cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5277727.v1
title: Tables of human adipose tissue cell type-specific genes

description: The data set includes:1) "Celltype_enriched.txt" files separated by ";" that contain genes significantly enriched in one cell type compared to other three analyzed hWAT cell types according to the analysis described in R markdown file:http://figshare.com/s/509ea9441af442a735acAdjusted p-value &lt;0.05 for all pairwise comparisons, moderated F-statistics p-value &lt;0.05 (from R package/bioconductor package Limma).<br>2) "Celltype_enriched_collected.txt" files separated by ";". These files contain tables that include mean expression of the gene in a fraction where it is enriched, log fold change (logFC) and adjusted P values (adj.P.val) compared to each of other fractions. Minimal logFC and maximal adj.P.Val against other fractions are included as separate columns to enable easy sorting of the data in search for best expressed, best enriched or most specific genes. <br>3) R-code used to generate "Celltype_enriched_collected.txt" tables is provided.<br>4) In addition, a table with 100 highest-ranked genes from each fraction (based on highest logFC_min and lowest adj.P.val_max) is also included ("Selected_enriched_genes_all_fractions" - separated by tab).
DOI: 10.6084/m9.figshare.5277697
title: Abaqus model from Multi-parameter actuation of a neutrally stable shell: a flexible gear-less motor

description: Abaqus .inp files to reproduce the finite element simulation of the shell actuation and identification tests
DOI: 10.6084/m9.figshare.5277697.v1
title: Abaqus model from Multi-parameter actuation of a neutrally stable shell: a flexible gear-less motor

description: Abaqus .inp files to reproduce the finite element simulation of the shell actuation and identification tests
DOI: 10.6084/m9.figshare.5277673
title: Uniform curvature model from Multi-parameter actuation of a neutrally stable shell: a flexible gear-less motor

description: Mathemaica file deducing the material properties of the shell from Classical Laminate Plate Theory, and implementing of the uniform curvature model
DOI: 10.6084/m9.figshare.5277658
title: Differential expression in obese vs non-obese adipocyte - nominal significance

description: DIfferential expression of lean_obese adipocytes from adipose tissue. PLEASE NOTE: nominal significance, as all adjusted p-values &gt; 0.05. Reported genes have log fold change &gt; 0.585<br>
DOI: 10.6084/m9.figshare.5277673.v1
title: Uniform curvature model from Multi-parameter actuation of a neutrally stable shell: a flexible gear-less motor

description: Mathemaica file deducing the material properties of the shell from Classical Laminate Plate Theory, and implementing of the uniform curvature model
DOI: 10.6084/m9.figshare.5277655
title: PISA_2012

description: Test and questionnaire results of about half million student in 66 countries. The main dataset is ~500,000 rows by ~700 columns dataframe with mixed datatype.
DOI: 10.6084/m9.figshare.5277649
title: Re-evaluating conservation priorities of New World tarantulas (Araneae: Theraphosidae) in a molecular framework indicates non-monophyly of the genera, <i>Aphonopelma</i> and <i>Brachypelma</i>

