cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4546834
title: Tardigrades microbiome Scripts and data

description: Mothur and R commands used in the paper: "The microbial community of tardigrades: environmental influence and species-specificity of microbiome structure and composition"R working space containing a Phyloseq object with the OTU table, phylogenetic tree and taxonomy used.Fasta file containing a representative sequence for each OTU.
DOI: 10.6084/m9.figshare.4546570
title: A general algorithm for computing simultaneous prediction intervals for the (log)-location-scale family of distributions

description: Making predictions of future realized values of random variables based on currently available data is a frequent task in statistical applications. In some applications, the interest is to obtain a two-sided simultaneous prediction interval (SPI) to contain at least <i>k</i> out of <i>m</i> future observations with a certain confidence level based on <i>n</i> previous observations from the same distribution. A closely related problem is to obtain a one-sided upper (or lower) simultaneous prediction bound (SPB) to exceed (or be exceeded) by at least <i>k</i> out of <i>m</i> future observations. In this paper, we provide a general approach for computing SPIs and SPBs based on data from a particular member of the (log)-location-scale family of distributions with complete or right censored data. The proposed simulation-based procedure can provide exact coverage probability for complete and Type II censored data. For Type I censored data, our simulation results show that our procedure provides satisfactory results in small samples. We use three applications to illustrate the proposed simultaneous prediction intervals and bounds.
DOI: 10.6084/m9.figshare.4546570.v1
title: A general algorithm for computing simultaneous prediction intervals for the (log)-location-scale family of distributions

description: Making predictions of future realized values of random variables based on currently available data is a frequent task in statistical applications. In some applications, the interest is to obtain a two-sided simultaneous prediction interval (SPI) to contain at least <i>k</i> out of <i>m</i> future observations with a certain confidence level based on <i>n</i> previous observations from the same distribution. A closely related problem is to obtain a one-sided upper (or lower) simultaneous prediction bound (SPB) to exceed (or be exceeded) by at least <i>k</i> out of <i>m</i> future observations. In this paper, we provide a general approach for computing SPIs and SPBs based on data from a particular member of the (log)-location-scale family of distributions with complete or right censored data. The proposed simulation-based procedure can provide exact coverage probability for complete and Type II censored data. For Type I censored data, our simulation results show that our procedure provides satisfactory results in small samples. We use three applications to illustrate the proposed simultaneous prediction intervals and bounds.
DOI: 10.5287/bodleian:b7xod0p8d
title: Input file dataset for "Stabilisation of short-wavelength instabilities by parallel-to-the-field shear in long-wavelength E x B flows" arXiv:1911.04999
DOI: 10.6084/m9.figshare.4545952
title: Data and Syntax for TDDS and 12 moral dilemmas

description: Dataset Containing TDDS and 12 Moral DIlemmas used in the publication: Individual Differences in Moral Disgust Do Not Predict Utilitarian Judgments, Sexual and Pathogen Disgust Do. This is the data used in the publication:<br><br><b>Laakasuo, M., Sundvall, J. & Drosinou, M. (2017).</b> Individual Differences in Moral Disgust Do Not Predict Utilitarian Judgments, Sexual and Pathogen Disgust Do. <i>Scientific Reports, 7</i>:45526, DOI: 10.1038/srep45526<br>
DOI: 10.6084/m9.figshare.4545784
title: RespiratoryPathogenDetectionData.xlsx

description: Detection histories of respiratory pathogens for individual bighorn sheep that were sampled using several specified diagnostic protocols.
DOI: 10.6084/m9.figshare.4545724
title: Data used in Van Wynsberge et al. 2017 (Plos one)

description: Asking author permission and additional guidelines is required before any use of this dataset. <br>
DOI: 10.6084/m9.figshare.4545742
title: Tableau 1. Marché bancaire. Répartition entre les secteurs "banques" / non-banques (Mds d'écus)

description: Données relatives au marché bancaire. Source: Commission européenne.<br>
DOI: 10.6084/m9.figshare.4545724.v1
title: Data used in Van Wynsberge et al. 2017 (Plos one)

description: Asking author permission and additional guidelines is required before any use of this dataset. <br>
DOI: 10.6084/m9.figshare.4545706
title: The cranial osteology of <i>Buitreraptor gonzalezorum</i> Makovicky, ApesteguÍa, and AgnolÍn, 2005 (Theropoda, Dromaeosauridae), from the Late Cretaceous of Patagonia, Argentina

