cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1008433.v1
title: A Monte Carlo-Adjusted Goodness-of-Fit Test for Parametric Models Describing Spatial Point Patterns

description: Assessing the goodness-of-fit (GOF) for intricate parametric spatial point process models is important for many application fields. When the probability density of the statistic of the GOF test is intractable, a commonly used procedure is the Monte Carlo GOF test. Additionally, if the data comprise a single dataset, a popular version of the test plugs a parameter estimate in the hypothesized parametric model to generate data for the Monte Carlo GOF test. In this case, the test is invalid because the resulting empirical level does not reach the nominal level. In this article, we propose a method consisting of nested Monte Carlo simulations which has the following advantages: the bias of the resulting empirical level of the test is eliminated, hence the empirical levels can always reach the nominal level, and information about inhomogeneity of the data can be provided. We theoretically justify our testing procedure using Taylor expansions and demonstrate that it is correctly sized through various simulation studies. In our first data application, we discover, in agreement with Illian et al., that <i>Phlebocarya filifolia</i> plants near Perth, Australia, can follow a homogeneous Poisson clustered process that provides insight into the propagation mechanism of these plants. In our second data application, we find, in contrast to Diggle, that a pairwise interaction model provides a good fit to the micro-anatomy data of amacrine cells designed for analyzing the developmental growth of immature retina cells in rabbits. This article has supplementary material online.
DOI: 10.6084/m9.figshare.1008429.v1
title: Fast Kalman Filtering and Forward–Backward Smoothing via a Low-Rank Perturbative Approach

description: Kalman filtering-smoothing is a fundamental tool in statistical time-series analysis. However, standard implementations of the Kalman filter-smoother require <i>O</i>(<i>d</i><sup>3</sup>) time and <i>O</i>(<i>d</i><sup>2</sup>) space per time step, where <i>d</i> is the dimension of the state variable, and are therefore impractical in high-dimensional problems. In this article we note that if a relatively small number of observations are available per time step, the Kalman equations may be approximated in terms of a low-rank perturbation of the prior state covariance matrix in the absence of any observations. In many cases this approximation may be computed and updated very efficiently (often in just <i>O</i>(<i>k</i><sup>2</sup><i>d</i>) or <i>O</i>(<i>k</i><sup>2</sup><i>d</i> + <i>kd</i>log <i>d</i>) time and space per time step, where <i>k</i> is the rank of the perturbation and in general <i>k</i> ≪ <i>d</i>), using fast methods from numerical linear algebra. We justify our approach and give bounds on the rank of the perturbation as a function of the desired accuracy. For the case of smoothing, we also quantify the error of our algorithm because of the low-rank approximation and show that it can be made arbitrarily low at the expense of a moderate computational cost. We describe applications involving smoothing of spatiotemporal neuroscience data. This article has online supplementary material.
DOI: 10.6084/m9.figshare.1008430.v1
title: Automated Factor Slice Sampling

description: Markov chain Monte Carlo (MCMC) algorithms offer a very general approach for sampling from arbitrary distributions. However, designing and tuning MCMC algorithms for each new distribution can be challenging and time consuming. It is particularly difficult to create an efficient sampler when there is strong dependence among the variables in a multivariate distribution. We describe a two-pronged approach for constructing efficient, automated MCMC algorithms: (1) we propose the “factor slice sampler,” a generalization of the univariate slice sampler where we treat the selection of a coordinate basis (factors) as an additional tuning parameter, and (2) we develop an approach for automatically selecting tuning parameters to construct an efficient factor slice sampler. In addition to automating the factor slice sampler, our tuning approach also applies to the standard univariate slice samplers. We demonstrate the efficiency and general applicability of our automated MCMC algorithm with a number of illustrative examples. This article has online supplementary materials.
DOI: 10.6084/m9.figshare.1008425
title: Pyridinedicarboxylic Acid Diamides as Selective Ligands for Extraction and Separation of Trivalent Lanthanides and Actinides: DFT Study