description: We present a mtDNA gene tree of tarantula spiders (Araneae: Mygalomorphae: Theraphosidae) based on the mitochondrial <i>16S-tRNA (leu)-ND1</i> gene region as a promising initial molecular hypothesis to clarify the taxonomy of the largest subfamily, Theraphosinae. Many species of this New World subfamily are traded widely as exotic pets, yet few scientific studies on them exist, and the robustness of many supposed taxonomic groupings is debatable. Yet the validity of taxon names and knowledge of their distinctiveness is vital for trade regulation, most notably for the Neotropical genus <i>Brachypelma</i> Simon 1891, which is listed under CITES (Appendix II, see online supplemental material, which is available from the article's Taylor & Francis Online page at https://doi.org/10.1080/14772000.2017.1346719). The use of molecular markers for tarantula taxonomy has been limited until recently, with most previous studies relying on morphological methods. Our findings, from newly collected molecular data, have several nomenclatural implications, suggesting a need for a rigorous overhaul of Theraphosinae classification at multiple hierarchical levels. Here, we take steps toward a revised classification, favouring division of Theraphosinae into three tribes: the Theraphosini trib. nov., the Hapalopini trib. nov., and the Grammostolini trib. nov. We also make conservation recommendations for two non-monophyletic genera. Firstly, we recover <i>Aphonopelma</i> Pocock 1901 as polyphyletic, finding that the large radiation into the USA and Mexico is taxonomically distinct from at least three other lineages distributed throughout Central America, one of which includes the type species of the genus. Secondly, and importantly for conservation, we find diphyly in the CITES listed genus <i>Brachypelma</i> Simon 1891, where our data strongly favour a division into two distinct smaller genera. We consider only the lineage with endemics in the Pacific coastal zone of Mexico to be of conservation concern. Finally, we also make suggestions on the future direction of revisionary research for the Theraphosidae as a whole. http://zoobank.org/urn:lsid:zoobank.org:pub:B37F7795-3F92-4334-A0C7-65C8026EE1FB
DOI: 10.6084/m9.figshare.5277658.v2
title: Differential expression in obese vs non-obese adipocyte - nominal significance

description: DIfferential expression of lean_obese adipocytes from adipose tissue. PLEASE NOTE: nominal significance, as all adjusted p-values &gt; 0.05. Reported genes have log fold change &gt; 0.585<br>
DOI: 10.6084/m9.figshare.5277649.v1
title: Re-evaluating conservation priorities of New World tarantulas (Araneae: Theraphosidae) in a molecular framework indicates non-monophyly of the genera, <i>Aphonopelma</i> and <i>Brachypelma</i>

description: We present a mtDNA gene tree of tarantula spiders (Araneae: Mygalomorphae: Theraphosidae) based on the mitochondrial <i>16S-tRNA (leu)-ND1</i> gene region as a promising initial molecular hypothesis to clarify the taxonomy of the largest subfamily, Theraphosinae. Many species of this New World subfamily are traded widely as exotic pets, yet few scientific studies on them exist, and the robustness of many supposed taxonomic groupings is debatable. Yet the validity of taxon names and knowledge of their distinctiveness is vital for trade regulation, most notably for the Neotropical genus <i>Brachypelma</i> Simon 1891, which is listed under CITES (Appendix II, see online supplemental material, which is available from the article's Taylor & Francis Online page at https://doi.org/10.1080/14772000.2017.1346719). The use of molecular markers for tarantula taxonomy has been limited until recently, with most previous studies relying on morphological methods. Our findings, from newly collected molecular data, have several nomenclatural implications, suggesting a need for a rigorous overhaul of Theraphosinae classification at multiple hierarchical levels. Here, we take steps toward a revised classification, favouring division of Theraphosinae into three tribes: the Theraphosini trib. nov., the Hapalopini trib. nov., and the Grammostolini trib. nov. We also make conservation recommendations for two non-monophyletic genera. Firstly, we recover <i>Aphonopelma</i> Pocock 1901 as polyphyletic, finding that the large radiation into the USA and Mexico is taxonomically distinct from at least three other lineages distributed throughout Central America, one of which includes the type species of the genus. Secondly, and importantly for conservation, we find diphyly in the CITES listed genus <i>Brachypelma</i> Simon 1891, where our data strongly favour a division into two distinct smaller genera. We consider only the lineage with endemics in the Pacific coastal zone of Mexico to be of conservation concern. Finally, we also make suggestions on the future direction of revisionary research for the Theraphosidae as a whole. http://zoobank.org/urn:lsid:zoobank.org:pub:B37F7795-3F92-4334-A0C7-65C8026EE1FB
DOI: 10.6084/m9.figshare.5277658.v1
title: Differential expression in obese vs non-obese adipocyte - nominal significance

