cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12048729.v1
title: DECM Machine Ready Corpus

description: <i>The DECM Corpus </i>is a digital corpus of the texts of <i>Relaciones Geográficas</i> <i>de Nueva España </i>(the Geographic Reports of New Spain) with different versions, including a machine ready version, a gold standard annotated dataset and an automatically annotated version ready for text mining and machine learning experiments.This is the DECM Machine Ready Corpus. This version includes text only files (.txt) containing each of the 10 volumes originally edited by Rene Acuña, the 2 volumes edited by Mercedes de la Garza, the <i>Suma de Visita</i> edited by Del Paso y Troncoso, a file with the original text of the Crown mandate (<i>Instrucción</i>), and metadata for this collection. This version contains only the original text of each of the RGs as transcribed by the scholars, excluding any editorial note, commentary, or historical work. This can be therefore used directly for corpus linguistics analyses, visualisations, etc.
DOI: 10.6084/m9.figshare.12048624
title: Research Data EGILMEZ_KOCA.docx.docx

description: The data collected via Qualitative data interview. Quantitative data, with consensus and filling the semantic scale form to see the alternatives to each other. Instruments: M-MACBETH program. The participants were gathered together to reach a consensus on 4 main criteria, with 11 alternatives formed as a result of the qualitative phase. They were asked to assign to evaluate the comparison of alternatives through a semantic scale (extreme to very weak) over another.<br>In the data collection part: the participants were aware of Health 4.0 concept due to their expertise. The in-depth interviews were held in 2 weeks and lasted app. 35 mins. Data manually coded by the authors in order to create the main criteria to be evaluated in Study 2 (quantitative- MACBETH) through the given common statements. The group of participants had a meeting lasted 3 hrs to fill the provided form on a consensus basis.<br>
DOI: 10.6084/m9.figshare.12048633
title: Table 2. Ustekinumab dosing, interval, levels, duration of therapy, and complication

description: ustekinumab dose, interval, drug level, duration of therapy, and complications observed in pediatric Crohn Disease patients
DOI: 10.6084/m9.figshare.12048624.v2
title: Research Data EGILMEZ_KOCA.docx.docx

description: The data collected via Qualitative data interview. Quantitative data, with consensus and filling the semantic scale form to see the alternatives to each other. Instruments: M-MACBETH program. The participants were gathered together to reach a consensus on 4 main criteria, with 11 alternatives formed as a result of the qualitative phase. They were asked to assign to evaluate the comparison of alternatives through a semantic scale (extreme to very weak) over another.<br>In the data collection part: the participants were aware of Health 4.0 concept due to their expertise. The in-depth interviews were held in 2 weeks and lasted app. 35 mins. Data manually coded by the authors in order to create the main criteria to be evaluated in Study 2 (quantitative- MACBETH) through the given common statements. The group of participants had a meeting lasted 3 hrs to fill the provided form on a consensus basis.<br>
DOI: 10.6084/m9.figshare.12047478
title: A crop type dataset for consistent land cover classification in Central Asia

description: Land cover is a key variable in the context of climate change. In particular, crop type information is essential to understand the spatial distribution of water usage and anticipate the risk of water scarcity and the consequent danger of food insecurity. This applies to arid regions such as the Aral Sea Basin (ASB), Central Asia, where agriculture relies heavily on irrigation. Here, remote sensing is valuable to map crop types, but its quality depends on consistent ground-truth data. Yet, in the ASB, such data is missing. Addressing this issue, we collected thousands of polygons on crop types, 97.7% of which in Uzbekistan and the remaining in Tajikistan. We collected 8,196 samples between 2015 and 2018, 213 in 2011 and 26 in 2008. Our data compiles samples for 40 crop types and is dominated by “cotton” (40%) and “wheat”, (25%). These data were meticulously validated using expert knowledge and remote sensing data and relied on transferable, open-source workflows that will assure the consistency of future sampling campaigns.<br>
DOI: 10.6084/m9.figshare.12048624.v1
title: Research Data EGILMEZ_KOCA.docx.docx

