cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1067053.v2
title: Variable Selection Diagnostics Measures for High-Dimensional Regression

description: Many exciting results have been obtained on model selection for high-dimensional data in both efficient algorithms and theoretical developments. The powerful penalized regression methods can give sparse representations of the data even when the number of predictors is much larger than the sample size. One important question then is: How do we know when a sparse pattern identified by such a method is reliable? In this work, besides investigating instability of model selection methods in terms of variable selection, we propose variable selection deviation measures that give one a proper sense on how many predictors in the selected set are likely trustworthy in certain aspects. Simulation and a real data example demonstrate the utility of these measures for application.
DOI: 10.6084/m9.figshare.1067051.v1
title: Tree-Structured Mixed-Effects Regression Modeling for Longitudinal Data

description: Tree-structured models have been widely used because they function as interpretable prediction models that offer easy data visualization. A number of tree algorithms have been developed for univariate response data and can be extended to analyze multivariate response data. We propose a tree algorithm by combining the merits of a tree-based model and a mixed-effects model for longitudinal data. We alleviate variable selection bias through residual analysis, which is used to solve problems that exhaustive search approaches suffer from, such as undue preference to split variables with more possible splits, expensive computational cost, and end-cut preference. Most importantly, our tree algorithm discovers trends over time on each of the subspaces from recursive partitioning, while other tree algorithms predict responses. We investigate the performance of our algorithm with both simulation and real data studies. We also develop an R package melt that can be used conveniently and freely. Additional results are provided as online supplementary material.
DOI: 10.6084/m9.figshare.1067052.v2
title: Graphical Aids for the Analysis of Two-Level Nonregular Designs

description: The complex alias pattern between main effects and two-factor interactions for two-level nonregular designs has been considered a problem when analyzing these designs. If only a few two-factor interactions are active, however, the pattern induced into the estimated main effects contrasts from the active interactions may be very structured. This is, in particular, true for the 12-run and the 20-run Plackett–Burman (PB) designs, probably the two most important designs for physical experimentation. This article presents a graphical method for the analysis of nonregular two-level designs. The method consists of two steps. The first step is called contrast plots interpretation and is directed toward revealing the cause for the pattern observed in contrast plots. The second step is called alias reduction and aims at simplifying the interpretation of the contrast plots by reducing the aliasing caused by effects that, with a high degree of certainty, may be considered active. The method is tested on the 12-run PB design both with simulated and real data and on the 20-run PB design for one particular case with real data. Supplementary materials (MINITAB codes for performing calculations and plots) are available online.
DOI: 10.6084/m9.figshare.1067053.v1
title: Variable Selection Diagnostics Measures for High-Dimensional Regression

description: Many exciting results have been obtained on model selection for high-dimensional data in both efficient algorithms and theoretical developments. The powerful penalized regression methods can give sparse representations of the data even when the number of predictors is much larger than the sample size. One important question then is: How do we know when a sparse pattern identified by such a method is reliable? In this work, besides investigating instability of model selection methods in terms of variable selection, we propose variable selection deviation measures that give one a proper sense on how many predictors in the selected set are likely trustworthy in certain aspects. Simulation and a real data example demonstrate the utility of these measures for application.
DOI: 10.6084/m9.figshare.1067049.v1
title: A Graphical Goodness-of-Fit Test for Dependence Models in Higher Dimensions

description: This article introduces a graphical goodness-of-fit test for copulas in more than two dimensions. The test is based on pairs of variables and can thus be interpreted as a first-order approximation of the underlying dependence structure. The idea is to first transform pairs of data columns with the Rosenblatt transform to bivariate standard uniform distributions under the null hypothesis. This hypothesis can be graphically tested with a matrix of bivariate scatterplots, Q-Q plots, or other transformations. Furthermore, additional information can be encoded as background color, such as measures of association or (approximate) <i>p</i>-values of tests of independence. The proposed goodness-of-fit test is designed as a basic graphical tool for detecting deviations from a postulated, possibly high-dimensional, dependence model. Various examples are given and the methodology is applied to a financial dataset. An implementation is provided by the R package copula. Supplementary material for this article is available online, which provides the R package copula and reproduces all the graphical results of this article.
DOI: 10.6084/m9.figshare.1067050.v1
title: Adaptive Bayesian Nonstationary Modeling for Large Spatial Datasets Using Covariance Approximations

