Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
352
datasets available to search
ShareScore release 0.9.0
Dataset results
352 results for “Data Enrichment”
Data from: Precipitation and nitrogen enrichment impact carbon exchange and stability: From antagonism to synergy with increasing shrub encroachment
Open the record for dataset details and reuse information.
Data from: Connectivity and nutrient enrichment affect the productivity and stability of aquatic meta-ecosystems
Open the record for dataset details and reuse information.
Data from: Enriched East Asian oxygen isotope of precipitation indicates reduced summer seasonality in regional climate and westerlies
Open the record for dataset details and reuse information.
Reproduction data for Lespedeza capitata: BioCON : Biodiversity, Elevated CO2, and N Enrichment
BioCON (Biodiversity, CO2, and Nitrogen) is an ecological experiment started in 1997 at the University of Minnesota's Cedar Creek Ecosystem Science Reserve. BioCON's goal is to explore the ways in which plant communities will respond to three environmental changes that are known to be occurring on a global scale: increasing nitrogen deposition, increasing atmospheric CO2, and decreasing biodiversity. Why Biodiversity, CO2, and Nitrogen? While there are many uncertainties in global change biology, there are also some well documented facts. Some of these are: 1. The amount of carbon dioxide (CO2) in the atmosphere is rising. Since the industrial revolution, the CO2 concentration in the atmosphere has increased from approximately 275 parts per million (ppm) to about 378 ppm today. This has been largely the result of fossil fuel burning. It is expected that CO2 levels will continue to rise, and that by the year 2050 these levels will be approximately 550 ppm. CO2 is the raw material for photosynthesis and is known to affect plant growth and development. 2. The amount of nitrogen moving through terrestrial ecosystems has increased in the recent past. While natural "background" levels of nitrogen fixation have remained constant, human additions to the system through fertilizer production and fossil fuel use have increased dramatically. Nitrogen is a key nutrient for plant growth and plays a critical role in plant community structure and composition in many environments. 3. Biodiversity levels are falling. While the research and data are not as complete as they are for CO2 and nitrogen, data indicate that the number of species globally, is being reduced. Perhaps more important for ecosystem function, diversity levels on local to regional scales have fallen due to land use change, biotic invasion and many other drivers. While much is known about how each of these factors affects ecosystem functioning, many questions remain. There is also little data on how these issues affe
Reproduction data for Solidago rigida: BioCON : Biodiversity, Elevated CO2, and N Enrichment
BioCON (Biodiversity, CO2, and Nitrogen) is an ecological experiment started in 1997 at the University of Minnesota's Cedar Creek Ecosystem Science Reserve. BioCON's goal is to explore the ways in which plant communities will respond to three environmental changes that are known to be occurring on a global scale: increasing nitrogen deposition, increasing atmospheric CO2, and decreasing biodiversity. Why Biodiversity, CO2, and Nitrogen? While there are many uncertainties in global change biology, there are also some well documented facts. Some of these are: 1. The amount of carbon dioxide (CO2) in the atmosphere is rising. Since the industrial revolution, the CO2 concentration in the atmosphere has increased from approximately 275 parts per million (ppm) to about 378 ppm today. This has been largely the result of fossil fuel burning. It is expected that CO2 levels will continue to rise, and that by the year 2050 these levels will be approximately 550 ppm. CO2 is the raw material for photosynthesis and is known to affect plant growth and development. 2. The amount of nitrogen moving through terrestrial ecosystems has increased in the recent past. While natural "background" levels of nitrogen fixation have remained constant, human additions to the system through fertilizer production and fossil fuel use have increased dramatically. Nitrogen is a key nutrient for plant growth and plays a critical role in plant community structure and composition in many environments. 3. Biodiversity levels are falling. While the research and data are not as complete as they are for CO2 and nitrogen, data indicate that the number of species globally, is being reduced. Perhaps more important for ecosystem function, diversity levels on local to regional scales have fallen due to land use change, biotic invasion and many other drivers. While much is known about how each of these factors affects ecosystem functioning, many questions remain. There is also little data on how these issues affe