description: The data collected via Qualitative data interview. Quantitative data, with consensus and filling the semantic scale form to see the alternatives to each other. Instruments: M-MACBETH program. The participants were gathered together to reach a consensus on 4 main criteria, with 11 alternatives formed as a result of the qualitative phase. They were asked to assign to evaluate the comparison of alternatives through a semantic scale (extreme to very weak) over another.<br>In the data collection part: the participants were aware of Health 4.0 concept due to their expertise. The in-depth interviews were held in 2 weeks and lasted app. 35 mins. Data manually coded by the authors in order to create the main criteria to be evaluated in Study 2 (quantitative- MACBETH) through the given common statements. The group of participants had a meeting lasted 3 hrs to fill the provided form on a consensus basis.<br>
DOI: 10.6084/m9.figshare.12048633.v2
title: Table 2. Ustekinumab dosing, interval, levels, duration of therapy, and complication

description: ustekinumab dose, interval, drug level, duration of therapy, and complications observed in pediatric Crohn Disease patients
DOI: 10.6084/m9.figshare.12048633.v1
title: Table 2. Ustekinumab dosing, interval, levels, duration of therapy, and complication

description: ustekinumab dose, interval, drug level, duration of therapy, and complications observed in pediatric Crohn Disease patients
DOI: 10.6084/m9.figshare.12047466
title: Data

description: Data for Baethke et al - Minerals<br>
DOI: 10.6084/m9.figshare.12047478.v1
title: A Crop Type Dataset for Consistent Land Cover Classification in Central Asia and Beyond

description: This dataset offers thousands of polygons on crop types collected within the Aral Sea Basin (ASB). It was collected in the scope of the project Central Asia Waters (CAWa, https://www.cawa-project.net/) and consists of the first extensive, open-source dataset of crop samples in this data scarce region. The samples were collected using GPS devices, and were later translated into field polygons with the support of high-resolution imagery. The thematic quality of the samples was validated using remote sensing and expert knowledge on crop phenology, a process supported by local experts familiar with the landscape.<br>This data was collected in support of efficient agricultural management through detailed, multi-temporal agricultural mapping. However, it can support other mapping applications. <br>
DOI: 10.6084/m9.figshare.12047466.v1
title: Data

description: Data for Baethke et al - Minerals<br>
DOI: 10.6084/m9.figshare.12047415
title: Does bilingualism protect against dementia? A meta-analysis

description: Attached are the datasets of effect sizes and the R-script we used to analyze our data for the "Does bilingualism protect against dementia? A meta-analysis" accepted at Psychonomic Bulletin and Review. <br>For comments or questions, please do not hesitate to contact either JAEA or JG.
DOI: 10.6084/m9.figshare.12047397
title: SI for Paper Self-Assembly, Adaptive Response and in,out-Stereoisomerism of Large Orthoformate Cryptands

description: Additional Supporting information for computational studies for the paper "Self-Assembly, Adaptive Response and in,out-Stereoisomerism of Large Orthoformate Cryptands"by Henrik Löw, Elena Mena-Osteritz, Kathleen M. Mullen, Christof M. Jäger,* and Max von Delius*<br><br>- QM calculation structures and truncated output files- MD simulation paramter, input and analysis files (rmsd, PCA, lie, etc)
DOI: 10.6084/m9.figshare.12047397.v1
title: SI for Paper Self-Assembly, Adaptive Response and in,out-Stereoisomerism of Large Orthoformate Cryptands

description: Additional Supporting information for computational studies for the paper "Self-Assembly, Adaptive Response and in,out-Stereoisomerism of Large Orthoformate Cryptands"by Henrik Löw, Elena Mena-Osteritz, Kathleen M. Mullen, Christof M. Jäger,* and Max von Delius*<br><br>- QM calculation structures and truncated output files- MD simulation paramter, input and analysis files (rmsd, PCA, lie, etc)
DOI: 10.6084/m9.figshare.12047241
title: Temporal trade-off between gymnosperm resistance and resilience increases forest sensitivity to extreme drought