description: This article presents a general approach to solving the urgent practical problem of separation of 4f-(lanthanides, Ln<sup>3+</sup>) and 5f-elements (actinides, An<sup>3+</sup>) very similar in properties based on the DFT quantum-chemical supercomputer simulation of Ln<sup>3+</sup> and An<sup>3+</sup> complexes with polydentate nitrogen-containing heterocyclic ligands. The method allows to calculate the geometry parameters of ligands and complexes and the metal to ligand binding energies with accuracy, permitting a direct comparison of calculation results with the experimental data, and estimate selectivity factors for separation of Eu<sup>3+</sup>/Am<sup>3+</sup> model pair cations (<b><i>SF<sub>Am/Eu</sub></i></b>) in extraction experiments on a semi-quantitative level.The applicability of the method and the approach demonstrated by DFT-modeling (nonempirical PBE functional, extended relativistic full-electron basis set) of a large series of diamides of pyridine-2,6-dicarboxylic (dipicolinic) acid (<b>L</b>) with different substituents at the amide nitrogen atoms and in the pyridine cycle, as well as their complexes [<b>LM</b>]<sup>3+</sup>, <b>(H<sub>2</sub>O)<sub>n</sub>M(NO<sub>3</sub>)<sub>3</sub></b> (n = 3, 4), and <b>LM(NO<sub>3</sub>)<sub>3</sub></b> (<b>M</b> = <b>Eu, Am</b>).Based on the theoretical analysis a new model is proposed that describes the mechanism of Ln<sup>3+</sup> and An<sup>3+</sup> extraction in two-phase system highly acidic water solution-organic solvent, according to which the formation of An<sup>3+</sup> and Ln<sup>3+</sup> complexes occurs at the water/organic interface as a substitution reaction of hydroxonium ion in a cavity of a protonated ligand for the metal cation.Calculation results confirm the experimentally established higher extraction ability of dipicolinic acid diamides containing one aryl and one alkyl substituent at the amide nitrogen atoms compared to the N,N,N′,N′-tetraalkyl diamides (“effect of anomalous aryl strengthening”). Based on the simulation results the structure of the modified ligand <b>L</b> suggested that it should ensure maximum An<sup>3+</sup>/Ln<sup>3</sup>separation selectivity in the series of dipicolinic acid diamides.
DOI: 10.6084/m9.figshare.1008427
title: Boosted Varying-Coefficient Regression Models for Product Demand Prediction

description: Estimating the aggregated market demand for a product in a dynamic market is critical to manufacturers and retailers. Motivated by the need for a statistical demand prediction model for laptop pricing at Hewlett-Packard, we have developed a novel boosting-based varying-coefficient regression model. The developed model uses regression trees as the base learner, and is generally applicable to varying-coefficient models with a large number of mixed-type varying-coefficient variables, which proves to be challenging for conventional nonparametric smoothing methods. The proposed method works well in both predicting the response and estimating the coefficient surface, based on a simulation study. Finally, we have applied this methodology to real-world mobile computer sales data, and demonstrated its superiority by comparing with elastic net- and kernel regression-based varying-coefficient model. Computer codes for boosted varying-coefficient regression are available online as supplementary materials.
DOI: 10.6084/m9.figshare.1008423
title: Comet Assay welding fumes

description: At least 50 total cell comets from 2 independent experiments were measured for the percentage of DNA in comet tails per condition. This was calculated by determining the background-corrected fluorescence from: the nuclear region of interest in a cell (nuclear ROI) and the total cell fluorescence for a defined region of interest (total cell ROI). ImageJ software was used to measure the “integrated density” (the sum of the values of the pixels in the selection) for regions of interest, and Microsoft Excel was used to calculate the corrected fluorescence values and ratios of nuclear ROI to total cell ROI. This was converted to a percentage of DNA in the “tail” (100 – [(nuclear ROI/total cell ROI) X 100]), with elevated percentages indicating DNA damage. Area: Area of selection in square pixels Integrated Density - Calculates and displays two values: "IntDen" (the product of Area and Mean Gray Value) and "RawIntDen" (the sum of the values of the pixels in the image or selection). CTCF: corrected total cell fluorescence. (intDen - (area x mean fluor bkgd)
DOI: 10.6084/m9.figshare.1008427.v1
title: Boosted Varying-Coefficient Regression Models for Product Demand Prediction

