cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8063765.v1
title: Beyond prediction: A framework for inference with variational approximations in mixture models

description: Variational inference is a popular method for estimating model parameters and conditional distributions in hierarchical and mixed models, which arise frequently in many settings in the health, social, and biological sciences. Variational inference in a frequentist context works by approximating intractable conditional distributions with a tractable family and optimizing the resulting lower bound on the log-likelihood. The variational objective function is typically less computationally intensive to optimize than the true likelihood, enabling scientists to fit rich models even with extremely large datasets. Despite widespread use, little is known about the general theoretical properties of estimators arising from variational approximations to the log-likelihood, which hinders their use in inferential statistics. In this paper we connect such estimators to profile <i>M</i>-estimation, which enables us to provide regularity conditions for consistency and asymptotic normality of variational estimators. Our theory also motivates three methodological improvements to variational inference: estimation of the asymptotic model-robust covariance matrix, a one-step correction that improves estimator efficiency, and an empirical assessment of consistency. We evaluate the proposed results using simulation studies and data on marijuana use from the National Longitudinal Study of Youth.
DOI: 10.6084/m9.figshare.8063579
title: Data (part) from Penk 2005 MSc thesis

description: <b>Data (part) from:</b><br>Penk MR (2005) Investigation into the food sources of the cockle (<i>Cerastoderma edule</i>) in Dublin Bay: multiple stable isotopes approach. MSc thesis. Centre for the Environment, University of Dublin, Trinity College, Ireland<br><b>Sample preparation:<br></b>Cerastoderma edule (Linnaeus, 1758) were frozen directly upon collection. They were thawed and processed within two months of collection. Adductor muscle tissues were extracted, rinsed with Milli Q water and acidified in 10% HCl to remove any shell remains. They were than rinsed twice with Milli Q water and dried for 24 hrs at 60°C. Dried samples were crushed using mortar and pestle, placed in plastic 10 ml tubes and retained for analysis.<br><br>Sediment samples were dried at 60°C rinsed with Milli Q water and sieved through a 63 μm sieve using a soft paintbrush. Particles obtained after sieving (&lt;63 μm) were placed in the oven at 60°C to evaporate all water. Dry particles were placed in glass beakers. Samples were then acidified by adding 10% HCl (at approximately five times sample volume) to remove carbonates. Beakers were than placed on a warm place to evaporate all acid. Dry sediment samples were than rinsed by adding Milli Q water to the beakers (five times the sample volume) and the beakers placed on a warm plate until dry. Rinsing was repeated three times to remove acid residues by evaporation. Dry samples were then crushed using a mortar and pestle, placed in plastic tubes and retained for analysis.<br><b>Sample processing:<br></b>Samples were weighed into microanalytical capsules on a Sartorius MC5 microanalytical balance. Samples were than analyzed on 18 August 2005 for stable isotopes of C and N ratios using a Thermo Delta Plus continuous flow isotope ratio mass spectrometer (CF-IRMS) coupled to a CE Instruments 1112 Flash elemental analyser (EA) by a Conflo III interface. Results were obtained in relation to international standards (atmospheric nitrogen and carbon from PeeDee Belemnite) and presented as standard delta connotations Additionally, %N, %C as well as C:N ratio values have been obtained. The precision of the elemental analyser has been established on L-Alanine standard samples (for Δ13C: 0.82‰, for Δ15: 0.21‰).<br>
DOI: 10.6084/m9.figshare.8063624.v1
title: SLEUTH model data

description: Data includes the urban layer, the slope layer, the hill-shade layer, the transportation layer and the exclusion layers for three scenarios.
DOI: 10.6084/m9.figshare.8063726.v1
title: parins-fukuchi_supp.zip

description: raw data and scripts from a submitted paper<br>
DOI: 10.6084/m9.figshare.8063579.v2
title: Data (part) from Penk 2005 MSc thesis