description: Raw datasets are available from public sources, which are used in the paper "Temporal trade-off between gymnosperm resistance and resilience increases forest sensitivity to extreme drought". doi:10.1038/s41559-020-1217-3https://www.nature.com/articles/s41559-020-1217-3<br>The datasets include:<br>raw data of tree-ring widths from https://www1.ncdc.noaa.gov/pub/data/paleo/treering/; the Climatic Research Unit (CRU), version TS 4.01 from https://crudata.uea.ac.uk/cru/data/hrg/; the gridded SPEI data (SPEIbase v2.5) from http://digital.csic.es/handle/10261/153475; the Regridded Harmonized World Soil Database v1.2 from https://daac.ornl.gov/SOILS/guides/HWSD.html; canopy height from https://webmap.ornl.gov/ogc/dataset.jsp?dg_id=10023_1; maximum rooting depth from https://wci.earth2observe.eu/thredds/catalog/usc/root-depth/catalog.html; wood density from https://datadryad.org/handle/10255/dryad.235; SLA, Nm, and Pm from https://github.com/abhirupdatta/global_maps_of_plant_traits; HSM and P50 from https://www.nature.com/articles/nature11688; isohydricity data from https://github.com/agkonings/isohydricity; tree density from https://elischolar.library.yale.edu/yale_fes_data/1/ ;above ground biomass of tropical forest plots from http://www.forestplots.net/data-packages/brienen-et-al-2015.<br>Please cite the corresponding papers correctly and follow the data usage license when using these datasets.
DOI: 10.6084/m9.figshare.12047235
title: TPCs

description: Temperature is one of the most important environmental factors driving the genome-to-phenome relationship. Metabolic rates and related biological processes are predicted to increase with temperature due to the biophysical laws of chemical reactions. However, selection can also act on these processes across scales of biological organization, from individual enzymes to whole organisms. Although individual some studies have examined thermal responses across multiple scales, there is no general consensus on how these responses vary depending on the level of organization, or whether rates actually follow predicted theoretical patterns (e.g., Arrhenius-like exponential responses or thermal performance curves with showing peak responsess). Here, we performed a meta-analysis on studies where these rates were measured across the same set of temperatures, but at multiplethree levels of biological organization: enzyme activities, mitochondrial respiration, and/or whole-animal metabolic rates. Our final dataset consisted of 235 pairwise comparisons among between levels of organization from 13 publications. Thermal responses differed drastically across levels of biological organization, sometimes showing completely opposite patterns. We developed a new effect size metric, ‘organizational disagreement’, to quantify the difference in responses among levels of biological organization. Overall, rates at higher levels of biological organization (e.g., whole animal metabolic rates) increased more quickly with temperature than rates at lower levels, contrary to our predictions. Taxa and tissues examined generally did not affect organizational disagreement. Theoretical TPCs, where rates increase to a peak value and then drop, were only rarely observed (12%), while exponential increases following Arrhenius predictions were more common (29%). Our results suggest classic assumptions about thermal responses in biological rates are not supported by empirical datasets. Responses may differ across levels due to differing selection pressures or differing consequences of biochemical laws with increasing organization. TPCs may be rare because a broad range of test temperatures are rarely investigated (averaging only four test temperatures in our dataset). We advocate for more studies where thermal responses are measured across multiple levels of biological organization and for authors to explicitly address organizational disagreement in their interpretations. These results further emphasize the complexity of connecting the genome to the phenome when environmental plasticity is incorporated: the impact of the environment on the phenotype can depend on the scale of organization considered.<br>Here are the supplemental data associated with this project. They include:<br>File S1: All 235 pairwise comparisons of thermal responses used to calculate the organizational disagreement effect size metric.<br>File S2: The OD metric and its variance for each of the 235 comparisons.<br>File S3: The 189 thermal responses examined. <br>File S4: The R code used to perform the analyses and generate most of the figures.
DOI: 10.6084/m9.figshare.12047238
title: Long-term serial culture of Piscirickettsia salmonis leads to a genomic and transcriptomic reorganization affecting bacterial in vitro virulence

