cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11968521
title: A Computationally More Efficient Bayesian Approach for Estimating Continuous-Time Models

description: Continuous-time modeling is gaining in popularity as more and more intensive longitudinal data need to be analyzed. Current Bayesian software implementations of continuous-time models suffer from rather high, inadequate run times. Therefore, we apply a model reformulation approach to reduce run time. In a simulation study, we investigate the estimation quality and run time gain. We then illustrate our optimized Bayesian continuous-time model estimation and compare it to established continuous-time modeling software using an empirical example. Parameter estimates and inference statistics were very comparable, while run times were very different. Our approach reduces the run times for Bayesian estimations of continuous-time models from hours to minutes.
DOI: 10.6084/m9.figshare.11981397.v1
title: Factor Score Regression in Connected Measurement Models Containing Cross-Loadings

description: Factor Score Regression (FSR) methods have received increased interest in the quantitative literature, with Croon’s <i>bias-correcting</i> method gaining particular traction. By fixing measurement parameters in place in an initial step, FSR methods aim to stymie the proliferation of bias in larger structural models that may contain misspecification. Although Croon’s approach was originally derived for factor models exhibiting simple structure and conditionally independent unique factors, Hayes and Usami recently extended this method to connected measurement models featuring correlated uniquenesses. In this article, we demonstrate that their formulas also correct bias in models that feature cross-loadings. We begin by discussing bias in SEMs that incorrectly impose simple structure. We then describe Croon’s approach in connected measurement models featuring cross-loadings and compare its performance to two other state-of-the-art FSR approaches both analytically and via a simulated demonstration.
DOI: 10.6084/m9.figshare.11866056
title: semopy: A Python Package for Structural Equation Modeling

description: Structural equation modeling (SEM) is a multivariate statistical technique for estimating complex relationships between observed and latent variables. Although numerous SEM packages currently exist, they each have limitations and more importantly they are not free or open-source. The only package that is both free and open-source is lavaan. However, because this package is written in R, it is often difficult to integrate it with other programming language functionalities. This paper provides an overview of a new Python package called semopy that was specifically developed to overcome these limitations. Using illustrative examples we introduce the new package and then compare its performance in accuracy and execution time to lavaan.
DOI: 10.6084/m9.figshare.11981397
title: Factor Score Regression in Connected Measurement Models Containing Cross-Loadings

description: Factor Score Regression (FSR) methods have received increased interest in the quantitative literature, with Croon’s <i>bias-correcting</i> method gaining particular traction. By fixing measurement parameters in place in an initial step, FSR methods aim to stymie the proliferation of bias in larger structural models that may contain misspecification. Although Croon’s approach was originally derived for factor models exhibiting simple structure and conditionally independent unique factors, Hayes and Usami recently extended this method to connected measurement models featuring correlated uniquenesses. In this article, we demonstrate that their formulas also correct bias in models that feature cross-loadings. We begin by discussing bias in SEMs that incorrectly impose simple structure. We then describe Croon’s approach in connected measurement models featuring cross-loadings and compare its performance to two other state-of-the-art FSR approaches both analytically and via a simulated demonstration.
DOI: 10.6084/m9.figshare.11968521.v3
title: A Computationally More Efficient Bayesian Approach for Estimating Continuous-Time Models

description: Continuous-time modeling is gaining in popularity as more and more intensive longitudinal data need to be analyzed. Current Bayesian software implementations of continuous-time models suffer from rather high, inadequate run times. Therefore, we apply a model reformulation approach to reduce run time. In a simulation study, we investigate the estimation quality and run time gain. We then illustrate our optimized Bayesian continuous-time model estimation and compare it to established continuous-time modeling software using an empirical example. Parameter estimates and inference statistics were very comparable, while run times were very different. Our approach reduces the run times for Bayesian estimations of continuous-time models from hours to minutes.
DOI: 10.6084/m9.figshare.11866056.v1
title: semopy: A Python Package for Structural Equation Modeling

