cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25390/caryinstitute.7395032.v1
title: Cary Environmental Monitoring Program Daily Meteorological and Solar Radiation Data: 1988-2017

description: The Cary Institute of Ecosystem Studies Environmental Monitoring Program is a long-term data collection program designed to understand how the environment changes over time. The program includes monitoring of climate including temperature and precipitation, as well as variables related to air pollution, such as acid deposition and ozone, and water pollution and other streamwater chemistry. Our solar radiation monitoring includes diffuse and global photosynthetically active radiation (PAR), diffuse and global shortwave radiation, net radiation and UV. Long-term monitoring of solar radiation provides us with an understanding of atmospheric energy dynamics, which can affect natural and human systems. The Cary Institute of Ecosystem Studies, Environmental Monitoring Program furnishes data under the following conditions: The data have received quality assurance scrutiny by our program, and, although we are confident of the accuracy of these data, the Cary Institute will not be held liable for errors in these data. Data are subject to change resulting from updates in data screening or models used. Data citation: The following is a standard citation for referencing data from the Cary Institute of Ecosystem Studies, Environmental Monitoring Program:<br>Cary Institute of Ecosystem Studies, Environmental Monitoring Program. 2008 (or current year). Cary Institute of Ecosystem Studies, Box AB, Millbrook, NY 12545, www.caryinstitute.org. <br>Those wishing to publish data from the Cary Institute of Ecosystem Studies, Environmental Monitoring Program are encouraged to contact Data Manager Vicky Kelly, kellyv@caryinstitute.org.<br><br>
DOI: 10.6084/m9.figshare.7396037.v2
title: Linares_Dataset

description: Dataset related to a manuscript submitted to Scientific Data Journal.
DOI: 10.7284/120101
title: PTU (Pressure, Temperature, Humidity) data collected during research cruise OC1409A using a Vaisala PTU300 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7396037.v1
title: Linhares_Dataset

description: Dataset related to a manuscript submitted to Scientific Data Journal.
DOI: 10.7284/120103
title: Radiometer data collected during research cruise OC1409A using a RMR Co. PRP instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7393559
title: Hyoid bone movement label

description: The hyoid bone movement labeled by one human rater
DOI: 10.6084/m9.figshare.7393565
title: Novel approaches to sampling pollinators in whole landscapes: a lesson for landscape-wide biodiversity monitoring

description: ContextBiodiversity monitoring programs require fast, reliable and cost-effective methods for biodiversity assessment in landscapes. Sampling pollinators across entire landscapes is challenging, as trapping needs to cover many habitat types.ObjectivesWe developed and tested a landscape-wide sampling design for pollinators. We assessed the predictability and stability of pollinator biodiversity estimates in agricultural landscapes, and tested how estimates were affected by sampled habitat, landscape composition and spatial scale.MethodsWe sampled pollinators using pan traps at 250 locations in 10 replicated landscapes measuring 1 × 1 km and calculated bee richness predictions based on different sample sizes. Traps were placed regularly in each landscape, sampling each habitat proportionally to its area. Landscapes contained semi-natural habitats, crop fields and forests and differed in the amount of a mass-flowering crop (oilseed rape).ResultsRegular sampling reflected local habitat amount. Compared with cereal fields, significantly more pollinators occurred in oilseed rape, and fewer in forests. Sampling in only one habitat type led to biased estimates of landscape-wide bee species richness, even when sample size was increased. The spatial scale of best predictions depended on the sampled habitat. Species richness was overestimated when sampling was limited to semi-natural habitats and underestimated in oilseed rape fields. Precision increased with the number of sampling points per landscape.ConclusionsTo study landscape-wide pollinator biodiversity, we suggest to sample multiple sites per landscape in a broad range of resource-providing habitat types, with sample sizes proportional to habitat amount. Our approach will also be useful for biodiversity monitoring programs in general.
DOI: 10.6084/m9.figshare.7393565.v2
title: Novel approaches to sampling pollinators in whole landscapes: a lesson for landscape-wide biodiversity monitoring

