cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5491804
title: Ecosystem service supply by European landscapes under alternative land-use and environmental policies

description: The European Union (EU) 2020 Biodiversity strategy aims at guaranteeing and enhancing the future supply of ecosystem services (‘ES’) in the member states. In an <i>ex-ante</i> assessment of plausible environmental policies, we projected the supply of 10 ES under 3 policy alternatives of land-use change (‘Nature Protection’, ‘Payment for carbon sequestration’ and ‘Payment for recreational services’) in the 27 EU member states (EU27). We assessed changes in supply of individual services across administrative units (at the NUTS-2 and EU27 levels) as well as bundles (at the EU27 level) between 2010 and 2040. Results show that the policy options only marginally affected ES bundles but several services could change substantially at the EU27 level (e.g. energy content from agricultural production and pollination). Wood supply, carbon sequestration and moderation of wind disturbance responded very differently across policy alternatives. At the NUTS-2 level, biocontrol of pests, carbon sequestration, moderation of wind disturbance and wood supply showed the most contrasted deviation from their regional supply in 2010. Finally, while payments for carbon sequestration benefited carbon sequestration as expected, specific payments for recreation services failed to promote them. Our analyses suggest that protecting nature appeared to be the best way of fostering ES supply within Europe.<b>EDITED BY</b> Rob Alkemade <b>EDITED BY</b> Rob Alkemade
DOI: 10.6084/m9.figshare.5491804.v1
title: Ecosystem service supply by European landscapes under alternative land-use and environmental policies

description: The European Union (EU) 2020 Biodiversity strategy aims at guaranteeing and enhancing the future supply of ecosystem services (‘ES’) in the member states. In an <i>ex-ante</i> assessment of plausible environmental policies, we projected the supply of 10 ES under 3 policy alternatives of land-use change (‘Nature Protection’, ‘Payment for carbon sequestration’ and ‘Payment for recreational services’) in the 27 EU member states (EU27). We assessed changes in supply of individual services across administrative units (at the NUTS-2 and EU27 levels) as well as bundles (at the EU27 level) between 2010 and 2040. Results show that the policy options only marginally affected ES bundles but several services could change substantially at the EU27 level (e.g. energy content from agricultural production and pollination). Wood supply, carbon sequestration and moderation of wind disturbance responded very differently across policy alternatives. At the NUTS-2 level, biocontrol of pests, carbon sequestration, moderation of wind disturbance and wood supply showed the most contrasted deviation from their regional supply in 2010. Finally, while payments for carbon sequestration benefited carbon sequestration as expected, specific payments for recreation services failed to promote them. Our analyses suggest that protecting nature appeared to be the best way of fostering ES supply within Europe.<b>EDITED BY</b> Rob Alkemade <b>EDITED BY</b> Rob Alkemade
DOI: 10.6084/m9.figshare.5491723
title: Effect of Adalimumab on Peripheral Blood Mononuclear Cells in Non-Infectious Uveitis

description: <i>Purpose:</i> This study analyzed the effect of adalimumab on peripheral blood mononuclear cells (PBMCs) in uveitis. <i>Methods:</i> PBMCs and serum S100A12 levels from 14 uveitis patients and 28 healthy controls were analyzed. Patient samples were taken before (w0), and 6 (w6) and 12 (w12) weeks after initiation of adalimumab therapy. <i>Results:</i> Monocytes expressing CD124, CD86, CD39, CD115, and MHCII were decreased in patients. Adalimumab induced CD86+ and CD39+ monocytes, and further decreased the frequency of MHCII- and CD124-positive cells. Patients (w0) had increased percentages of Th1-, Th17-, and Th2 cells and T cell subsets showed a pro-inflammatory polarization (<i>p</i> = 0.02 ratio Th17/Treg patients w0 vs controls), which was reduced upon adalimumab treatment (<i>p</i> = 0.05 w0 vs w6). S100A12 levels were increased in patients (<i>p</i> = 0.02) and reduced under treatment (<i>p</i> = 0.02 for w6/w12). <i>Conclusions:</i> The phenotype of PBMCs from uveitis patients is modified upon adalimumab treatment. Serum S100A12 levels reflect the systemic immune response.
DOI: 10.6084/m9.figshare.5491723.v1
title: Effect of Adalimumab on Peripheral Blood Mononuclear Cells in Non-Infectious Uveitis