description: Gaussian process models have been widely used in spatial statistics but face tremendous modeling and computational challenges for very large nonstationary spatial datasets. To address these challenges, we develop a Bayesian modeling approach using a nonstationary covariance function constructed based on adaptively selected partitions. The partitioned nonstationary class allows one to knit together local covariance parameters into a valid global nonstationary covariance for prediction, where the local covariance parameters are allowed to be estimated within each partition to reduce computational cost. To further facilitate the computations in local covariance estimation and global prediction, we use the full-scale covariance approximation (FSA) approach for the Bayesian inference of our model. One of our contributions is to model the partitions stochastically by embedding a modified treed partitioning process into the hierarchical models that leads to automated partitioning and substantial computational benefits. We illustrate the utility of our method with simulation studies and the global Total Ozone Matrix Spectrometer (TOMS) data. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.1067052.v1
title: Graphical Aids for the Analysis of Two-Level Nonregular Designs

description: The complex alias pattern between main effects and two-factor interactions for two-level nonregular designs has been considered a problem when analyzing these designs. If only a few two-factor interactions are active, however, the pattern induced into the estimated main effects contrasts from the active interactions may be very structured. This is, in particular, true for the 12-run and the 20-run Plackett–Burman (PB) designs, probably the two most important designs for physical experimentation. This article presents a graphical method for the analysis of nonregular two-level designs. The method consists of two steps. The first step is called contrast plots interpretation and is directed toward revealing the cause for the pattern observed in contrast plots. The second step is called alias reduction and aims at simplifying the interpretation of the contrast plots by reducing the aliasing caused by effects that, with a high degree of certainty, may be considered active. The method is tested on the 12-run PB design both with simulated and real data and on the 20-run PB design for one particular case with real data. Supplementary materials (MINITAB codes for performing calculations and plots) are available online.
DOI: 10.6084/m9.figshare.1067047
title: Emissivity of LaB6 at 1622K from 550 nm to 2400 nm.

description: Emissivity of LaB6 at 1622K from 550 nm to 2400 nm. For a paper describing the acquisition of this data see: J. M. D. Kowalczyk, M. R. Hadmack, E. B. Szarmes, and J. M. J. Madey. Emissivity of Lanthanum<br>Hexaboride Thermionic Electron Gun Cathode. International Journal of Thermophysics, 35(8):1538–<br>1544, Aug. 2014. doi:10.1007/s10765-014-1712-3.
DOI: 10.6084/m9.figshare.1067046
title: Genetic variation brown trout Chile & Falklands

description: C. Monzón-Argüello, S. Consuegra, G. Gajardo, F. Marco-Rius, D.M. Fowler, J. DeFaveri & C. Garcia de Leaniz. (2014). Contrasting patterns of genetic and phenotypic differentiation in two invasive salmonids in the Southern Hemisphere. <em>Evol App</em> (in press)
DOI: 10.6084/m9.figshare.1067046.v1
title: Genetic variation brown trout Chile & Falklands

description: C. Monzón-Argüello, S. Consuegra, G. Gajardo, F. Marco-Rius, D.M. Fowler, J. DeFaveri & C. Garcia de Leaniz. (2014). Contrasting patterns of genetic and phenotypic differentiation in two invasive salmonids in the Southern Hemisphere. <em>Evol App</em> (in press)
DOI: 10.6084/m9.figshare.1067047.v1
title: Emissivity of LaB6 at 1622K from 550 nm to 2400 nm.

