cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12901334.v3
title: Aesculus hippocastanum 2020

description: Unique genotypes of individuals from various <i>Aesculus </i>species, identified with using twelve new SSR markers designed for <i>A. hippocastanum</i>. Stands for <i>A. hippocastanum</i>: 1 – Ondria, 2 – Kalampaka, 3 – Dasos Nanitsa, 4 – Vaeni, 5 – Mariolata, 6 – Karitsa, 7 – Perivoli. Stands for others species: P - AMU Botanical Garden in Poznań, K – Kórnik Arboretum.
DOI: 10.6084/m9.figshare.12901334.v2
title: Aesculus hippocastanum 2020

description: Unique genotypes of individuals from various <i>Aesculus </i>species, identified with using twelve new SSR markers designed for <i>A. hippocastanum</i>. Stands for <i>A. hippocastanum</i>: 1 – Ondria, 2 – Kalampaka, 3 – Dasos Nanitsa, 4 – Vaeni, 5 – Mariolata, 6 – Karitsa, 7 – Perivoli. Stands for others species: P - AMU Botanical Garden in Poznań, K – Kórnik Arboretum.
DOI: 10.6084/m9.figshare.5504608
title: Attenborougharion Hyman & Köhler

description: Details of specimens used in the description of the new genus <i>Attenborougharion </i>Hyman & Köhler, 2017 (Mollusca: Pulmonata: Helicarionidae) are presented here. The following species were examined: <i>Attenborougharion rubicundus </i>(Dartnall & Kershaw, 1978); <i>Helicarion cuvieri </i>Férussac, 1821; <i>Helicarion </i>cf. <i>cuvieri </i>Férussac, 1821; <i>Helicarion leopardinus </i>Iredale, 1941; <i>Helicarion mastersi </i>(Cox, 1868); <i>Helicarion </i>cf. <i>mastersi </i>(Cox, 1868); and <i>Helicarion niger </i>(Quoy & Gaimard, 1832).<br>
DOI: 10.6084/m9.figshare.5504608.v1
title: Attenborougharion Hyman & Köhler

description: Details of specimens used in the description of the new genus <i>Attenborougharion </i>Hyman & Köhler, 2017 (Mollusca: Pulmonata: Helicarionidae) are presented here. The following species were examined: <i>Attenborougharion rubicundus </i>(Dartnall & Kershaw, 1978); <i>Helicarion cuvieri </i>Férussac, 1821; <i>Helicarion </i>cf. <i>cuvieri </i>Férussac, 1821; <i>Helicarion leopardinus </i>Iredale, 1941; <i>Helicarion mastersi </i>(Cox, 1868); <i>Helicarion </i>cf. <i>mastersi </i>(Cox, 1868); and <i>Helicarion niger </i>(Quoy & Gaimard, 1832).<br>
DOI: 10.22003/xfel.eu-data-002012-00
title: Serial Femtosecond Crystallography at MHz repetition rates
DOI: 10.22003/xfel.eu-data-002038-00
title: Structural dynamics induced by and studied with XFEL pulses
DOI: 10.22003/xfel.eu-data-002252-00
title: Single shot time-resolved imaging of ultrafast thermal skyrmion nucleation and annihilation in a ferromagnet
DOI: 10.22003/xfel.eu-data-002046-00
title: XFEL pump - optical probe study of ultrafast energy dissipation in semiconductors
DOI: 10.22003/xfel.eu-data-002191-00
title: Resolving low-frequency structural dynamics at the HED scientific instrument
DOI: 10.22003/xfel.eu-data-002207-00
title: Cavitation Dynamics Studied by Time-Resolved High-Resolution X-Ray Holography
DOI: 10.22003/xfel.eu-data-900099-00
title: SASE2 Photon Beam Measurements
DOI: 10.6084/m9.figshare.5504194
title: Shan Han Lun

description: Text of Shan Han Lun for testing extract_formula.py program
DOI: 10.6084/m9.figshare.5504125
title: test.db.gz

description: Test sqlite database file to use within the cRegulome R package
DOI: 10.6084/m9.figshare.5504116
title: raw data.xls