Reproduction data for Asclepias tuberosa: BioCON : Biodiversity, Elevated CO2, and N Enrichment
BioCON (Biodiversity, CO2, and Nitrogen) is an ecological experiment started in 1997 at the University of Minnesota's Cedar Creek Ecosystem Science Reserve. BioCON's goal is to explore the ways in which plant communities will respond to three environmental changes that are known to be occurring on a global scale: increasing nitrogen deposition, increasing atmospheric CO2, and decreasing biodiversity. Why Biodiversity, CO2, and Nitrogen? While there are many uncertainties in global change biology, there are also some well documented facts. Some of these are: 1. The amount of carbon dioxide (CO2) in the atmosphere is rising. Since the industrial revolution, the CO2 concentration in the atmosphere has increased from approximately 275 parts per million (ppm) to about 378 ppm today. This has been largely the result of fossil fuel burning. It is expected that CO2 levels will continue to rise, and that by the year 2050 these levels will be approximately 550 ppm. CO2 is the raw material for photosynthesis and is known to affect plant growth and development. 2. The amount of nitrogen moving through terrestrial ecosystems has increased in the recent past. While natural "background" levels of nitrogen fixation have remained constant, human additions to the system through fertilizer production and fossil fuel use have increased dramatically. Nitrogen is a key nutrient for plant growth and plays a critical role in plant community structure and composition in many environments. 3. Biodiversity levels are falling. While the research and data are not as complete as they are for CO2 and nitrogen, data indicate that the number of species globally, is being reduced. Perhaps more important for ecosystem function, diversity levels on local to regional scales have fallen due to land use change, biotic invasion and many other drivers. While much is known about how each of these factors affects ecosystem functioning, many questions remain. There is also little data on how these issues affe
Reproduction data for Petalostemum villosum: BioCON : Biodiversity, Elevated CO2, and N Enrichment
BioCON (Biodiversity, CO2, and Nitrogen) is an ecological experiment started in 1997 at the University of Minnesota's Cedar Creek Ecosystem Science Reserve. BioCON's goal is to explore the ways in which plant communities will respond to three environmental changes that are known to be occurring on a global scale: increasing nitrogen deposition, increasing atmospheric CO2, and decreasing biodiversity. Why Biodiversity, CO2, and Nitrogen? While there are many uncertainties in global change biology, there are also some well documented facts. Some of these are: 1. The amount of carbon dioxide (CO2) in the atmosphere is rising. Since the industrial revolution, the CO2 concentration in the atmosphere has increased from approximately 275 parts per million (ppm) to about 378 ppm today. This has been largely the result of fossil fuel burning. It is expected that CO2 levels will continue to rise, and that by the year 2050 these levels will be approximately 550 ppm. CO2 is the raw material for photosynthesis and is known to affect plant growth and development. 2. The amount of nitrogen moving through terrestrial ecosystems has increased in the recent past. While natural "background" levels of nitrogen fixation have remained constant, human additions to the system through fertilizer production and fossil fuel use have increased dramatically. Nitrogen is a key nutrient for plant growth and plays a critical role in plant community structure and composition in many environments. 3. Biodiversity levels are falling. While the research and data are not as complete as they are for CO2 and nitrogen, data indicate that the number of species globally, is being reduced. Perhaps more important for ecosystem function, diversity levels on local to regional scales have fallen due to land use change, biotic invasion and many other drivers. While much is known about how each of these factors affects ecosystem functioning, many questions remain. There is also little data on how these issues affe
Reproduction data for Achillea millefolium: BioCON : Biodiversity, Elevated CO2, and N Enrichment