description: Estimating the aggregated market demand for a product in a dynamic market is critical to manufacturers and retailers. Motivated by the need for a statistical demand prediction model for laptop pricing at Hewlett-Packard, we have developed a novel boosting-based varying-coefficient regression model. The developed model uses regression trees as the base learner, and is generally applicable to varying-coefficient models with a large number of mixed-type varying-coefficient variables, which proves to be challenging for conventional nonparametric smoothing methods. The proposed method works well in both predicting the response and estimating the coefficient surface, based on a simulation study. Finally, we have applied this methodology to real-world mobile computer sales data, and demonstrated its superiority by comparing with elastic net- and kernel regression-based varying-coefficient model. Computer codes for boosted varying-coefficient regression are available online as supplementary materials.
DOI: 10.6084/m9.figshare.1008425.v2
title: Pyridinedicarboxylic Acid Diamides as Selective Ligands for Extraction and Separation of Trivalent Lanthanides and Actinides: DFT Study

description: This article presents a general approach to solving the urgent practical problem of separation of 4f-(lanthanides, Ln<sup>3+</sup>) and 5f-elements (actinides, An<sup>3+</sup>) very similar in properties based on the DFT quantum-chemical supercomputer simulation of Ln<sup>3+</sup> and An<sup>3+</sup> complexes with polydentate nitrogen-containing heterocyclic ligands. The method allows to calculate the geometry parameters of ligands and complexes and the metal to ligand binding energies with accuracy, permitting a direct comparison of calculation results with the experimental data, and estimate selectivity factors for separation of Eu<sup>3+</sup>/Am<sup>3+</sup> model pair cations (<b><i>SF<sub>Am/Eu</sub></i></b>) in extraction experiments on a semi-quantitative level.The applicability of the method and the approach demonstrated by DFT-modeling (nonempirical PBE functional, extended relativistic full-electron basis set) of a large series of diamides of pyridine-2,6-dicarboxylic (dipicolinic) acid (<b>L</b>) with different substituents at the amide nitrogen atoms and in the pyridine cycle, as well as their complexes [<b>LM</b>]<sup>3+</sup>, <b>(H<sub>2</sub>O)<sub>n</sub>M(NO<sub>3</sub>)<sub>3</sub></b> (n = 3, 4), and <b>LM(NO<sub>3</sub>)<sub>3</sub></b> (<b>M</b> = <b>Eu, Am</b>).Based on the theoretical analysis a new model is proposed that describes the mechanism of Ln<sup>3+</sup> and An<sup>3+</sup> extraction in two-phase system highly acidic water solution-organic solvent, according to which the formation of An<sup>3+</sup> and Ln<sup>3+</sup> complexes occurs at the water/organic interface as a substitution reaction of hydroxonium ion in a cavity of a protonated ligand for the metal cation.Calculation results confirm the experimentally established higher extraction ability of dipicolinic acid diamides containing one aryl and one alkyl substituent at the amide nitrogen atoms compared to the N,N,N′,N′-tetraalkyl diamides (“effect of anomalous aryl strengthening”). Based on the simulation results the structure of the modified ligand <b>L</b> suggested that it should ensure maximum An<sup>3+</sup>/Ln<sup>3</sup>separation selectivity in the series of dipicolinic acid diamides.
DOI: 10.6084/m9.figshare.1008414
title: Intracellular ROS production in cells following treatment with welding fumes

description: RAW 264.7 cells were pre-treated with DCFH-DA, exposed to suspensions of welding fumes, and plates were read each hour to measure intracellular ROS represented as arbitrary fluorescence units. Values represent means from triplicate wells run in 3 independent experiments.
DOI: 10.6084/m9.figshare.1008423.v1
title: Comet Assay welding fumes

description: At least 50 total cell comets from 2 independent experiments were measured for the percentage of DNA in comet tails per condition. This was calculated by determining the background-corrected fluorescence from: the nuclear region of interest in a cell (nuclear ROI) and the total cell fluorescence for a defined region of interest (total cell ROI). ImageJ software was used to measure the “integrated density” (the sum of the values of the pixels in the selection) for regions of interest, and Microsoft Excel was used to calculate the corrected fluorescence values and ratios of nuclear ROI to total cell ROI. This was converted to a percentage of DNA in the “tail” (100 – [(nuclear ROI/total cell ROI) X 100]), with elevated percentages indicating DNA damage. Area: Area of selection in square pixels Integrated Density - Calculates and displays two values: "IntDen" (the product of Area and Mean Gray Value) and "RawIntDen" (the sum of the values of the pixels in the image or selection). CTCF: corrected total cell fluorescence. (intDen - (area x mean fluor bkgd)
DOI: 10.6084/m9.figshare.1008425.v1
title: Pyridinedicarboxylic Acid Diamides as Selective Ligands for Extraction and Separation of Trivalent Lanthanides and Actinides: DFT Study