description: DIfferential expression of lean_obese adipocytes from adipose tissue. PLEASE NOTE: nominal significance, as all adjusted p-values &gt; 0.05. Reported genes have log fold change &gt; 0.585<br>
DOI: 10.34760/5f479998aea5a
title: Skeleton 3750 
title: 2
DOI: 10.34760/5f466940838f1
title: Skeleton 5114 
title: 2
DOI: 10.6084/m9.figshare.5277151
title: Chapter_7_Sup_Results_tables_Lead_SCA.xlsx

description: Supplementary results tables for Chapter 7 of Samuel C. Andrew's PhD thesis.
DOI: 10.6084/m9.figshare.5277139
title: Chapter_4_Supplementary_data_ZBS_170614.xlsx

description: Supplementary Data for Chapter 4 of Samuel C. Andrew's PhD thesis.
DOI: 10.6084/m9.figshare.5277142
title: Chapter_5_Andrew_HOSP_structure_Sup_Data.xlsx

description: Supplementary Microsatellite data for Chapter 5 of Samuel C. Andrew's PhD thesis.
DOI: 10.6084/m9.figshare.5277145
title: Chapter_6_LA_ Sup_Results_tables_SCA.xlsx

description: Supplementary Results for Chapter 6 of Samuel C. Andrew's PhD thesis.
DOI: 10.6084/m9.figshare.5277151.v1
title: Chapter_7_Sup_Results_tables_Lead_SCA.xlsx

description: Supplementary results tables for Chapter 7 of Samuel C. Andrew's PhD thesis.
DOI: 10.6084/m9.figshare.5277145.v1
title: Chapter_6_LA_ Sup_Results_tables_SCA.xlsx

description: Supplementary Results for Chapter 6 of Samuel C. Andrew's PhD thesis.
DOI: 10.6084/m9.figshare.5277142.v1
title: Chapter_5_Andrew_HOSP_structure_Sup_Data.xlsx

description: Supplementary Microsatellite data for Chapter 5 of Samuel C. Andrew's PhD thesis.
DOI: 10.6084/m9.figshare.5277139.v1
title: Chapter_4_Supplementary_data_ZBS_170614.xlsx

description: Supplementary Data for Chapter 4 of Samuel C. Andrew's PhD thesis.
DOI: 10.6084/m9.figshare.5277025
title: Nelson Marina, New Zealand: SST and salinity data

description: Time series of sea surface temperature (SST, °C) and salinity (PSU) recorded every 10 minutes at Nelson marina, the top of the South Island, New Zealand (S 41° 15’ 21”, E 173° 16’ 33.31”) between February 2012 and January 2014 using a HOBO U24-002-C logger (http://www.onsetcomp.com/products/data-loggers/u24-002-c) deployed from a floating pontoon at ~1 m depth (n = 81,164). The logger sensor was cleaned on a monthly basis using a soft cloth to reduce biofouling accumulation.<br>This data was collected as environmental ancillary data for marine pest biocontrol research published as:<br>Atalah, J., Newcombe, E.M., Hopkins, G.A., Forrest, B.M., 2014. Potential biocontrol agents for biofouling on artificial structures. Biofouling 30, 999-1010.<br>
DOI: 10.6084/m9.figshare.5277025.v1
title: Nelson Marina, New Zealand: SST and salinity data

description: Time series of sea surface temperature (SST, °C) and salinity (PSU) recorded every 10 minutes at Nelson marina, the top of the South Island, New Zealand (S 41° 15’ 21”, E 173° 16’ 33.31”) between February 2012 and January 2014 using a HOBO U24-002-C logger (http://www.onsetcomp.com/products/data-loggers/u24-002-c) deployed from a floating pontoon at ~1 m depth (n = 81,164). The logger sensor was cleaned on a monthly basis using a soft cloth to reduce biofouling accumulation.<br>This data was collected as environmental ancillary data for marine pest biocontrol research published as:<br>Atalah, J., Newcombe, E.M., Hopkins, G.A., Forrest, B.M., 2014. Potential biocontrol agents for biofouling on artificial structures. Biofouling 30, 999-1010.<br>
DOI: 10.6084/m9.figshare.5276908
title: mutation_data.zip

