cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6287693
title: Superheat: An R Package for Creating Beautiful and Extendable Heatmaps for Visualizing Complex Data

description: The technological advancements of the modern era have enabled the collection of huge amounts of data in science and beyond. Extracting useful information from such massive datasets is an ongoing challenge as traditional data visualization tools typically do not scale well in high-dimensional settings. An existing visualization technique that is particularly well suited to visualizing large datasets is the heatmap. Although heatmaps are extremely popular in fields such as bioinformatics, they remain a severely underutilized visualization tool in modern data analysis. This article introduces superheat, a new R package that provides an extremely flexible and customizable platform for visualizing complex datasets. Superheat produces attractive and extendable heatmaps to which the user can add a response variable as a scatterplot, model results as boxplots, correlation information as barplots, and more. The goal of this article is two-fold: (1) to demonstrate the potential of the heatmap as a core visualization method for a range of data types, and (2) to highlight the customizability and ease of implementation of the superheat R package for creating beautiful and extendable heatmaps. The capabilities and fundamental applicability of the superheat package will be explored via three reproducible case studies, each based on publicly available data sources.
DOI: 10.6084/m9.figshare.14151268.v1
title: Additional file 4 of Comprehensive analysis of the transcriptome‐wide m6A methylome in invasive malignant pleomorphic adenoma

description: Additional file 4. Table S4. Number of altered m6A peaks in human chromosomes.
DOI: 10.6084/m9.figshare.6287690.v1
title: Algorithms for Fitting the Constrained Lasso

description: We compare alternative computing strategies for solving the constrained lasso problem. As its name suggests, the constrained lasso extends the widely used lasso to handle linear constraints, which allow the user to incorporate prior information into the model. In addition to quadratic programming, we employ the alternating direction method of multipliers (ADMM) and also derive an efficient solution path algorithm. Through both simulations and benchmark data examples, we compare the different algorithms and provide practical recommendations in terms of efficiency and accuracy for various sizes of data. We also show that, for an arbitrary penalty matrix, the generalized lasso can be transformed to a constrained lasso, while the converse is not true. Thus, our methods can also be used for estimating a generalized lasso, which has wide-ranging applications. Code for implementing the algorithms is freely available in both the Matlab toolbox SparseReg and the Julia package ConstrainedLasso. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.13627193
title: Additional file 3 of Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach

description: Additional file 2. bioBakery workflows.
DOI: 10.6084/m9.figshare.13627196
title: Additional file 4 of Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach

description: Additional file 3. Multivariate tests for taxa associated with metadata.
DOI: 10.6084/m9.figshare.13627202
title: Additional file 6 of Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach

description: Additional file 5. Metadata.
DOI: 10.6084/m9.figshare.13627205
title: Additional file 7 of Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach

description: Additional file 6. Relative abundances of several taxa changed significantly after PMA treatment.
DOI: 10.6084/m9.figshare.13627208
title: Additional file 8 of Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach

description: Additional file 7:. All sample taxonomy.
DOI: 10.6084/m9.figshare.13627211.v1
title: Additional file 9 of Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach

description: Additional file 8:. All sample meta.
DOI: 10.6084/m9.figshare.13627196.v1
title: Additional file 4 of Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach

description: Additional file 3. Multivariate tests for taxa associated with metadata.
DOI: 10.6084/m9.figshare.6287681
title: Local Gaussian Process Model for Large-Scale Dynamic Computer Experiments

description: The recent accelerated growth in the computing power has generated popularization of experimentation with dynamic computer models in various physical and engineering applications. Despite the extensive statistical research in computer experiments, most of the focus had been on the theoretical and algorithmic innovations for the design and analysis of computer models with scalar responses. In this article, we propose a computationally efficient statistical emulator for a large-scale dynamic computer simulator (i.e., simulator which gives time series outputs). The main idea is to first find a good local neighborhood for every input location, and then emulate the simulator output via a singular value decomposition (SVD) based Gaussian process (GP) model. We develop a new design criterion for sequentially finding this local neighborhood set of training points. Several test functions and a real-life application have been used to demonstrate the performance of the proposed approach over a naive method of choosing local neighborhood set using the Euclidean distance among design points. The supplementary material, which contains proof of the theoretical results, detailed algorithms, additional simulation results, and <i>R</i> codes, are available online.
DOI: 10.6084/m9.figshare.13627193.v1
title: Additional file 3 of Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach

description: Additional file 2. bioBakery workflows.
DOI: 10.6084/m9.figshare.13627208.v1
title: Additional file 8 of Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach

