensional radiation profile of a poloidal cross section of a fusion device based on line-integrated measurements along several lines of sight. The reconstruction process is computationally intensive, and in practice, only a few reconstructions are usually computed per pulse. In this work, we trained a deep neural network based on a large collection of sample tomograms that have been produced at JET over several years. Once trained, the network is able to reproduce those results with high accuracy. More importantly, it can compute all the tomographic reconstructions for a given pulse in just a few seconds. This makes it possible to visualize several phenomena—such as plasma heating, disruptions, and impurity transport—over the course of the entire pulse.
DOI: 10.6084/m9.figshare.5849991
title: Supporting information for "Modeling Palladium Surfaces with Density Functional Theory, Neural Networks and Molecular Dynamics"

description: This data set can be used to reproduce most of the figures and analysis in our paper "Modeling Palladium Surfaces with Density Functional Theory, Neural Networks and Molecular Dynamics". The details for how to use this dataset are in the supporting information file for that paper.<br>Note, the original data was posted here: <br>https://figshare.com/articles/Data_zip/4347956/1<br><br>This dataset supercedes that one.
DOI: 10.6084/m9.figshare.5849991.v1
title: Supporting information for "Modeling Palladium Surfaces with Density Functional Theory, Neural Networks and Molecular Dynamics"

description: This data set can be used to reproduce most of the figures and analysis in our paper "Modeling Palladium Surfaces with Density Functional Theory, Neural Networks and Molecular Dynamics". The details for how to use this dataset are in the supporting information file for that paper.<br>Note, the original data was posted here: <br>https://figshare.com/articles/Data_zip/4347956/1<br><br>This dataset supercedes that one.
DOI: 10.6084/m9.figshare.5849976
title: Supplimentary data.xlsx

description: In this study, a predictive model based GPR will be developed and evaluated on the basis of its ability to accurately estimate the influence of six physical parameters on D<sub>eff</sub>.
DOI: 10.6084/m9.figshare.5849976.v2
title: Supplimentary data.xlsx

description: In this study, a predictive model based GPR will be developed and evaluated on the basis of its ability to accurately estimate the influence of six physical parameters on D<sub>eff</sub>.
DOI: 10.6084/m9.figshare.5849976.v1
title: Supplimentary data.xlsx

description: In this study, a predictive model based GPR will be developed and evaluated on the basis of its ability to accurately estimate the influence of six physical parameters on D<sub>eff</sub>.
DOI: 10.6084/m9.figshare.5849964
title: bioRxiv vs arXiv unique content uploads

description: This Excel spreadsheet (.xlsx format) compares the first 51 months of unique uploads to both the bioRxiv and arXiv prepress servers.<br>The arXiv preprint server received approximately 30,000 unique papers over the 51 month period compared with approximately 20,000 papers on bioRxiv.
DOI: 10.6084/m9.figshare.5849964.v2
title: bioRxiv vs arXiv unique content uploads

description: This Excel spreadsheet (.xlsx format) compares the first 51 months of unique uploads to both the bioRxiv and arXiv prepress servers.<br>The arXiv preprint server received approximately 30,000 unique papers over the 51 month period compared with approximately 20,000 papers on bioRxiv.
DOI: 10.6084/m9.figshare.5849964.v1
title: bioRxiv vs arXiv unique content uploads

description: This Excel spreadsheet (.xlsx format) compares the first 51 months of uploads to both the bioXriv and arXiv prepress servers.
DOI: 10.6084/m9.figshare.5849916
title: Crossref Citation Links - January 2018

description: An effort by eLife Sciences to make citation data more accessible.http://elifesciences.org/<br>The citation links are an extract of the Crossref bulk dump (January 2018) that is available here: https://figshare.com/account/articles/5845554<br>The source code that produced the file can be found here:https://github.com/elifesciences/datacapsule-crossref
DOI: 10.6084/m9.figshare.5849901
title: Dataset for: Expression of Striated Activator of Rho-Signaling (STARS) in human skeletal muscle following acute exercise and long-term training