description: <i>Buitreraptor gonzalezorum</i> is a paravian theropod from the Late Cretaceous of Patagonia that has been recovered as an unenlagiine dromaeosaurid in several phylogenies. It was preliminarily described in a brief article, but a detailed osteology has not been published to date. Here we provide a thorough osteological description of the skull of the holotype, which preserves the maxillae, nasals, frontals, parietals, postorbitals, quadrates, and many mandibular bones, together with some in situ and isolated teeth. The isolated occipital condyle is the only element preserved from the braincase. Diagnostic cranial characters of this taxon include elongate skull; maxillary fenestra not dorsally displaced; posteriorly expanded postantral wall; quadrate with expanded lateral flange and a posterior pneumatic foramen; straight anterior border of the supratemporal fossa; nutrient foramina within a well-marked lateral groove on the dentary; and small, fluted teeth without denticles. <i>Buitreraptor</i> shares traits with <i>Austroraptor cabazai</i>, the only other unenlagiine to preserve cranial remains, although they also differ in the morphology of the maxillary fenestra and the presence/absence of interdental plates. A phylogenetic analysis was performed, recovering <i>Buitreraptor</i> as an unenlagiine dromaeosaurid, in agreement with previous works. The phylogenetic implications of some characters are discussed, including characters not previously considered for this taxon, such as the presence of the mylohyoid foramen. The distribution and codings of some characters are reconsidered, with an evaluation of how they influence the phylogenetic position of <i>Buitreraptor</i> and paravian relationships overall. SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP Citation for this article: Gianechini, F. A., P. J. Makovicky, and S. Apesteguía. 2017. The cranial osteology of <i>Buitreraptor gonzalezorum</i> Makovicky, Apesteguía, and Agnolín, 2005 (Theropoda, Dromaeosauridae), from the Late Cretaceous of Patagonia, Argentina. Journal of Vertebrate Paleontology. DOI: 10. 10.1080/02724634.2017.1255639.
DOI: 10.6084/m9.figshare.4545742.v1
title: Marché bancaire

description: Données relatives au marché bancaire<br>
DOI: 10.6084/m9.figshare.4545742.v3
title: Tableau 1. Marché bancaire. Répartition entre les secteurs "banques" / non-banques (Mds d'écus)

description: Données relatives au marché bancaire. Source: Commission européenne.<br>
DOI: 10.6084/m9.figshare.4545694
title: Identification of HuR target circular RNAs uncovers suppression of PABPN1 translation by <i>CircPABPN1</i>

description: HuR influences gene expression programs and hence cellular phenotypes by binding to hundreds of coding and noncoding linear RNAs. However, whether HuR binds to circular RNAs (circRNAs) and impacts on their function is unknown. Here, we have identified <i>en masse</i> circRNAs binding HuR in human cervical carcinoma HeLa cells. One of the most prominent HuR target circRNAs was hsa_circ_0031288, renamed <i>CircPABPN1</i> as it arises from the <i>PABPN1</i> pre-mRNA. Further analysis revealed that HuR did not influence <i>CircPABPN1</i> abundance; interestingly, however, high levels of <i>CircPABPN1</i> suppressed HuR binding to <i>PABPN1</i> mRNA. Evaluation of <i>PABPN1</i> mRNA polysomes indicated that PABPN1 translation was modulated positively by HuR and hence negatively by <i>CircPABPN1</i>. We propose that the extensive binding of <i>CircPABPN1</i> to HuR prevents HuR binding to <i>PABPN1</i> mRNA and lowers PABPN1 translation, providing the first example of competition between a circRNA and its cognate mRNA for an RBP that affects translation.
DOI: 10.6084/m9.figshare.4545682
title: Long-term effects on the incidence of second primary cancers in a randomized trial of two and five years of adjuvant tamoxifen

