cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7039850
title: Deconstructing progression of amyotrophic lateral sclerosis in stages: a Markov modeling approach

description: <i>Objectives:</i> Propose an empirical amyotrophic lateral sclerosis (ALS) staging approach called Fine’til 9 (FT9) based on how many of the patient’s ALS functional rating scale (ALSFRS-R) subscores are 9 or less (of normal 12). Gain insights into progression of ALS by applying Markov models to ALS stages by multiple systems (King’s, Milan–Torino system (MITOS) and FT9). <i>Methods:</i> Patients from the Pooled Resource Open-Access ALS Clinical Trials (PRO-ACT) dataset were staged using ALSFRS-R responses. Risks of progression through stages and death were estimated, as were effects of prognostic variables on these risks. <i>Results:</i> A total of 29,947 time points in 3199 patients from the PRO-ACT dataset were assigned stages. Although the three systems were moderately correlated, MITOS stages were heavily skewed toward advanced disease, whereas King’s and FT9 stages were more balanced. Non-sequential progression was observed with King’s system. Markov models adequately described transitions from stage to stage in the first year of observation, but underestimated risks beyond that point. Regardless of staging method, initial rate of ALSFRS-R decline had a powerful effect on rate of progression through sequential stages, whereas age predominantly influenced stage-specific mortality. <i>Conclusion:</i> King’s and FT9 are more sensitive to observed progression of disease in clinical trials than MITOS. FT9 can partition the course similar to King’s, and may have advantages of sequential progression and easy applicability to retrospective data. Markov transition intensity estimates may be of value for counseling, health economic studies, and research design. In particular, this framework permits estimation of multidimensional effects of variables (including treatment) on outcome.
DOI: 10.6084/m9.figshare.7039850.v1
title: Deconstructing progression of amyotrophic lateral sclerosis in stages: a Markov modeling approach

description: <i>Objectives:</i> Propose an empirical amyotrophic lateral sclerosis (ALS) staging approach called Fine’til 9 (FT9) based on how many of the patient’s ALS functional rating scale (ALSFRS-R) subscores are 9 or less (of normal 12). Gain insights into progression of ALS by applying Markov models to ALS stages by multiple systems (King’s, Milan–Torino system (MITOS) and FT9). <i>Methods:</i> Patients from the Pooled Resource Open-Access ALS Clinical Trials (PRO-ACT) dataset were staged using ALSFRS-R responses. Risks of progression through stages and death were estimated, as were effects of prognostic variables on these risks. <i>Results:</i> A total of 29,947 time points in 3199 patients from the PRO-ACT dataset were assigned stages. Although the three systems were moderately correlated, MITOS stages were heavily skewed toward advanced disease, whereas King’s and FT9 stages were more balanced. Non-sequential progression was observed with King’s system. Markov models adequately described transitions from stage to stage in the first year of observation, but underestimated risks beyond that point. Regardless of staging method, initial rate of ALSFRS-R decline had a powerful effect on rate of progression through sequential stages, whereas age predominantly influenced stage-specific mortality. <i>Conclusion:</i> King’s and FT9 are more sensitive to observed progression of disease in clinical trials than MITOS. FT9 can partition the course similar to King’s, and may have advantages of sequential progression and easy applicability to retrospective data. Markov transition intensity estimates may be of value for counseling, health economic studies, and research design. In particular, this framework permits estimation of multidimensional effects of variables (including treatment) on outcome.
DOI: 10.6084/m9.figshare.7039799
title: Phylogenetic, functional and taxonomic richness have both positive and negative effects on ecosystem multifunctionality

description: Data from "Phylogenetic and functional attributes of subordinate species are key for the multifunctionality of terrestrial ecosystems"
DOI: 10.6084/m9.figshare.7039796
title: Crassigyrinus NMSG1984.15.3partB metatarsals TIFFs

description: see paper for details:Herbst, E., Hutchinson, J.R. 2018. New insights into the morphology of the Carboniferous tetrapod <i>Crassigyrinus scoticus </i>from computed tomography. Earth and Environmental Science Transactions of the Royal Society of Edinburgh, published online. https://doi.org/10.1017/S1755691018000804
DOI: 10.6084/m9.figshare.7039796.v2
title: Crassigyrinus NMSG1984.15.3partB metatarsals TIFFs

description: see paper for details:Herbst, E., Hutchinson, J.R. 2018. New insights into the morphology of the Carboniferous tetrapod <i>Crassigyrinus scoticus </i>from computed tomography. Earth and Environmental Science Transactions of the Royal Society of Edinburgh, published online. https://doi.org/10.1017/S1755691018000804
DOI: 10.6084/m9.figshare.7039775
title: Crassigyrinus NMSG1984.15.3partA metatarsals, neural arch TIFFs