description: This data was used in our study "Reliability and validity study of Sino-Nasal Outcome test 22 (Thai version) in chronic rhinosinusitis".
DOI: 10.6084/m9.figshare.5504101
title: cRegulome.db.gz

description: A database sqlite file for microRNA/transcription factors-gene correlations in cancer
DOI: 10.6084/m9.figshare.5504116.v1
title: raw data.xls

description: This data was used in our study "Reliability and validity study of Sino-Nasal Outcome test 22 (Thai version) in chronic rhinosinusitis".
DOI: 10.6084/m9.figshare.5504089
title: Origin of directionally tuned responses in lower limb muscles to unpredictable upper limb disturbances

description: Ramp and hold perturbations were applied to the hand while standing. Body kinematics, ground reaction force, hand force and EMG from upper limb, trunk and lower limb muscles were recorded. Format of Matlab files is described in readme.pdf.<br>
DOI: 10.6084/m9.figshare.5504086
title: Robust_TIE_Solver.m

description: This function is utilized to robustly solve the transport-of-intensity equation (TIE) for retrieving the pseudo-phase of samples.
DOI: 10.6084/m9.figshare.5504089.v1
title: Origin of directionally tuned responses in lower limb muscles to unpredictable upper limb disturbances

description: Ramp and hold perturbations were applied to the hand while standing. Body kinematics, ground reaction force, hand force and EMG from upper limb, trunk and lower limb muscles were recorded. Format of Matlab files is described in readme.pdf.<br>
DOI: 10.6084/m9.figshare.5504125.v1
title: test.db.gz

description: Test sqlite database file to use within the cRegulome R package
DOI: 10.6084/m9.figshare.5504101.v1
title: cRegulome.db.gz

description: A database sqlite file for microRNA/transcription factors-gene correlations in cancer
DOI: 10.6084/m9.figshare.5504086.v1
title: Robust_TIE_Solver.m

description: This function is utilized to compute the pseudo-phase of samples based on TIE.
DOI: 10.6084/m9.figshare.5504101.v2
title: cRegulome.db.gz

description: A database sqlite file for microRNA/transcription factors-gene correlations in cancer
DOI: 10.6084/m9.figshare.5504125.v2
title: test.db.gz

description: Test sqlite database file to use within the cRegulome R package
DOI: 10.6084/m9.figshare.5504101.v4
title: cRegulome.db.gz

description: A database sqlite file for microRNA/transcription factors-gene correlations in cancer
DOI: 10.6084/m9.figshare.5504125.v3
title: test.db.gz

description: Test sqlite database file to use within the cRegulome R package
DOI: 10.6084/m9.figshare.5504026
title: Influence of grazing intensity on patterns and structuring processes in plant-pollinator networks in a subtropical grassland

description: Understanding how disturbances influence interactions networks is a central but still poorly explored issue in ecology and management. To test how the structure of plant-pollinator networks and the structuring importance of morphological traits, phenological overlap and relative abundance are influenced by grazing in a subtropical grassland community.Twelve sampling plots were allocated in order to cover a grazing gradient ranging from overgrazed to ungrazed sites. For each sampling plot, we created a quantitative matrix containing all observed pair wise insect–plant interactions and described morphology, phenology and abundances of each species. We then fitted series of models to test the influence of grazing intensity on metrics describing networks structure; and used probabilistic matrices, maximum likelihood analyses and models selection to investigate the determinants of frequencies of interactions. Grazing intensity influenced connectance, specialization and interaction evenness, while number of species and links, nestedness and modularity were more stable. Species abundance was the most important determinant of frequencies of interaction regardless the grazing intensity. In contrast to northern hemisphere pollination networks, the studied subtropical plant-pollinator networks and their structuring processes were remarkably consistent along the gradient of grazing intensity. We argue that the dominance of Asteraceae species – that are selectively avoided by cattle – play a crucial role in attracting a wide range of pollinators and thereby structuring plant-pollinator interactions, conferring resistance to these networks.
DOI: 10.6084/m9.figshare.5504101.v3
title: cRegulome.db.gz

description: A database sqlite file for microRNA/transcription factors-gene correlations in cancer
DOI: 10.6084/m9.figshare.5504086.v3
title: Robust_TIE_Solver.m