description: Data analyzed in Prominent features of the amino acid mutation landscape in cancer <br>bioRxiv 136002; doi: https://doi.org/10.1101/136002
DOI: 10.6084/m9.figshare.5277004
title: Bengston BES data .xlsx

description: This is the data for "Life-history and behavioral trait covariation across three years in Temnothorax ants" but S. Bengston
DOI: 10.6084/m9.figshare.5277004.v1
title: Bengston BES data .xlsx

description: This is the data for "Life-history and behavioral trait covariation across three years in Temnothorax ants" but S. Bengston
DOI: 10.6084/m9.figshare.5276899
title: Estimating orthant probabilities of high dimensional Gaussian vectors with an application to set estimation

description: The computation of Gaussian orthant probabilities has been extensively studied for low dimensional vectors. Here we focus on the high dimensional case and we present a two step procedure relying on both deterministic and stochastic techniques. The proposed estimator relies indeed on splitting the probability into a low dimensional term and a remainder. While the low dimensional probability can be estimated by fast and accurate quadrature, the remainder requires Monte Carlo sampling. We further refine the estimation by using a novel asymmetric nested Monte Carlo (anMC) algorithm for the remainder and we highlight cases where this approximation brings substantial efficiency gains. The proposed methods are compared against state-of-the-art techniques in a numerical study, which also calls attention to the advantages and drawbacks of the procedure. Finally the proposed method is applied to derive conservative estimates of excursion sets of expensive to evaluate deterministic functions under a Gaussian random field prior, without requiring a Markov assumption.
DOI: 10.6084/m9.figshare.5276899.v1
title: Estimating orthant probabilities of high dimensional Gaussian vectors with an application to set estimation

description: The computation of Gaussian orthant probabilities has been extensively studied for low dimensional vectors. Here we focus on the high dimensional case and we present a two step procedure relying on both deterministic and stochastic techniques. The proposed estimator relies indeed on splitting the probability into a low dimensional term and a remainder. While the low dimensional probability can be estimated by fast and accurate quadrature, the remainder requires Monte Carlo sampling. We further refine the estimation by using a novel asymmetric nested Monte Carlo (anMC) algorithm for the remainder and we highlight cases where this approximation brings substantial efficiency gains. The proposed methods are compared against state-of-the-art techniques in a numerical study, which also calls attention to the advantages and drawbacks of the procedure. Finally the proposed method is applied to derive conservative estimates of excursion sets of expensive to evaluate deterministic functions under a Gaussian random field prior, without requiring a Markov assumption.
DOI: 10.6084/m9.figshare.5276896.v1
title: A Generalized Estimating Equation approach to Multivariate Adaptive Regression Splines

description: Multivariate adaptive regression splines (MARS) is a popular nonparametric regression tool often used for prediction and for uncovering important data patterns between the response and predictor variables. The standard MARS algorithm assumes responses are normally distributed and independent, but in this paper we relax both of these assumptions by extending MARS to generalized estimating equations. We refer to this MARS-for-GEEs algorithm as “MARGE”. Our algorithm makes use of fast forward selection techniques, such that in the univariate case, MARGE has similar computation speed to a standard MARS implementation. Through simulation we show that the proposed algorithm has improved predictive performance than the original MARS algorithm when using correlated and/or non-normal response data. MARGE is also competitive with alternatives in the literature, especially for problems with multiple interacting predictors. We apply MARGE to various ecological examples with different data types.
DOI: 10.6084/m9.figshare.5276686
title: Do patients with thyroid cancer perceive adequate access to psychosocial support? A mixed methods survey of patients attending a UK cancer centre

description: Do patients with thyroid cancer perceive adequate access to psychosocial support? A mixed methods survey of patients attending a UK cancer centre
DOI: 10.6084/m9.figshare.5272453
title: Price-per-unit_data_and_analysis