description: ContextBiodiversity monitoring programs require fast, reliable and cost-effective methods for biodiversity assessment in landscapes. Sampling pollinators across entire landscapes is challenging, as trapping needs to cover many habitat types.ObjectivesWe developed and tested a landscape-wide sampling design for pollinators. We assessed the predictability and stability of pollinator biodiversity estimates in agricultural landscapes, and tested how estimates were affected by sampled habitat, landscape composition and spatial scale.MethodsWe sampled pollinators using pan traps at 250 locations in 10 replicated landscapes measuring 1 × 1 km and calculated bee richness predictions based on different sample sizes. Traps were placed regularly in each landscape, sampling each habitat proportionally to its area. Landscapes contained semi-natural habitats, crop fields and forests and differed in the amount of a mass-flowering crop (oilseed rape).ResultsRegular sampling reflected local habitat amount. Compared with cereal fields, significantly more pollinators occurred in oilseed rape, and fewer in forests. Sampling in only one habitat type led to biased estimates of landscape-wide bee species richness, even when sample size was increased. The spatial scale of best predictions depended on the sampled habitat. Species richness was overestimated when sampling was limited to semi-natural habitats and underestimated in oilseed rape fields. Precision increased with the number of sampling points per landscape.ConclusionsTo study landscape-wide pollinator biodiversity, we suggest to sample multiple sites per landscape in a broad range of resource-providing habitat types, with sample sizes proportional to habitat amount. Our approach will also be useful for biodiversity monitoring programs in general.
DOI: 10.7284/120104
title: Radiometer data collected during research cruise OC1409A using a Biospherical QSR-2200 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7393550
title: Analyzing the Speech Act

description: Data sets about the gender disagreement strategies<br>
DOI: 10.6084/m9.figshare.7393559.v1
title: Hyoid bone movement label

description: The hyoid bone movement labeled by one human rater
DOI: 10.6084/m9.figshare.7393544
title: The neck sensor signals

description: The neck sensor signals<br>
DOI: 10.7284/120105
title: Rain Gauge data collected during research cruise OC1409A using a RM Young 50202 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7393514
title: The hyoid bone movement comparison between computer calculation and two human raters

description: Three hyoid bone movements (coordinate values) for one swallow are listed in this file. The first two columns are the predicted hyoid bone movement based on the computer calculation, in which the input were the sensor signals. The third and forth columns are hyoid bone movements labeled by a human rater based on the X-ray videos, and the fifth and sixth columns are also hyoid bone movements labeled by another human rater.<br>The data in the excel file were also used for drawing the Figure 4(c)
DOI: 10.6084/m9.figshare.7393550.v1
title: data set - updated.xlsx

description: Data sets about the gender disagreement strategies
DOI: 10.7284/120096
title: Singlebeam Echosounder data collected during research cruise OC1409A using a Knudsen 3260 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/120098
title: Singlebeam Echosounder data collected during research cruise OC1409A using a Knudsen 3260 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7393493
title: pMPPla107 variants

description: Variants found on the pMPPla107 in six DBL408 (P. stutzeri) lines after 500 generations of evolution.
DOI: 10.7284/120106
title: Speedlog data collected during research cruise OC1409A using a Furuno DS-50 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/120094
title: Water Temperature data collected during research cruise OC1409A using a Sea-Bird SBE-48 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/120107
title: Water Temperature data collected during research cruise OC1409A using a Sea-Bird SBE-38 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/120108
title: Transmissometer data collected during research cruise OC1409A using a WET Labs C-Star instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/120109
title: TSG (Thermosalinograph) data collected during research cruise OC1409A using a Sea-Bird SBE-45 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/120124
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise OC1409B using a Hawaii UHDAS instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/120111
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise OC1409B using a Sea-Bird SBE-911+ instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/120114
title: Fluorometer data collected during research cruise OC1409B using a WET Labs WETStar instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/117350
title: GNSS (Global Navigation Satellite System) data collected during research cruise OC1409B using a Ashtech ADU5 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/120115
title: Gyrocompass data collected during research cruise OC1409B using a Sperry MK-37 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7393415
title: P. stutzeri Chromosomal Variants

description: Variants found on the chromosome of six DBL408 (P. stutzeri) lines after 500 generations of evolution.
DOI: 10.7284/120117
title: Hygrometer data collected during research cruise OC1409B using a Vaisala HMT300 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7393367
title: ABC–CDE: Toward Approximate Bayesian Computation With Complex High-Dimensional Data and Limited Simulations