description: <b>Background:</b> Tamoxifen is a well established treatment for breast cancer, but its long-term effects on the incidence of secondary cancers are not fully evaluated. <b>Material and methods:</b> We have studied 4128 postmenopausal patients with early stage breast cancer who were alive and free of breast cancer recurrence after two years of tamoxifen, and who were randomized to receive totally two or five years of therapy. <b>Results:</b> Compared to patients randomized to two years of tamoxifen the incidence of contralateral breast cancer [hazard ratio (HR) 0.73; 95% CI 0.56–0.96] and of lung cancer (HR 0.45; 95% CI 0.27–0.77), especially squamous cell and small cell lung cancer, were reduced in the five-year group, and similar results were seen when restricting the analysis to the 10-year period after treatment stopped. An increased incidence of endometrial cancer was observed in the five-year group, but the excess risk decreased over time. <b>Conclusion:</b> Further studies of the effects of tamoxifen on the risk of different histological types of lung cancer are needed.
DOI: 10.6084/m9.figshare.4545742.v2
title: Tableau 1. Marché bancaire (Mds d'écus)

description: Données relatives au marché bancaire. Source: Commission européenne.<br>
DOI: 10.6084/m9.figshare.4545694.v1
title: Identification of HuR target circular RNAs uncovers suppression of PABPN1 translation by <i>CircPABPN1</i>

description: HuR influences gene expression programs and hence cellular phenotypes by binding to hundreds of coding and noncoding linear RNAs. However, whether HuR binds to circular RNAs (circRNAs) and impacts on their function is unknown. Here, we have identified <i>en masse</i> circRNAs binding HuR in human cervical carcinoma HeLa cells. One of the most prominent HuR target circRNAs was hsa_circ_0031288, renamed <i>CircPABPN1</i> as it arises from the <i>PABPN1</i> pre-mRNA. Further analysis revealed that HuR did not influence <i>CircPABPN1</i> abundance; interestingly, however, high levels of <i>CircPABPN1</i> suppressed HuR binding to <i>PABPN1</i> mRNA. Evaluation of <i>PABPN1</i> mRNA polysomes indicated that PABPN1 translation was modulated positively by HuR and hence negatively by <i>CircPABPN1</i>. We propose that the extensive binding of <i>CircPABPN1</i> to HuR prevents HuR binding to <i>PABPN1</i> mRNA and lowers PABPN1 translation, providing the first example of competition between a circRNA and its cognate mRNA for an RBP that affects translation.
DOI: 10.6084/m9.figshare.4545682.v1
title: Long-term effects on the incidence of second primary cancers in a randomized trial of two and five years of adjuvant tamoxifen

description: <b>Background:</b> Tamoxifen is a well established treatment for breast cancer, but its long-term effects on the incidence of secondary cancers are not fully evaluated. <b>Material and methods:</b> We have studied 4128 postmenopausal patients with early stage breast cancer who were alive and free of breast cancer recurrence after two years of tamoxifen, and who were randomized to receive totally two or five years of therapy. <b>Results:</b> Compared to patients randomized to two years of tamoxifen the incidence of contralateral breast cancer [hazard ratio (HR) 0.73; 95% CI 0.56–0.96] and of lung cancer (HR 0.45; 95% CI 0.27–0.77), especially squamous cell and small cell lung cancer, were reduced in the five-year group, and similar results were seen when restricting the analysis to the 10-year period after treatment stopped. An increased incidence of endometrial cancer was observed in the five-year group, but the excess risk decreased over time. <b>Conclusion:</b> Further studies of the effects of tamoxifen on the risk of different histological types of lung cancer are needed.
DOI: 10.6084/m9.figshare.4545697.v1
title: Penalized Estimation in Large-Scale Generalized Linear Array Models

description: Large-scale generalized linear array models (GLAMs) can be challenging to fit. Computation and storage of its tensor product design matrix can be impossible due to time and memory constraints, and previously considered design matrix free algorithms do not scale well with the dimension of the parameter vector. A new design matrix free algorithm is proposed for computing the penalized maximum likelihood estimate for GLAMs, which, in particular, handles nondifferentiable penalty functions. The proposed algorithm is implemented and available via the R package glamlasso. It combines several ideas—previously considered separately—to obtain sparse estimates while at the same time efficiently exploiting the GLAM structure. In this article, the convergence of the algorithm is treated and the performance of its implementation is investigated and compared to that of glmnet on simulated as well as real data. It is shown that the computation time for glamlasso scales favorably with the size of the problem when compared to glmnet. Supplementary materials, in the form of R code, data and visualizations of results, are available online.
DOI: 10.6084/m9.figshare.4545697.v2
title: Penalized Estimation in Large-Scale Generalized Linear Array Models