description: <b>Data (part) from:</b><br>Penk MR (2005) Investigation into the food sources of the cockle (<i>Cerastoderma edule</i>) in Dublin Bay: multiple stable isotopes approach. MSc thesis. Centre for the Environment, University of Dublin, Trinity College, Ireland<br><b>Sample preparation:<br></b>Cerastoderma edule (Linnaeus, 1758) were frozen directly upon collection. They were thawed and processed within two months of collection. Adductor muscle tissues were extracted, rinsed with Milli Q water and acidified in 10% HCl to remove any shell remains. They were than rinsed twice with Milli Q water and dried for 24 hrs at 60°C. Dried samples were crushed using mortar and pestle, placed in plastic 10 ml tubes and retained for analysis.<br><br>Sediment samples were dried at 60°C rinsed with Milli Q water and sieved through a 63 μm sieve using a soft paintbrush. Particles obtained after sieving (&lt;63 μm) were placed in the oven at 60°C to evaporate all water. Dry particles were placed in glass beakers. Samples were then acidified by adding 10% HCl (at approximately five times sample volume) to remove carbonates. Beakers were than placed on a warm place to evaporate all acid. Dry sediment samples were than rinsed by adding Milli Q water to the beakers (five times the sample volume) and the beakers placed on a warm plate until dry. Rinsing was repeated three times to remove acid residues by evaporation. Dry samples were then crushed using a mortar and pestle, placed in plastic tubes and retained for analysis.<br><b>Sample processing:<br></b>Samples were weighed into microanalytical capsules on a Sartorius MC5 microanalytical balance. Samples were than analyzed on 18 August 2005 for stable isotopes of C and N ratios using a Thermo Delta Plus continuous flow isotope ratio mass spectrometer (CF-IRMS) coupled to a CE Instruments 1112 Flash elemental analyser (EA) by a Conflo III interface. Results were obtained in relation to international standards (atmospheric nitrogen and carbon from PeeDee Belemnite) and presented as standard delta connotations Additionally, %N, %C as well as C:N ratio values have been obtained. The precision of the elemental analyser has been established on L-Alanine standard samples (for Δ13C: 0.82‰, for Δ15: 0.21‰).<br>
DOI: 10.6084/m9.figshare.8063579.v1
title: Data (part) from Penk 2005 MSc thesis

description: <b>Data (part) from:</b><br>Penk MR (2005) Investigation into the food sources of the cockle (<i>Cerastoderma edule</i>) in Dublin Bay: multiple stable isotopes approach. MSc thesis. Centre for the Environment, University of Dublin, Trinity College, Ireland<br><b>Sample preparation:<br></b>Cerastoderma edule (Linnaeus, 1758) were frozen directly upon collection. They were thawed and processed within two months of collection. Adductor muscle tissues were extracted, rinsed with Milli Q water and acidified in 10% HCl to remove any shell remains. They were than rinsed twice with Milli Q water and dried for 24 hrs at 60°C. Dried samples were crushed using mortar and pestle, placed in plastic 10 ml tubes and retained for analysis.<br><br>Sediment samples were dried at 60°C rinsed with Milli Q water and sieved through a 63 μm sieve using a soft paintbrush. Particles obtained after sieving (&lt;63 μm) were placed in the oven at 60°C to evaporate all water. Dry particles were placed in glass beakers. Samples were then acidified by adding 10% HCl (at approximately five times sample volume) to remove carbonates. Beakers were than placed on a warm place to evaporate all acid. Dry sediment samples were than rinsed by adding Milli Q water to the beakers (five times the sample volume) and the beakers placed on a warm plate until dry. Rinsing was repeated three times to remove acid residues by evaporation. Dry samples were then crushed using a mortar and pestle, placed in plastic tubes and retained for analysis.<br><b>Sample processing:<br></b>Samples were weighed into microanalytical capsules on a Sartorius MC5 microanalytical balance. Samples were than analyzed on 18 August 2005 for stable isotopes of C and N ratios using a Thermo Delta Plus continuous flow isotope ratio mass spectrometer (CF-IRMS) coupled to a CE Instruments 1112 Flash elemental analyser (EA) by a Conflo III interface. Results were obtained in relation to international standards (atmospheric nitrogen and carbon from PeeDee Belemnite) and presented as standard delta connotations Additionally, %N, %C as well as C:N ratio values have been obtained. The precision of the elemental analyser has been established on L-Alanine standard samples (for Δ13C: 0.82‰, for Δ15: 0.21‰).<br>
DOI: 10.6084/m9.figshare.12724058
title: Metadata record for: HIT-COVID, a global database tracking public health interventions to COVID-19

description: This dataset contains key characteristics about the data described in the Data Descriptor HIT-COVID, a global database tracking public health interventions to COVID-19. <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.12724058.v1
title: Metadata record for: HIT-COVID, a global database tracking public health interventions to COVID-19