description: <i>Purpose:</i> This study analyzed the effect of adalimumab on peripheral blood mononuclear cells (PBMCs) in uveitis. <i>Methods:</i> PBMCs and serum S100A12 levels from 14 uveitis patients and 28 healthy controls were analyzed. Patient samples were taken before (w0), and 6 (w6) and 12 (w12) weeks after initiation of adalimumab therapy. <i>Results:</i> Monocytes expressing CD124, CD86, CD39, CD115, and MHCII were decreased in patients. Adalimumab induced CD86+ and CD39+ monocytes, and further decreased the frequency of MHCII- and CD124-positive cells. Patients (w0) had increased percentages of Th1-, Th17-, and Th2 cells and T cell subsets showed a pro-inflammatory polarization (<i>p</i> = 0.02 ratio Th17/Treg patients w0 vs controls), which was reduced upon adalimumab treatment (<i>p</i> = 0.05 w0 vs w6). S100A12 levels were increased in patients (<i>p</i> = 0.02) and reduced under treatment (<i>p</i> = 0.02 for w6/w12). <i>Conclusions:</i> The phenotype of PBMCs from uveitis patients is modified upon adalimumab treatment. Serum S100A12 levels reflect the systemic immune response.
DOI: 10.6084/m9.figshare.5491675
title: Drivers of Change and Sustainability in Linked Social–Ecological Systems: An Analysis in the Volta River Basin of Ghana, West Africa

description: Understanding the nature and relative importance of various drivers of change is crucial for sustainable management of natural resources and in prioritizing management efforts, allocating limited resources, and understanding cumulative effects. For this article, we employed structured an expert judgments approach to identify, characterize, and assess the relative importance of the key biophysical and socioeconomic drivers of change within the Volta River Basin, West Africa. Precipitation variability, water availability, land use change, drought events, and population growth were perceived as most important, while biodiversity loss, social conflicts, pest and disease occurrence, urbanization, and pollution were viewed as less critical. A majority of these drivers were characterized as “slow” acting processes as compared to rapidly changing drivers. Intra- and interexpert groups agreement were found to be significant and convergent, indicating the reliability of the results. The implications of these results for sustainable water resources management and agricultural production are discussed.
DOI: 10.6084/m9.figshare.5491678
title: Dataset for: Clean pure shift 2D J-resolved spectroscopy

description: 2D J-resolved spectroscopy is one of the oldest and conceptually most elegant ways to separate homonuclear scalar couplings from chemical shift information. In practice, the classical experiment suffers from a number of complications that limits accuracy and resolution, including phasetwist lineshapes, strong coupling artifacts and the need for shearing the spectrum by 45° to obtain a (J,δ)-representation. Here, a novel pure shift 2DJ experiment based on the TSE-PSYCHE experiment is reported that deals with all these issues. Previous experiments proposed z-filtration to avoid excessive artifacts caused by chunked pure shift acquisition. It will be shown that these artifacts can also easily be avoided by means of the Pell-Keeler method. As opposed to its z-filtered counterparts, the new experiment provides pure shift 2DJ spectra that are free of artifacts from pulse imperfections and minimize responses related to strong coupling. In this way, multiplet analysis becomes possible at maximal resolution and a minimum of spectral complications.
DOI: 10.6084/m9.figshare.5491672
title: Dataset for: Time-to-event data with time-varying biomarkers measured only at study entry, with applications to Alzheimer’s disease

description: Relating time-varying biomarkers of Alzheimer’s disease (AD) to time-to-event using a Cox model is complicated by the fact that AD biomarkers are sparsely collected, typically only at study entry; this is problematic since Cox regression with time-varying covariates requires observation of the covariate process at all failure times. The analysis might be simplified by using study entry as the time origin and treating the time-varying covariate measured at study entry as a fixed baseline covariate. In this paper, we first derive conditions under which using an incorrect time origin of study entry results in consistent estimation of regression parameters when the time-varying covariate is continuous and fully observed. We then derive conditions under which treating the time-varying covariate as fixed at study entry results in consistent estimation. We provide methods for estimating the regression parameter when a functional form can be assumed for the time-varying biomarker, which is measured only at study entry. We demonstrate our analytical results in a simulation study and apply our methods to data from the Rush Religious Orders Study and Memory and Aging Project, and data from the Alzheimer’s Disease Neuroimaging Initiative.
DOI: 10.6084/m9.figshare.5491675.v1
title: Drivers of Change and Sustainability in Linked Social–Ecological Systems: An Analysis in the Volta River Basin of Ghana, West Africa

