cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1514983
title: High resolution distance ambulated time series in Japanese quail in a home-cage environment over a 6.5 day period (ALL SERIES)

description: Each data point represents the distance moved (cm) by the center of the animal recorded at 0.5s time interval (xi), over a 6.5 day period .The total number of data points is approximately 1.070.000. In this experiment in a whole, the locomotor activity of 24 adult females quail (100-140 days old) was evaluated in a home-cage environment in a white wooden box measuring 40 x 40 x 40 cm (width x length x height, respectively) with a wire mesh floor. A metal bar wall divided the box in two same-size zones (feeding, nesting), and an opening served as a door allowing the bird to move freely between compartments. A video camera that automatically switched to infrared recording after lights were turned off was suspended 1.5m above the box. It was connected to a computer in an adjacent room and could be accessed remotely by experimenters. Testing began at approximately 1:00 PM, when 12 quail were placed in a box, and transported to a nearby experimental room. Each bird was then placed individually in the feeding zone of one of the boxes. During the following 6.5 days, the birds’ locomotor activity was continuously recorded. Testing ended at 9 PM the 7th day. Daily maintenance activities (egg collection, cleaning and feeding) were performed between 12 and 12:30 PM; the activity during this period was not included in time series, which in total implied a loss of 2% from the data set. Since only 12 birds could be tested simultaneously, two consecutive groups of 12 individuals were evaluated (group 1 and group 2). We used the commercially available ANY-MAZE@ computer program to register the center of the animals coordinates (x,y) at 0.5 s intervals.
DOI: 10.6084/m9.figshare.1515002.v4
title: Capturing Dynamics of Biased Attention

description: Simulation study to assess characteristics of ABV and TL-BS indices.
DOI: 10.6084/m9.figshare.1514982
title: High resolution zone location time series in Japanese quail in a home-cage environment over a 6.5 day period (ALL SERIES)

description: Each data point represents the zone of the box the animal was positioned in (see description bellow) recorded at 0.5s time interval, over a 6.5 day period.The total number of data points is approximately 1.070.000. In this experiment in a whole, the locomotor activity of 24 adult females quail (100-140 days old) was evaluated in a home-cage environment in a white wooden box measuring 40 x 40 x 40 cm (width x length x height, respectively) with a wire mesh floor. A metal bar wall divided the box in two same-size compartments (feeding, nesting), and a 7.5 x 7.5 cm opening served as a door allowing the bird to move freely between compartments. In the feeding compartment, a feeder and an automatic nipple drinker (with drainage) were positioned, while in the nesting compartment, a small white rubber nest measuring 15 x 15 cm was placed. Each of these two compartments were then imaginarily divided into two zones, resulting in a total of 4 zones of equal dimensions for data analysis. Zone 1: Feeding compartment with automatic nipple drinker and feeder. Zone 2: Feeding compartment from which the bird has access to the door that connects both compartments. Zone 3: Nesting compartment where a 15 x 15 cm small rubber nest was placed. Zone 4: Nesting compartment from which the bird has access to the door that connects both compartments. A video camera that automatically switched to infrared recording after lights were turned off was suspended 1.5m above the box. It was connected to a computer in an adjacent room and could be accessed remotely by experimenters. Testing began at approximately 1:00 PM, when 12 quail were placed in a box, and transported to a nearby experimental room. Each bird was then placed individually in the feeding zone of one of the boxes. During the following 6.5 days, the birds’ locomotor activity was continuously recorded. Testing ended at 9 PM the 7th day. Daily maintenance activities (egg collection, cleaning and feeding) were performed between 12 and 12:30 PM; the activity during this period was not included in time series, which in total implied a loss of 2% from the data set. Since only 12 birds could be tested simultaneously, two consecutive groups of 12 individuals were evaluated (group 1 and group 2). We used the commercially available ANY-MAZE@ computer program to register the center of the animals coordinates (x,y) and located the zone the animal was positioned in at 0.5 s intervals.
DOI: 10.6084/m9.figshare.1515055.v3
title: Modified EPIRICE

description: EPIRICE model (Savary et al., 2012) was modified to fit in a national scale application in Korea, and used for the climate change impact analysis in Korea (Kim et al., 2015). - References *Savary, S., A. Nelson, L. Willocquet, I. Pangga, and J. Aunario, 2012. Modeling and mapping potential epidemics of rice diseases globally. Crop Protection 34, 6–17. *Kim, K.-H., Cho, J., Lee, Y.H., and Lee, W.-S. 2015. Predicting potential epidemics of rice leaf blast and sheath blight in South Korea under the RCP 4.5 and RCP 8.5 climate change scenarios using a rice disease epidemiology model, EPIRICE. Agricultural and Forest Meteorology, 203, 191-207.
DOI: 10.6084/m9.figshare.1515002.v5
title: Capturing Dynamics of Biased Attention