description: ABSTRACTThis paper presents a general approach to solving urgent practical problem of separation of very similar in properties 4f-(lanthanides, Ln3+) and 5f-elements (actinides, An3+) based on the DFT quantum-chemical supercomputer simulation of Ln3+ and An3+ complexes with polydentate nitrogen-containing heterocyclic ligands. The method allows to calculate the geometry parameters of ligands and complexes and the metal to ligand binding energies with accuracy, permitting a direct comparison of calculation results with the experimental data, and estimate selectivity factors for separation of Eu3+/Am3+ model pair cations (SFAm/Eu) in extraction experiments on semi-quantitative level.The applicability of the method and the approach demonstrated by DFT-modeling (nonempirical РВЕ functional, extended relativistic full-electron basis set) of a large series of diamides of pyridine-2,6-dicarboxylic (dipicolinic) acid (L) with different substituents at the amide nitrogen atoms and in the pyridine cycle, as well as their complexes [LM]3+, (H2O)nM(NO3)3 (n = 3, 4), and LM(NO3)3 (M = Eu, Am).Based on the theoretical analysis new model proposed that describes the mechanism of Ln3+ and An3+ extraction in two-phase system highly acidic water solution - organic solvent, which adequately explains the experimentally observed influence of acidity and bulk hydrophobic anions on the extraction equilibrium. According to this model, the formation of An3+ and Ln3+ complexes occurs at the water/organic interface as a substitution reaction of hydroxonium ion in a cavity of a protonated ligand for the metal cation.Calculation results confirm the experimentally established higher extraction ability of dipicolinic acid diamides containing one aryl and one alkyl substituent at the amide nitrogen atoms compared to the N,N,N∕,N∕-tetraalkyl diamides (“effect of anomalous aryl strengthening”). It is shown that the reason for this effect is a smaller “ligand pre-organization energy” for the first, calculated as the difference in the energies of unfolded conformations of free ligands and syn–syn-conformations of bound ligands. Based on simulation results the structure of modified ligand L suggested, which should ensure maximum An3+/Ln3separation selectivity in the series of dipicolinic acid diamides.
DOI: 10.6084/m9.figshare.1008411
title: Electron spin resonance measurement of •OH radicals following reaction of welding fumes with H2O2 or RAW 264.7 cells

description: Values represent mean ESR spectra peak heights from 3 experiments. The lower table is the same as above, except using cellular ESR.
DOI: 10.6084/m9.figshare.1008335
title: A first attempt at modelling roe deer (Capreolus capreolus) distributions over Europe

description: The presence of roe deer can be an important component within ecological and epidemiological systems contributing to the risk and spread of a range of vector-borne diseases. Deer are important hosts for many vectors, and may therefore serve as a focal point or attractant for vectors or may themselves act as a reservoir for vector-borne disease. Three spatial modelling techniques were used to generate an ensemble model describing the proportion of suitable roe deer habitat within recorded distributions for Europe as identified from diverse sources. The resulting model is therefore an index of presence, which may be useful in supporting the modelling of vector-borne disease across Europe.
DOI: 10.6084/m9.figshare.1008334
title: A first attempt at modelling red deer (Cervus elaphus) distributions over Europe

description: The presence of red deer may be a contributing factor within the ecological and epidemiological systems contributing to the risk and spread of a range of vector-borne diseases. Deer are importan hosts for many vectors, and may therefore serve as a focal point or attractant for vectors or may themselves become a reservoir for vector-borne disease. Three spatial modelling techniques were used to generate an ensemble model describing the proportion of suitable red deer habitat within recorded distributions for Europe as identified from diverse sources. The resulting model is therefore an index of presence, which may be useful in supporting the modelling of vector-borne disease across Europe.
DOI: 10.6084/m9.figshare.1008403
title: Mitochondrial dysfunction following incubations with welding fumes