description: Aim: The Striated Activator of Rho-Signaling (STARS) protein acts as a link between external stimuli and exercise adaptation such as muscle hypertrophy. However, the acute and long-term adaptational response of STARS is still unclear. This study aimed at investigating the acute and long-term endurance training response on the mRNA and protein expression of STARS and its related upstream and downstream factors in human skeletal muscle. Methods: mRNA and protein levels of STARS and related factors were assessed in skeletal muscle of healthy young men and women following an acute bout of endurance exercise (n=20) or 12 weeks of one-legged training (n=23). Muscle biopsies were obtained before (acute and long-term), at 30 min, 2h and 6h following acute exercise, and at 24 hrs following both acute exercise and long-term training. Results: Following acute exercise, STARS mRNA was significantly elevated 3.9-fold at 30 minutes returning back to baseline 24 hours after exercise. STARS protein levels were were numerically but non-significantly increased 7.2-fold at 24 hours. No changes of STARS or ERRα mRNA or STARS protein expression were seen following long-term training. PGC-1α mRNA increased 1.7-fold following long-term training. MRTF-A mRNA was increased both following acute exercise and long-term training, in contrast to SRF mRNA and protein which did not change. Conclusion: STARS mRNA is acutely upregulated with exercise, but there is no cumulative effect to long-term training as seen in PGC-1α mRNA expression. Exercise intensity might play a role in manifestation of protein expression, suggesting a more complex regulation of STARS.
DOI: 10.6084/m9.figshare.5849901.v1
title: Dataset for: Expression of Striated Activator of Rho-Signaling (STARS) in human skeletal muscle following acute exercise and long-term training

description: Aim: The Striated Activator of Rho-Signaling (STARS) protein acts as a link between external stimuli and exercise adaptation such as muscle hypertrophy. However, the acute and long-term adaptational response of STARS is still unclear. This study aimed at investigating the acute and long-term endurance training response on the mRNA and protein expression of STARS and its related upstream and downstream factors in human skeletal muscle. Methods: mRNA and protein levels of STARS and related factors were assessed in skeletal muscle of healthy young men and women following an acute bout of endurance exercise (n=20) or 12 weeks of one-legged training (n=23). Muscle biopsies were obtained before (acute and long-term), at 30 min, 2h and 6h following acute exercise, and at 24 hrs following both acute exercise and long-term training. Results: Following acute exercise, STARS mRNA was significantly elevated 3.9-fold at 30 minutes returning back to baseline 24 hours after exercise. STARS protein levels were were numerically but non-significantly increased 7.2-fold at 24 hours. No changes of STARS or ERRα mRNA or STARS protein expression were seen following long-term training. PGC-1α mRNA increased 1.7-fold following long-term training. MRTF-A mRNA was increased both following acute exercise and long-term training, in contrast to SRF mRNA and protein which did not change. Conclusion: STARS mRNA is acutely upregulated with exercise, but there is no cumulative effect to long-term training as seen in PGC-1α mRNA expression. Exercise intensity might play a role in manifestation of protein expression, suggesting a more complex regulation of STARS.
DOI: 10.6084/m9.figshare.5849766
title: Experimental plant community_biomass_evenness.xlsx

description: The data file contains the plant biomass data from the mesocosm experiment. The data file consists of 3 sheets. Sheet 1 contains the metadata explaining the column headings in sheet 2 and 3. Sheet 2 contains the biomass data of the six plant species per mesocosm (identified by pot code). Each mesocosm was fertilized with dung from 1 of 5 different herbivore species in either a low or high amount. Sheet 3 contains the total biomass of the experimental plant community, so the sum of biomass from all plant species per mesocosm. It also contains the evenness of the experimental plant community based on Pielou's evenness index (see methods section in paper for more details).
DOI: 10.6084/m9.figshare.5849766.v2
title: Experimental plant community_biomass_evenness.xlsx

