cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.5393816
title: An Optimized North America MODIS Leaf Area Index (LAI) Dataset for Air Quality Modeling

description: Air Quality Research Division, Environment and Climate Change Canada, 4905 Dufferin Street, Toronto, Ontario, M3H 5T4, Canada Email: Junhua.zhang@ec.gc.ca Leaf Area Index (LAI) is used in air quality models for land surface processes and for calculating biogenic emissions. MODIS LAI product provided by NASA (https://modis.gsfc.nasa.gov/data/dataprod/mod15.php) has been widely used in the air quality modeling community for such purposes. However, limitations of MODIS LAI product have been seen for some geographic areas, particularly unreasonably low LAI over the evergreen needleleaf boreal forests in the northern hemisphere during wintertime due to snow cover and low sun angle. Missing retrievals over urban areas and areas with persistent cloud cover are also seen. Considerable efforts have been made to improve the MODIS LAI product. However, some issues are still persistent, such as the very low LAI over boreal forests during wintertime. In order to solve these issues for supporting regional air quality modelling, the 8-day MODIS Collection 6 (C6) LAI product at 500m resolution (MCD15A2H) was examined for North America. Statistics were calculated by month and by land cover type defined in the “Land Cover Type 1” science data set (SDS) of the Collection 6 MODIS Land Cover (MCD12Q1) product. Comparisons with LAI calculated from the EPA’s Biogenic Emissions Landuse Database, version 4 (BELD4, https://www.epa.gov/air-emissions-modeling/biogenic-emission-sources) were also done (Zhang et al., 2020). Based on the analysis, an updated monthly LAI dataset was calculated based on 1) 17-year (2003-2019) average of MODIS summer-time peak LAI, 2) fraction of evergreen and deciduous for each pixel from BELD4, and 3) monthly profiles of LAI for evergreen and deciduous vegetation species from MODIS LAI (Zhang et al., 2021). This is the final LAI dataset for North America compiled using the 17 years of MODIS LAI product complemented by information from BELD4. REFERENCES: Zhang, J., M. D. Moran, P. A. Makar, and S. Kharol, 2020. Examination of MODIS Leaf Area Index (LAI) Product for Air Quality Modelling. 19th CMAS Conference, 26-30 Oct., Virtual [see https://www.cmascenter.org/conference/2020/slides/ZhangJ_MODIS_LAI_CMAS_2020.pdf]. Zhang, J., P. A. Makar, S. Kharol, M. D. Moran, and C. McLinden, 2021. Examination and Processing of MODIS Leaf Area Index (LAI) Product for Air Quality Modelling. 2021 Meteorology and Climate - Modeling for Air Quality Conference, Sep 14-17, 2021, Virtual
DOI: 10.5281/zenodo.5393815
title: An Optimized North America MODIS Leaf Area Index (LAI) Dataset for Air Quality Modeling

description: Air Quality Research Division, Environment and Climate Change Canada, 4905 Dufferin Street, Toronto, Ontario, M3H 5T4, Canada Email: Junhua.zhang@ec.gc.ca Leaf Area Index (LAI) is used in air quality models for land surface processes and for calculating biogenic emissions. MODIS LAI product provided by NASA (https://modis.gsfc.nasa.gov/data/dataprod/mod15.php) has been widely used in the air quality modeling community for such purposes. However, limitations of MODIS LAI product have been seen for some geographic areas, particularly unreasonably low LAI over the evergreen needleleaf boreal forests in the northern hemisphere during wintertime due to snow cover and low sun angle. Missing retrievals over urban areas and areas with persistent cloud cover are also seen. Considerable efforts have been made to improve the MODIS LAI product. However, some issues are still persistent, such as the very low LAI over boreal forests during wintertime. In order to solve these issues for supporting regional air quality modelling, the 8-day MODIS Collection 6 (C6) LAI product at 500m resolution (MCD15A2H) was examined for North America. Statistics were calculated by month and by land cover type defined in the “Land Cover Type 1” science data set (SDS) of the Collection 6 MODIS Land Cover (MCD12Q1) product. Comparisons with LAI calculated from the EPA’s Biogenic Emissions Landuse Database, version 4 (BELD4, https://www.epa.gov/air-emissions-modeling/biogenic-emission-sources) were also done (Zhang et al., 2020). Based on the analysis, an updated monthly LAI dataset was calculated based on 1) 17-year (2003-2019) average of MODIS summer-time peak LAI, 2) fraction of evergreen and deciduous for each pixel from BELD4, and 3) monthly profiles of LAI for evergreen and deciduous vegetation species from MODIS LAI (Zhang et al., 2021). This is the final LAI dataset for North America compiled using the 17 years of MODIS LAI product complemented by information from BELD4. REFERENCES: Zhang, J., M. D. Moran, P. A. Makar, and S. Kharol, 2020. Examination of MODIS Leaf Area Index (LAI) Product for Air Quality Modelling. 19th CMAS Conference, 26-30 Oct., Virtual [see https://www.cmascenter.org/conference/2020/slides/ZhangJ_MODIS_LAI_CMAS_2020.pdf]. Zhang, J., P. A. Makar, S. Kharol, M. D. Moran, and C. McLinden, 2021. Examination and Processing of MODIS Leaf Area Index (LAI) Product for Air Quality Modelling. 2021 Meteorology and Climate - Modeling for Air Quality Conference, Sep 14-17, 2021, Virtual
DOI: 10.5519/qd.io1d3k3l
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (4898397 records)
DOI: 10.3886/e149341
title: Ethno-Territorial Civil War: Conventional vs. Guerrilla Strategies

