cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5432722.v3
title: Calculating the Malliavin Derivative of some numerical model using the Malliavin Weight Sampling method

description: The Malliavin calculus suggests a methodology, called the Malliavin Weight Sampling method, for computing the derivative of an expected quantity of a stochastic system with respect to the parameters of its underlying stochastic variable. This repository shows how to apply this method to some problems found in classical mechanics, including problems solved using numerical methods like finite elements (FEniCS) and finite differences.<br>This code was used to generate the results in the paper:<br>Calculating the Malliavin derivative of some stochastic mechanics problems, Hauseux P, Hale JS, Bordas SPA (2017) PLOS ONE 12(12): e0189994 https://doi.org/10.1371/journal.pone.0189994<br><br>This repository is for archive purposes. Please see the bitbucket repository below for the latest version.
DOI: 10.6084/m9.figshare.5432620
title: Clustering and classification problems in genetics through <i>U</i>-statistics

description: Genetic data are frequently categorical and have complex dependence structures that are not always well understood. For this reason, clustering and classification based on genetic data, while highly relevant, are challenging statistical problems. Here we consider a versatile <i>U</i>-statistics-based approach for non-parametric clustering that allows for an unconventional way of solving these problems. In this paper we propose a statistical test to assess group homogeneity taking into account multiple testing issues and a clustering algorithm based on dissimilarities within and between groups that highly speeds up the homogeneity test. We also propose a test to verify classification significance of a sample in one of two groups. We present Monte Carlo simulations that evaluate size and power of the proposed tests under different scenarios. Finally, the methodology is applied to three different genetic data sets: global human genetic diversity, breast tumour gene expression and Dengue virus serotypes. These applications showcase this statistical framework's ability to answer diverse biological questions in the high dimension low sample size scenario while adapting to the specificities of the different datatypes.
DOI: 10.6084/m9.figshare.5432620.v2
title: Clustering and classification problems in genetics through <i>U</i>-statistics

description: Genetic data are frequently categorical and have complex dependence structures that are not always well understood. For this reason, clustering and classification based on genetic data, while highly relevant, are challenging statistical problems. Here we consider a versatile <i>U</i>-statistics-based approach for non-parametric clustering that allows for an unconventional way of solving these problems. In this paper we propose a statistical test to assess group homogeneity taking into account multiple testing issues and a clustering algorithm based on dissimilarities within and between groups that highly speeds up the homogeneity test. We also propose a test to verify classification significance of a sample in one of two groups. We present Monte Carlo simulations that evaluate size and power of the proposed tests under different scenarios. Finally, the methodology is applied to three different genetic data sets: global human genetic diversity, breast tumour gene expression and Dengue virus serotypes. These applications showcase this statistical framework's ability to answer diverse biological questions in the high dimension low sample size scenario while adapting to the specificities of the different datatypes.
DOI: 10.6084/m9.figshare.5432620.v1
title: Clustering and classification problems in genetics through <i>U</i>-statistics

description: Genetic data are frequently categorical and have complex dependence structures that are not always well understood. For this reason, clustering and classification based on genetic data, while highly relevant, are challenging statistical problems. Here we consider a versatile <i>U</i>-statistics-based approach for non-parametric clustering that allows for an unconventional way of solving these problems. In this paper we propose a statistical test to assess group homogeneity taking into account multiple testing issues and a clustering algorithm based on dissimilarities within and between groups that highly speeds up the homogeneity test. We also propose a test to verify classification significance of a sample in one of two groups. We present Monte Carlo simulations that evaluate size and power of the proposed tests under different scenarios. Finally, the methodology is applied to three different genetic data sets: global human genetic diversity, breast tumour gene expression and Dengue virus serotypes. These applications showcase this statistical framework's ability to answer diverse biological questions in the high dimension low sample size scenario while adapting to the specificities of the different datatypes.
DOI: 10.6084/m9.figshare.5432182
title: Peruvian Scientific Journals 2015