description: Data and analysis for price-per-unit
DOI: 10.6084/m9.figshare.5272411
title: REFPROP Thermodynamic Reference Files: 1-hexene, 1-pentene, 1,2,4-trimethylbenzene, 1,3,5-trimethylbenzene, 2-methylexane

description: REFPROP thermodynamic reference files for the Peng-Robinson EOS:<br> 1-hexene (1HEXENE.FLD)1-pentene (1PENTENE.FLD)1,2,4-trimethylbenzene (124TRIMETHYLBENZENE.FLD)1,3,5-trimethylbenzene (135TRIMETHYLBENZENE.FLD)2-methylhexane (isoc7.FLD)<br>
DOI: 10.6084/m9.figshare.5276686.v1
title: Do patients with thyroid cancer perceive adequate access to psychosocial support? A mixed methods survey of patients attending a UK cancer centre

description: Do patients with thyroid cancer perceive adequate access to psychosocial support? A mixed methods survey of patients attending a UK cancer centre
DOI: 10.34760/5f466167208ad
title: Skeleton 4446 
title: 2
DOI: 10.6084/m9.figshare.5272453.v1
title: Price-per-unit_data_and_analysis

description: Data and analysis for price-per-unit
DOI: 10.6084/m9.figshare.5272255
title: Dashlane Installer - 4.8.4.34239_NO_TYPE_nolog_world_v8.exe

description: Dashlane Installer - 4.8.4.34239_NO_TYPE_nolog_world_v8.exe
DOI: 10.6084/m9.figshare.5272411.v1
title: REFPROP Thermodynamic Reference Files

description: REFPROP thermodynamic reference files for the Peng-Robinson EOS:<br> 1-hexene (1HEXENE.FLD)1-pentene (1PENTENE.FLD)1,2,4-trimethylbenzene (124TRIMETHYLBENZENE.FLD)1,3,5-trimethylbenzene (135TRIMETHYLBENZENE.FLD)2-methylhexane (isoc7.FLD)<br>
DOI: 10.6084/m9.figshare.5272255.v1
title: Dashlane Installer - 4.8.4.34239_NO_TYPE_nolog_world_v8.exe

description: Dashlane Installer - 4.8.4.34239_NO_TYPE_nolog_world_v8.exe
DOI: 10.6084/m9.figshare.5272036
title: Dash clustering and NOE dist analysis of SAM MDs

description: Collection of MD analysis scripts for cluster analysis and distance analysis:<br><b>running amberdash:</b>amberdash uses the commandline provided amberdash.inptext. It needs the information about the dihedral angles to be clustered (seed.tor) the MD trajectories used (seed.trajin) and a corresponding toppology file for the MD (seed.trj).<br><b>dashstate-trajectories.pl:</b>Script creates and runs cpptraj input that reads original MD trajectories and dash.out to create first multiple short dashstate trajectory files which are combined into Dihedcluster[n].trj files containing all structures per cluster.<br><b>analyseDihedclusters.pl:</b>uses ptraj to read individual Dihedcluster[n].trj trajectory files and calculates rmsd, partial rmsd, defined dihedral angles, individual distances, averaged distances, r^-6 averaged distances and their histograms and standard deviations.<br>In this example this is printed into several files including a summary file for the ditance analysis used for NOE fitting afterwards.<br>
DOI: 10.6084/m9.figshare.5272111
title: Ambiguous sequences at different cut off levels - (Item E)

description: For the evaluation of ambiguous sequences in microbial reference genomes we assessed different cut of levels for the generation of a curated microbial genome database. For each sequence fragment we determined the ratio between the number of negative BLAST hits (query genus ≠ subject genus) and all BLAST hits.<br><br>For a detailed description of this analysis, see the Supplemental Materials section of the publication.<br><br><b>Reference</b> <b>Kirstahler P, Bjerrum SS, Friis-Møller A, </b><b>la Cour M, Aarestrup FM, Westh H., and Pamp SJ. (2018) </b>Genomics-Based Identification of Microorganisms in Human Ocular Body Fluid.<b> </b><b>Scientific Reports</b>, doi:10.1038/s41598-018-22416-4.
DOI: 10.6084/m9.figshare.5272027
title: MK2 Phosphoscan dataset_Menon et al 2017.xlsx