description: In ethno-territorial civil wars, which factors influence whether rebels choose and retain conventional warfare as their primary military strategy throughout the conflict, or whether they use guerrilla warfare as a primary strategy during periods judged to be less advantageous to conventional warfare? We find some support for the traditionally dominant explanation—relative power. We also find that rebel leaders with more intense, far-reaching nationalist goals are more likely to employ guerrilla warfare as a primary war strategy. By contrast, status quo conditions or a high level of state democracy do not have significant influences.
DOI: 10.3886/e149341v1
title: Ethno-Territorial Civil War: Conventional vs. Guerrilla Strategies

description: In ethno-territorial civil wars, which factors influence whether rebels choose and retain conventional warfare as their primary military strategy throughout the conflict, or whether they use guerrilla warfare as a primary strategy during periods judged to be less advantageous to conventional warfare? We find some support for the traditionally dominant explanation—relative power. We also find that rebel leaders with more intense, far-reaching nationalist goals are more likely to employ guerrilla warfare as a primary war strategy. By contrast, status quo conditions or a high level of state democracy do not have significant influences.
DOI: 10.5281/zenodo.5458010
title: Adela reaumurella decontaminated FSCR

description: .
DOI: 10.5281/zenodo.5458009
title: Adela reaumurella decontaminated FSCR

description: .
DOI: 10.5281/zenodo.5458036
title: Adranes taylori decontaminated FSCR

description: .
DOI: 10.5281/zenodo.5458035
title: Adranes taylori decontaminated FSCR

description: .
DOI: 10.5281/zenodo.5458044
title: Absolute units in Arabidopsis clock models up to U2020.3