description: General characteristics of peruvian scientific journals (2015).<br><br>Santillán-Aldana, J.; Arakaki, M.; de la Vega, A.; Calderón-Carranza, M.; Pacheco-Mendoza, J. (2017). Características generales de las revistas científicas peruanas. <em>Revista Española de Documentación Científica</em>, 40 (3): e182. doi: http://dx.doi.org/10.3989/redc.2017.3.1419<br>
DOI: 10.6084/m9.figshare.5432176
title: Complete data.sav

description: reader study on breast tomosynthesis
DOI: 10.6084/m9.figshare.5432182.v1
title: Peruvian Scientific Journals 2015

description: General characteristics of peruvian scientific journals (2015).<br><br>Santillán-Aldana, J.; Arakaki, M.; de la Vega, A.; Calderón-Carranza, M.; Pacheco-Mendoza, J. (2017). Características generales de las revistas científicas peruanas. <em>Revista Española de Documentación Científica</em>, 40 (3): e182. doi: http://dx.doi.org/10.3989/redc.2017.3.1419<br>
DOI: 10.6084/m9.figshare.5432176.v1
title: Complete data Reader 1.sav

description: reader study on breast tomosynthesis
DOI: 10.6084/m9.figshare.5432152
title: VHFPT 2.0.zip

description: images to run the study in your own software, as well as livecode app
DOI: 10.6084/m9.figshare.5432119
title: TsNAC1 ChIP-on-chip Log2 Ratio Data.zip

description: To explore the candidate downstream target genes of TsNAC1 in Arabidopsis.
DOI: 10.6084/m9.figshare.5432128
title: A corpus of 42 books from European languages embracing four families.

description: A corpus of 42 books, three for each of 14 different European languages taken from the page www.gutenberg.org. The titles of the oeuvres and authors are written in the romanized way given in the page. The texts were chosen by no other reason that to be representative of each language and avoiding, as much as possible, the repetitive texts like poetry. <br>
DOI: 10.6084/m9.figshare.5432116
title: TsNAC1 ChIP-on-chip Peaks Data.zip

description: The peaks data of the candidate target genes of TsNAC1 in Arabidopsis.
DOI: 10.6084/m9.figshare.5432119.v1
title: TsNAC1 ChIP-on-chip Log2 Ratio Data.zip

description: To explore the candidate downstream target genes of TsNAC1 in Arabidopsis.
DOI: 10.6084/m9.figshare.5432110
title: TsNAC1 cHIP-on-chip Annotation file.zip

description: To explore the candidate downstream target genes of TsNAC1 in Arabidopsis.
DOI: 10.6084/m9.figshare.5432113
title: TsNAC1 ChIP-on-chip row data.zip

description: Input and ChIP DNA were labelled with Cy3- and Cy5-labelled random 9-mers, respectively. HE1, HE3 were two lines of TsNAC1.
DOI: 10.6084/m9.figshare.5432128.v2
title: A corpus of 42 books from European languages embracing four families.

description: A corpus of 42 books, three for each of 14 different European languages taken from the page www.gutenberg.org. The titles of the oeuvres and authors are written in the romanized way given in the page. The texts were chosen by no other reason that to be representative of each language and avoiding, as much as possible, the repetitive texts like poetry. <br>
DOI: 10.6084/m9.figshare.5432107
title: R code and Raw Data for Clark et al. 2017 Diversity and Distributions

description: These datasets and the associated R scripts provide working examples of (a) running mixed models to predict parasite local distinctiveness, using a host phylogeny as the random term and running models across multiple host phylogenetic trees to account for uncertainty; (b) calculating host and parasite phylogenetic turnover across sets of phylogenies
DOI: 10.6084/m9.figshare.5432113.v1
title: TsNAC1 ChIP-on-chip row data.zip

description: Input and ChIP DNA were labelled with Cy3- and Cy5-labelled random 9-mers, respectively. HE1, HE3 were two lines of TsNAC1.
DOI: 10.6084/m9.figshare.5432095
title: The corpus

description: To each of these books we have calculated the Approximate Entropy and classified the values obtained with a Linear Discriminant Analysis.<br>
DOI: 10.6084/m9.figshare.5432128.v1
title: The corpus