description: see paper for details:Herbst, E., Hutchinson, J.R. 2018. New insights into the morphology of the Carboniferous tetrapod <i>Crassigyrinus scoticus </i>from computed tomography. Earth and Environmental Science Transactions of the Royal Society of Edinburgh, published online. https://doi.org/10.1017/S1755691018000804
DOI: 10.6084/m9.figshare.7039790
title: pmoA_mapping_Scotland_Appendix S1_NSIS_2_dataset

description: The present dataset is part of the supplementary section of a manuscript (Nazaries <i>et al.</i> 2018 – Environmental drivers of the geographical distribution of methanotrophs: insights from a national survey – manuscript accepted; in production by Soil Biology and Biochemistry) with the aim of mapping the geographical distribution of important methanotrophs (i.e. methane-oxidising bacteria) and their community structure.<br>The first tab (called "Information") of the spreadsheet provided here gives the details (metadata) of the variables available, namely: abbreviation, description (or full name), unit and eventual comments. The second tab (called "NSIS_2 dataset") contains the actual raw data values of this NSIS_2 dataset. It is the collection of 62 climo-edaphic properties and terrain attributes, with a total number of 697 soil samples. It was created for a national-wide soil survey in Scotland named the National Soils Inventory of Scotland re-sampling (NSIS_2). For more details, see link below for Lilly <i>et al.</i> 2010 (see link below).Soil sampling was executed by the James Hutton Institute (Aberdeen) between 2006 and 2009 following a 20-km<sup>2</sup> grid (for details, see Yao <i>et al.</i> 2013 – doi: 10.1111/1462-2920.12141).<br> pmoA genes of methanotrophs were isolated by PCR and enzyme restriction was performed using the T-RFLP method (Terminal-Restriction Length Polymorphism – see Singh <i>et al.</i> 2006 – doi:10.1128/AEM.00510-06). The pmoA terminal-restriction fragments (or T-RF) were retained to analyse the methanotroph community structure (122 T-RFs/OTU in total) and bio-geography (see Nazaries <i>et al.</i> 2018 – Environmental drivers of the geographical distribution of methanotrophs: insights from a national survey – manuscript accepted; in production by Soil Biology and Biochemistry). The present dataset corresponds to the Appendix S1 of the manuscript.. From this dataset, the three most abundant T-RFs (pmoA fragments 33 base-pair (bp) long, pmoA-81 and pmoA-130) were modeled to predict their geographical distribution across Scotland in relation to the common ecosystem habitats found across Scotland and their most important physico-chemical soil properties. In order to achieve this, a novel hybrid geo-statistical modelling approach was adopted as summarised in <b>Figure 1</b> of Nazaries <i>et al.</i> 2018 (Environmental drivers of the geographical distribution of methanotrophs: insights from a national survey – manuscript accepted; in production by Soil Biology and Biochemistry).
DOI: 10.6084/m9.figshare.7039796.v1
title: Crassigyrinus NMSG1984.15.3partB metatarsals TIFFs

description: see paper for details:Herbst, E., Hutchinson, J.R. 2018. New insights into the morphology of the Carboniferous tetrapod <i>Crassigyrinus scoticus </i>from computed tomography. Earth and Environmental Science Transactions of the Royal Society of Edinburgh, in press.
DOI: 10.6084/m9.figshare.7039772
title: Crassigyrinus NMSG1975.5.5 R Ischium, L ilum, non-Crassi interclavicle TIFFs

description: see paper for details:Herbst, E., Hutchinson, J.R. 2018. New insights into the morphology of the Carboniferous tetrapod <i>Crassigyrinus scoticus </i>from computed tomography. Earth and Environmental Science Transactions of the Royal Society of Edinburgh, published online. https://doi.org/10.1017/S1755691018000804
DOI: 10.6084/m9.figshare.7039790.v1
title: pmoA_mapping_Scotland_Appendix S1_NSIS_2_dataset