description: Additional file 7:. All sample taxonomy.
DOI: 10.6084/m9.figshare.11531010
title: MOESM16 of Transcriptomic and metabolomic analyses provide insight into the volatile compounds of citrus leaves and flowers

description: Additional file 16: Table S9. Differentially expressed genes between the balloon (F1) and fully open (F2) flower stages.
DOI: 10.6084/m9.figshare.11531010.v1
title: MOESM16 of Transcriptomic and metabolomic analyses provide insight into the volatile compounds of citrus leaves and flowers

description: Additional file 16: Table S9. Differentially expressed genes between the balloon (F1) and fully open (F2) flower stages.
DOI: 10.6084/m9.figshare.7336328.v1
title: Research on the Folding Patterns and Deployment Dynamics of Inflatable Capsule Structures

description: ABSTRACT: The folding patterns and deployment dynamic characteristics of conical inflatable capsule structures were investigated. A six-fold-line method of packing a conical shell surface was designed. The fold-line layouts and relation formulas of the fold angles were determined. The folded state of the inflatable capsule structure was parametrically modeled; then, the deployment dynamic analysis model was established using ANSYS/LS-DYNA software. The dynamic characteristics of the inflatable capsule structure in orbit were numerically simulated. Thus, the deployment configurations and the time history curves of the dynamic characteristics were obtained. The results verified the feasibility of the fold pattern and the deployment dynamic analysis model. The influences of the residual gases from the packing process on the subsequent deployment process were investigated. The results indicated that a small amount of residual gas can lead to structures that cannot deploy smoothly, and two methods were presented to avoid this challenge. These works provide technical support for the structural designs of this type of inflatable capsule structure.
DOI: 10.6084/m9.figshare.1569546
title: Petrogenesis of Early Cretaceous volcanic rocks of the Manketouebo Formation in the Wuchagou region, central Great Xing’an Range, NE China, and tectonic implications: geochronological, geochemical, and Hf isotopic evidence

description: This study presents new whole-rock major and trace element geochemistry, zircon U–Pb ages, and Hf-isotope compositions for volcanic rocks from the Manketouebo Formation of the central Great Xing’an Range, NE China. These data provide precise ages and information on the petrogenesis and source of the magmas that formed this formation, furthering our understanding of the geodynamic setting of the large-scale late Mesozoic magmatism in the Great Xing’an Range and other areas in NE China. The Manketouebo Formation in the study area is dominated by rhyolites and rhyolitic tuffs with minor trachydacites. The LA-ICP-MS zircon U–Pb dating indicates that these volcanic rocks formed between 143 and 139 Ma. The volcanic rocks contain high silica (66.70–79.91 wt.%) and total alkali (5.93–9.72 wt.%) concentrations, and low concentrations of MgO (0.08–1.15 wt.%), total FeO (0.68–4.50 wt.%), and CaO (0.10–2.56 wt.%). They are enriched in large-ion lithophile elements (LILEs; e.g. Rb, Th, and U) and light rare earth elements (LREEs), and depleted in high field strength elements (HFSEs; e.g. Nb, Ta, Ti, and P) and heavy rare earth elements (HREEs), indicating that they are similar to highly fractionated I-type igneous rocks. All of the magmatic zircons from the analysed samples have high initial <sup>176</sup>Hf/<sup>177</sup>Hf ratios (0.282900–0.283093), positive <i>ε</i><sub>Hf</sub>(<i>t</i>) values (7.48–14.19), and young Hf two-stage model ages (954–344 Ma) that suggest the primary magma that formed the volcanic rocks of the Manketouebo Formation was derived from the partial melting of Neoproterozoic to Phanerozoic juvenile crustal material, indicating in turn that significant crustal growth occurred at this time within the Xing’an Terrane. These data, combined with previous research into the spatial–temporal distribution of Mesozoic volcanic rocks in NE China, suggest that the Early Cretaceous magmatism in the Great Xing’an Range was influenced by both the subduction of the Palaeo-Pacific Plate and the closure of the Mongol–Okhotsk Ocean. This was a crucial period in the transformation from the Mongol–Okhotsk Ocean to the Palaeo-Pacific tectonic regimes. In summary, the early stages of Early Cretaceous magmatism in this area were related to the closure of the Mongol–Okhotsk Ocean, whereas the later stages of magmatism in this area and elsewhere in NE China were related to the subduction of the Palaeo-Pacific Plate.
DOI: 10.6084/m9.figshare.13627199
title: Additional file 5 of Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach

description: Additional file 4. PERMANOVA FDR adjusted.
DOI: 10.6084/m9.figshare.13627199.v1
title: Additional file 5 of Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach

description: Additional file 4. PERMANOVA FDR adjusted.
DOI: 10.6084/m9.figshare.11531022
title: MOESM18 of Transcriptomic and metabolomic analyses provide insight into the volatile compounds of citrus leaves and flowers

description: Additional file 18: Table S10. Expression levels of TPS genes, CYP450 genes and the volatile compound content in flowers.
DOI: 10.6084/m9.figshare.11531022.v1
title: MOESM18 of Transcriptomic and metabolomic analyses provide insight into the volatile compounds of citrus leaves and flowers

description: Additional file 18: Table S10. Expression levels of TPS genes, CYP450 genes and the volatile compound content in flowers.
DOI: 10.6084/m9.figshare.11531031
title: MOESM1 of Transcriptomic and metabolomic analyses provide insight into the volatile compounds of citrus leaves and flowers

description: Additional file 1: Table S1. Volatiles in citrus leaves (Î¼g/g). U: undetectable.
DOI: 10.6084/m9.figshare.11531031.v1
title: MOESM1 of Transcriptomic and metabolomic analyses provide insight into the volatile compounds of citrus leaves and flowers

description: Additional file 1: Table S1. Volatiles in citrus leaves (Î¼g/g). U: undetectable.
DOI: 10.6084/m9.figshare.11531040
title: MOESM21 of Transcriptomic and metabolomic analyses provide insight into the volatile compounds of citrus leaves and flowers

description: Additional file 21: Table S12. Primers used in the cloning of STPS and construction of expression vectors.
DOI: 10.6084/m9.figshare.11531040.v1
title: MOESM21 of Transcriptomic and metabolomic analyses provide insight into the volatile compounds of citrus leaves and flowers

description: Additional file 21: Table S12. Primers used in the cloning of STPS and construction of expression vectors.
DOI: 10.15468/dl.prydfz
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "HasCoordinate is true",
 "TaxonKey is Loxosceles misteca Gertsch, 1958",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 9 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016056-191105090559680/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zdej4a
title: Occurrence Download

description: A dataset containing 82 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cinclus schulzi Cabanis, 1882",
 "HasCoordinate is true"
 ]
}

 The dataset includes 82 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000551-150410134957023/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34816/efa.archives.819763
title: Malia-N596-739-ASO2014-04-0410-Photo9

description: Référence : N596-739<br />Publication(s) : Inédit<br />Période(s) : Âge du Bronze; Minoen<br />Domaine : Fouille<br />
DOI: 10.34816/efa.archives.819764
title: Malia-N596-740-ASO2014-04-0410-Photo10

description: Référence : N596-740<br />Publication(s) : Inédit<br />Période(s) : Âge du Bronze; Minoen<br />Domaine : Fouille<br />
DOI: 10.34816/efa.archives.819765
title: Malia-N596-741-ASO2014-04-0410-Photo11

description: Référence : N596-741<br />Publication(s) : Inédit<br />Période(s) : Âge du Bronze; Minoen<br />Domaine : Fouille<br />
DOI: 10.15468/dl.3xg7vf
title: Occurrence Download

description: A dataset containing 508047 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Russian Federation",
 {
 "or" : [
 "Geometry POLYGON((40.253906 60.042903,40.253906 57.433123,48.164062 57.433123,48.164062 60.042903,40.253906 60.042903))",
 "Geometry POLYGON((56 57,56 67,84 67,84 57,56 57))"
 ]
 },
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 508047 records from 93 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000551-150422101436696/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9zgfvw
title: Occurrence Download

description: A dataset containing 346 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((17.05124 38.90952,17.07564 38.87629,17.16712 38.89409,17.22505 38.93324,17.222 38.98067,17.20371 39.05056,17.05124 38.90952))",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 346 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002124-231002084531237/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.oored9
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "HasCoordinate is true",
 "TaxonKey is Loxosceles arizonica Gertsch & Mulaik, 1940",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016058-191105090559680/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.h7r27c
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Perezia pygmea Wedd."
 ]
}

 The dataset includes 7 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0184372-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.oqslnd
title: Occurrence Download

description: A dataset containing 1682 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Loasaceae",
 "Country is Peru"
 ]
}