description: Three books for 14 different European languages taken from the web site www.gutenberg.org. The titles and authors are written in the romanized way given in the page. <br>
DOI: 10.6084/m9.figshare.5432089
title: Primary data Bebbington et al. 2017 PNAS.xlsx

description: Primary data used to produce the results reported in the study. Each tab contains the data relating to one of the analyses.
DOI: 10.6084/m9.figshare.5432089.v1
title: Primary data Bebbington et al. 2017 PNAS.xlsx

description: Primary data used to produce the results reported in the study. Each tab contains the data relating to one of the analyses.
DOI: 10.6084/m9.figshare.5432047
title: Dataset for: A biologically inspired neurocomputational model for audio-visual integration and causal inference

description: Recently, experimental and theoretical research has focused on the brain’s abilities to extract information from a noisy sensory environment and how cross-modal inputs are processed to solve the causal inference problem to provide the best estimate of external events. Despite the empirical evidence suggesting that the nervous system uses a statistically optimal and probabilistic approach in addressing these problems, little is known about the brain’s architecture needed to implement these computations. The aim of this work is to realize a mathematical model, based on physiologically plausible hypotheses, to analyze the neural mechanisms underlying multisensory perception and causal inference. The model consists of three layers topologically organized: two encode auditory and visual stimuli, separately, and are reciprocally connected via excitatory synapses and send excitatory connections to the third downstream layer. This synaptic organization realizes two mechanisms of cross-modal interactions: the first is responsible for the sensory representation of the external stimuli while the second solves the causal inference problem. We tested the network by comparing its results to behavioral data reported in the literature. Among others, the network can account for the ventriloquism illusion, the pattern of sensory bias and the percept of unity as a function of the spatial auditory-visual distance, and the dependence of the auditory error on the causal inference. Finally, simulations results are consistent with probability matching as the perceptual strategy used in auditory-visual spatial localization tasks, agreeing with the behavioral data. The model makes untested predictions that can be investigated in future behavioral experiments.
DOI: 10.6084/m9.figshare.5432047.v1
title: Dataset for: A biologically inspired neurocomputational model for audio-visual integration and causal inference

description: Recently, experimental and theoretical research has focused on the brain’s abilities to extract information from a noisy sensory environment and how cross-modal inputs are processed to solve the causal inference problem to provide the best estimate of external events. Despite the empirical evidence suggesting that the nervous system uses a statistically optimal and probabilistic approach in addressing these problems, little is known about the brain’s architecture needed to implement these computations. The aim of this work is to realize a mathematical model, based on physiologically plausible hypotheses, to analyze the neural mechanisms underlying multisensory perception and causal inference. The model consists of three layers topologically organized: two encode auditory and visual stimuli, separately, and are reciprocally connected via excitatory synapses and send excitatory connections to the third downstream layer. This synaptic organization realizes two mechanisms of cross-modal interactions: the first is responsible for the sensory representation of the external stimuli while the second solves the causal inference problem. We tested the network by comparing its results to behavioral data reported in the literature. Among others, the network can account for the ventriloquism illusion, the pattern of sensory bias and the percept of unity as a function of the spatial auditory-visual distance, and the dependence of the auditory error on the causal inference. Finally, simulations results are consistent with probability matching as the perceptual strategy used in auditory-visual spatial localization tasks, agreeing with the behavioral data. The model makes untested predictions that can be investigated in future behavioral experiments.
DOI: 10.6084/m9.figshare.5432107.v1
title: R code for Clark et al. 2017 Diversity and Distributions

description: These datasets and the associated R script provide a working example of running mixed models to predict parasite local distinctiveness, using a host phylogeny as the random term and running models across multiple host phylogenetic trees to account for uncertainty.
DOI: 10.6084/m9.figshare.5431981
title: Reconciling conflicting models for global control of cell-cycle transcription