description: The present dataset is part of the supplementary section of a manuscript (Nazaries <i>et al.</i> 2018 – Environmental drivers of the geographical distribution of methanotrophs: insights from a national survey – manuscript accepted; in production by Soil Biology and Biochemistry) with the aim of mapping the geographical distribution of important methanotrophs (i.e. methane-oxidising bacteria) and their community structure.<br>The first tab (called "Information") of the spreadsheet provided here gives the details (metadata) of the variables available, namely: abbreviation, description (or full name), unit and eventual comments. The second tab (called "NSIS_2 dataset") contains the actual raw data values of this NSIS_2 dataset. It is the collection of 62 climo-edaphic properties and terrain attributes, with a total number of 697 soil samples. It was created for a national-wide soil survey in Scotland named the National Soils Inventory of Scotland re-sampling (NSIS_2). For more details, see link below for Lilly <i>et al.</i> 2010 (see link below).Soil sampling was executed by the James Hutton Institute (Aberdeen) between 2006 and 2009 following a 20-km<sup>2</sup> grid (for details, see Yao <i>et al.</i> 2013 – doi: 10.1111/1462-2920.12141).<br> pmoA genes of methanotrophs were isolated by PCR and enzyme restriction was performed using the T-RFLP method (Terminal-Restriction Length Polymorphism – see Singh <i>et al.</i> 2006 – doi:10.1128/AEM.00510-06). The pmoA terminal-restriction fragments (or T-RF) were retained to analyse the methanotroph community structure (122 T-RFs/OTU in total) and bio-geography (see Nazaries <i>et al.</i> 2018 – Environmental drivers of the geographical distribution of methanotrophs: insights from a national survey – manuscript accepted; in production by Soil Biology and Biochemistry). The present dataset corresponds to the Appendix S1 of the manuscript.. From this dataset, the three most abundant T-RFs (pmoA fragments 33 base-pair (bp) long, pmoA-81 and pmoA-130) were modeled to predict their geographical distribution across Scotland in relation to the common ecosystem habitats found across Scotland and their most important physico-chemical soil properties. In order to achieve this, a novel hybrid geo-statistical modelling approach was adopted as summarised in <b>Figure 1</b> of Nazaries <i>et al.</i> 2018 (Environmental drivers of the geographical distribution of methanotrophs: insights from a national survey – manuscript accepted; in production by Soil Biology and Biochemistry).
DOI: 10.6084/m9.figshare.7039775.v2
title: Crassigyrinus NMSG1984.15.3partA metatarsals, neural arch TIFFs

description: see paper for details:Herbst, E., Hutchinson, J.R. 2018. New insights into the morphology of the Carboniferous tetrapod <i>Crassigyrinus scoticus </i>from computed tomography. Earth and Environmental Science Transactions of the Royal Society of Edinburgh, published online. https://doi.org/10.1017/S1755691018000804
DOI: 10.6084/m9.figshare.7039772.v2
title: Crassigyrinus NMSG1975.5.5 R Ischium, L ilum, non-Crassi interclavicle TIFFs

description: see paper for details:Herbst, E., Hutchinson, J.R. 2018. New insights into the morphology of the Carboniferous tetrapod <i>Crassigyrinus scoticus </i>from computed tomography. Earth and Environmental Science Transactions of the Royal Society of Edinburgh, published online. https://doi.org/10.1017/S1755691018000804
DOI: 10.6084/m9.figshare.7039772.v1
title: Crassigyrinus NMSG1975.5.5 R Ischium, L ilum, non-Crassi interclavicle TIFFs

description: see paper for details:Herbst, E., Hutchinson, J.R. 2018. New insights into the morphology of the Carboniferous tetrapod <i>Crassigyrinus scoticus </i>from computed tomography. Earth and Environmental Science Transactions of the Royal Society of Edinburgh, in press.
DOI: 10.6084/m9.figshare.7039775.v1
title: Crassigyrinus NMSG1984.15.3partA metatarsals, neural arch TIFFs

description: see paper for details:Herbst, E., Hutchinson, J.R. 2018. New insights into the morphology of the Carboniferous tetrapod <i>Crassigyrinus scoticus </i>from computed tomography. Earth and Environmental Science Transactions of the Royal Society of Edinburgh, in press.
DOI: 10.6084/m9.figshare.7039760
title: Crassigyrinus NHMUKVPR10000 slab midthoracic TIFFs

description: see paper for details:Herbst, E., Hutchinson, J.R. 2018. New insights into the morphology of the Carboniferous tetrapod <i>Crassigyrinus scoticus </i>from computed tomography. Earth and Environmental Science Transactions of the Royal Society of Edinburgh, published online. https://doi.org/10.1017/S1755691018000804
DOI: 10.6084/m9.figshare.7039745
title: Crassigyrinus NHMUKVPR10000 'immediately presacral rib', centra TIFFs