description: This dataset contains key characteristics about the data described in the Data Descriptor HIT-COVID, a global database tracking public health interventions to COVID-19. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format
DOI: 10.17028/rd.lboro.8063387
title: Dynamics: all states, 15 modes

description: Input and output files of the dynamics using all states and 15 modes.<br><b>PREP</b> - general preparation filesPREP/LVC.template - LVC parameters usedPREP/ref_dyn.bash - script for generating diabatic initital conditions<br>MCTDH/pop.out - reference diabatic populations at the MCTDH level<br><b>AFSSH_E</b>, <b>EDC_Eph-plus</b>, etc. - SHARC runsAFSSH_E/input.new - SHARC input file for AFSSH/<i>E</i>AFSSH_E/pop3.out - Number of trajectories in each MCH state (multiplets summed up) for AFSSH/<i>E</i><br>AFSSH_E/pop9.out - Quantum amplitudes in MCH picture (multiplets summed up) for AFSSH/<i>E</i><br>AFSSH_E/pop13.out - Transform diagonal populations to MCH states (multiplets summed up) - classical - for AFSSH/<i>E</i>AFSSH_E/pop15.out - Transform diagonal populations to MCH states (multiplets summed up) - mixed quantum/classical - for AFSSH/<i>E</i><br>AFSSH_E/pop20.out - Quantum amplitudes in diabatic picture - quantum - for AFSSH/<i>E</i><br>AFSSH_E/pop21.out - Quantum amplitudes in diabatic picture - classical - for AFSSH/<i>E</i><br>AFSSH_E/pop22.out - Quantum amplitudes in diabatic picture - mixed quantum/classical - for AFSSH/<i>E</i><i><br></i>
DOI: 10.6084/m9.figshare.8063369
title: datasets.zipConfocal Microscopy Images of Cardiomyocyte Development Stages

description: Datasets of confocal microscopy images of cardiomyocytes aimed at development of image recognition systems. Images of live and healthy cardiomyocytes were assigned into 5 classes according to their development stages. The least developed cardiomyocytes were considered to be at stage~1 (class 1) while the most developed ones were assigned stage~5 (class 5). All other images belong to a class 0. We provide three datasets of the cardiomyocyte images. The resolution of images is 1024 x 1024 px. Datasets T-XXX-A and T-XXX-B are aimed at training of image recognition systems, while a dataset E-XXX-A is aimed at their evaluation. The dataset T-XXX-B is T-XXX-A extended about manually modified images, so that T-XXX-B is 3 times bigger compared to T-XXX-A. We also provide a Python script which allow augmentation of the images by their flipping and rotation. The script further allows resizing of the images and it generates a csv file that consists of records about each generated image. The records specify all operations that were used for its generation.<br>
DOI: 10.6084/m9.figshare.8063357
title: Data (part) from Penk et al 2015 Diversity and Distributions

description: Data (part) from:<br>Penk MR, Donohue I, Récoules V & Irvine K (2015) Elevated temperatures interact with habitat quality to undermine survival of ectotherms in climatic refugia. Diversity and Distributions, 21: 200–210.<br><br>Laboratory experiments:<br>The effect of temperature on survival of <i>Mysis salemaai</i> in hypoxia was examined over 24 hrs in a flow-through closed-circuit experimental system. Oxygen concentration was manipulated in a 5-L reservoir by bubbling either air or nitrogen gas through water, which was then circulated at 0.5 L min 1 using a submersible pump through a 1-L experimental bottle. The entire unit was submerged in either a 10 or 15 °C water bath.
DOI: 10.6084/m9.figshare.8063366
title: Izuddin et al., 2019 - Availability of orchid mycorrhizal fungi on roadside trees in a tropical urban landscape (sequencing data)

description: These DNA sequences were obtained from bark and orchid root samples via Illumina® MiSeq sequencer (Illumina, Inc., San Diego, California, USA) and ware used in the article "Availability of orchid mycorrhizal fungi on roadside trees in a tropical urban landscape" by Izuddin et al. (2019). They were assembled using PEAR 0.9.11 (by Zhang et al. 2014, "PEAR: a fast and accurate Illumina Paired-end reAd mergeR"). The primer combinations used were ITS86F / ITS4 and ITS1 / ITS4-TUL.
DOI: 10.17028/rd.lboro.8063387.v2
title: Dynamics: all states, 15 modes