description: Emissivity of LaB6 at 1622K from 550 nm to 2400 nm. For a paper describing the acquisition of this data see: J.M.D. Kowalczyk, M.R. Hadmack, E.B. Szarmes, and J.M.J. Madey, "Emissivity of lanthanum hexaboride thermionic electron gun cathode," International Journal of Thermophysics (in revision) 2014.
DOI: 10.6084/m9.figshare.1067011
title: Dataset - Fearfulness Affects quail Maternal Care and Subsequent Offspring Development

description: <strong>Abstract</strong><br>Our study investigated relationships between a precocial bird’s fearfulness and maternal care, and the implication of maternal care as a vector for non-genomic transmission of fearfulness to chicks. We compared care given to chicks between two sets of female Japanese quail selected to present either high (LTI) or low fearfulness (STI). Chicks, from a broiler line, were adopted by these females following a sensitization procedure. Chicks’ fearfulness after separation from their mother was assessed by well-established procedures. LTIs took longer to present maternal responses, pecked chicks more during the first days post-hatch, presented impaired maternal vocal behaviour and were globally less active than STI females. Chicks mothered by LTIs presented more fearful reactions than did chicks mothered by STIs, supporting the hypothesis of a non-genetic maternal transmission of fearfulness. We suggest that the longer latencies required by LTIs to become maternal are a consequence of their greater fear of chicks, and that their lower general and vocal activity could be components of a heightened antipredatory strategy. We discuss the transmission of maternal fearfulness to fostered chicks, taking into account the possible implication of several well-known mechanisms underlying maternal effects.
DOI: 10.6084/m9.figshare.1067011.v1
title: Dataset - Fearfulness Affects quail Maternal Care and Subsequent Offspring Development

description: <strong>Abstract</strong><br>Our study investigated relationships between a precocial bird’s fearfulness and maternal care, and the implication of maternal care as a vector for non-genomic transmission of fearfulness to chicks. We compared care given to chicks between two sets of female Japanese quail selected to present either high (LTI) or low fearfulness (STI). Chicks, from a broiler line, were adopted by these females following a sensitization procedure. Chicks’ fearfulness after separation from their mother was assessed by well-established procedures. LTIs took longer to present maternal responses, pecked chicks more during the first days post-hatch, presented impaired maternal vocal behaviour and were globally less active than STI females. Chicks mothered by LTIs presented more fearful reactions than did chicks mothered by STIs, supporting the hypothesis of a non-genetic maternal transmission of fearfulness. We suggest that the longer latencies required by LTIs to become maternal are a consequence of their greater fear of chicks, and that their lower general and vocal activity could be components of a heightened antipredatory strategy. We discuss the transmission of maternal fearfulness to fostered chicks, taking into account the possible implication of several well-known mechanisms underlying maternal effects.
DOI: 10.6084/m9.figshare.1066994
title: Phylogenomic exploration with aTRAM: slides only

description: Assembling genes without genomes: phylogenomic exploration with aTRAM
DOI: 10.6084/m9.figshare.1066903
title: Genetic determinism in the Finnish upper secondary school biology textbooks

description: In the excel file “all models” tab includes properties on all analyzed gene models: the book, the page, the epistemological features (named as in the article), context where the model was situated, the model and the hybridization percentage. “Proportion of historical models” counts the total number and proportion of historic models. “Structure of the books” tab shows the sequence of contents in all analyzed books. “Definitions of key concepts” shows the original passages which includes definitions of genes, alleles, dominance, recessive or environmental effects on phenotype and translations in English with book details and page numbers.<br> “Examples” tab show all the examples used in the books and “Named scientist” lists all the scientists which have been named in the textbooks.The numbers refer to the page numbers in books.<br><br>Article at the moment in press for NorDiNa - Nordic Studies in Science Education
DOI: 10.6084/m9.figshare.1066953
title: University of Sussex APC data (2013-14)

description: Version 3 This data was collected by Information Power Ltd on behalf of Jisc Collections in March and April 2014, along with the APC expenditure of 23 other UK higher education institutions. As of April 2014, it lists all known APCs paid by the University of Sussex during 2013 and the first two months of 2014. It is likely that many more articles published by University of Sussex authors were open access, but the full extent is not known. Some figures were estimated, and the data should not be treated as 100% accurate. It has been publicly released with the permission of University of Sussex library. <strong>UPDATE</strong>: The original file published on 24 June 2014 was replaced on 25 June 2014 to include PLOS articles (although the prices paid are mostly estimates). It was updated again on 3 July 2014 to include a completed column stating whether journals are hybrid or fully open access.
DOI: 10.6084/m9.figshare.1066994.v1
title: Phylogenomic exploration with aTRAM: slides only