description: Simulation study to assess characteristics of ABV and TL-BS indices.
DOI: 10.6084/m9.figshare.1514895
title: 8TSPA

description: 8TSPA
DOI: 10.6084/m9.figshare.1514896
title: Gaussian Job Archive for C52H74N4O10Zn2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1514952
title: Open Notebook Science Challenge Solubility Dataset

description: A collection of 9730 organic and aqueous solubility measurements collected from the literature and measured using open notebook science. Measurements with assumed incorrect values are marked DONOTUSE.
DOI: 10.6084/m9.figshare.1514889
title: Gaussian Job Archive for C52H74N4O10Zn2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1514895.v1
title: 8TSPA

description: 8TSPA
DOI: 10.6084/m9.figshare.1514887
title: Gaussian Job Archive for C8H4O3

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1514888
title: Gaussian Job Archive for C52H74N4O10Zn2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1514889.v1
title: Gaussian Job Archive for C52H74N4O10Zn2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1514896.v1
title: Gaussian Job Archive for C52H74N4O10Zn2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1515002.v6
title: Capturing Dynamics of Biased Attention

description: Simulation study to assess characteristics of ABV and TL-BS indices.
DOI: 10.6084/m9.figshare.1514885
title: Gaussian Job Archive for C45H70N4O9Zn2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1514886
title: Gaussian Job Archive for C45H70N4O9Zn2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1514887.v1
title: Gaussian Job Archive for C8H4O3

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1514888.v1
title: Gaussian Job Archive for C52H74N4O10Zn2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1514884
title: Gaussian Job Archive for C45H70N4O9Zn2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1514885.v1
title: Gaussian Job Archive for C45H70N4O9Zn2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1514886.v1
title: Gaussian Job Archive for C45H70N4O9Zn2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1514882
title: Gaussian Job Archive for C44H70N4O7Zn2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1514883
title: Gaussian Job Archive for C45H70N4O9Zn2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1515002.v7
title: Capturing Dynamics of Biased Attention

description: Simulation study to assess characteristics of ABV and TL-BS indices.
DOI: 10.6084/m9.figshare.1514880
title: Gaussian Job Archive for C6H10O

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1514881
title: Gaussian Job Archive for CO2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1514884.v1
title: Gaussian Job Archive for C45H70N4O9Zn2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1514882.v1
title: Gaussian Job Archive for C44H70N4O7Zn2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1514883.v1
title: Gaussian Job Archive for C45H70N4O9Zn2

description: Archive of work produced using the resources of the Imperial College High Performance Computing Service.
DOI: 10.6084/m9.figshare.1514867
title: Data from: Bayesian Survival Trees for Clustered Observations, Applied to Tooth Prognosis

description: Tooth loss from periodontal disease or dental caries (decay) afflicts most adults over the course of their lives. Survival tree methods for correlated observations have shown potential for developing objective tooth prognosis systems, however the current tech- nology suffers either from prohibitive computational expense or unrealistic simplifying assumptions to overcome computational demands. In this article Bayesian tree meth- ods are developed for correlated survival data, relying on a computationally feasible, yet flexible, frailty model with piecewise constant hazard function. Bayesian stochastic search methods, using a Laplace approximated marginal likelihood, are detailed for tree construction and posterior ensemble averaged variable importance ranking and amal- gamation procedures are developed. The proposed methods are used to assign each tooth from the VA Dental Longitudinal Study to one of five prognosis categories and evaluate the effects of clinical factors and genetic polymorphisms in predicting tooth loss. The prognostic rules established may be used in clinical practice to optimize tooth retention and devise periodontal treatment plans.
DOI: 10.6084/m9.figshare.1514868
title: Data from: Survival Analysis with Electronic Health Record Data: Experiments with Chronic Kidney Disease

description: This paper presents a detailed survival analysis for chronic kidney disease (CKD). The analysis is based on the EHR data comprising almost two decades of clinical observations collected at New York-Presbyterian, a large hospital in New York City with one of the oldest electronic health records in the United States. Our survival analysis approach centers around Bayesian multiresolution hazard modeling, with an objective to capture the changing hazard of CKD over time, adjusted for patient clinical covariates and kidney-related laboratory tests. Special attention is paid to statistical issues common to all EHR data, such as cohort definition, missing data and censoring, variable selection, and potential for joint survival and longitudinal modeling, all of which are discussed alone and within the EHR CKD context.
DOI: 10.6084/m9.figshare.1514870
title: Measures of Agreement Between Many Raters for Ordinal Classifications