BioCON (Biodiversity, CO2, and Nitrogen) is an ecological experiment started in 1997 at the University of Minnesota's Cedar Creek Ecosystem Science Reserve. BioCON's goal is to explore the ways in which plant communities will respond to three environmental changes that are known to be occurring on a global scale: increasing nitrogen deposition, increasing atmospheric CO2, and decreasing biodiversity. Why Biodiversity, CO2, and Nitrogen? While there are many uncertainties in global change biology, there are also some well documented facts. Some of these are: 1. The amount of carbon dioxide (CO2) in the atmosphere is rising. Since the industrial revolution, the CO2 concentration in the atmosphere has increased from approximately 275 parts per million (ppm) to about 378 ppm today. This has been largely the result of fossil fuel burning. It is expected that CO2 levels will continue to rise, and that by the year 2050 these levels will be approximately 550 ppm. CO2 is the raw material for photosynthesis and is known to affect plant growth and development. 2. The amount of nitrogen moving through terrestrial ecosystems has increased in the recent past. While natural "background" levels of nitrogen fixation have remained constant, human additions to the system through fertilizer production and fossil fuel use have increased dramatically. Nitrogen is a key nutrient for plant growth and plays a critical role in plant community structure and composition in many environments. 3. Biodiversity levels are falling. While the research and data are not as complete as they are for CO2 and nitrogen, data indicate that the number of species globally, is being reduced. Perhaps more important for ecosystem function, diversity levels on local to regional scales have fallen due to land use change, biotic invasion and many other drivers. While much is known about how each of these factors affects ecosystem functioning, many questions remain. There is also little data on how these issues affe
Reproduction data for grasses: BioCON : Biodiversity, Elevated CO2, and N Enrichment
BioCON (Biodiversity, CO2, and Nitrogen) is an ecological experiment started in 1997 at the University of Minnesota's Cedar Creek Ecosystem Science Reserve. BioCON's goal is to explore the ways in which plant communities will respond to three environmental changes that are known to be occurring on a global scale: increasing nitrogen deposition, increasing atmospheric CO2, and decreasing biodiversity. Why Biodiversity, CO2, and Nitrogen? While there are many uncertainties in global change biology, there are also some well documented facts. Some of these are: 1. The amount of carbon dioxide (CO2) in the atmosphere is rising. Since the industrial revolution, the CO2 concentration in the atmosphere has increased from approximately 275 parts per million (ppm) to about 378 ppm today. This has been largely the result of fossil fuel burning. It is expected that CO2 levels will continue to rise, and that by the year 2050 these levels will be approximately 550 ppm. CO2 is the raw material for photosynthesis and is known to affect plant growth and development. 2. The amount of nitrogen moving through terrestrial ecosystems has increased in the recent past. While natural "background" levels of nitrogen fixation have remained constant, human additions to the system through fertilizer production and fossil fuel use have increased dramatically. Nitrogen is a key nutrient for plant growth and plays a critical role in plant community structure and composition in many environments. 3. Biodiversity levels are falling. While the research and data are not as complete as they are for CO2 and nitrogen, data indicate that the number of species globally, is being reduced. Perhaps more important for ecosystem function, diversity levels on local to regional scales have fallen due to land use change, biotic invasion and many other drivers. While much is known about how each of these factors affects ecosystem functioning, many questions remain. There is also little data on how these issues affe
Reproduction data for Amorpha canescens: BioCON : Biodiversity, Elevated CO2, and N Enrichment
BioCON (Biodiversity, CO2, and Nitrogen) is an ecological experiment started in 1997 at the University of Minnesota's Cedar Creek Ecosystem Science Reserve. BioCON's goal is to explore the ways in which plant communities will respond to three environmental changes that are known to be occurring on a global scale: increasing nitrogen deposition, increasing atmospheric CO2, and decreasing biodiversity. Why Biodiversity, CO2, and Nitrogen? While there are many uncertainties in global change biology, there are also some well documented facts. Some of these are: 1. The amount of carbon dioxide (CO2) in the atmosphere is rising. Since the industrial revolution, the CO2 concentration in the atmosphere has increased from approximately 275 parts per million (ppm) to about 378 ppm today. This has been largely the result of fossil fuel burning. It is expected that CO2 levels will continue to rise, and that by the year 2050 these levels will be approximately 550 ppm. CO2 is the raw material for photosynthesis and is known to affect plant growth and development. 2. The amount of nitrogen moving through terrestrial ecosystems has increased in the recent past. While natural "background" levels of nitrogen fixation have remained constant, human additions to the system through fertilizer production and fossil fuel use have increased dramatically. Nitrogen is a key nutrient for plant growth and plays a critical role in plant community structure and composition in many environments. 3. Biodiversity levels are falling. While the research and data are not as complete as they are for CO2 and nitrogen, data indicate that the number of species globally, is being reduced. Perhaps more important for ecosystem function, diversity levels on local to regional scales have fallen due to land use change, biotic invasion and many other drivers. While much is known about how each of these factors affects ecosystem functioning, many questions remain. There is also little data on how these issues affe