description: The propagation of intracellular bacteria in culture mediums implies physiological adaptation to an artificial environment. If these conditions are persistent enough time, a permanent adaptation to the new environment can be expected. This study aimed to explore the genomic and transcriptomic rearrangements that the intracellular bacterium <i>Piscirickettsia salmoni</i>s undergo during a long-term serial culture experiment and the potential impact on virulence. Here, PacBio and Illumina sequencing were conducted after 200 passages (~2 years) of <i>P. salmonis</i> in a cell-free culture medium. The results evidenced genomic rearrangements of the <i>P. salmonis</i> genome during the continuous culture period, where a chromosome segment of 35 Kb was translocated from the P0 bacterial chromosome to a P200 plasmid. Notably, the genomic structure of this segment revealed the presence of the Dot/Icm secretion system, which has been previously associated with <i>P. salmonis</i> pathogenesis. On the other hand, a reduced transcriptomic response was evidenced in <i>P. salmonis</i> after 200 passages affecting the expression of different pathways including iron acquisition and metabolism. Furthermore, <i>in vitro</i> infections revealed that after 200 passages <i>P. salmonis</i> is less capable of generating cytopathic effects than the original P0 form. Overall, our results evidence that the continuous propagation of <i>P. salmonis</i> leads to genomic and transcriptomic rearrangement that impact on bacterial virulence. These results open new perspectives about the adaptation of intracellular bacteria to artificial culture conditions, providing useful information to develop live attenuated vaccines against <i>P. salmonis</i> in salmon aquaculture.
DOI: 10.6084/m9.figshare.12047238.v1
title: Long-term serial culture of Piscirickettsia salmonis leads to a genomic and transcriptomic reorganization affecting bacterial in vitro virulence

description: The propagation of intracellular bacteria in culture mediums implies physiological adaptation to an artificial environment. If these conditions are persistent enough time, a permanent adaptation to the new environment can be expected. This study aimed to explore the genomic and transcriptomic rearrangements that the intracellular bacterium <i>Piscirickettsia salmoni</i>s undergo during a long-term serial culture experiment and the potential impact on virulence. Here, PacBio and Illumina sequencing were conducted after 200 passages (~2 years) of <i>P. salmonis</i> in a cell-free culture medium. The results evidenced genomic rearrangements of the <i>P. salmonis</i> genome during the continuous culture period, where a chromosome segment of 35 Kb was translocated from the P0 bacterial chromosome to a P200 plasmid. Notably, the genomic structure of this segment revealed the presence of the Dot/Icm secretion system, which has been previously associated with <i>P. salmonis</i> pathogenesis. On the other hand, a reduced transcriptomic response was evidenced in <i>P. salmonis</i> after 200 passages affecting the expression of different pathways including iron acquisition and metabolism. Furthermore, <i>in vitro</i> infections revealed that after 200 passages <i>P. salmonis</i> is less capable of generating cytopathic effects than the original P0 form. Overall, our results evidence that the continuous propagation of <i>P. salmonis</i> leads to genomic and transcriptomic rearrangement that impact on bacterial virulence. These results open new perspectives about the adaptation of intracellular bacteria to artificial culture conditions, providing useful information to develop live attenuated vaccines against <i>P. salmonis</i> in salmon aquaculture.
DOI: 10.6084/m9.figshare.12047193
title: Metadata record for: Reactants, products, and transition states of elementary chemical reactions based on quantum chemistry

description: This dataset contains key characteristics about the data described in the Data Descriptor Reactants, products, and transition states of elementary chemical reactions based on quantum chemistry. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format
DOI: 10.6084/m9.figshare.12047235.v2
title: TPCs