description: see paper for details:Herbst, E., Hutchinson, J.R. 2018. New insights into the morphology of the Carboniferous tetrapod <i>Crassigyrinus scoticus </i>from computed tomography. Earth and Environmental Science Transactions of the Royal Society of Edinburgh, published online. https://doi.org/10.1017/S1755691018000804
DOI: 10.6084/m9.figshare.7039760.v2
title: Crassigyrinus NHMUKVPR10000 slab midthoracic TIFFs

description: see paper for details:Herbst, E., Hutchinson, J.R. 2018. New insights into the morphology of the Carboniferous tetrapod <i>Crassigyrinus scoticus </i>from computed tomography. Earth and Environmental Science Transactions of the Royal Society of Edinburgh, published online. https://doi.org/10.1017/S1755691018000804
DOI: 10.6084/m9.figshare.7039760.v1
title: Crassigyrinus NHMUKVPR10000 slab midthoracic TIFFs

description: see paper for details:Herbst, E., Hutchinson, J.R. 2018. New insights into the morphology of the Carboniferous tetrapod <i>Crassigyrinus scoticus </i>from computed tomography. Earth and Environmental Science Transactions of the Royal Society of Edinburgh, in press.
DOI: 10.6084/m9.figshare.7039745.v1
title: Crassigyrinus NHMUKVPR10000 'immediately presacral rib', centra TIFFs

description: see paper for details:Herbst, E., Hutchinson, J.R. 2018. New insights into the morphology of the Carboniferous tetrapod <i>Crassigyrinus scoticus </i>from computed tomography. Earth and Environmental Science Transactions of the Royal Society of Edinburgh, in press.
DOI: 10.6084/m9.figshare.7039745.v2
title: Crassigyrinus NHMUKVPR10000 'immediately presacral rib', centra TIFFs

description: see paper for details:Herbst, E., Hutchinson, J.R. 2018. New insights into the morphology of the Carboniferous tetrapod <i>Crassigyrinus scoticus </i>from computed tomography. Earth and Environmental Science Transactions of the Royal Society of Edinburgh, published online. https://doi.org/10.1017/S1755691018000804
DOI: 10.6084/m9.figshare.7039733
title: Crassigyrinus NHMUKVPR10000 cervical slab piece TIFFs

description: see paper for details:Herbst, E., Hutchinson, J.R. 2018. New insights into the morphology of the Carboniferous tetrapod <i>Crassigyrinus scoticus </i>from computed tomography. Earth and Environmental Science Transactions of the Royal Society of Edinburgh, published online. https://doi.org/10.1017/S1755691018000804 <br>
DOI: 10.6084/m9.figshare.7039733.v2
title: Crassigyrinus NHMUKVPR10000 cervical slab piece TIFFs

description: see paper for details:Herbst, E., Hutchinson, J.R. 2018. New insights into the morphology of the Carboniferous tetrapod <i>Crassigyrinus scoticus </i>from computed tomography. Earth and Environmental Science Transactions of the Royal Society of Edinburgh, published online. https://doi.org/10.1017/S1755691018000804 <br>
DOI: 10.6084/m9.figshare.7039733.v1
title: Crassigyrinus NHMUKVPR10000 cervical slab piece TIFFs

description: see paper for details:Herbst, E., Hutchinson, J.R. 2018. New insights into the morphology of the Carboniferous tetrapod <i>Crassigyrinus scoticus </i>from computed tomography. Earth and Environmental Science Transactions of the Royal Society of Edinburgh, in press.<br>
DOI: 10.6084/m9.figshare.7039697
title: Supplementary Material for: Intradialytic Activities and Health-Related Quality of Life Among Hemodialysis Patients