Lysimeter data: BioCON : Biodiversity, Elevated CO2, and N Enrichment
BioCON (Biodiversity, CO2, and Nitrogen) is an ecological experiment started in 1997 at the University of Minnesota's Cedar Creek Ecosystem Science Reserve. BioCON's goal is to explore the ways in which plant communities will respond to three environmental changes that are known to be occurring on a global scale: increasing nitrogen deposition, increasing atmospheric CO2, and decreasing biodiversity. Why Biodiversity, CO2, and Nitrogen? While there are many uncertainties in global change biology, there are also some well documented facts. Some of these are: 1. The amount of carbon dioxide (CO2) in the atmosphere is rising. Since the industrial revolution, the CO2 concentration in the atmosphere has increased from approximately 275 parts per million (ppm) to about 378 ppm today. This has been largely the result of fossil fuel burning. It is expected that CO2 levels will continue to rise, and that by the year 2050 these levels will be approximately 550 ppm. CO2 is the raw material for photosynthesis and is known to affect plant growth and development. 2. The amount of nitrogen moving through terrestrial ecosystems has increased in the recent past. While natural "background" levels of nitrogen fixation have remained constant, human additions to the system through fertilizer production and fossil fuel use have increased dramatically. Nitrogen is a key nutrient for plant growth and plays a critical role in plant community structure and composition in many environments. 3. Biodiversity levels are falling. While the research and data are not as complete as they are for CO2 and nitrogen, data indicate that the number of species globally, is being reduced. Perhaps more important for ecosystem function, diversity levels on local to regional scales have fallen due to land use change, biotic invasion and many other drivers. While much is known about how each of these factors affects ecosystem functioning, many questions remain. There is also little data on how these issues affe
MitoFinder: efficient automated large-scale extraction of mitogenomic data in target enrichment phylogenomics
<p><strong>MitoFinder: efficient automated large-scale extraction of mitogenomic data in target enrichment phylogenomics</strong></p> <p>Rémi Allio<sup>1</sup>, Alex Schomaker-Bastos<sup>2,†</sup>, Jonathan Romiguier<sup>1</sup>, Francisco Prosdocimi<sup>2</sup>, Benoit Nabholz<sup>1</sup>, and Frédéric Delsuc<sup>1</sup></p> <p><sup>1</sup><em>Institut des Sciences de l’Evolution de Montpellier (ISEM), CNRS, EPHE, IRD, Université de Montpellier, Montpellier, France.</em></p> <p><sup>2</sup><em>Laboratório Multidisciplinar para Análise de Dados (LAMPADA), Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil.</em></p> <p><sup>†</sup><em> In Memoriam (08/01/2015) </em></p> <p> </p> <p><em><strong>Correspondence</strong></em></p> <p>Rémi Allio</p> <p>Email: <a href="mailto:remi.allio@umontpelier.fr">remi.allio@umontpellier.fr</a></p> <p>Frédéric Delsuc</p> <p>Email: <a href="mailto:frederic.delsuc@umontpellier.fr">frederic.delsuc@umontpellier.fr</a></p> <p> </p> <p><strong><em>Running head</em></strong></p> <p>Mitochondrial signal from UCE capture data</p> <p> </p> <p><strong>Abstract</strong><strong> </strong></p> <p>Thanks to the development of high-throughput sequencing technologies, target enrichment sequencing of nuclear ultraconserved DNA elements (UCEs) now allows routinely inferring phylogenetic relationships from thousands of genomic markers. Recently, it has been shown that mitochondrial DNA (mtDNA) is frequently sequenced alongside the targeted loci in such capture experiments. Despite its broad evolutionary interest, mtDNA is rarely assembled and used in conjunction with nuclear markers in capture-based studies. Here, we developed MitoFinder, a user-friendly bioinformatic pipeline, to efficiently assemble and annotate mitogenomic data from hundreds of UCE libraries. As a case study, we used ants (Formicidae) for which 501 UCE libraries have been sequenced whereas only 29 mitogenomes are available. We compared the efficiency of four different assemblers (IDBA-UD, MEGAHIT, MetaSPAdes, and Trinity) for assembling both UCE and mtDNA loci. Using MitoFinder, we show that metagenomic assemblers, in particular MetaSPAdes, are well suited to assemble both UCEs and mtDNA. Mitogenomic signal was successfully extracted from all 501 UCE libraries allowing confirming species identification using COI barcoding. Moreover, our automated procedure retrieved 296 cases in which the mitochondrial genome was assembled in a single contig, thus increasing the number of available ant mitogenomes by an order of magnitude. By leveraging the power of metagenomic assemblers, MitoFinder provides an efficient tool to extract complementary mitogenomic data from UCE libraries, allowing testing for potential mito-nuclear discordance. Our approach is potentially applicable to other sequence capture methods, transcriptomic data, and whole genome shotgun sequencing in diverse taxa.