description: The dataset presents mathematical models of the gene regulatory network of the circadian clock, in the plant <em>Arabidopsis thaliana.</em> The work is published in Urquiza-Garcia and Millar, <strong>Testing the inferred transcription rates of a dynamic, gene network model in absolute units</strong>, In Silico Plants, 2021. Starting from the P2011 model, this project corrects theoretical issues (EC steady state binding assumption) to form an intermediate model (published as U2019.1), rescales parameters to match absolute RNA levels from the TiMet WP1a RNA dataset of Flis et al. 2015 in U2019.2, then reoptimises globally to match RNA timeseries, period and amplitude constraints to produce the U2019.3 model. This project then replaces regulation of the PRRs with repression by later-expressed genes (instead of activation by earlier ones, as in P2011/P2012/U2019) in the U2019.1 model, to create the U2020.1 model, then also rescales to match the RNA levels in the U2020.2 model, and performs a global reoptimisation as above to form U2020.3. The input data files, the computational environment for model development (a Docker image in the 'Reproducibility Toolset' assay) and the relevant model files are included here, as published in Urquiza and Millar, In Silico Plants, 2021. The biorXiv preprint version of the publication is linked inside the archive structure. The DOI for the publication was not yet available but is now: 10.1093/insilicoplants/diab022. This version 3 replaces 10.5281/zenodo.5150823 (version 2), as model files for the earlier KF2014 models were omitted in error from versions 1 and 2. There are no other changes.
description: The dataset is structured as a Research Object with an internal ISA hierarchy, which is automatically generated by the Snapshot function of the FAIRDOMHub.org repository. The Research Object is a .ZIP file with the ISA hierarchy reflected in its subfolder structure. There is metadata at multiple levels of the hierarchy, including in the datafile records. The model files are in Antimony and SBML formats. The KF2014 model in SBML format was excluded from the "snapshot" due to an unresolved technical error in FAIRDOMHub.org, and will be included in a later version of this deposit if possible. The file is publicly available from the live resource by searching for "F2014".
description: {"references": ["Urquiza-Garc\u00eda, U., & Millar, A. J. (2021). Testing the inferred transcription rates of a dynamic, gene network model in absolute units. biorXiv, Cold Spring Harbor Laboratory. https://doi.org/10.1101/2021.03.18.436071", "Urquiza-Garc\u00eda, U., & Millar, A. J. (2021). Testing the inferred transcription rates of a dynamic, gene network model in absolute units. in silico Plants. http://dx.doi.org/10.1093/insilicoplants/diab022"]}
DOI: 10.5281/zenodo.5150793
title: Absolute units in Arabidopsis clock models up to U2020.3

description: The dataset presents mathematical models of the gene regulatory network of the circadian clock, in the plant <em>Arabidopsis thaliana.</em> The work is published in Urquiza-Garcia and Millar, <strong>Testing the inferred transcription rates of a dynamic, gene network model in absolute units</strong>, In Silico Plants, 2021. Starting from the P2011 model, this project corrects theoretical issues (EC steady state binding assumption) to form an intermediate model (published as U2019.1), rescales parameters to match absolute RNA levels from the TiMet WP1a RNA dataset of Flis et al. 2015 in U2019.2, then reoptimises globally to match RNA timeseries, period and amplitude constraints to produce the U2019.3 model. This project then replaces regulation of the PRRs with repression by later-expressed genes (instead of activation by earlier ones, as in P2011/P2012/U2019) in the U2019.1 model, to create the U2020.1 model, then also rescales to match the RNA levels in the U2020.2 model, and performs a global reoptimisation as above to form U2020.3. The input data files, the computational environment for model development (a Docker image in the 'Reproducibility Toolset' assay) and the relevant model files are included here, as published in Urquiza and Millar, In Silico Plants, 2021. The biorXiv preprint version of the publication is linked inside the archive structure. The DOI for the publication was not yet available but is now: 10.1093/insilicoplants/diab022. This version 3 replaces 10.5281/zenodo.5150823 (version 2), as model files for the earlier KF2014 models were omitted in error from versions 1 and 2. There are no other changes.
description: The dataset is structured as a Research Object with an internal ISA hierarchy, which is automatically generated by the Snapshot function of the FAIRDOMHub.org repository. The Research Object is a .ZIP file with the ISA hierarchy reflected in its subfolder structure. There is metadata at multiple levels of the hierarchy, including in the datafile records. The model files are in Antimony and SBML formats. The KF2014 model in SBML format was excluded from the "snapshot" due to an unresolved technical error in FAIRDOMHub.org, and will be included in a later version of this deposit if possible. The file is publicly available from the live resource by searching for "F2014".
description: {"references": ["Urquiza-Garc\u00eda, U., & Millar, A. J. (2021). Testing the inferred transcription rates of a dynamic, gene network model in absolute units. biorXiv, Cold Spring Harbor Laboratory. https://doi.org/10.1101/2021.03.18.436071", "Urquiza-Garc\u00eda, U., & Millar, A. J. (2021). Testing the inferred transcription rates of a dynamic, gene network model in absolute units. in silico Plants. http://dx.doi.org/10.1093/insilicoplants/diab022"]}
DOI: 10.34740/kaggle/ds/1572619
title: Cars for sale in Moldova
DOI: 10.5281/zenodo.5425432
title: Data and code for the manuscript: "An ecological explanation for hyperallometric scaling of reproduction"