description: Structural equation modeling (SEM) is a multivariate statistical technique for estimating complex relationships between observed and latent variables. Although numerous SEM packages currently exist, they each have limitations and more importantly they are not free or open-source. The only package that is both free and open-source is lavaan. However, because this package is written in R, it is often difficult to integrate it with other programming language functionalities. This paper provides an overview of a new Python package called semopy that was specifically developed to overcome these limitations. Using illustrative examples we introduce the new package and then compare its performance in accuracy and execution time to lavaan.
DOI: 10.6084/m9.figshare.14361587.v2
title: Canopy and understory nitrogen addition have different effects on fine root dynamics in a temperate forest: implications for soil carbon storage

description: Here, we conducted a field experiment comparing the effects of canopy addition of N (CAN) with understory addition of N (UAN) at three N-addition rates (0, 25, and 50 kg N ha<sup>–</sup><sup>1</sup> yr<sup>–</sup><sup>1</sup>) on fine root dynamics in a temperate deciduous forest. Fine root production and biomass were significantly higher with CAN than with UAN. At the same N-addition rate, increases in fine root production with CAN were at least 2-times greater than with UAN. At the high N-addition rate and relative to the Control, fine root biomass was significantly increased by 23.5% by CAN but was significantly decreased by 12.2% by UAN.
DOI: 10.6084/m9.figshare.14361587.v1
title: Canopy and understory nitrogen addition have different effects on fine root dynamics in a temperate forest: implications for soil carbon storage

description: Here, we conducted a field experiment comparing the effects of canopy addition of N (CAN) with understory addition of N (UAN) at three N-addition rates (0, 25, and 50 kg N ha<sup>–</sup><sup>1</sup> yr<sup>–</sup><sup>1</sup>) on fine root dynamics in a temperate deciduous forest. Fine root production and biomass were significantly higher with CAN than with UAN. At the same N-addition rate, increases in fine root production with CAN were at least 2-times greater than with UAN. At the high N-addition rate and relative to the Control, fine root biomass was significantly increased by 23.5% by CAN but was significantly decreased by 12.2% by UAN.
DOI: 10.5281/zenodo.4740941
title: Nucleocytoviricota phylogenies and alignments

description: Reference phylogenies and alignments for the Nucleocytoviricota
DOI: 10.5281/zenodo.4730954
title: Nucleocytoviricota phylogenies and alignments

description: Reference phylogenies and alignments for the Nucleocytoviricota
DOI: 10.5281/zenodo.4740942
title: BC Ophiolitic UMR Mineralogy, Physical Properties, and ME Geochemistry

description: This is a dataset comprises: major-element geochemistry, physical properties (magnetic susceptibility, natural remanent magnetization, density, porosity), and mineralogy (XRD and TGA) for ophiolitic ultramafic rocks in British Columbia.
description: {"references": ["Hansen et al. (2005) - Carbonated serpentinite (listwanite) at Atlin, British Columbia: a geological analogue to carbon dioxide sequestration, The Canadian Mineralogist: v43, 225-239", "Zagorevski (2020) - Whole-rock geochemical data compilation supporting Geo-mapping for Energy and Minerals Cordillera syntheses, British Columbia and Yukon, Geological Survey of Canada, Open File 8674, 5p", "McGoldrick et al. (2017) - Geochemistry of volcanic and plutonic rocks from the Nahlin ophiolite with implications for the Permo-Triassic arc in the Cache Creek terrane, northwestern British Columbia, Canadian Journal of Earth Sciences, v54, 1214-1227", "McGoldrick et al. (2018) - Contrasting thermal and melting histories for segments of mantle lithosphere in the Nahlin ophiolite, British Columbia, Canada, Contributions to Mineralogy and Petrology, v173:25", "Milidragoic and Grundy (2019) - Geochemistry and petrology of rocks in the Decar area, central British Columbia: Petrologically constrained subdivision of the Cache Creek complex. In: Geological Fieldwork 2018, British Columbia Ministry of Energy, Mines and Petroleum Resources, British Columbia Geological Survey Paper 2019-01, 55-77"]}
DOI: 10.15468/mceqbx
title: A review of the subfamily Methochinae from Taiwan (Hymenoptera: Tiphiidae) with description of a new species and redescription of the known species