description: Large-scale generalized linear array models (GLAMs) can be challenging to fit. Computation and storage of its tensor product design matrix can be impossible due to time and memory constraints, and previously considered design matrix free algorithms do not scale well with the dimension of the parameter vector. A new design matrix free algorithm is proposed for computing the penalized maximum likelihood estimate for GLAMs, which, in particular, handles nondifferentiable penalty functions. The proposed algorithm is implemented and available via the R package glamlasso. It combines several ideas—previously considered separately—to obtain sparse estimates while at the same time efficiently exploiting the GLAM structure. In this article, the convergence of the algorithm is treated and the performance of its implementation is investigated and compared to that of glmnet on simulated as well as real data. It is shown that the computation time for glamlasso scales favorably with the size of the problem when compared to glmnet. Supplementary materials, in the form of R code, data and visualizations of results, are available online.
DOI: 10.6084/m9.figshare.4545697.v3
title: Penalized Estimation in Large-Scale Generalized Linear Array Models

description: Large-scale generalized linear array models (GLAMs) can be challenging to fit. Computation and storage of its tensor product design matrix can be impossible due to time and memory constraints, and previously considered design matrix free algorithms do not scale well with the dimension of the parameter vector. A new design matrix free algorithm is proposed for computing the penalized maximum likelihood estimate for GLAMs, which, in particular, handles nondifferentiable penalty functions. The proposed algorithm is implemented and available via the R package glamlasso. It combines several ideas—previously considered separately—to obtain sparse estimates while at the same time efficiently exploiting the GLAM structure. In this article, the convergence of the algorithm is treated and the performance of its implementation is investigated and compared to that of glmnet on simulated as well as real data. It is shown that the computation time for glamlasso scales favorably with the size of the problem when compared to glmnet. Supplementary materials, in the form of R code, data and visualizations of results, are available online.
DOI: 10.6084/m9.figshare.4545697.v4
title: Penalized estimation in large-scale generalized linear array models

description: Large-scale generalized linear array models (GLAMs) can be challenging to fit. Computation and storage of its tensor product design matrix can be impossible due to time and memory constraints, and previously considered design matrix free algorithms do not scale well with the dimension of the parameter vector. A new design matrix free algorithm is proposed for computing the penalized maximum likelihood estimate for GLAMs, which, in particular, handles nondifferentiable penalty functions. The proposed algorithm is implemented and available via the R package glamlasso. It combines several ideas – previously considered separately – to obtain sparse estimates while at the same time efficiently exploiting the GLAM structure. In this paper the convergence of the algorithm is treated and the performance of its implementation is investigated and compared to that of glmnet on simulated as well as real data. It is shown that the computation time for glamlasso scales favorably with the size of the problem when compared to glmnet. Supplementary materials, in the form of R code, data and visualizations of results, are available online.
DOI: 10.6084/m9.figshare.4543435.v1
title: A comprehensive public data set of running biomechanics and the effects of running speed on lower extremity kinematics and kinetics

description: The data set comprises raw and processed lower extremity gait kinematics and kinetics signals of 28 subjects in different file formats (c3d and txt). A file of metadata (in txt and xls formats), including demographics, running characteristics, foot-strike patterns, and muscle strength and flexibility measurements is provided. In addition, a model file (mdh) and a pipeline file (v3s) for the Visual 3D software program are also provided.The data were collected using a three-dimensional (3D) motion-capture system and an instrumented treadmill while the subjects ran at 2.5 m/s, 3.5 m/s, and 4.5 m/s wearing standard neutral shoes.<br>
DOI: 10.6084/m9.figshare.4543435.v2
title: A public data set of running biomechanics and the effects of running speed on lower extremity kinematics and kinetics

description: The data set comprises raw and processed lower extremity gait kinematics and kinetics signals of 28 subjects in different file formats (c3d and txt). A file of metadata (in txt and xls formats), including demographics, running characteristics, foot-strike patterns, and muscle strength and flexibility measurements is provided. In addition, a model file (mdh) and a pipeline file (v3s) for the Visual 3D software program are also provided.The data were collected using a three-dimensional (3D) motion-capture system and an instrumented treadmill while the subjects ran at 2.5 m/s, 3.5 m/s, and 4.5 m/s wearing standard neutral shoes.<br>
DOI: 10.6084/m9.figshare.4543303
title: Theoretical study of Si<sup>+</sup>(<sup>2</sup><i>P<sub>J</sub></i>)–RG complexes and transport of Si<sup>+</sup>(<sup>2</sup><i>P<sub>J</sub></i>) in RG (RG = He–Ar)