description: The data file contains the plant biomass data from the mesocosm experiment. The data file consists of 3 sheets. Sheet 1 contains the metadata explaining the column headings in sheet 2 and 3. Sheet 2 contains the biomass data of the six plant species per mesocosm (identified by pot code). Each mesocosm was fertilized with dung from 1 of 5 different herbivore species in either a low or high amount. Sheet 3 contains the total biomass of the experimental plant community, so the sum of biomass from all plant species per mesocosm. It also contains the evenness of the experimental plant community based on Pielou's evenness index (see methods section in paper for more details).
DOI: 10.6084/m9.figshare.5849766.v1
title: Experimental plant community_biomass_evenness.xlsx

description: The data file contains the plant biomass data from the mesocosm experiment. The data file consists of 3 sheets. Sheet 1 contains the metadata explaining the column headings in sheet 2 and 3. Sheet 2 contains the biomass data of the six plant species per mesocosm (identified by pot code). Each mesocosm was fertilized with dung from 1 of 5 different herbivore species in either a low or high amount. Sheet 3 contains the total biomass of the experimental plant community, so the sum of biomass from all plant species per mesocosm. It also contains the evenness of the experimental plant community based on Pielou's evenness index (see methods section in paper for more details).
DOI: 10.6084/m9.figshare.5849763
title: Herbivore dung_CNP.xlsx

description: The data file contains the carbon, nitrogen and phosphorus concentration of herbivore dung collected in the study. The data file consists of 2 sheets. Sheet 1 is the metadata explaining the column headings in sheet 2. Sheet 2 contains the dung nutrient data of the herbivore species collected in three different areas during two seasons.
DOI: 10.6084/m9.figshare.5849763.v2
title: Herbivore dung_CNP.xlsx

description: The data file contains the carbon, nitrogen and phosphorus concentration of herbivore dung collected in the study. The data file consists of 2 sheets. Sheet 1 is the metadata explaining the column headings in sheet 2. Sheet 2 contains the dung nutrient data of the herbivore species collected in three different areas during two seasons.
DOI: 10.6084/m9.figshare.5849763.v1
title: Herbivore dung_CNP.xlsx

description: The data file contains the carbon, nitrogen and phosphorus concentration of herbivore dung collected in the study. The data file consists of 2 sheets. Sheet 1 is the metadata explaining the column headings in sheet 2. Sheet 2 contains the dung nutrient data of the herbivore species collected in three different areas during two seasons.
DOI: 10.6084/m9.figshare.5849724
title: Material and outcomes of the OSCAR user testing session

description: This fileset contains all the material and the outcomes of a user testing session we run for testing the usability of OSCAR, the OpenCitations RDF Search Application, available at https://github.com/ivanhb/OSCAR.<br>
DOI: 10.6084/m9.figshare.5849694
title: Emotions, trust, and motivation in ICT mediated work

description: This dataset contains data from three experiments (results of two questionnaires and one game - trust game). The aim of the study was to investigate the changes that the employment of ICT mediated collaboration induces in team members in comparison to face-to-face collaboration. Our results reveal that online collaboration results in a decrease of positive emotions, motivation, and trust.
DOI: 10.6084/m9.figshare.5849694.v1
title: Emotions, trust, and motivation in ICT mediated work

description: This dataset contains data from three experiments (results of two questionnaires and one game - trust game). The aim of the study was to investigate the changes that the employment of ICT mediated collaboration induces in team members in comparison to face-to-face collaboration. Our results reveal that online collaboration results in a decrease of positive emotions, motivation, and trust.
DOI: 10.6084/m9.figshare.5849634.v2
title: Integrating Ecopath with Ecosim into the MSP software - conceptual design