description: Input and output files of the dynamics using all states and 15 modes.<br><b>PREP</b> - general preparation filesPREP/LVC.template - LVC parameters usedPREP/ref_dyn.bash - script for generating diabatic initital conditions<br>MCTDH/pop.out - reference diabatic populations at the MCTDH level<br><b>AFSSH_E</b>, <b>EDC_Eph-plus</b>, etc. - SHARC runsAFSSH_E/input.new - SHARC input file for AFSSH/<i>E</i>AFSSH_E/pop3.out - Number of trajectories in each MCH state (multiplets summed up) for AFSSH/<i>E</i><br>AFSSH_E/pop9.out - Quantum amplitudes in MCH picture (multiplets summed up) for AFSSH/<i>E</i><br>AFSSH_E/pop13.out - Transform diagonal populations to MCH states (multiplets summed up) - classical - for AFSSH/<i>E</i>AFSSH_E/pop15.out - Transform diagonal populations to MCH states (multiplets summed up) - mixed quantum/classical - for AFSSH/<i>E</i><br>AFSSH_E/pop20.out - Quantum amplitudes in diabatic picture - quantum - for AFSSH/<i>E</i><br>AFSSH_E/pop21.out - Quantum amplitudes in diabatic picture - classical - for AFSSH/<i>E</i><br>AFSSH_E/pop22.out - Quantum amplitudes in diabatic picture - mixed quantum/classical - for AFSSH/<i>E</i><i><br></i>
DOI: 10.17028/rd.lboro.8063387.v1
title: Dynamics: all states, 15 modes

description: Input and output files of the dynamics using all states and 15 modes.<br><b>PREP</b> - general preparation filesPREP/LVC.template - LVC parameters usedPREP/ref_dyn.bash - script for generating diabatic initital conditions<br>MCTDH/pop.out - reference diabatic populations at the MCTDH level<br><b>AFSSH_E</b>, <b>EDC_Eph-plus</b>, etc. - SHARC runsAFSSH_E/input.new - SHARC input file for AFSSH/<i>E</i>AFSSH_E/pop.out - diabatic populations for AFSSH/<i>E</i>
DOI: 10.6084/m9.figshare.8063366.v2
title: Izuddin et al., 2019 - Availability of orchid mycorrhizal fungi on roadside trees in a tropical urban landscape (sequencing data)

description: These DNA sequences were obtained from bark and orchid root samples via Illumina® MiSeq sequencer (Illumina, Inc., San Diego, California, USA) and ware used in the article "Availability of orchid mycorrhizal fungi on roadside trees in a tropical urban landscape" by Izuddin et al. (2019). They were assembled using PEAR 0.9.11 (by Zhang et al. 2014, "PEAR: a fast and accurate Illumina Paired-end reAd mergeR"). The primer combinations used were ITS86F / ITS4 and ITS1 / ITS4-TUL.
DOI: 10.6084/m9.figshare.8063366.v1
title: Izuddin et al., 2019 - Availability of orchid mycorrhizal fungi on roadside trees in a tropical urban landscape (sequencing data)

description: These DNA sequences were obtained from bark and orchid root samples via Illumina® MiSeq sequencer (Illumina, Inc., San Diego, California, USA) and ware used in the article "Availability of orchid mycorrhizal fungi on roadside trees in a tropical urban landscape" by Izuddin et al. (2019). They were assembled using PEAR 0.9.11 (by Zhang et al. 2014, "PEAR: a fast and accurate Illumina Paired-end reAd mergeR"). The primer combinations used were ITS86F / ITS4 and ITS1 / ITS4-TUL.
DOI: 10.6084/m9.figshare.8063357.v2
title: Data (part) from Penk et al 2015 Diversity and Distributions

description: Data (part) from:<br>Penk MR, Donohue I, Récoules V & Irvine K (2015) Elevated temperatures interact with habitat quality to undermine survival of ectotherms in climatic refugia. Diversity and Distributions, 21: 200–210.<br><br>Laboratory experiments:<br>The effect of temperature on survival of <i>Mysis salemaai</i> in hypoxia was examined over 24 hrs in a flow-through closed-circuit experimental system. Oxygen concentration was manipulated in a 5-L reservoir by bubbling either air or nitrogen gas through water, which was then circulated at 0.5 L min 1 using a submersible pump through a 1-L experimental bottle. The entire unit was submerged in either a 10 or 15 °C water bath.
DOI: 10.6084/m9.figshare.8063357.v1
title: Data from Penk et al 2015 Diversity and Distributions