 The dataset includes 1682 records from 36 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000551-150523225239109/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34816/efa.archives.819766
title: Malia-N596-742-ASO2014-04-0410-Photo12

description: Référence : N596-742<br />Publication(s) : Inédit<br />Période(s) : Âge du Bronze; Minoen<br />Domaine : Fouille<br />
DOI: 10.15468/dl.2pvnav
title: Occurrence Download

description: A dataset containing 2403 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((4.83591 44.29648,4.81289 44.29513,4.79501 44.29156,4.77422 44.28888,4.75835 44.28731,4.75232 44.28239,4.76193 44.27837,4.77668 44.28038,4.80082 44.28195,4.81065 44.28418,4.8263 44.28865,4.83233 44.28686,4.83748 44.28754,4.83591 44.29648))",
 "PublishingOrg is one of (dca4d666-c9e0-4712-b658-0d1bc3f39d48, b3bf3a83-1f68-4541-a03f-330d30d567f5, f9912a00-84a9-11d9-8952-b8a03c50a862, 2cd829bb-b713-433d-99cf-64bef11e5b3e, ada9d123-ddb4-467d-8891-806ea8d94230, c8d737e0-2ff8-42e8-b8fc-6b805d26fc5f, 1928bdf0-f5d2-11dc-8c12-b8a03c50a862)"
 ]
}

 The dataset includes 2403 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0054657-231002084531237/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xtlrnc
title: Occurrence Download

description: A dataset containing 645 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Year 1969-2019",
 "HasCoordinate is true",
 "TaxonKey is Pteropus conspicillatus Gould, 1850",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 645 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020241-191105090559680/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34816/efa.archives.819767
title: Malia-N596-743-ASO2014-04-0410-Photo13

description: Référence : N596-743<br />Publication(s) : Inédit<br />Période(s) : Âge du Bronze; Minoen<br />Domaine : Fouille<br />
DOI: 10.34816/efa.archives.819768
title: Malia-N596-744-ASO2014-04-0410-Photo14

description: Référence : N596-744<br />Publication(s) : Inédit<br />Période(s) : Âge du Bronze; Minoen<br />Domaine : Fouille<br />
DOI: 10.15468/dl.zemyyq
title: Occurrence Download

description: A dataset containing 6047 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Baiomys taylori (Thomas, 1887)"
 ]
}

 The dataset includes 6047 records from 58 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000551-150528172251762/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34816/efa.archives.819769
title: Malia-N596-745-ASO2014-04-0410-Photo15

description: Référence : N596-745<br />Publication(s) : Inédit<br />Période(s) : Âge du Bronze; Minoen<br />Domaine : Fouille<br />
DOI: 10.15468/dl.5yue3f
title: Occurrence Download

description: A dataset containing 1162 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Dioscorea sagittifolia Pax"
 ]
}

 The dataset includes 1162 records from 53 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0177637-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jk98re
title: Occurrence Download

description: A dataset containing 504 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Astragalus asper Jacq."
 ]
}

 The dataset includes 504 records from 49 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0211487-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34816/efa.archives.819770
title: Malia-N596-746-ASO2014-04-0410-Photo16

description: Référence : N596-746<br />Publication(s) : Inédit<br />Période(s) : Âge du Bronze; Minoen<br />Domaine : Fouille<br />
DOI: 10.34816/efa.archives.819771
title: Malia-N596-747-ASO2014-04-0410-Photo17

description: Référence : N596-747<br />Publication(s) : Inédit<br />Période(s) : Âge du Bronze; Minoen<br />Domaine : Fouille<br />
DOI: 10.15468/dl.pk2vxv
title: Occurrence Download

description: A dataset containing 51013 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Helianthus L."
 ]
}

 The dataset includes 51013 records from 430 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000551-150831095807960/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34816/efa.archives.819772
title: Malia-N596-748-ASO2014-04-0410-Photo18

description: Référence : N596-748<br />Publication(s) : Inédit<br />Période(s) : Âge du Bronze; Minoen<br />Domaine : Fouille<br />
DOI: 10.15468/dl.46zvd6
title: Occurrence Download

description: A dataset containing 374 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Totoaba Villamar, 1980"
 ]
}

 The dataset includes 374 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012569-230918134249559/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bcvbzq
title: Occurrence Download

description: A dataset containing 849 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Pl@ntNet automatically identified occurrences",
 "TaxonKey is Quercus pubescens Willd.",
 "Year 1000-2021"
 ]
}

 The dataset includes 849 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0211503-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34816/efa.archives.819773
title: Malia-N596-749-ASO2014-04-0410-Photo19

description: Référence : N596-749<br />Publication(s) : Inédit<br />Période(s) : Âge du Bronze; Minoen<br />Domaine : Fouille<br />
DOI: 10.34816/efa.archives.819774
title: Malia-N596-750-ASO2014-04-0410-Photo20

description: Référence : N596-750<br />Publication(s) : Inédit<br />Période(s) : Âge du Bronze; Minoen<br />Domaine : Fouille<br />