description: This dataset contains the digitized treatments in Plazi based on the original journal article Narita, Keisuke, Mita, Toshiharu (2021): A review of the subfamily Methochinae from Taiwan (Hymenoptera: Tiphiidae) with description of a new species and redescription of the known species. Zootaxa 4964 (2): 303-329, DOI: https://doi.org/10.11646/zootaxa.4964.2.4
DOI: 10.6084/m9.figshare.14549145
title: Luminex analysis final dataset_Dr.Paul Katongole.xlsx

description: Dataset of Cytokine concentrations for patients with Prostate cancer and normal Health controls at the Uganda Cancer Institute.
DOI: 10.6084/m9.figshare.14549145.v1
title: Luminex analysis final dataset_Dr.Paul Katongole.xlsx

description: Dataset of Cytokine concentrations for patients with Prostate cancer and normal Health controls at the Uganda Cancer Institute.
DOI: 10.5281/zenodo.4740965
title: Britain Breathing 2020 Air Quality and Meteorological Dataset

description: This data set is a collection of daily mean and maximum values for a range of air quality and meterological measurements and model forecasts for the UK for the year 2020. The dataset contains Temperature, Relative Humidity, and Pressure data, downloaded from the Met Office MIDAS archives via the MEDMI server (https://www.data-mashup.org.uk/). Also downloaded from the MEDMI server are daily pollen measurements for the UK. PM10, PM2.5, NO2, NOx (as NO2), O3, and SO2 measurements from the DEFRA AURN network, and also model forecasts of the same made using the EMEP model. The tools used to download and process these measurement datasets are available here: https://zenodo.org/record/4545257 The dataset is designed for use with the region estimator toolset, available here: https://zenodo.org/record/4589993 Emissions over the UK for the EMEP model runs were generated using the NAEI 2016 UK emission dataset, available in netcdf form here: https://zenodo.org/record/3997165#.X9KUBF6nzUI. The running scripts, and operation inputs for EMEP, are available here: https://zenodo.org/record/3997301#.X9KUAF6nzUI and https://zenodo.org/record/3997271#.X9KV1F6nzUI. This dataset is an extension of the Britain Breathing 2016-2019 Air Quality and Meteorological Dataset, available here: https://zenodo.org/record/4416028#.YIrJfOvTXUL. The file 'site_location_data.csv' in this dataset contains the location metadata (site_id, latitude, longitude, postcode area) for the dataset here too. The dataset is presented in CSV format as the file 'turing_aq_daily_met_pollen_pollution_data_2020.csv', described below. The columns intended to be used as indexes are: timestamp, date of measurements on that row site_id, measurement site ID, corresponding to sites in the three networks: AURN [indicated by AQ], MIDAS [indicated by WEATHER], or pollen [indicated by POLLEN]. The data columns are: O3, PM10, PM2.5, NO2, NOXasNO2, SO2, daily mean and maximum values in ug/m3 (all with "_max", "_mean", and "_flag" tags) AURN measurement data O3_EMEP, NO2_EMEP, SO2_EMEP, NOXasNO2_EMEP, PM2.5_EMEP, PM10_EMEP, daily mean and maximum values in ug/m3 (all with "_max", and "_mean" tags) EMEP model forecasts alnus, ambrosia, artemisia, betula, corylus, fraxinus, platanus, poaceae, quercus, salix, ulmus, urtica, daily pollen grain counts temperature, relativehumidity, pressure, daily mean and maximum values in degC, %, and hPa (all with "_max", "_mean", and "_flag" tags). Met Office measurement data The "_flag" columns indicate data points which have been partially, or fully, imputed. The values for these will be in the range 0-1, and indicate the fraction of the hourly values within that day that are imputed (0 = none, 1 = all 24 hourly datapoints are imputed). No imputation has been carried out for this dataset, so the "_flag" data in this dataset will always be zero (the number of hourly data points used to calculate the daily mean and maximum are not recorded in this dataset).
DOI: 10.5281/zenodo.4727908
title: Britain Breathing 2020 Air Quality and Meteorological Dataset