description: Code, data, and data objects underlying the analyses presented in the manuscript "An ecological explanation for hyperallometric scaling of reproduction". A version of the manuscript is available on bioRxiv: https://doi.org/10.1101/2021.03.12.435090 Abstract for the manuscript: "In wild populations, large individuals have disproportionately higher reproductive output than smaller individuals. Some theoretical models explain this pattern – termed reproductive hyperallometry – by individuals allocating a greater fraction of available energy towards reproductive effort as they grow. Here, we propose an ecological explanation for this observation: differences between individuals in rates of resource assimilation, where greater assimilation causes both increased reproduction and body size, resulting in reproductive hyperallometry at the level of the population. We illustrate this effect by determining the relationship between size and reproduction in wild and lab-reared Trinidadian guppies. We show that (i) reproduction increased disproportionately with body size in the wild but not in the lab, where resource competition was eliminated; (ii) in the wild, hyperallometry was greatest during the wet season, when resource competition is strongest; and (iii) detection of hyperallometric scaling of reproduction at the population level was inevitable if individual differences in assimilation were ignored. We propose that ecologically-driven variation in assimilation – caused by size-dependent resource competition, niche expansion, and chance – contributes substantially to hyperallometric scaling of reproduction in natural populations. We recommend that mechanistic models incorporate such ecologically-caused variation when seeking to explain reproductive hyperallometry.' The zip file contains: 1. A single R script for running the analyses, generating the results, and producing the figures given in the manuscript - size_reproduction_scaling_lab_wild.R 2. Two .csv files containing the wild and lab datasets used in the study: - wild_guppy_data_81-87.csv (the wild dataset)<br> - senecence_long_data.csv (the lab dataset) 3. A folder containing 14 model objects. These are the models produced by running the R script. These are provided to save the user time. The model object names correspond to the models described in Table 1 of the manuscript. 4. A READ_ME.txt file.
DOI: 10.5281/zenodo.5425431
title: Data and code for the manuscript: "An ecological explanation for hyperallometric scaling of reproduction"

description: Code, data, and data objects underlying the analyses presented in the manuscript "An ecological explanation for hyperallometric scaling of reproduction". A version of the manuscript is available on bioRxiv: https://doi.org/10.1101/2021.03.12.435090 Abstract for the manuscript: "In wild populations, large individuals have disproportionately higher reproductive output than smaller individuals. Some theoretical models explain this pattern – termed reproductive hyperallometry – by individuals allocating a greater fraction of available energy towards reproductive effort as they grow. Here, we propose an ecological explanation for this observation: differences between individuals in rates of resource assimilation, where greater assimilation causes both increased reproduction and body size, resulting in reproductive hyperallometry at the level of the population. We illustrate this effect by determining the relationship between size and reproduction in wild and lab-reared Trinidadian guppies. We show that (i) reproduction increased disproportionately with body size in the wild but not in the lab, where resource competition was eliminated; (ii) in the wild, hyperallometry was greatest during the wet season, when resource competition is strongest; and (iii) detection of hyperallometric scaling of reproduction at the population level was inevitable if individual differences in assimilation were ignored. We propose that ecologically-driven variation in assimilation – caused by size-dependent resource competition, niche expansion, and chance – contributes substantially to hyperallometric scaling of reproduction in natural populations. We recommend that mechanistic models incorporate such ecologically-caused variation when seeking to explain reproductive hyperallometry.' The zip file contains: 1. A single R script for running the analyses, generating the results, and producing the figures given in the manuscript - size_reproduction_scaling_lab_wild.R 2. Two .csv files containing the wild and lab datasets used in the study: - wild_guppy_data_81-87.csv (the wild dataset)<br> - senecence_long_data.csv (the lab dataset) 3. A folder containing 14 model objects. These are the models produced by running the R script. These are provided to save the user time. The model object names correspond to the models described in Table 1 of the manuscript. 4. A READ_ME.txt file.
DOI: 10.6084/m9.figshare.14479809.v3
title: A resistance assessment report and bioinformatic analysis of predicted resistance genes of Staph. aureus

description: A resistance assessment report and bioinformatic analysis of predicted resistance genes of <i>Staph. aureus </i>isolated from 23 Chinese Rubing and Rushan cheese samples collected from local market outlets in Yunnan province, China between July 2019 to June 2020.
DOI: 10.5281/zenodo.5443258
title: Vorau Abbey library Cod. 253 dataset for Document Layout Analysis