description: Assembling genes without genomes: phylogenomic exploration with aTRAM
DOI: 10.6084/m9.figshare.1066902
title: APPLICATIONS OF GEOGRAPHICAL INFORMATION SYSTEM AND REMOTE SENSING TECHNIQUES IN HYPSOMETRIC ANALYSIS OF MAN RIVER BASIN IN AKOLA AND BULDHANA DISTRICTS, MAHARASHTRA, INDIA

description: Hypsometric analysis of watershed (area-elevation analysis) has generally been used to<br>reveal the stages of geomorphic development (stabilized, mature and young). Hypsometric integral<br>quantifies the geologic stages of development and erosion prone-ness of the watersheds. Hypsometric<br>integral is estimated by the graphical plot of the measured contour elevation and encompassed area by<br>using empirical formulae
DOI: 10.6084/m9.figshare.1066902.v1
title: APPLICATIONS OF GEOGRAPHICAL INFORMATION SYSTEM AND REMOTE SENSING TECHNIQUES IN HYPSOMETRIC ANALYSIS OF MAN RIVER BASIN IN AKOLA AND BULDHANA DISTRICTS, MAHARASHTRA, INDIA

description: Hypsometric analysis of watershed (area-elevation analysis) has generally been used to<br>reveal the stages of geomorphic development (stabilized, mature and young). Hypsometric integral<br>quantifies the geologic stages of development and erosion prone-ness of the watersheds. Hypsometric<br>integral is estimated by the graphical plot of the measured contour elevation and encompassed area by<br>using empirical formulae
DOI: 10.6084/m9.figshare.1066903.v2
title: Genetic determinism in the Finnish upper secondary school biology textbooks

description: In the excel file “all models” tab includes properties on all analyzed gene models: the book, the page, the epistemological features (named as in the article), context where the model was situated, the model and the hybridization percentage. “Proportion of historical models” counts the total number and proportion of historic models. “Structure of the books” tab shows the sequence of contents in all analyzed books. “Definitions of key concepts” shows the original passages which includes definitions of genes, alleles, dominance, recessive or environmental effects on phenotype and translations in English with book details and page numbers.<br> “Examples” tab show all the examples used in the books and “Named scientist” lists all the scientists which have been named in the textbooks.The numbers refer to the page numbers in books.<br><br>Article at the moment in press for NorDiNa - Nordic Studies in Science Education
DOI: 10.6084/m9.figshare.1066903.v1
title: Finnish upper secondary school textbooks include outdated gene models

description: In the excel file “all models” tab includes properties on all analyzed gene models: the book, the page, the epistemological features (named as in the article), context where the model was situated, the model and the hybridization percentage. “Proportion of historical models” counts the total number and proportion of historic models. “Structure of the books” tab shows the sequence of contents in all analyzed books. “Definitions of key concepts” shows the original passages which includes definitions of genes, alleles, dominance, recessive or environmental effects on phenotype and translations in English with book details and page numbers.<br> “Examples” tab show all the examples used in the books and “Named scientist” lists all the scientists which have been named in the textbooks.The numbers refer to the page numbers in books.<br>
DOI: 10.6084/m9.figshare.1066953.v1
title: Sussex APC data (2013-14)

description: This data was collected by Information Power Ltd on behalf of Jisc Collections in March and April 2014, along with the APC expenditure of 23 other UK higher education institutions. As of April 2014, it lists all known APCs paid by the University of Sussex during 2013 and the first two months of 2014. It is likely that many more articles published by University of Sussex authors were open access, but the full extent is not known. Some figures were estimated, and the data should not be treated as 100% accurate. It has been publicly released with the permission of University of Sussex library.
DOI: 10.6084/m9.figshare.1066953.v2
title: Sussex APC data (2013-14)

description: This data was collected by Information Power Ltd on behalf of Jisc Collections in March and April 2014, along with the APC expenditure of 23 other UK higher education institutions. As of April 2014, it lists all known APCs paid by the University of Sussex during 2013 and the first two months of 2014. It is likely that many more articles published by University of Sussex authors were open access, but the full extent is not known. Some figures were estimated, and the data should not be treated as 100% accurate. It has been publicly released with the permission of University of Sussex library. <strong>UPDATE</strong>: The original file published on 24 June 2014 has been replaced with this one as of 25 June 2014. It now includes PLOS articles (although the prices paid are mostly estimates).
DOI: 10.6084/m9.figshare.1066953.v4
title: University of Sussex APC data (2013-14)