</p> <p> </p> <p><strong><em>Figures & Tables</em></strong></p> <p><strong>Figure 1.</strong> Conceptualization of the pipeline used to assemble and extract UCE and mitochondrial signal from ultraconserved element sequencing data.</p> <p><strong>Figure 2</strong>. Comparison of the efficiency of the assemblers in terms of: A) computational time, B) number of potentially mitochondrial contigs identified, and C) number of mitochondrial genes annotated. Violin plots reflect the data distribution with a horizontal line indicating the median. Note that for the three metagenomic assemblers, 5 CPUs were used compared to 35 CPUs for Trinity. Plots were obtained using PlotsOfData (Postma & Goedhart 2019).</p> <p><strong>Figure 3.</strong> Phylogenomic relationships of ants (Formicidae). AA) Mito-nuclear phylogenetic differences among subfamily relationships based on the UCE and mtDNA supermatrices obtained with the assembler MetaSPAdes assembler. Clades corresponding to subfamilies were collapsed. Inter-subfamily relationships with UFBS < 95% were collapsed. Non-maximal node support values are reported. B) The topology obtained reflects the results of phylogenetic analyses based on the amino acid mitochondrial supermatrix (using MetaSPAdes as assembler). Histograms reflect the percent of UCEs (light grey) and mitochondrial genes (dark grey) recovered for each species. Illustrative pictures (*): <em>Diacamma sp</em>. (Ponerinae; top left), <em>Formica sp</em>. (Formicinae; top right), and <em>Messor barbarus </em>(Myrmicinae; bottom right).</p> <p><strong>Table 1. </strong>Summary statistics on assembly results according to the assembler used. The values are averages over the 501 assemblies, except for the assembly time, which is a median value. The two tables report specific statistics for A) ultraconserved elements data, and B) mitochondrial data. Note that 35 CPUs were used for Trinity whereas 5 CPUs were used for other assemblers.</p> <p><strong>Table 2.</strong> Statistical comparison between the performances of the different assemblers. Statistical significance was estimated with a paired non parametric test (paired wilcoxon test). *** = <em>p</em><0.001; ** = <em>p</em><0.01; * = <em>p</em><0.05; NS = <em>p</em>>0.05; and (+)/(-) is the result of the comparison between the row and the column.</p> <p> </p> <p><strong><em>Appendices</em></strong></p> <p><strong>Appendix S1.</strong> List of the 501 UCE libraries (SRA accessions) and associated metadata.</p> <p><strong>Appendix S2.</strong> Summary statistics on mitochondrial signal recovered per species and depending on the assembler used. The table provides the number of contigs and genes recovered with MitoFinder and the size of each annotated gene.</p> <p><strong>Appendix S3.</strong> Summary statistics of barcoding analyses. Detailed results for both BOLDsystem and Megablast analyses are provided for each CO1 recovered with MitoFinder using MetaSPAdes.</p> <p><strong>Appendix S4.</strong> Detailed results of tree distance analyses realized with Dquad (Ranwez, Criscuolo, & Douzery 2010). Trees obtained with each assembler with mitochondrial amino acid supermatrix, mitochondrial nucleotide supermatrix, and UCE nucleotide supermatrix were compared with each others.</p> <p><strong>Appendix S5</strong>. List of Genbank accession numbers for newly generated mitchondrial contigs.</p> <p> </p> <p><strong><em>Zenodo supplementary files</em></strong></p> <p><strong>Assembly_results.tar.gz</strong> Contains all contigs obtained for each species with the different assemblers implemented in MitoFinder.</p> <p><strong>MitoFinder_annotations.tar.gz</strong> Contains MitoFinder annotations for each species. (based on the contigs obtained with MetaSPAdes)</p> <p><strong>UCE_results.tar.gz</strong> Contains all annotated UCE obtained for each species after UCE identification with PHYLUCE. (MetaSPAdes)</p> <p><strong>Final_mtDNA_alignments.tar.gz</strong> Contains the final mitochondrial gene alignments. (MetaSPAdes)</p> <p><strong>Final_UCE_alignments.tar.gz</strong> Contains the final UCE alignments. (MetaSPAdes)</p> <p><strong>Final_mtDNA_matrices.tar.gz</strong> Contains the final mi tochondrial supermatrices (AA and NT) used for the phylogenetic analyses. (MetaSPAdes)</p> <p><strong>Metaspades_final_UCE_matrix.phy</strong> The final UCE supermatrix used for the phylogenetic analyses. (MetaSPAdes)</p>