description: This function is utilized to robustly solve the transport-of-intensity equation (TIE) for retrieving the pseudo-phase of samples.
DOI: 10.6084/m9.figshare.5504125.v4
title: test.db.gz

description: Test sqlite database file to use within the cRegulome R package
DOI: 10.6084/m9.figshare.5504026.v1
title: Influence of grazing intensity on patterns and structuring processes in plant-pollinator networks in a subtropical grassland

description: Understanding how disturbances influence interactions networks is a central but still poorly explored issue in ecology and management. To test how the structure of plant-pollinator networks and the structuring importance of morphological traits, phenological overlap and relative abundance are influenced by grazing in a subtropical grassland community.Twelve sampling plots were allocated in order to cover a grazing gradient ranging from overgrazed to ungrazed sites. For each sampling plot, we created a quantitative matrix containing all observed pair wise insect–plant interactions and described morphology, phenology and abundances of each species. We then fitted series of models to test the influence of grazing intensity on metrics describing networks structure; and used probabilistic matrices, maximum likelihood analyses and models selection to investigate the determinants of frequencies of interactions. Grazing intensity influenced connectance, specialization and interaction evenness, while number of species and links, nestedness and modularity were more stable. Species abundance was the most important determinant of frequencies of interaction regardless the grazing intensity. In contrast to northern hemisphere pollination networks, the studied subtropical plant-pollinator networks and their structuring processes were remarkably consistent along the gradient of grazing intensity. We argue that the dominance of Asteraceae species – that are selectively avoided by cattle – play a crucial role in attracting a wide range of pollinators and thereby structuring plant-pollinator interactions, conferring resistance to these networks.
DOI: 10.6084/m9.figshare.5504086.v4
title: Robust_TIE_Solver.m

description: This function is utilized to robustly solve the transport-of-intensity equation (TIE) for retrieving the pseudo-phase of samples.
DOI: 10.6084/m9.figshare.5504125.v5
title: test.db.gz

description: Test sqlite database file to use within the cRegulome R package
DOI: 10.6084/m9.figshare.5504026.v2
title: Influence of grazing intensity on patterns and structuring processes in plant-pollinator networks in a subtropical grassland

description: Understanding how disturbances influence interactions networks is a central but still poorly explored issue in ecology and management. To test how the structure of plant-pollinator networks and the structuring importance of morphological traits, phenological overlap and relative abundance are influenced by grazing in a subtropical grassland community.Twelve sampling plots were allocated in order to cover a grazing gradient ranging from overgrazed to ungrazed sites. For each sampling plot, we created a quantitative matrix containing all observed pair wise insect–plant interactions and described morphology, phenology and abundances of each species. We then fitted series of models to test the influence of grazing intensity on metrics describing networks structure; and used probabilistic matrices, maximum likelihood analyses and models selection to investigate the determinants of frequencies of interactions. Grazing intensity influenced connectance, specialization and interaction evenness, while number of species and links, nestedness and modularity were more stable. Species abundance was the most important determinant of frequencies of interaction regardless the grazing intensity. In contrast to northern hemisphere pollination networks, the studied subtropical plant-pollinator networks and their structuring processes were remarkably consistent along the gradient of grazing intensity. We argue that the dominance of Asteraceae species – that are selectively avoided by cattle – play a crucial role in attracting a wide range of pollinators and thereby structuring plant-pollinator interactions, conferring resistance to these networks.
DOI: 10.6084/m9.figshare.5504125.v7
title: test.db.gz

description: Test sqlite database file to use within the cRegulome R package
DOI: 10.6084/m9.figshare.5503819
title: WikiProjects Machine Readable Dataset

description: Machine readable format of WikiProjects listed at https://en.wikipedia.org/wiki/Wikipedia:WikiProject_Council/Directory<br>The dataset is generated using the code at - https://github.com/wiki-ai/drafttopic/<br>The dataset is modeled in the form of a nested tree structure after the original hierarchical mappings on the WikiProejcts home page and its child pages.<br>* Each non-leaf entry represents a sub-category with a name and some associated information like the level in the page it was parsed at and the root url of the page it was parsed from.* Each non-leaf node has a mandatory key "topics" which leads to further sub-categories within it.* Each leaf node is a WikiProject entry, with actual WikiProject name and its active status.
DOI: 10.6084/m9.figshare.5504086.v5
title: Robust_TIE_Solver.m