description: Understanding the nature and relative importance of various drivers of change is crucial for sustainable management of natural resources and in prioritizing management efforts, allocating limited resources, and understanding cumulative effects. For this article, we employed structured an expert judgments approach to identify, characterize, and assess the relative importance of the key biophysical and socioeconomic drivers of change within the Volta River Basin, West Africa. Precipitation variability, water availability, land use change, drought events, and population growth were perceived as most important, while biodiversity loss, social conflicts, pest and disease occurrence, urbanization, and pollution were viewed as less critical. A majority of these drivers were characterized as “slow” acting processes as compared to rapidly changing drivers. Intra- and interexpert groups agreement were found to be significant and convergent, indicating the reliability of the results. The implications of these results for sustainable water resources management and agricultural production are discussed.
DOI: 10.6084/m9.figshare.5491648
title: Protein Sequence and Feature Data used to develop the ECemble enzyme classification methodology

description: This dataset relates to the development of ECemble, an approach to identifying enzymes and enzyme classes and study the human gut metabolic pathways, using an ensemble of machine-learning methods to accurately model and predict enzymes from protein sequences. ECemble has been used to predict entire complements of enzymes from ten sequenced proteomes including the human proteome, as well as predicting enzymes encoded by the human gut microbiome from gut metagenomic samples, and to study the role played by the microbe-derived enzymes in the human metabolism. This dataset includes enzyme and non-enzyme sequence data (FASTA format and Identifiers) and sequence features from Pfam, Prosite and Superfamily databases used to develop ECemble enzyme classification methodology. The files include: <b>Enzyme Data : </b>64,950 sequences (Fasta File | Sequence ID File) <b>Non-enzyme Data : </b>128,475 sequences (Fasta File | Sequence ID File) <b>All Data : </b>193,425 sequences (Fasta File | Sequence ID File) <b>List of Unique Features :</b> 14,241 featuresThese files are in .txt format and can be opened by any open source or standard word processing software.<br>
DOI: 10.6084/m9.figshare.5491672.v1
title: Dataset for: Time-to-event data with time-varying biomarkers measured only at study entry, with applications to Alzheimer’s disease

description: Relating time-varying biomarkers of Alzheimer’s disease (AD) to time-to-event using a Cox model is complicated by the fact that AD biomarkers are sparsely collected, typically only at study entry; this is problematic since Cox regression with time-varying covariates requires observation of the covariate process at all failure times. The analysis might be simplified by using study entry as the time origin and treating the time-varying covariate measured at study entry as a fixed baseline covariate. In this paper, we first derive conditions under which using an incorrect time origin of study entry results in consistent estimation of regression parameters when the time-varying covariate is continuous and fully observed. We then derive conditions under which treating the time-varying covariate as fixed at study entry results in consistent estimation. We provide methods for estimating the regression parameter when a functional form can be assumed for the time-varying biomarker, which is measured only at study entry. We demonstrate our analytical results in a simulation study and apply our methods to data from the Rush Religious Orders Study and Memory and Aging Project, and data from the Alzheimer’s Disease Neuroimaging Initiative.
DOI: 10.6084/m9.figshare.5491678.v1
title: Dataset for: Clean pure shift 2D J-resolved spectroscopy

description: 2D J-resolved spectroscopy is one of the oldest and conceptually most elegant ways to separate homonuclear scalar couplings from chemical shift information. In practice, the classical experiment suffers from a number of complications that limits accuracy and resolution, including phasetwist lineshapes, strong coupling artifacts and the need for shearing the spectrum by 45° to obtain a (J,δ)-representation. Here, a novel pure shift 2DJ experiment based on the TSE-PSYCHE experiment is reported that deals with all these issues. Previous experiments proposed z-filtration to avoid excessive artifacts caused by chunked pure shift acquisition. It will be shown that these artifacts can also easily be avoided by means of the Pell-Keeler method. As opposed to its z-filtered counterparts, the new experiment provides pure shift 2DJ spectra that are free of artifacts from pulse imperfections and minimize responses related to strong coupling. In this way, multiplet analysis becomes possible at maximal resolution and a minimum of spectral complications.
DOI: 10.6084/m9.figshare.5491621
title: textFile Hello.world!