description: VORAU-253 is a music manuscript referred to as Cod. 253 of the Vorau Abbey library, which was provided by the Austrian Academy of Sciences. It is written in German Gothic notation and dated around year 1450. This manuscript is interesting because of the complexity of its layout, where staff, text and decorations are intertwined to<br> compose the structure of the document. This database is a subset of 228 pages of the archive, using 128 randomly selected pages for training/validation and 100 for test. The database was manually annotated into the following three layout regions: * staff: represents the regions that contains a set of horizontal lines and spaces where each one represent a different musical pitch. This region type does not contain text lines. Hence, no baselines. * lyrics: are the words that are sung appear below their corresponding staff, and other text in the document. In all cases, text to be sung and the other text are assigned to different layout regions under the lyrics label. * drop-capital: is a decorated letter that might appear at the beginning of a word or text line. As it is a single big letter, it contain no text lines nor baselines. On average each page contains 12.5 [7,23] text lines distributed over an average of 10.5[7,15] ``lyrics'' regions. Moreover, each page contains 22.3[14,28] layout regions on average.
DOI: 10.5281/zenodo.5443257
title: Vorau Abbey library Cod. 253 dataset for Document Layout Analysis

description: VORAU-253 is a music manuscript referred to as Cod. 253 of the Vorau Abbey library, which was provided by the Austrian Academy of Sciences. It is written in German Gothic notation and dated around year 1450. This manuscript is interesting because of the complexity of its layout, where staff, text and decorations are intertwined to<br> compose the structure of the document. This database is a subset of 228 pages of the archive, using 128 randomly selected pages for training/validation and 100 for test. The database was manually annotated into the following three layout regions: * staff: represents the regions that contains a set of horizontal lines and spaces where each one represent a different musical pitch. This region type does not contain text lines. Hence, no baselines. * lyrics: are the words that are sung appear below their corresponding staff, and other text in the document. In all cases, text to be sung and the other text are assigned to different layout regions under the lyrics label. * drop-capital: is a decorated letter that might appear at the beginning of a word or text line. As it is a single big letter, it contain no text lines nor baselines. On average each page contains 12.5 [7,23] text lines distributed over an average of 10.5[7,15] ``lyrics'' regions. Moreover, each page contains 22.3[14,28] layout regions on average.
DOI: 10.5281/zenodo.5458366
title: Dataset_PostOP_MRI_findings_following_conventional_and_extralevator_APE_in_LRC

description: Dataset on which the research presented in the above article is based.
DOI: 10.5281/zenodo.5458365
title: Dataset_PostOP_MRI_findings_following_conventional_and_extralevator_APE_in_LRC

description: Dataset on which the research presented in the above article is based.
DOI: 10.5281/zenodo.5458356
title: Alcedo semitorquata decontaminated FSCR

description: .
DOI: 10.5281/zenodo.5458355
title: Alcedo semitorquata decontaminated FSCR

description: .
DOI: 10.3886/e149221
title: Trends in Differences in Health Status and Health Care Access and Affordability by Race and Ethnicity in the United States, 1999-2018.

description: We include here the code files used to obtain the results reported in the study below:<br>Mahajan S, Caraballo C, Lu Y, et al. Trends in Differences in Health Status and Health Care Access and Affordability by Race and Ethnicity in the United States, 1999-2018. JAMA. 2021;326(7):637–648. doi:10.1001/jama.2021.9907<br>In the study above, we used data from the National Health Interview Survey from years 1999 to 2018 to investigate the trends in racial and ethnic disparities in health status, severe psychological distress, functional limitation, lack of health insurance coverage, lack of a usual source of care, no recent health care utilization, and unmet medical needs due to cost.<br><br>
description: Adult noninstitutionalized population of the United States.<br>.
description: All the data used in this study are publicly available. We obtained the data from the Integrated Public Use Microdata Series website (https://nhis.ipums.org/nhis/). Reference: Lynn A. Blewett, Julia A. Rivera Drew, Miriam L. King and Kari C.W. Williams. IPUMS Health Surveys: National Health Interview Survey, Version 6.4 [dataset]. Minneapolis, MN: IPUMS, 2019. https://doi.org/10.18128/D070.V6.4<br>