description: We calculate accurate interatomic potentials for the interaction of a singly charged silicon cation with a rare gas atom of helium, neon or argon. We employ the RCCSD(T) method, and basis sets of quadruple-ζ and quintuple-ζ quality; each point is counterpoise-corrected and extrapolated to the basis set limit. We consider the lowest electronic state of the silicon atomic cation, Si<sup>+</sup>(<sup>2</sup> <i>P</i>), and calculate the interatomic potentials for the terms that arise from this: <sup>2</sup>Π and <sup>2</sup>Σ<sup>+</sup>. We additionally calculate the interatomic potentials for the respective spin-orbit levels, and examine the effect on the spectroscopic parameters; we also derive effective ionic radii for C<sup>+</sup> and Si<sup>+</sup>. Finally, we employ each set of potentials to calculate transport coefficients, and compare these to available data for Si<sup>+</sup> in He.
DOI: 10.6084/m9.figshare.4543261
title: d15N from Ficken & Wright 2017 (Biogeoscience)

description: This file contains data on the d15N values of soil pre and post burn. Data were collected in the summer of 2014.
DOI: 10.6084/m9.figshare.4545697.v5
title: Penalized Estimation in Large-Scale Generalized Linear Array Models

description: Large-scale generalized linear array models (GLAMs) can be challenging to fit. Computation and storage of its tensor product design matrix can be impossible due to time and memory constraints, and previously considered design matrix free algorithms do not scale well with the dimension of the parameter vector. A new design matrix free algorithm is proposed for computing the penalized maximum likelihood estimate for GLAMs, which, in particular, handles nondifferentiable penalty functions. The proposed algorithm is implemented and available via the R package glamlasso. It combines several ideas—previously considered separately—to obtain sparse estimates while at the same time efficiently exploiting the GLAM structure. In this article, the convergence of the algorithm is treated and the performance of its implementation is investigated and compared to that of glmnet on simulated as well as real data. It is shown that the computation time for glamlasso scales favorably with the size of the problem when compared to glmnet. Supplementary materials, in the form of R code, data and visualizations of results, are available online.
DOI: 10.6084/m9.figshare.4543261.v1
title: d15N from Ficken & Wright 2017 (Biogeoscience)

description: This file contains data on the d15N values of soil pre and post burn. Data were collected in the summer of 2014.
DOI: 10.6084/m9.figshare.4543255
title: Contributions of microbial activity and ash deposition to post-fire nitrogen availability in a pine savanna

description: This file contains data on inorganic nitrogen availability, soil moisture, soil organic matter, and soil pH across sites. It also contains data on soil d15N before and after prescribed burns. Data were collected in summer 2014.<br><br>
DOI: 10.6084/m9.figshare.4543303.v2
title: Theoretical study of Si<sup>+</sup>(<sup>2</sup><i>P<sub>J</sub></i>)–RG complexes and transport of Si<sup>+</sup>(<sup>2</sup><i>P<sub>J</sub></i>) in RG (RG = He–Ar)

description: We calculate accurate interatomic potentials for the interaction of a singly charged silicon cation with a rare gas atom of helium, neon or argon. We employ the RCCSD(T) method, and basis sets of quadruple-ζ and quintuple-ζ quality; each point is counterpoise-corrected and extrapolated to the basis set limit. We consider the lowest electronic state of the silicon atomic cation, Si<sup>+</sup>(<sup>2</sup> <i>P</i>), and calculate the interatomic potentials for the terms that arise from this: <sup>2</sup>Π and <sup>2</sup>Σ<sup>+</sup>. We additionally calculate the interatomic potentials for the respective spin-orbit levels, and examine the effect on the spectroscopic parameters; we also derive effective ionic radii for C<sup>+</sup> and Si<sup>+</sup>. Finally, we employ each set of potentials to calculate transport coefficients, and compare these to available data for Si<sup>+</sup> in He.