description: Screening and diagnostic procedures often require a physician’s subjective interpretation of a patient’s test result using an ordered categorical scale to define the patient’s disease severity. Due to wide variability observed between physicians’ ratings, many large-scale studies have been conducted to quantify agreement between multiple experts’ ordinal classifications in common diagnostic procedures such as mammography. However, very few statistical approaches are available to assess agreement in these large-scale settings. Existing summary measures of agreement rely on extensions of Cohen’s kappa [1 - 5]. These are prone to prevalence and marginal distribution issues, become increasingly complex for more than three experts or are not easily implemented. Here we propose a model-based approach to assess agreement in large-scale studies based upon a framework of ordinal generalized linear mixed models. A summary measure of agreement is proposed for multiple experts assessing the same sample of patients’ test results according to an ordered categorical scale. This measure avoids some of the key flaws associated with Cohen’s kappa and its extensions. Simulation studies are conducted to demonstrate the validity of the approach with comparison to commonly used agreement measures. The proposed methods are easily implemented using the software package R and are applied to two large-scale cancer agreement studies.
DOI: 10.6084/m9.figshare.1514866
title: Data from: Posterior Singular Spectrum Analysis

description: A method is proposed for finding interesting underlying features of a time series, such as trends, maxima, minima and oscillations. A combination of Singular Spectrum Analysis (SSA) and Bayesian modeling is used where the credibility of SSA signal components are analyzed via posterior simulation. The potential of the technique is demonstrated using artificial and real data examples. Our analysis of a Bayesian re- construction of post Ice Age temperature variation lends support for the presence oscillations detected in previous studies of the paleoclimate.
DOI: 10.6084/m9.figshare.1514868.v2
title: Data from: Survival Analysis with Electronic Health Record Data: Experiments with Chronic Kidney Disease

description: This paper presents a detailed survival analysis for chronic kidney disease (CKD). The analysis is based on the EHR data comprising almost two decades of clinical observations collected at New York-Presbyterian, a large hospital in New York City with one of the oldest electronic health records in the United States. Our survival analysis approach centers around Bayesian multiresolution hazard modeling, with an objective to capture the changing hazard of CKD over time, adjusted for patient clinical covariates and kidney-related laboratory tests. Special attention is paid to statistical issues common to all EHR data, such as cohort definition, missing data and censoring, variable selection, and potential for joint survival and longitudinal modeling, all of which are discussed alone and within the EHR CKD context.
DOI: 10.6084/m9.figshare.1513948
title: Pulication data for Plos

description: Pulication data for Plos
DOI: 10.6084/m9.figshare.1514866.v2
title: Data from: Posterior Singular Spectrum Analysis

description: A method is proposed for finding interesting underlying features of a time series, such as trends, maxima, minima and oscillations. A combination of Singular Spectrum Analysis (SSA) and Bayesian modeling is used where the credibility of SSA signal components are analyzed via posterior simulation. The potential of the technique is demonstrated using artificial and real data examples. Our analysis of a Bayesian re- construction of post Ice Age temperature variation lends support for the presence oscillations detected in previous studies of the paleoclimate.
DOI: 10.6084/m9.figshare.1514867.v2
title: Data from: Bayesian Survival Trees for Clustered Observations, Applied to Tooth Prognosis

description: Tooth loss from periodontal disease or dental caries (decay) afflicts most adults over the course of their lives. Survival tree methods for correlated observations have shown potential for developing objective tooth prognosis systems, however the current tech- nology suffers either from prohibitive computational expense or unrealistic simplifying assumptions to overcome computational demands. In this article Bayesian tree meth- ods are developed for correlated survival data, relying on a computationally feasible, yet flexible, frailty model with piecewise constant hazard function. Bayesian stochastic search methods, using a Laplace approximated marginal likelihood, are detailed for tree construction and posterior ensemble averaged variable importance ranking and amal- gamation procedures are developed. The proposed methods are used to assign each tooth from the VA Dental Longitudinal Study to one of five prognosis categories and evaluate the effects of clinical factors and genetic polymorphisms in predicting tooth loss. The prognostic rules established may be used in clinical practice to optimize tooth retention and devise periodontal treatment plans.
DOI: 10.6084/m9.figshare.1513948.v1
title: Pulication data for Plos

description: Pulication data for Plos
DOI: 10.6084/m9.figshare.1514866.v1
title: Posterior Singular Spectrum Analysis