description: Models for the control of global cell-cycle transcription have advanced from a CDK-APC/C oscillator, a transcription factor (TF) network, to coupled CDK-APC/C and TF networks. Nonetheless, current models were challenged by a recent study that concluded that the cell-cycle transcriptional program is primarily controlled by a CDK-APC/C oscillator in budding yeast. Here we report an analysis of the transcriptome dynamics in cyclin mutant cells that were not queried in the previous study. We find that B-cyclin oscillation is not essential for control of phase-specific transcription. Using a mathematical model, we demonstrate that the function of network TFs can be retained in the face of significant reductions in transcript levels. Finally, we show that cells arrested at mitotic exit with non-oscillating levels of B-cyclins continue to cycle transcriptionally. Taken together, these findings support a critical role of a TF network and a requirement for CDK activities that need not be periodic.
DOI: 10.6084/m9.figshare.5432107.v2
title: R code for Clark et al. 2017 Diversity and Distributions

description: These datasets and the associated R scripts provide working examples of (a) running mixed models to predict parasite local distinctiveness, using a host phylogeny as the random term and running models across multiple host phylogenetic trees to account for uncertainty; (b) calculating host and parasite phylogenetic turnover across sets of phylogenies
DOI: 10.6084/m9.figshare.5431981.v1
title: Reconciling conflicting models for global control of cell-cycle transcription

description: Models for the control of global cell-cycle transcription have advanced from a CDK-APC/C oscillator, a transcription factor (TF) network, to coupled CDK-APC/C and TF networks. Nonetheless, current models were challenged by a recent study that concluded that the cell-cycle transcriptional program is primarily controlled by a CDK-APC/C oscillator in budding yeast. Here we report an analysis of the transcriptome dynamics in cyclin mutant cells that were not queried in the previous study. We find that B-cyclin oscillation is not essential for control of phase-specific transcription. Using a mathematical model, we demonstrate that the function of network TFs can be retained in the face of significant reductions in transcript levels. Finally, we show that cells arrested at mitotic exit with non-oscillating levels of B-cyclins continue to cycle transcriptionally. Taken together, these findings support a critical role of a TF network and a requirement for CDK activities that need not be periodic.
DOI: 10.6084/m9.figshare.5431930.v1
title: Vote shares Union-FDP (German Election 2017)

description: These are vote shares of Union-FDP, calculated based on a pooled survey (at each date pooled sample was calculated based on aggregation of polls from different German pollsters). For each date this data set provides a subset of 500 simulations from a Dirichlet distribution, which is the (Bayesian) Posterior distribution of a Multinomial Likelihood (pooled survey) and a uninformative (flat) Dirichlet-Prior. Each simulation provides a possible election outcome. The vote shares provided here are based on "redistributed votes" (i.e. votes of parties below 5% threshold are redistributed proportionally to parties above the 5% threshold).
DOI: 10.6084/m9.figshare.5432107.v3
title: R code and Raw Data for Clark et al. 2017 Diversity and Distributions

description: These datasets and the associated R scripts provide working examples of (a) running mixed models to predict parasite local distinctiveness, using a host phylogeny as the random term and running models across multiple host phylogenetic trees to account for uncertainty; (b) calculating host and parasite phylogenetic turnover across sets of phylogenies
DOI: 10.6084/m9.figshare.5432107.v5
title: R code and Raw Data for Clark et al. 2017 Diversity and Distributions

description: These datasets and the associated R scripts provide working examples of (a) running mixed models to predict parasite local distinctiveness, using a host phylogeny as the random term and running models across multiple host phylogenetic trees to account for uncertainty; (b) calculating host and parasite phylogenetic turnover across sets of phylogenies
DOI: 10.6084/m9.figshare.5427310
title: Gazepoint GP3 manuscript code and data

description: All code, functions, and data required to generate the plots in the manuscript titled "Assessing the performance of the Gazepoint GP3 eye-tracker for gaze event detection using a visual search task" by Notaro et al, using main script GNotaro_Gazepointmainscript.m. The code produces plots regarding gaze event detection (i.e. short fixation events) within a visual search task. <br>(Note: run main .m script and reference Matlab data folder within matlab.zip when prompted; original raw data files in gazepointdata.zip; matlab variable eparticipant with all random indexes and values reported in manuscript located in eparticipant_struct.mat (in compressed .rar file here); if errors, check paths to files and functions!)<br>All human data anonymized and acquired under approved CPHS protocol (#21522)
DOI: 10.6084/m9.figshare.5432107.v4
title: R code and Raw Data for Clark et al. 2017 Diversity and Distributions