description: This function is utilized to robustly solve the transport-of-intensity equation (TIE) for retrieving the pseudo-phase of samples.
DOI: 10.6084/m9.figshare.5504125.v6
title: test.db.gz

description: Test sqlite database file to use within the cRegulome R package
DOI: 10.6084/m9.figshare.5503816
title: Appendix-1 and subject programs

description: This folder contains Appendix-1 and the source code of the subject programs we used in the experiments.
DOI: 10.6084/m9.figshare.5504086.v6
title: Robust_TIE_Solver.m

description: This function is utilized to robustly solve the transport-of-intensity equation (TIE) for retrieving the pseudo-phase of samples.
DOI: 10.6084/m9.figshare.5503819.v3
title: WikiProjects Machine Readable Dataset

description: Machine readable format of WikiProjects listed at https://en.wikipedia.org/wiki/Wikipedia:WikiProject_Council/Directory<br>The dataset is generated using the code at - https://github.com/wiki-ai/drafttopic/<br>The dataset is modeled in the form of a nested tree structure after the original hierarchical mappings on the WikiProejcts home page and its child pages.<br>* Each non-leaf entry represents a sub-category with a name and some associated information like the level in the page it was parsed at and the root url of the page it was parsed from.* Each non-leaf node has a mandatory key "topics" which leads to further sub-categories within it.* Each leaf node is a WikiProject entry, with actual WikiProject name and its active status.
DOI: 10.6084/m9.figshare.5503732
title: An Extension of Generalized Linear Models to Finite Mixture Outcome Distributions

description: Finite mixture distributions arise in sampling a heterogeneous population. Data drawn from such a population will exhibit extra variability relative to any single subpopulation. Statistical models based on finite mixtures can assist in the analysis of categorical and count outcomes when standard generalized linear models (GLMs) cannot adequately express variability observed in the data. We propose an extension of GLMs where the response follows a finite mixture distribution and the regression of interest is linked to the mixture’s mean. This approach may be preferred over a finite mixture of regressions when the population mean is of interest; here, only one regression must be specified and interpreted in the analysis. A technical challenge is that the mixture’s mean is a composite parameter that does not appear explicitly in the density. The proposed model maintains its link to the regression through a certain random effects structure and is completely likelihood-based. We consider typical GLM cases where means are either real-valued, constrained to be positive, or constrained to be on the unit interval. The resulting model is applied to two example datasets through Bayesian analysis. Supporting the extra variation is seen to improve residual plots and produce widened prediction intervals reflecting the uncertainty. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.5503819.v2
title: WikiProjects Machine Readable Dataset

description: Machine readable format of WikiProjects listed at https://en.wikipedia.org/wiki/Wikipedia:WikiProject_Council/Directory<br>The dataset is generated using the code at - https://github.com/wiki-ai/drafttopic/<br>The dataset is modeled in the form of a nested tree structure after the original hierarchical mappings on the WikiProejcts home page and its child pages.<br>* Each non-leaf entry represents a sub-category with a name and some associated information like the level in the page it was parsed at and the root url of the page it was parsed from.* Each non-leaf node has a mandatory key "topics" which leads to further sub-categories within it.* Each leaf node is a WikiProject entry, with actual WikiProject name and its active status.
DOI: 10.6084/m9.figshare.5503732.v1
title: An Extension of Generalized Linear Models to Finite Mixture Outcome Distributions

description: Finite mixture distributions arise in sampling a heterogeneous population. Data drawn from such a population will exhibit extra variability relative to any single subpopulation. Statistical models based on finite mixtures can assist in the analysis of categorical and count outcomes when standard generalized linear models (GLMs) cannot adequately express variability observed in the data. We propose an extension of GLMs where the response follows a finite mixture distribution and the regression of interest is linked to the mixture’s mean. This approach may be preferred over a finite mixture of regressions when the population mean is of interest; here, only one regression must be specified and interpreted in the analysis. A technical challenge is that the mixture’s mean is a composite parameter that does not appear explicitly in the density. The proposed model maintains its link to the regression through a certain random effects structure and is completely likelihood-based. We consider typical GLM cases where means are either real-valued, constrained to be positive, or constrained to be on the unit interval. The resulting model is applied to two example datasets through Bayesian analysis. Supporting the extra variation is seen to improve residual plots and produce widened prediction intervals reflecting the uncertainty. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.5504086.v7
title: Robust_TIE_Solver.m