description: This data set is a collection of daily mean and maximum values for a range of air quality and meterological measurements and model forecasts for the UK for the year 2020. The dataset contains Temperature, Relative Humidity, and Pressure data, downloaded from the Met Office MIDAS archives via the MEDMI server (https://www.data-mashup.org.uk/). Also downloaded from the MEDMI server are daily pollen measurements for the UK. PM10, PM2.5, NO2, NOx (as NO2), O3, and SO2 measurements from the DEFRA AURN network, and also model forecasts of the same made using the EMEP model. The tools used to download and process these measurement datasets are available here: https://zenodo.org/record/4545257 The dataset is designed for use with the region estimator toolset, available here: https://zenodo.org/record/4589993 Emissions over the UK for the EMEP model runs were generated using the NAEI 2016 UK emission dataset, available in netcdf form here: https://zenodo.org/record/3997165#.X9KUBF6nzUI. The running scripts, and operation inputs for EMEP, are available here: https://zenodo.org/record/3997301#.X9KUAF6nzUI and https://zenodo.org/record/3997271#.X9KV1F6nzUI. This dataset is an extension of the Britain Breathing 2016-2019 Air Quality and Meteorological Dataset, available here: https://zenodo.org/record/4416028#.YIrJfOvTXUL. The file 'site_location_data.csv' in this dataset contains the location metadata (site_id, latitude, longitude, postcode area) for the dataset here too. The dataset is presented in CSV format as the file 'turing_aq_daily_met_pollen_pollution_data_2020.csv', described below. The columns intended to be used as indexes are: timestamp, date of measurements on that row site_id, measurement site ID, corresponding to sites in the three networks: AURN [indicated by AQ], MIDAS [indicated by WEATHER], or pollen [indicated by POLLEN]. The data columns are: O3, PM10, PM2.5, NO2, NOXasNO2, SO2, daily mean and maximum values in ug/m3 (all with "_max", "_mean", and "_flag" tags) AURN measurement data O3_EMEP, NO2_EMEP, SO2_EMEP, NOXasNO2_EMEP, PM2.5_EMEP, PM10_EMEP, daily mean and maximum values in ug/m3 (all with "_max", and "_mean" tags) EMEP model forecasts alnus, ambrosia, artemisia, betula, corylus, fraxinus, platanus, poaceae, quercus, salix, ulmus, urtica, daily pollen grain counts temperature, relativehumidity, pressure, daily mean and maximum values in degC, %, and hPa (all with "_max", "_mean", and "_flag" tags). Met Office measurement data The "_flag" columns indicate data points which have been partially, or fully, imputed. The values for these will be in the range 0-1, and indicate the fraction of the hourly values within that day that are imputed (0 = none, 1 = all 24 hourly datapoints are imputed). No imputation has been carried out for this dataset, so the "_flag" data in this dataset will always be zero (the number of hourly data points used to calculate the daily mean and maximum are not recorded in this dataset).
DOI: 10.15468/xw5be5
title: Revisiting the type of Cespitularia stolonifera Gohar, 1938 leads to the description of a new genus and a species of the family Xeniidae (Octocorallia, Alcyonacea)

description: This dataset contains the digitized treatments in Plazi based on the original journal article Benayahu, Yehuda, Van Ofwegen, Leen P., Ruiz Allais, J. P., Mcfadden, Catherine S. (2021): Revisiting the type of Cespitularia stolonifera Gohar, 1938 leads to the description of a new genus and a species of the family Xeniidae (Octocorallia, Alcyonacea). Zootaxa 4964 (2): 330-344, DOI: https://doi.org/10.11646/zootaxa.4964.2.5
DOI: 10.6084/m9.figshare.12601048.v1
title: Inverse time trends of peptic ulcer and reflux esophagitis show significant association with reduced prevalence of <i>Helicobacter pylori</i> infection