description: These datasets and the associated R scripts provide working examples of (a) running mixed models to predict parasite local distinctiveness, using a host phylogeny as the random term and running models across multiple host phylogenetic trees to account for uncertainty; (b) calculating host and parasite phylogenetic turnover across sets of phylogenies
DOI: 10.6084/m9.figshare.5427307
title: Dissipation kinetics and safety evaluation of tebuconazole and trifloxystrobin in tea under tropical field conditions

description: Dissipation kinetics of tebuconazole, trifloxystrobin and its acid metabolite residues were studied in tea under tropical field conditions using GC-MS (SIM). The average recoveries ranged from 80.7% to 105.8%, with a RSD of &lt;9.3%. Dissipation rate for both doses applied followed first-order kinetics, with half-lives in green leaves in the range of 2.8–3.3 and 2.9–3.3 days; ranges in processed tea were 2.7–3.6 days for trifloxystrobin and 3.0–3.1 days for tebuconazole. The trifloxystrobin residues were not transferred into the tea infusion during the infusion process; tebuconazole did transfer, in the range of 14.3–18.9%. As the theoretical maximum residue contributions on tea from initial deposits were found to be less than the maximum permissible intake values, at the recommended application dose a withdrawal period of 23 days before consumption should be applied to reduce risk.
DOI: 10.6084/m9.figshare.5427301.v1
title: Hydrogeological mapping of heterogeneous and multi-layered ophiolitic aquifers (Mountain Prinzera, northern Apennines, Italy)

description: A few hydrogeological studies have been carried out worldwide in peridotite aquifer systems, despite their wide distribution. The ophiolites are one of the main groundwater reservoir within the northern Apennines (Italy). This paper suggests the graphical solution to set the hydrogeological map of heterogeneous, multi-layered ophiolitic aquifers mapped on large scale (1:1600). The site investigation area is an ophiolite outcrop of the External Ligurian of the northern Apennines: the Mountain Prinzera rock complex area (44°38′30″N, 10°5′E; Parma Province, Emilia-Romagna Region). The hydrogeological characteristics of the tested aquifer system do not allow setting a hydrogeological map by applying usual graphical approaches. The hydrogeological map in such complex aquifer systems will show the classic hydrogeological data but must put in evidence above all (i) the main heterogeneities of the system, from the hydraulic point of view and (ii) the modifications of groundwater scenarios and pathways over time. The hydrogeological database of Mt Prinzera aquifer was managed in ESRI ArcGIS 10.0 software.
DOI: 10.6084/m9.figshare.5427307.v1
title: Dissipation kinetics and safety evaluation of tebuconazole and trifloxystrobin in tea under tropical field conditions

description: Dissipation kinetics of tebuconazole, trifloxystrobin and its acid metabolite residues were studied in tea under tropical field conditions using GC-MS (SIM). The average recoveries ranged from 80.7% to 105.8%, with a RSD of &lt;9.3%. Dissipation rate for both doses applied followed first-order kinetics, with half-lives in green leaves in the range of 2.8–3.3 and 2.9–3.3 days; ranges in processed tea were 2.7–3.6 days for trifloxystrobin and 3.0–3.1 days for tebuconazole. The trifloxystrobin residues were not transferred into the tea infusion during the infusion process; tebuconazole did transfer, in the range of 14.3–18.9%. As the theoretical maximum residue contributions on tea from initial deposits were found to be less than the maximum permissible intake values, at the recommended application dose a withdrawal period of 23 days before consumption should be applied to reduce risk.
DOI: 10.6084/m9.figshare.5427295
title: Myocardial Stiffening in a mouse model of persistent truncus arteriosus

description: Data for PLOS ONE article
DOI: 10.6084/m9.figshare.5427277
title: The Evolution of Institutional Repository Technology and Scholarly Communications

description: A webinar with advice and perspectives from experts on the future directions for the institutional repository