description: Temperature is one of the most important environmental factors driving the genome-to-phenome relationship. Metabolic rates and related biological processes are predicted to increase with temperature due to the biophysical laws of chemical reactions. However, selection can also act on these processes across scales of biological organization, from individual enzymes to whole organisms. Although individual some studies have examined thermal responses across multiple scales, there is no general consensus on how these responses vary depending on the level of organization, or whether rates actually follow predicted theoretical patterns (e.g., Arrhenius-like exponential responses or thermal performance curves with showing peak responsess). Here, we performed a meta-analysis on studies where these rates were measured across the same set of temperatures, but at multiplethree levels of biological organization: enzyme activities, mitochondrial respiration, and/or whole-animal metabolic rates. Our final dataset consisted of 235 pairwise comparisons among between levels of organization from 13 publications. Thermal responses differed drastically across levels of biological organization, sometimes showing completely opposite patterns. We developed a new effect size metric, ‘organizational disagreement’, to quantify the difference in responses among levels of biological organization. Overall, rates at higher levels of biological organization (e.g., whole animal metabolic rates) increased more quickly with temperature than rates at lower levels, contrary to our predictions. Taxa and tissues examined generally did not affect organizational disagreement. Theoretical TPCs, where rates increase to a peak value and then drop, were only rarely observed (12%), while exponential increases following Arrhenius predictions were more common (29%). Our results suggest classic assumptions about thermal responses in biological rates are not supported by empirical datasets. Responses may differ across levels due to differing selection pressures or differing consequences of biochemical laws with increasing organization. TPCs may be rare because a broad range of test temperatures are rarely investigated (averaging only four test temperatures in our dataset). We advocate for more studies where thermal responses are measured across multiple levels of biological organization and for authors to explicitly address organizational disagreement in their interpretations. These results further emphasize the complexity of connecting the genome to the phenome when environmental plasticity is incorporated: the impact of the environment on the phenotype can depend on the scale of organization considered.<br>Here are the supplemental data associated with this project. They include:<br>File S1: All 235 pairwise comparisons of thermal responses used to calculate the organizational disagreement effect size metric.<br>File S2: The OD metric and its variance for each of the 235 comparisons.<br>File S3: The 189 thermal responses examined. <br>File S4: The R code used to perform the analyses and generate most of the figures.
DOI: 10.6084/m9.figshare.12047193.v1
title: Metadata record for: Reactants, products, and transition states of elementary chemical reactions based on quantum chemistry

description: This dataset contains key characteristics about the data described in the Data Descriptor Reactants, products, and transition states of elementary chemical reactions based on quantum chemistry. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format
DOI: 10.6084/m9.figshare.12047241.v2
title: Trade-off between gymnosperm resistance and resilience increases forest sensitivity to extreme drought

description: Raw datasets are available from public sources, which are used in the paper "Trade-off between gymnosperm resistance and resilience increases forest sensitivity to extreme drought".<br>The datasets include:raw data of tree-ring widths from https://www1.ncdc.noaa.gov/pub/data/paleo/treering/; the Climatic Research Unit (CRU), version TS 4.01 from https://crudata.uea.ac.uk/cru/data/hrg/; the gridded SPEI data (SPEIbase v2.5) from http://digital.csic.es/handle/10261/153475; the Regridded Harmonized World Soil Database v1.2 from https://daac.ornl.gov/SOILS/guides/HWSD.html; canopy height from https://webmap.ornl.gov/ogc/dataset.jsp?dg_id=10023_1; maximum rooting depth from https://wci.earth2observe.eu/thredds/catalog/usc/root-depth/catalog.html; wood density from https://datadryad.org/handle/10255/dryad.235; SLA, Nm, and Pm from https://github.com/abhirupdatta/global_maps_of_plant_traits; HSM and P50 from https://www.nature.com/articles/nature11688; isohydricity data from https://github.com/agkonings/isohydricity; tree density from https://elischolar.library.yale.edu/yale_fes_data/1/ ;above ground biomass of tropical forest plots from http://www.forestplots.net/data-packages/brienen-et-al-2015.<br>Please cite the corresponding papers correctly and follow the data usage license when using these datasets.
DOI: 10.6084/m9.figshare.12046980
title: Quantile risk hedging - Applied Economics

description: For research purpose only.
DOI: 10.6084/m9.figshare.12046980.v1
title: Quantile risk hedging - Applied Economics

description: For research purpose only.