RAW data: Knockdown of UTX/KDM6A Enriches Precursor Cell Populations in Urothelial Cell Cultures and Cell Lines - single cell RNAseq - Fastq format and UMI counts
<p>This data set of the single cell sequencing experiment of the urothelial cell line HBLAK belongs to the publication: "Knockdown of UTX/KDM6A Enriches Precursor Cell Populations in Urothelial Cell Cultures and Cell Lines" Cancers 2020, 12(4), 1023; https://doi.org/10.3390/cancers12041023.</p> <p> </p>
Neutron Reflectometry data and code for the manuscript entitled: 'Enrichment of charged monomers explains non-monotonic polymer volume fraction profiles of multi-stimulus responsive copolymer brushes'
<p>Contained in the zip file is the reduced neutron reflectometry data, the code used to analyse the data and jupyter notebooks used implement this code. Data is for proposal number PP4274, experiment number PPR6490 on the Platypus Reflectometer at ANSTO, Australia. The data is name with measurement numbers. The attached excel document describes the condition which corresponds to measurement number. </p>
Data from: Synergistic effects of nitrogen and CO2 enrichment on alpine grassland biomass and community structure
<p>Global environmental change is altering Earth's ecosystems. However, much research has focused on ecosystem-level responses, and we know substantially less about community-level responses to global change stressors.<br> <br> Here we conducted a 6-year field experiment in a high-altitude (4600 m above sea level) alpine grassland on the Tibetan Plateau to explore the effects of nitrogen (N) addition and rising atmospheric CO2 concentration on plant communities.<br> <br> Our results showed that N and CO2 enrichment had synergistic effects on alpine grassland communities. Adding nitrogen or CO2 alone did not alter total community biomass, species diversity, or community composition, whereas adding both resources together increased community biomass, reduced species diversity, and altered community composition. The observed decline in species diversity under simultaneous N and CO2 enrichment was associated with greater community biomass and lower soil water content, and driven by the loss of species characterized simultaneously by tall stature and small specific leaf area.<br> <br> Our findings point to the co-limitation of alpine plant community biomass and structure by nitrogen and CO2, emphasizing the need for future studies to consider multiple aspects of global environmental change together to gain a more complete understanding of their ecological consequences.</p>
Data from: An enhanced target-enrichment bait set for Hexacorallia provides phylogenomic resolution of the staghorn corals (Acroporidae) and close relatives
<p>Targeted enrichment of genomic DNA can profoundly increase the phylogenetic resolution of clades and inform taxonomy. Here, we redesign a custom bait set previously developed for the cnidarian class Anthozoa to more efficiently target and capture ultraconserved elements (UCEs) and exonic loci within the subclass Hexacorallia. We test this enhanced bait set (targeting 2,476 loci) on 99 specimens of scleractinian corals spanning both the "complex" (Acroporidae, Agariciidae) and "robust" (Fungiidae) clades.Focused sampling in the staghorn corals (genus <i>Acropora</i>)highlights the ability of sequence capture to inform the taxonomy of a clade previously deficient in molecular resolution. A mean of 1850 (± 298) loci were captured per taxon (955 UCEs, 894 exons), and a 75% complete concatenated alignment of 96 samples included 1792 loci (991 UCE, 801 exons) and ~1.87 million base pairs. Maximum likelihood and Bayesian analyses recovered robust molecular relationships and revealed that species-level relationships within the <i>Acropora</i>are incongruent with traditional morphological groupings. Both UCE and exon datasets delineated six well-supported clades within <i>Acropora.</i>The enhanced bait set will facilitate investigations of the evolutionary history of many important groups of reef corals, particularly where previous molecular marker development has been unsuccessful.</p>
Evaluating Elements of Web-based Data Enrichment for Pseudo-Relevance Feedback Retrieval
<p>This data archive accompanies our work, in which we analyze a pseudo-relevance retrieval method that is based on the results of web search engines. By enriching topics with text data from web search engine result pages and linked contents, we train topic-specific and cost-efficient classifiers that can be used to search test collections for relevant documents. Building up on attempts that were initially made at TREC Common Core 2018 by Grossman and Cormack, we address the questions of system performance over time considering different search engines, queries and test collections. Our experimental results show how and to which extent the considered components affect the retrieval performance. Overall, the analyzed method is robust in terms of average retrieval performance and a promising way to use web content for the data enrichment of relevance feedback methods.</p>