description: <b><i>Background:</i></b> Health-related quality of life (HRQOL) reflects a patient’s perceived disease burden, treatment effectiveness, and health status. Given the time burden and physiologic effects of hemodialysis, patients who spend dialysis time (9–15 h/week) physically or intellectually engaged may have better HRQOL. We characterized the intradialytic activities and explored their association with HRQOL. <b><i>Methods:</i></b> In a cross-sectional study of 431 hemodialysis patients, we ascertained kidney-disease-specific quality of life, measured frailty, and surveyed participants about their usual active intradialytic activities (reading, playing games, doing puzzles, chatting, or other) and passive intradialytic activities (watching TV or sleeping). We used adjusted ordered logistic regression to identify correlates of the activity index (the sum of active intradialytic activities) and adjusted linear regression to quantify the association between the activity index and physical-, mental-, and kidney-disease-specific HRQOL. <b><i>Results:</i></b> The 2 most common intradialytic activities were passive activities (watching TV = 87.9%; sleeping = 72.4%). Participants who were female (aOR 1.85, 95% CI 1.28–2.66; <i>p</i> = 0.001), nonfrail (aOR 1.70, 95% CI 1.06–2.70; <i>p </i>= 0.03), and nonsmokers (aOR 2.61, 95% CI 1.39–4.90; <i>p</i> = 0.003) had a higher intradialytic activity index after adjustment. Higher intradialytic activity index was associated with better mental- (0.83 points, 95% CI 0.04–1.62; <i>p</i> = 0.04) and kidney-disease-specific HRQOL (1.70 points, 95% CI 0.47–2.93; <i>p</i> = 0.007), but not physical HRQOL. <b><i>Conclusions:</i></b> Hemodialysis patients with more active intradialytic activities report better mental and kidney-disease-specific HRQOL. These results should be confirmed in a prospective study with a broader cohort of hemodialysis patients. Dialysis providers may consider offering patients with low levels of activity additional support and opportunities to engage in beneficial intradialytic activities.
DOI: 10.6084/m9.figshare.7039697.v1
title: Supplementary Material for: Intradialytic Activities and Health-Related Quality of Life Among Hemodialysis Patients

description: <b><i>Background:</i></b> Health-related quality of life (HRQOL) reflects a patient’s perceived disease burden, treatment effectiveness, and health status. Given the time burden and physiologic effects of hemodialysis, patients who spend dialysis time (9–15 h/week) physically or intellectually engaged may have better HRQOL. We characterized the intradialytic activities and explored their association with HRQOL. <b><i>Methods:</i></b> In a cross-sectional study of 431 hemodialysis patients, we ascertained kidney-disease-specific quality of life, measured frailty, and surveyed participants about their usual active intradialytic activities (reading, playing games, doing puzzles, chatting, or other) and passive intradialytic activities (watching TV or sleeping). We used adjusted ordered logistic regression to identify correlates of the activity index (the sum of active intradialytic activities) and adjusted linear regression to quantify the association between the activity index and physical-, mental-, and kidney-disease-specific HRQOL. <b><i>Results:</i></b> The 2 most common intradialytic activities were passive activities (watching TV = 87.9%; sleeping = 72.4%). Participants who were female (aOR 1.85, 95% CI 1.28–2.66; <i>p</i> = 0.001), nonfrail (aOR 1.70, 95% CI 1.06–2.70; <i>p </i>= 0.03), and nonsmokers (aOR 2.61, 95% CI 1.39–4.90; <i>p</i> = 0.003) had a higher intradialytic activity index after adjustment. Higher intradialytic activity index was associated with better mental- (0.83 points, 95% CI 0.04–1.62; <i>p</i> = 0.04) and kidney-disease-specific HRQOL (1.70 points, 95% CI 0.47–2.93; <i>p</i> = 0.007), but not physical HRQOL. <b><i>Conclusions:</i></b> Hemodialysis patients with more active intradialytic activities report better mental and kidney-disease-specific HRQOL. These results should be confirmed in a prospective study with a broader cohort of hemodialysis patients. Dialysis providers may consider offering patients with low levels of activity additional support and opportunities to engage in beneficial intradialytic activities.
DOI: 10.6084/m9.figshare.7039688
title: models for verification

description: The three models can be opened by finite element software MSC.Patran & Nastran.
DOI: 10.5281/zenodo.4005595
title: Vegetation plots of Tuscan Archipelago

description: This dataset contains 1561 vegetational plots (relevé) from the Tuscan Archipelago (Italy), which were analysed in Chiarucci et al. Journal of Vegetation Science. Each plot corresponds to a row and contains the list of species (1 for presence and 0 for absence), the island where it was collected, an EUNIS code describing the habitat and other descriptors such as the coordinates of the plot, the elevation, the substrate, etc. Beware that only the species list, the island and habitat identities are available for all the plots, whereas the other descriptors are present only in the cases the original sources provided the data or in the cases we successfully extracted from other sources.
DOI: 10.5281/zenodo.4005594
title: Vegetation plots of Tuscan Archipelago

description: This dataset contains 1561 vegetational plots (relevé) from the Tuscan Archipelago (Italy), which were analysed in Chiarucci et al. Journal of Vegetation Science. Each plot corresponds to a row and contains the list of species (1 for presence and 0 for absence), the island where it was collected, an EUNIS code describing the habitat and other descriptors such as the coordinates of the plot, the elevation, the substrate, etc. Beware that only the species list, the island and habitat identities are available for all the plots, whereas the other descriptors are present only in the cases the original sources provided the data or in the cases we successfully extracted from other sources.