description: Approximate Bayesian computation (ABC) is typically used when the likelihood is either unavailable or intractable but where data can be simulated under different parameter settings using a forward model. Despite the recent interest in ABC, high-dimensional data and costly simulations still remain a bottleneck in some applications. There is also no consensus as to how to best assess the performance of such methods without knowing the true posterior. We show how a nonparametric conditional density estimation (CDE) framework, which we refer to as ABC–CDE, help address three nontrivial challenges in ABC: (i) how to efficiently estimate the posterior distribution with limited simulations and different types of data, (ii) how to tune and compare the performance of ABC and related methods in estimating the posterior itself, rather than just certain properties of the density, and (iii) how to efficiently choose among a large set of summary statistics based on a CDE surrogate loss. We provide theoretical and empirical evidence that justify ABC–CDE procedures that <i>directly</i> estimate and assess the posterior based on an initial ABC sample, and we describe settings where standard ABC and regression-based approaches are inadequate. Supplemental materials for this article are available online.
DOI: 10.6084/m9.figshare.7393415.v1
title: P. stutzeri Chromosomal Variants

description: Variants found on the chromosome of six DBL408 (P. stutzeri) lines after 500 generations of evolution.
DOI: 10.7284/120116
title: PTU (Pressure, Temperature, Humidity) data collected during research cruise OC1409B using a Vaisala PTU300 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7393367.v2
title: ABC–CDE: Toward Approximate Bayesian Computation With Complex High-Dimensional Data and Limited Simulations

description: Approximate Bayesian computation (ABC) is typically used when the likelihood is either unavailable or intractable but where data can be simulated under different parameter settings using a forward model. Despite the recent interest in ABC, high-dimensional data and costly simulations still remain a bottleneck in some applications. There is also no consensus as to how to best assess the performance of such methods without knowing the true posterior. We show how a nonparametric conditional density estimation (CDE) framework, which we refer to as ABC–CDE, help address three nontrivial challenges in ABC: (i) how to efficiently estimate the posterior distribution with limited simulations and different types of data, (ii) how to tune and compare the performance of ABC and related methods in estimating the posterior itself, rather than just certain properties of the density, and (iii) how to efficiently choose among a large set of summary statistics based on a CDE surrogate loss. We provide theoretical and empirical evidence that justify ABC–CDE procedures that <i>directly</i> estimate and assess the posterior based on an initial ABC sample, and we describe settings where standard ABC and regression-based approaches are inadequate. Supplemental materials for this article are available online.
DOI: 10.6084/m9.figshare.7393415.v2
title: P. stutzeri Chromosomal Variants

description: Variants found on the chromosome of six DBL408 (P. stutzeri) lines after 500 generations of evolution.
DOI: 10.6084/m9.figshare.7393415.v3
title: P. stutzeri Chromosomal Variants

description: Variants found on the chromosome of six DBL408 (P. stutzeri) lines after 500 generations of evolution.
DOI: 10.6084/m9.figshare.7393367.v1
title: ABC-CDE: Towards Approximate Bayesian Computation with Complex High-Dimensional Data and Limited Simulations

description: Approximate Bayesian Computation (ABC) is typically used when the likelihood is either unavailable or intractable but where data can be simulated under different parameter settings using a forward model. Despite the recent interest in ABC, high-dimensional data and costly simulations still remain a bottleneck in some applications. There is also no consensus as to how to best assess the performance of such methods without knowing the true posterior. We show how a nonparametric conditional density estimation (CDE) framework, which we refer to as ABC-CDE, help address three nontrivial challenges in ABC: (i) how to efficiently estimate the posterior distribution with limited simulations and different types of data, (ii) how to tune and compare the performance of ABC and related methods in estimating the posterior itself, rather than just certain properties of the density, and (iii) how to efficiently choose among a large set of summary statistics based on a CDE surrogate loss. We provide theoretical and empirical evidence that justify ABC-CDE procedures that <i>directly</i> estimate and assess the posterior based on an initial ABC sample, and we describe settings where standard ABC and regression-based approaches are inadequate.
DOI: 10.7284/120118
title: Radiometer data collected during research cruise OC1409B using a Biospherical QSR-2200 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7393232
title: Average ROP grouped by history of stroke and gender

description: This file contains the statistics of Relative Overlapped Percentage of computer calculated Hyoid bone movement.
DOI: 10.7284/120119
title: Rain Gauge data collected during research cruise OC1409B using a RM Young 50202 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7393229
title: Fast and Accurate Approximation of the Full Conditional for Gamma Shape Parameters

description: The gamma distribution arises frequently in Bayesian models, but there is not an easy-to-use conjugate prior for the shape parameter of a gamma. This inconvenience is usually dealt with by using either Metropolis–Hastings moves, rejection sampling methods, or numerical integration. However, in models with a large number of shape parameters, these existing methods are slower or more complicated than one would like, making them burdensome in practice. It turns out that the full conditional distribution of the gamma shape parameter is well approximated by a gamma distribution, even for small sample sizes, when the prior on the shape parameter is also a gamma distribution. This article introduces a quick and easy algorithm for finding a gamma distribution that approximates the full conditional distribution of the shape parameter. We empirically demonstrate the speed and accuracy of the approximation across a wide range of conditions. If exactness is required, the approximation can be used as a proposal distribution for Metropolis–Hastings. Supplementary material for this article is available online.
DOI: 10.6084/m9.figshare.7393232.v1
title: Neck sensor-supported hyoid bone movement tracking during swallowing