description: Version 3 This data was collected by Information Power Ltd on behalf of Jisc Collections in March and April 2014, along with the APC expenditure of 23 other UK higher education institutions. As of April 2014, it lists all known APCs paid by the University of Sussex during 2013 and the first two months of 2014. It is likely that many more articles published by University of Sussex authors were open access, but the full extent is not known. Some figures were estimated, and the data should not be treated as 100% accurate. It has been publicly released with the permission of University of Sussex library. <strong>UPDATE</strong>: The original file published on 24 June 2014 was replaced on 25 June 2014 to include PLOS articles (although the prices paid are mostly estimates). It was updated again on 3 July 2014 to include a completed column stating whether journals are hybrid or fully open access.
DOI: 10.6084/m9.figshare.1066953.v3
title: University of Sussex APC data (2013-14)

description: Version 3 This data was collected by Information Power Ltd on behalf of Jisc Collections in March and April 2014, along with the APC expenditure of 23 other UK higher education institutions. As of April 2014, it lists all known APCs paid by the University of Sussex during 2013 and the first two months of 2014. It is likely that many more articles published by University of Sussex authors were open access, but the full extent is not known. Some figures were estimated, and the data should not be treated as 100% accurate. It has been publicly released with the permission of University of Sussex library. <strong>UPDATE</strong>: The original file published on 24 June 2014 was replaced on 25 June 2014 to include PLOS articles (although the prices paid are mostly estimates). It was updated again on 3 July 2014 to include a completed column stating whether journals are hybrid or fully open access.
DOI: 10.5517/ccdc.csd.cc24mnt8
title: CCDC 1985110: Experimental Crystal Structure Determination

description: Related Article: Jan Jirát, Vít Zvoníček, Martin Babor, Luděk Ridvan, Eliška Skořepová, Michal Dušek, Miroslav Šoóš|2020|Cryst.Growth Des.|20|5785|doi:10.1021/acs.cgd.0c00393
DOI: 10.5517/ccdc.csd.cc24mnv9
title: CCDC 1985111: Experimental Crystal Structure Determination

description: Related Article: Jan Jirát, Vít Zvoníček, Martin Babor, Luděk Ridvan, Eliška Skořepová, Michal Dušek, Miroslav Šoóš|2020|Cryst.Growth Des.|20|5785|doi:10.1021/acs.cgd.0c00393
DOI: 10.6084/m9.figshare.1066837
title: Taxonomic distribution of OTU for 16S rRNA gene sequences obtained with archeal (Arch), actinobacterial (Act) and universal (Univ) primers.

description: Supplementary data to manuscript entitled: “Paradox of the plankton” in exceptionally abundant rock biofilm by Karolina Tomczyk-Żak, Paweł Szczesny, Robert Gromadka and Urszula Zielenkiewicz.
DOI: 10.6084/m9.figshare.1066836
title: Taxonomic distribution of reads for 16S rRNA gene sequences obtained with archeal (Arch), actinobacterial (Act) and universal (Univ) primers.

description: Length of colored data stripes is proportional to sequence’s number. Supplementary data to manuscript entitled: “Paradox of the plankton” in exceptionally abundant rock biofilm by Karolina Tomczyk-Żak, Paweł Szczesny, Robert Gromadka and Urszula Zielenkiewicz.
DOI: 10.5517/ccdc.csd.cc24vhcw
title: CCDC 1991668: Experimental Crystal Structure Determination

description: Related Article: Jan Jirát, Vít Zvoníček, Martin Babor, Luděk Ridvan, Eliška Skořepová, Michal Dušek, Miroslav Šoóš|2020|Cryst.Growth Des.|20|5785|doi:10.1021/acs.cgd.0c00393
DOI: 10.6084/m9.figshare.1066835
title: Protocols of PCR amplification of 16S rRNA.

description: Supplementary data to manuscript entitled: “Paradox of the plankton” in exceptionally abundant rock biofilm by Karolina Tomczyk-Żak, Paweł Szczesny, Robert Gromadka and Urszula Zielenkiewicz.