description: A panel of MK2 (MAPKAPK-2)-target phosphopeptides identified by applying the Cell Signaling Technology Phosphoscan screening approach to the MK2/3 DKO cell culture model
DOI: 10.6084/m9.figshare.5272411.v3
title: REFPROP Thermodynamic Reference Files: 1-hexene, 1-pentene; 1,2,4-trimethylbenzene; 1,3,5-trimethylbenzene; 2-methylexane

description: REFPROP thermodynamic reference files for the Peng-Robinson EOS:<br> 1-hexene (1HEXENE.FLD)1-pentene (1PENTENE.FLD)1,2,4-trimethylbenzene (124TRIMETHYLBENZENE.FLD)1,3,5-trimethylbenzene (135TRIMETHYLBENZENE.FLD)2-methylhexane (isoc7.FLD)<br>
DOI: 10.6084/m9.figshare.5272027.v1
title: MK2 Phosphoscan dataset_Menon et al 2017.xlsx

description: A panel of MK2 (MAPKAPK-2)-target phosphopeptides identified by applying the Cell Signaling Technology Phosphoscan screening approach to the MK2/3 DKO cell culture model
DOI: 10.6084/m9.figshare.5272036.v1
title: Dash clustering and NOE dist analysis of SAM MDs

description: Collection of MD analysis scripts for cluster analysis and distance analysis:<br><b>running amberdash:</b>amberdash uses the commandline provided amberdash.inptext. It needs the information about the dihedral angles to be clustered (seed.tor) the MD trajectories used (seed.trajin) and a corresponding toppology file for the MD (seed.trj).<br><b>dashstate-trajectories.pl:</b>Script creates and runs cpptraj input that reads original MD trajectories and dash.out to create first multiple short dashstate trajectory files which are combined into Dihedcluster[n].trj files containing all structures per cluster.<br><b>analyseDihedclusters.pl:</b>uses ptraj to read individual Dihedcluster[n].trj trajectory files and calculates rmsd, partial rmsd, defined dihedral angles, individual distances, averaged distances, r^-6 averaged distances and their histograms and standard deviations.<br>In this example this is printed into several files including a summary file for the ditance analysis used for NOE fitting afterwards.<br>
DOI: 10.6084/m9.figshare.5272111.v2
title: Ambiguous sequences at different cut off levels - (Item E)

description: For the evaluation of ambiguous sequences in microbial reference genomes we assessed different cut of levels for the generation of a curated microbial genome database. For each sequence fragment we determined the ratio between the number of negative BLAST hits (query genus ≠ subject genus) and all BLAST hits.<br><br>For a detailed description of this analysis, see the Supplemental Materials section of the publication.<br><br><b>Reference</b> <b>Kirstahler P, Bjerrum SS, Friis-Møller A, </b><b>la Cour M, Aarestrup FM, Westh H., and Pamp SJ. (2018) </b>Genomics-Based Identification of Microorganisms in Human Ocular Body Fluid.<b> </b><b>Scientific Reports</b>, doi:10.1038/s41598-018-22416-4.
DOI: 10.6084/m9.figshare.5272111.v1
title: Ambiguous sequences at different cut off levels - (Item J)

description: For the evaluation of ambiguous sequences in microbial reference genomes we assessed different cut of levels for the generation of a curated microbial genome database. For each sequence fragment we determined the ratio between the number of negative BLAST hits (query genus ≠ subject genus) and all BLAST hits.<br><br>For a detailed description of this analysis, see the Supplemental Materials section of the publication.<br><br><b>Reference</b> <b>Kirstahler P, Bjerrum SS, Friis-Møller A, </b><b>la Cour M, Aarestrup FM, Westh H., and Pamp SJ. (2017) </b>Genomics-Based Identification of Microorganisms in Human Ocular Body Fluid.<b> Journal </b>Vol:Issue page-page.