description: This function is utilized to robustly solve the transport-of-intensity equation (TIE) for retrieving the pseudo-phase of samples.
DOI: 10.6084/m9.figshare.5503723
title: A new unified approach for the simulation of a wide class of directional distributions

description: The need for effective simulation methods for directional distributions has grown as they have become components in more sophisticated statistical models. A new acceptance-rejection method is proposed and investigated for the Bingham distribution on the sphere using the angular central Gaussian distribution as an envelope. It is shown that the proposed method has high efficiency and is also straightforward to use. Next, the simulation method is extended to the Fisher and Fisher-Bingham distributions on spheres and related manifolds. Together, these results provide a widely applicable and efficient methodology to simulate many of the standard models in directional data analysis. An R package simdd, available in the online supplementary material, implements these simulation methods.
DOI: 10.6084/m9.figshare.5503726
title: Gradient-based Regularization Parameter Selection for Problems with Non-smooth Penalty Functions

description: In high-dimensional and/or non-parametric regression problems, regularization (or penalization) is used to control model complexity and induce desired structure. Each penalty has a weight parameter that indicates how strongly the structure corresponding to that penalty should be enforced. Typically the parameters are chosen to minimize the error on a separate validation set using a simple grid search or a gradient-free optimization method. It is more efficient to tune parameters if the gradient can be determined, but this is often difficult for problems with non-smooth penalty functions. Here we show that for many penalized regression problems, the validation loss is actually smooth almost-everywhere with respect to the penalty parameters. We can therefore apply a modified gradient descent algorithm to tune parameters. Through simulation studies on example regression problems, we find that increasing the number of penalty parameters and tuning them using our method can decrease the generalization error.
DOI: 10.6084/m9.figshare.5503726.v1
title: Gradient-based Regularization Parameter Selection for Problems with Non-smooth Penalty Functions

description: In high-dimensional and/or non-parametric regression problems, regularization (or penalization) is used to control model complexity and induce desired structure. Each penalty has a weight parameter that indicates how strongly the structure corresponding to that penalty should be enforced. Typically the parameters are chosen to minimize the error on a separate validation set using a simple grid search or a gradient-free optimization method. It is more efficient to tune parameters if the gradient can be determined, but this is often difficult for problems with non-smooth penalty functions. Here we show that for many penalized regression problems, the validation loss is actually smooth almost-everywhere with respect to the penalty parameters. We can therefore apply a modified gradient descent algorithm to tune parameters. Through simulation studies on example regression problems, we find that increasing the number of penalty parameters and tuning them using our method can decrease the generalization error.
DOI: 10.6084/m9.figshare.5503816.v2
title: Subject programs source code

description: This folder contains the source code of the subject programs we used in the experiments.
DOI: 10.6084/m9.figshare.5504086.v8
title: Robust_TIE_Solver.m

description: This function is utilized to robustly solve the transport-of-intensity equation (TIE) for retrieving the pseudo-phase of samples.
DOI: 10.6084/m9.figshare.5503723.v1
title: A new unified approach for the simulation of a wide class of directional distributions

description: The need for effective simulation methods for directional distributions has grown as they have become components in more sophisticated statistical models. A new acceptance-rejection method is proposed and investigated for the Bingham distribution on the sphere using the angular central Gaussian distribution as an envelope. It is shown that the proposed method has high efficiency and is also straightforward to use. Next, the simulation method is extended to the Fisher and Fisher-Bingham distributions on spheres and related manifolds. Together, these results provide a widely applicable and efficient methodology to simulate many of the standard models in directional data analysis. An R package simdd, available in the online supplementary material, implements these simulation methods.
DOI: 10.6084/m9.figshare.5504086.v10
title: Robust_TIE_Solver.m

description: This function is utilized to robustly solve the transport-of-intensity equation (TIE) for retrieving the pseudo-phase of samples.