description: Data (part) from:<br>Penk MR, Donohue I, Récoules V & Irvine K (2015) Elevated temperatures interact with habitat quality to undermine survival of ectotherms in climatic refugia. Diversity and Distributions, 21: 200–210.<br><br>Laboratory experiments:<br>The effect of temperature on survival of <i>Mysis salemaai</i> in hypoxia was examined over 24 hrs in a flow-through closed-circuit experimental system. Oxygen concentration was manipulated in a 5-L reservoir by bubbling either air or nitrogen gas through water, which was then circulated at 0.5 L min 1 using a submersible pump through a 1-L experimental bottle. The entire unit was submerged in either a 10 or 15 °C water bath.
DOI: 10.17028/rd.lboro.8063312
title: Wigner distribution, 15 modes

description: These are the input/output files relevant to the Wigner distribution for the 15-mode model.<br>
DOI: 10.17028/rd.lboro.8063318
title: Wigner distribution all modes

description: These are the input/output files relevant to the Wigner distribution for the model containing all modes.
DOI: 10.17028/rd.lboro.8063312.v1
title: Wigner distribution, 15 modes

description: These are the input/output files relevant to the Wigner distribution for the 15-mode model.<br>
DOI: 10.17028/rd.lboro.8063318.v1
title: Wigner distribution all modes

description: These are the input/output files relevant to the Wigner distribution for the model containing all modes.
DOI: 10.6084/m9.figshare.8063216
title: The association between PTSD and cardiovascular disease and its risk factors in male veterans of the Iraq/Afghanistan conflicts: a systematic review

description: Military personnel with Post-Traumatic Stress Disorder (PTSD) can experience high levels of mental and physical health comorbidity, potentially indicating a high level of functional impairment that can impact on both military readiness and later ill-health. There is strong evidence to implicate PTSD as a contributory factor to Cardiovascular Disease (CVD) among serving personnel and veterans. This systematic review focusses on the association between PTSD and cardiovascular disease/risk factors in male, military serving and ex-serving personnel who served in the Iraq/Afghanistan conflicts. PUBMED, MEDLINE, PILOTS, EMBASE, PSYCINFO, and PSYCARTICLES were searched using PRISMA guidelines. Three hundred and forty-three records were identified, of which 20 articles were selected. PTSD was positively associated with the development of CVD, specifically circulatory diseases, including hypertension. PTSD was also positively associated with the following risk factors: elevated heart rate, tobacco use, dyslipidaemia, and obesity. Conflicting data is presented regarding heart rate variability and inflammatory markers. Future studies would benefit from a standardized methodological approach to investigating PTSD and physical health manifestations. It is suggested that clinicians offer health advice for CVD at an earlier age for ex-/serving personnel with PTSD.
DOI: 10.6084/m9.figshare.8063186
title: Document corpus of court case judgments

description: The data set contains Indian Supreme Court judgments. These cases are extracted using a web crawler from the website www.judis.nic.in. Preliminary pre-processing of removal of header/ metadata information from the document is performed.
DOI: 10.6084/m9.figshare.8063216.v2
title: The association between PTSD and cardiovascular disease and its risk factors in male veterans of the Iraq/Afghanistan conflicts: a systematic review

description: Military personnel with Post-Traumatic Stress Disorder (PTSD) can experience high levels of mental and physical health comorbidity, potentially indicating a high level of functional impairment that can impact on both military readiness and later ill-health. There is strong evidence to implicate PTSD as a contributory factor to Cardiovascular Disease (CVD) among serving personnel and veterans. This systematic review focusses on the association between PTSD and cardiovascular disease/risk factors in male, military serving and ex-serving personnel who served in the Iraq/Afghanistan conflicts. PUBMED, MEDLINE, PILOTS, EMBASE, PSYCINFO, and PSYCARTICLES were searched using PRISMA guidelines. Three hundred and forty-three records were identified, of which 20 articles were selected. PTSD was positively associated with the development of CVD, specifically circulatory diseases, including hypertension. PTSD was also positively associated with the following risk factors: elevated heart rate, tobacco use, dyslipidaemia, and obesity. Conflicting data is presented regarding heart rate variability and inflammatory markers. Future studies would benefit from a standardized methodological approach to investigating PTSD and physical health manifestations. It is suggested that clinicians offer health advice for CVD at an earlier age for ex-/serving personnel with PTSD.
DOI: 10.6084/m9.figshare.8063156
title: MAMEM SCI questionnaire study results.xlsx

description: MAMEM SCI questionnaire study results