description: A method is proposed for finding interesting underlying features of a time series, such as trends, maxima, minima and oscillations. A combination of Singular Spectrum Analysis (SSA) and Bayesian modeling is used where the credibility of SSA signal components are analyzed via posterior simulation. The potential of the technique is demonstrated using artificial and real data examples. Our analysis of a Bayesian re- construction of post Ice Age temperature variation lends support for the presence oscillations detected in previous studies of the paleoclimate.
DOI: 10.6084/m9.figshare.1514867.v1
title: Bayesian Survival Trees for Clustered Observations, Applied to Tooth Prognosis

description: Tooth loss from periodontal disease or dental caries (decay) afflicts most adults over the course of their lives. Survival tree methods for correlated observations have shown potential for developing objective tooth prognosis systems, however the current tech- nology suffers either from prohibitive computational expense or unrealistic simplifying assumptions to overcome computational demands. In this article Bayesian tree meth- ods are developed for correlated survival data, relying on a computationally feasible, yet flexible, frailty model with piecewise constant hazard function. Bayesian stochastic search methods, using a Laplace approximated marginal likelihood, are detailed for tree construction and posterior ensemble averaged variable importance ranking and amal- gamation procedures are developed. The proposed methods are used to assign each tooth from the VA Dental Longitudinal Study to one of five prognosis categories and evaluate the effects of clinical factors and genetic polymorphisms in predicting tooth loss. The prognostic rules established may be used in clinical practice to optimize tooth retention and devise periodontal treatment plans.
DOI: 10.6084/m9.figshare.1514868.v1
title: Survival Analysis with Electronic Health Record Data: Experiments with Chronic Kidney Disease

description: This paper presents a detailed survival analysis for chronic kidney disease (CKD). The analysis is based on the EHR data comprising almost two decades of clinical observations collected at New York-Presbyterian, a large hospital in New York City with one of the oldest electronic health records in the United States. Our survival analysis approach centers around Bayesian multiresolution hazard modeling, with an objective to capture the changing hazard of CKD over time, adjusted for patient clinical covariates and kidney-related laboratory tests. Special attention is paid to statistical issues common to all EHR data, such as cohort definition, missing data and censoring, variable selection, and potential for joint survival and longitudinal modeling, all of which are discussed alone and within the EHR CKD context.
DOI: 10.6084/m9.figshare.1513845
title: SGS Open Source Malaria 2015

description: Open Source malaria, student reports 2015
DOI: 10.6084/m9.figshare.1513853
title: American Civil War Era Financial Data

description: Miscellaneous financial and economic datasets from the period around the U.S. Civil War gathered from a variety of sources.
DOI: 10.6084/m9.figshare.1513854
title: Anvio v1.0.2-beta

description: OS X installer for anvi'o v1.0.2-beta.
DOI: 10.6084/m9.figshare.1513841
title: Shaw, M. Antimalarial Properties of Drugs in the Triazolopyrazine Series

description: Mackenzie Shaw, Open Source Malaria paper 2015
DOI: 10.6084/m9.figshare.1513853.v1
title: American Civil War Era Financial Data

description: Miscellaneous financial and economic datasets from the period around the U.S. Civil War gathered from a variety of sources.
DOI: 10.6084/m9.figshare.1513841.v1
title: Shaw, M. Antimalarial Properties of Drugs in the Triazolopyrazine Series

description: Mackenzie Shaw, Open Source Malaria paper 2015
DOI: 10.6084/m9.figshare.1513854.v1
title: Anvio v1.0.2-beta

description: OS X installer for anvi'o v1.0.2-beta.
DOI: 10.6084/m9.figshare.1513838
title: Retinopic mapping analysis

description: Matlab functions to analyse travelling wave retinotopic mapping data. Note that these functions are very old and their use is not recommended.
DOI: 10.6084/m9.figshare.1513840
title: Shepherd's Pi

description: Shepherd's Pi correlation - the method presented in our article "Better ways to improve standards in brain-behavior correlation analysis" in Front Hum Neurosci.
DOI: 10.6084/m9.figshare.1513839
title: Retinotopic mapping tutorial

description: My old retinotopic mapping tutorial and the associated Matlab functions for data analysis.
DOI: 10.6084/m9.figshare.1513845.v1
title: Open Source Malaria 2015

description: Open Source malaria, student reports 2015
DOI: 10.6084/m9.figshare.1513833
title: Data from global structure search of sulfur clusters

description: Raw data (structures and energies) from global structure search of sulfur clusters. The search was carried out using an evolutionary algorithm as implemented in the USPEX code, with VASP as the calculator and energies within density-functional theory with the PBE exchange-correlation functional as the fitness criteria. This is supporting data for a study of the free energy of mixed sulfur vapours.