description: Hyoid bone movement is an important physiological event during swallowing that contributes to normal swallowing function. In order to determine the adequate hyoid bone movement, clinicians conduct an X-ray videofluoroscopic swallowing study, which even though is the gold-standard technique, has limitations such as radiation exposure and cost. Here, we demonstrated the ability to track the hyoid bone movement using a non-invasive accelerometry sensor attached on the surface of the human neck. Specifically, deep neural networks were used to mathematically describe the relationship between hyoid bone movement and sensor signals. Training and validation of the system were conducted on a dataset of 400 swallows from 114 patients. Our experiments indicated the computer-aided hyoid bone movement prediction has a promising performance when compared with human experts' judgments, revealing that the universal pattern of the hyoid bone movement is acquirable by the highly nonlinear algorithm. Such a sensor-supported strategy offers an alternative and widely available method for online hyoid bone movement tracking without any radiation side-effects and provides a pronounced and flexible approach for identifying dysphagia and other swallowing disorders.
DOI: 10.6084/m9.figshare.7393226
title: “Critical Transitions” and “Avalanches” in Journal-Journal Citation Relations

description: Using the complete Journal Citation Reports (Science Citation Index, SCI, and Social Sciences Citation Index, SSCI) during the period 1994-2016 as data, we address the question of change and stability in the sciences at the level of the (n2) aggregated citation links between (n) journals. Information theory enables us to study longitudinal developments first at the level of cells and then to aggregate, since the Shannon-formulae are based on using Ss. Micro-developments in the data can thus be related to theorizing about the sciences in terms of distributed change (Price, 1976; cf. Kuhn, 1962).
DOI: 10.6084/m9.figshare.7393229.v2
title: Fast and Accurate Approximation of the Full Conditional for Gamma Shape Parameters

description: The gamma distribution arises frequently in Bayesian models, but there is not an easy-to-use conjugate prior for the shape parameter of a gamma. This inconvenience is usually dealt with by using either Metropolis–Hastings moves, rejection sampling methods, or numerical integration. However, in models with a large number of shape parameters, these existing methods are slower or more complicated than one would like, making them burdensome in practice. It turns out that the full conditional distribution of the gamma shape parameter is well approximated by a gamma distribution, even for small sample sizes, when the prior on the shape parameter is also a gamma distribution. This article introduces a quick and easy algorithm for finding a gamma distribution that approximates the full conditional distribution of the shape parameter. We empirically demonstrate the speed and accuracy of the approximation across a wide range of conditions. If exactness is required, the approximation can be used as a proposal distribution for Metropolis–Hastings. Supplementary material for this article is available online.
DOI: 10.6084/m9.figshare.7393304.v1
title: Global 'water table ratio' and 'groundwater response time' raster data

description: Data supporting the publication:<br>Cuthbert et al (2019) "Global patterns and dynamics of climate-groundwater interactions" Nature Climate Change http://dx.doi.org/10.1038/s41558-018-0386-4<br><br>See the ReadMe file uploaded with the data and the Methods section of the paper for details of the derivation of each dataset.<br>
DOI: 10.7284/120112
title: Singlebeam Echosounder data collected during research cruise OC1409B using a Knudsen 3260 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7393223
title: Intrinsic Data Depth for Hermitian Positive Definite Matrices

description: Nondegenerate covariance, correlation, and spectral density matrices are necessarily symmetric or Hermitian and positive definite. This article develops statistical data depths for collections of Hermitian positive definite matrices by exploiting the geometric structure of the space as a Riemannian manifold. The depth functions allow one to naturally characterize most central or outlying matrices, but also provide a practical framework for inference in the context of samples of positive definite matrices. First, the desired properties of an intrinsic data depth function acting on the space of Hermitian positive definite matrices are presented. Second, we propose two pointwise and integrated data depth functions that satisfy each of these requirements and investigate several robustness and efficiency aspects. As an application, we construct depth-based confidence regions for the intrinsic mean of a sample of positive definite matrices, which is applied to the exploratory analysis of a collection of covariance matrices in a multicenter clinical trial. Supplementary materials and an accompanying R-package are available online.