description: Recent prevalence and trends of gastric/duodenal ulcer (GU/DU) and reflux esophagitis (RE) are inadequate. We reviewed the records of consecutive 211,347 general population subjects from 1991 to 2015. During the 25 years, the prevalence of GU and DU has gradually decreased (from 3.0% to 0.3% and from 2.0% to 0.3%) whereas that of RE has markedly increased (from 2.0% to 22%). The prevalence of <i>Helicobacter pylori</i> (HP) infection has decreased from 49.8% (in 1996) to 31.2% (in 2010). Multivariable logistic regression analyses demonstrated that HP infection was positively associated with GU/DU and negatively associated with RE with statistical significance. The panel data analyses showed that reduced rate of HP infection is proportionally correlated with decrease of GU/DU and inversely correlated with increase of RE. It is further suggested other latent factors should be important for changed prevalence of these three acid-related diseases. Age-period-cohort analysis indicated the significant association of older age, male gender, and absence of HP infection with RE. The prevalence of GU and DU has gradually decreased whereas that of RE has markedly increased in Japan. Inverse time trends of peptic ulcer and reflux esophagitis are significantly associated with reduced prevalence of HP infection.KEY MESSAGESThe prevalence of gastric and duodenal ulcer has gradually decreased whereas that of reflux esophagitis has markedly increased in Japan.The prevalence of <i>Helicobacter pylori</i> infection in Japan has greatly decreased from 49.8% to 31.2% during the 14 years (from 1996 to 2010).Inverse time trends of peptic ulcer and reflux esophagitis are associated with reduced prevalence of <i>Helicobacter pylori</i> infection with statistical significance. The prevalence of gastric and duodenal ulcer has gradually decreased whereas that of reflux esophagitis has markedly increased in Japan. The prevalence of <i>Helicobacter pylori</i> infection in Japan has greatly decreased from 49.8% to 31.2% during the 14 years (from 1996 to 2010). Inverse time trends of peptic ulcer and reflux esophagitis are associated with reduced prevalence of <i>Helicobacter pylori</i> infection with statistical significance.
DOI: 10.6084/m9.figshare.12601048
title: Inverse time trends of peptic ulcer and reflux esophagitis show significant association with reduced prevalence of <i>Helicobacter pylori</i> infection

description: Recent prevalence and trends of gastric/duodenal ulcer (GU/DU) and reflux esophagitis (RE) are inadequate. We reviewed the records of consecutive 211,347 general population subjects from 1991 to 2015. During the 25 years, the prevalence of GU and DU has gradually decreased (from 3.0% to 0.3% and from 2.0% to 0.3%) whereas that of RE has markedly increased (from 2.0% to 22%). The prevalence of <i>Helicobacter pylori</i> (HP) infection has decreased from 49.8% (in 1996) to 31.2% (in 2010). Multivariable logistic regression analyses demonstrated that HP infection was positively associated with GU/DU and negatively associated with RE with statistical significance. The panel data analyses showed that reduced rate of HP infection is proportionally correlated with decrease of GU/DU and inversely correlated with increase of RE. It is further suggested other latent factors should be important for changed prevalence of these three acid-related diseases. Age-period-cohort analysis indicated the significant association of older age, male gender, and absence of HP infection with RE. The prevalence of GU and DU has gradually decreased whereas that of RE has markedly increased in Japan. Inverse time trends of peptic ulcer and reflux esophagitis are significantly associated with reduced prevalence of HP infection.KEY MESSAGESThe prevalence of gastric and duodenal ulcer has gradually decreased whereas that of reflux esophagitis has markedly increased in Japan.The prevalence of <i>Helicobacter pylori</i> infection in Japan has greatly decreased from 49.8% to 31.2% during the 14 years (from 1996 to 2010).Inverse time trends of peptic ulcer and reflux esophagitis are associated with reduced prevalence of <i>Helicobacter pylori</i> infection with statistical significance. The prevalence of gastric and duodenal ulcer has gradually decreased whereas that of reflux esophagitis has markedly increased in Japan. The prevalence of <i>Helicobacter pylori</i> infection in Japan has greatly decreased from 49.8% to 31.2% during the 14 years (from 1996 to 2010). Inverse time trends of peptic ulcer and reflux esophagitis are associated with reduced prevalence of <i>Helicobacter pylori</i> infection with statistical significance.