description: Ecopath International Initiative Research Organization (EII) has been commissioned to conceptualize the integration of the Ecopath with Ecosim (EwE) food web modelling approach into the Marine Spatial Planning (MSP) Challenge 2050 software.<br><br>The MSP Challenge 2050 serious game is an immersive, three-dimensional software system that educates stakeholders, planners and the general public about trade-offs and environmental consequences of planning decisions in the marine and coastal ecosystem over space and time (Stolte et al., 2013). The ecology component in the MSP software is a simplification of a EwE model of the North Sea based on Mackinson and Daskalov (2007). This food web model was recently reviewed and was deemed unsuitable to deliver useful ecological predictions, even for game purposes<br>(Steenbeek, 2015). Rather than fixing identified shortcomings in the MSP software, it has been decided to replace the MSP ecology calculations with a direct link to EwE.<br><br>This document provides the conceptual design of this linkage from the EwE point of view. A brief overview of EwE and its internal structure is given. Capabilities of EwE to<br>incorporate MSP player input into its food web dynamics, and the mechanisms to provide game feedback back to MSP, are identified. The essential data flow to and from EwE is explained, and a conceptual communication protocol between MSP and EwE is provided <br>
DOI: 10.6084/m9.figshare.5849634.v3
title: Integrating Ecopath with Ecosim into the MSP software - conceptual design

description: Ecopath International Initiative Research Organization (EII) has been commissioned to conceptualize the integration of the Ecopath with Ecosim (EwE) food web modelling approach into the Marine Spatial Planning (MSP) Challenge 2050 software.<br><br>The MSP Challenge 2050 serious game is an immersive, three-dimensional software system that educates stakeholders, planners and the general public about trade-offs and environmental consequences of planning decisions in the marine and coastal ecosystem over space and time (Stolte et al., 2013). The ecology component in the MSP software is a simplification of a EwE model of the North Sea based on Mackinson and Daskalov (2007). This food web model was recently reviewed and was deemed unsuitable to deliver useful ecological predictions, even for game purposes<br>(Steenbeek, 2015). Rather than fixing identified shortcomings in the MSP software, it has been decided to replace the MSP ecology calculations with a direct link to EwE.<br><br>This document provides the conceptual design of this linkage from the EwE point of view. A brief overview of EwE and its internal structure is given. Capabilities of EwE to<br>incorporate MSP player input into its food web dynamics, and the mechanisms to provide game feedback back to MSP, are identified. The essential data flow to and from EwE is explained, and a conceptual communication protocol between MSP and EwE is provided <br>
DOI: 10.6084/m9.figshare.5849547
title: Supplementary Material for: Sex Differences in the Impact of <b><i>BDNF</i></b> Genotype on the Longitudinal Relationship between Physical Activity and Cognitive Performance

description: <b><i>Background:</i></b> Physical activity may preserve cognitive function in older adults, but benefits vary by sex and genetic factors. <b><i>Objective:</i></b> We tested the longitudinal association between physical activity and cognitive performance to de termine whether a common genetic polymorphism for brain-derived neurotrophic factor <i>(BDNF</i> Val66Met<i>)</i> moderated this effect. <b><i>Methods:</i></b> In a 12-year longitudinal population-based sample of older adults (<i>n</i> = 2,218), we used growth curve modeling to investigate whether the benefits of physical activity on cognitive preservation differed by <i>BDNF</i> genotype and sex across multiple cognitive domains including processing speed, attention, working memory, and episodic verbal memory. <b><i>Results:</i></b> The relationship between physical activity and cognitive performance was dependent on <i>BDNF</i> carrier status in males (Δχ<sup>2</sup> [Δdf] = 12.94 [4], <i>p</i> = 0.01), but not in females (Δχ<sup>2</sup> [Δdf] = 4.38 [4], <i>p</i> = 0.36). Cognition benefited from physical activity in male <i>BDNF</i> <i>met</i> noncarriers, but not <i>met</i> carriers, whereas cognition was not statistically significantly related to physical activity in females regardless of genotype. <b><i>Conclusion:</i></b> We observed longitudinal, but not cross-sectional, effects of physical activity on cognitive performance. Our study highlights the importance of longitudinal follow-up and consideration of sex differences in the relationships between physical activity, <i>BDNF</i> genotype, and cognitive decline. The findings contribute to understanding gene-lifestyle interactions in promoting cognitive health.