description: ATP production, maximum respiration, and spare capacity were calculated from the mean oxygen consumption rates (OCR) from 5 independent experiments (6 replicate wells per condition each time). Values were normalized to PBS controls (represented as 100%).
DOI: 10.6084/m9.figshare.1008325
title: Type 1 error rate using TFCE for ERP

description: The archive contains codes used to create and analyze the data for 1) the review paper on clustering methods and 2) the OHBM poster on using TFCE to control the type 1 error rate over the whole space of EEG data analyzed - the data (ie the actual FWER measured per subject) are also availbale.
DOI: 10.6084/m9.figshare.1008331
title: Boreal forest coarse woody debris survey data

description: These are the 2007 survey data reported by Bond-Lamberty and Gower (2008), "Decay and fragmentation of coarse woody debris: revisiting a boreal black spruce chronosequence" in Ecosystems 11(6):831-840. Site codes and survey protocol are described in this publication-see link.
DOI: 10.6084/m9.figshare.1008403.v1
title: Mitochondrial dysfunction following incubations with welding fumes

description: ATP production, maximum respiration, and spare capacity were calculated from the mean oxygen consumption rates (OCR) from 5 independent experiments (6 replicate wells per condition each time). Values were normalized to PBS controls (represented as 100%).
DOI: 10.6084/m9.figshare.1008322
title: Land use change propensity maps

description: Land-use control and planning instruments face new challenges amid growing pressure for urbanization and annexation of valuable agricultural land and natural areas. This paper presents the land-use change propensity map, which shows the local potential for specific land-use changes. Propensity is derived empirically on the basis of historical land-use changes, with an explicit evaluation of characteristics that contributed to land-use change. Each step in creating a propensity map is described: selecting data that best represents land-use changes, identifying potential drivers of land-use change and the statistical inference of their impact on land-use change on the basis of observed historical land-use changes. The resulting propensity for land-use change is represented in the form of a binary logit model that evaluates the probability of specific land-use changes. A series of propensity maps for the territory of the Tábor microregion in the Czech Republic was created to demonstrate the method. The scale of the propensity maps is 1:310,000, and they cover an area of 1002 km<sup>2</sup>. Each propensity map represents the specific propensity for conversion from non-urban uses to family, multi-family and individual recreation houses. The evaluated propensity can be further compared to existing or proposed land-use regulations.
DOI: 10.6084/m9.figshare.1008319
title: Data used to quantify the complexity of the workflow on biodiversity-ecosystem functioning

description: The dataset represents the data directly derived from the workflow. Each row represents one port in the workflow. As most actors have multiple ports multiple rows represent one actors. The rows belonging to one actor are<br>further highlighted as they are separated by rows of NA. The dataset contains information about the purpose of the purpose of the actor, the description of the purpose, the position in the workflow, the lines of R code in the actor and the count of R functions used, the information about which additional R package have been used. Furthermore it contains information about the port name, whether the port has been used or not and if the port is an input or output port and the overall count of input and output ports of an actor. The dataset also contains information about the variable the ports handle (header from original dataset) and from which dataset the data comes from. Information about the structure of the input for each port is given as well as the length of the input and a lifecycle (how often has it been used) of the variable. Summary dataset: The dataset represents an aggregate by actor which is derived from the full dataset where each line represented an actor. In this dataset each line represents an actor. It contains information such as the ratio from output to input ports of an actor, a count of input and output ports, the actor purpose and R functions used in the actor. It also sums datasets identified by the id an actor deals with (domain_ids). It provides information about the whole line of code and the percent contribution of each actor to the total line of code. It also holds information about the used R packages, the total input and output port count as well as the actor position, a count of R packages used, a total count of datasets (domains), the total of R functions used and the the values for complexity (absolute and relative).
DOI: 10.6084/m9.figshare.1008325.v1
title: Type 1 error rate using clustering for ERP

description: The archive contains codes used to create and analyze the data for 1) the review paper on clustering methods and 2) the OHBM poster on using TFCE to control the type 1 error rate over the whole space of EEG data analyzed - the data (ie the actual FWER measured per subject) are also availbale.