description: Just a Hello World File<br>
DOI: 10.6084/m9.figshare.5491639
title: DNA-based identification of an echinoderm host for a deep-sea parasitic snail (Gastropoda: Eulimidae)

description: Eulimid gastropods (Caenogastropoda: Vanikoroidea) are exclusive parasites of echinoderms including all five classes of the phylum. However, many species have a long autonomous period and some tend to fall off the host during collection. This may result in a lack of host information for taxa, particularly those from the deep sea. The present study represents the first attempt to analyse the possible remains of host DNA in eulimid snails for a better understanding of their parasitic ecology. DNA extraction from the proboscis, polymerase chain reaction (PCR) with echinoderm-specific primers and sequencing of subclones successfully identified the ‘sea pig’, a holothurian of the genus <i>Scotoplanes</i> (Elasipodida: Elpidiidae) as the previously unknown host of <i>Crinolamia</i> sp. from bathyal depths off northern Japan. The morphological similarity between this eulimid and the type species of <i>Crinolamia</i> questions the alleged association of the latter with crinoids.
DOI: 10.6084/m9.figshare.5491648.v1
title: Protein Sequence and Feature Data used to develop the ECemble enzyme classification methodology

description: This dataset relates to the development of ECemble, an approach to identifying enzymes and enzyme classes and study the human gut metabolic pathways, using an ensemble of machine-learning methods to accurately model and predict enzymes from protein sequences. ECemble has been used to predict entire complements of enzymes from ten sequenced proteomes including the human proteome, as well as predicting enzymes encoded by the human gut microbiome from gut metagenomic samples, and to study the role played by the microbe-derived enzymes in the human metabolism. This dataset includes enzyme and non-enzyme sequence data (FASTA format and Identifiers) and sequence features from Pfam, Prosite and Superfamily databases used to develop ECemble enzyme classification methodology. The files include: <b>Enzyme Data : </b>64,950 sequences (Fasta File | Sequence ID File) <b>Non-enzyme Data : </b>128,475 sequences (Fasta File | Sequence ID File) <b>All Data : </b>193,425 sequences (Fasta File | Sequence ID File) <b>List of Unique Features :</b> 14,241 featuresThese files are in .txt format and can be opened by any open source or standard word processing software.<br>
DOI: 10.6084/m9.figshare.5491585
title: Supplemental Tables

description: All data in these tables were used to create the figures in the manuscript. Details on methodology can be found there.<br>
DOI: 10.6084/m9.figshare.5491591
title: Humidity-dependent mechanical properties, Raman

description: Mechanical measurements of stress and strain for specimens dried at 100torr, 200torr, wet, and Raman shift data.<br>Each folder comes with a metadata explanation / list file.
DOI: 10.6084/m9.figshare.5491585.v1
title: Supplemental Tables

description: All data in these tables were used to create the figures in the manuscript. Details on methodology can be found there.<br>
DOI: 10.6084/m9.figshare.5491621.v1
title: textFile Hello.world!

description: Just a Hello World File<br>
DOI: 10.6084/m9.figshare.5491639.v1
title: DNA-based identification of an echinoderm host for a deep-sea parasitic snail (Gastropoda: Eulimidae)

description: Eulimid gastropods (Caenogastropoda: Vanikoroidea) are exclusive parasites of echinoderms including all five classes of the phylum. However, many species have a long autonomous period and some tend to fall off the host during collection. This may result in a lack of host information for taxa, particularly those from the deep sea. The present study represents the first attempt to analyse the possible remains of host DNA in eulimid snails for a better understanding of their parasitic ecology. DNA extraction from the proboscis, polymerase chain reaction (PCR) with echinoderm-specific primers and sequencing of subclones successfully identified the ‘sea pig’, a holothurian of the genus <i>Scotoplanes</i> (Elasipodida: Elpidiidae) as the previously unknown host of <i>Crinolamia</i> sp. from bathyal depths off northern Japan. The morphological similarity between this eulimid and the type species of <i>Crinolamia</i> questions the alleged association of the latter with crinoids.
DOI: 10.6084/m9.figshare.5491582
title: Historical Schibler Map - 1909

description: This is a georeferenced historical forest cover map from 1909, cover the area of Davos, Switzerland. This was used to create the associated 1909 forest cover shapefile. Methods can be found in the associated manuscript.<br>
DOI: 10.6084/m9.figshare.5491591.v1
title: Humidity-dependent mechanical properties, Raman

description: Mechanical measurements of stress and strain for specimens dried at 100torr, 200torr, wet, and Raman shift data.<br>Each folder comes with a metadata explanation / list file.
DOI: 10.6084/m9.figshare.5491576
title: Forest Cover Shapefile - 1909

description: This shapefile represents the maximum extent of forest cover (all species) for the year 1909. Details on how this was created can be found in the associated manuscript.
DOI: 10.6084/m9.figshare.5491582.v1
title: Historical Schibler Map - 1909

description: This is a georeferenced historical forest cover map from 1909, cover the area of Davos, Switzerland. This was used to create the associated 1909 forest cover shapefile. Methods can be found in the associated manuscript.<br>
DOI: 10.6084/m9.figshare.5491576.v1
title: Forest Cover Shapefile - 1909

description: This shapefile represents the maximum extent of forest cover (all species) for the year 1909. Details on how this was created can be found in the associated manuscript.
DOI: 10.6084/m9.figshare.5491552
title: Διδακτικές Σημειώσεις Γραμμικής Άλγεβρας

description: Linear algebra
DOI: 10.6084/m9.figshare.5491519
title: Proa et al PeerJ Raw Data.zip

description: The form of the cranium can vary extensively among closely related species of papionins (Cercopithecidae, Primates), a fact that is often related to their adaptive differences to distinct diets. Yet, the form of the cranium can also vary greatly between males and females of the same species, even though both sexes tend to have the same diet. Here we use finite elements models and geometric morphometrics to test for differences in cranial biomechanical performance that could be attributed to differences in diet and feeding habits in male and female specimens of <i>Papio anubis</i> and <i>Theropithecus gelada</i>, two extant papionin species with known diets. It is expected that adaptation to that same diet must have occurred in both sexes, despite differences in form. Strain contour plots show that differences can be seen between male and female of each species, but differences between male and female <i>T. gelada </i>are much larger than those between male and female <i>P. anubis</i> for all bites. Nevertheless, larger differences in strain are seen between species, rather than between male and female of the same species. An analysis of deformations shows male and female of each species falling with each other, and away from the other species. <i>P. anubis</i> male and female deform almost identically, with the female deforming only slightly less than the male for all bites. Differences between male and female <i>T. gelada</i> are more marked, with the female deforming far less than the male particularly during incisor bites; the trajectory followed, though, is the same, with differences being mainly in magnitude of deformation. These results are an indicator that diet might have had a major adaptive effect on papionin cranial form, but they also indicate that papionin cranial form may be highly constrained by other non-masticatory functions. Also, these results highlight the difficulties in trying to interpret dietary ecology from modes and magnitudes of cranial deformation, which, being difficult in extant species with known diets and sexes, becomes extremely challenging when applied to extinct species.
DOI: 10.6084/m9.figshare.5491522
title: Forest Cover Shapefile - 2009

description: This shapefile represents the maximum extent of forest cover (all species) for the year 2009. Details on how this was created can be found in the associated manuscript.<br>
DOI: 10.6084/m9.figshare.5491492
title: Farmer and fisher entry decisions

description: Data to support statistical modeling of farmer and fisher entry and exit decisions in study communities of Nicaraguan Caribbean coast. The data file, fishprice.csv, was used to generate Fig. 5. The data file, roadexports.csv, was used to generate Fig. 6. The data file, foodoutlet.csv, was used to generate Fig. 7. All other data files were used to model farmer entry, farmer exit, fisher entry, and fisher exit decisions.