Data from: Multiple constraints cause positive and negative feedbacks limiting grassland soil CO2 efflux under CO2 enrichment
<p>Terrestrial ecosystems are increasingly enriched with resources such as atmospheric CO<sub>2</sub> that limit ecosystem processes. The consequences for ecosystem carbon cycling depend on the feedbacks from other limiting resources and plant community change, which remain poorly understood for soil CO<sub>2</sub> efflux, J<sub>CO2</sub>, a primary carbon flux from the biosphere to the atmosphere. We applied a unique CO<sub>2</sub> enrichment gradient (250 to 500 µL L<sup>-1</sup>) for eight years to grassland plant communities on soils from different landscape positions. We identified the trajectory of J<sub>CO2</sub> responses and feedbacks from other resources, plant diversity (effective species richness, exp(H)), and community change (plant species turnover). We found linear increases in J<sub>CO2</sub> on an alluvial sandy loam and a lowland clay soil, and an asymptotic increase on an upland silty clay soil. Structural equation modelling identified CO<sub>2</sub> as the dominant limitation on J<sub>CO2</sub> on the clay soil. In contrast with theory predicting limitation from a single limiting factor, the linear J<sub>CO2</sub> response on the sandy loam was reinforced by positive feedbacks from aboveground net primary productivity and exp(H), while the asymptotic J<sub>CO2</sub> response on the silty clay arose from a net negative feedback among exp(H), species turnover, and soil water potential. These findings support a multiple resource limitation view of the effects of global change drivers on grassland ecosystem carbon cycling and highlight a crucial role for positive or negative feedbacks between limiting resources and plant community structure. Incorporating these feedbacks will improve models of terrestrial carbon sequestration and ecosystem services.</p>
Data from: Axial xylem architecture of Larix decidua exposed to CO2 enrichment and soil warming at the treeline
1. Trees continuously adjust their axial xylem structure to meet changing needs imposed by ontogenetic and environmental changes. These axial structure-function responses need to be coordinated among competing biophysical constraints to avoid failure of the xylem system. Here, we investigated if ontogeny or experimental manipulation of CO2 and soil temperature influence these structure-function responses. 2. We performed detailed xylem cell anatomical quantification along the axis of 40-year-old Larix decidua trees planted at the Swiss treeline and exposed to a combination of elevated CO2 (+200 ppm) and soil warming (+4 °C) between 2001 and 2012. We assessed how mean hydraulic tracheid diameter (Dh), the cell wall reinforcement ((t/b)2), tracheid wall thickness (CWT) and the percent area of ray parenchyma (PERPAR) – proxies for hydraulic efficiency, hydraulic safety, biomechanical support and metabolic xylem functions, respectively – co-vary along the tree axis. 3. Dh increased from the stem apex to base, strictly following a power function (R2=0.81), independent from ontogeny and experimental treatments. In contrast, axial trends of (t/b)2 and CWT were either influenced by treatment and/or ontogeny, or showed no axial trend (PERPAR). Additionally, we found that a larger Dh only at the stem apex promoted primary and secondary growth. 4. Our approach of analyzing xylem anatomical traits along the tree axis and across tree-rings provides novel insights into xylem functional architecture and allows reconstructing xylem function over time. We conclude that the maintenance of hydraulic efficiency during ontogeny is very robust, as the conduit diameter undergoes a strong apical control, and plays a fundamental role for assimilation and tree growth. Instead, the other functional traits more plastically vary with ontogeny and environmental changes.
Data from: Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera
Gaining a genomic perspective on phylogeny requires the collection of data from many putatively independent loci across the genome. Among insects, an increasingly common approach to collecting this class of data involves transcriptome sequencing, because few insects have high-quality genome sequences available; assembling new genomes remains a limiting factor; the transcribed portion of the genome is a reasonable, reduced subset of the genome to target; and the data collected from transcribed portions of the genome are similar in composition to the types of data with which biologists have traditionally worked (e.g. exons). However, molecular techniques requiring RNA as a template, including transcriptome sequencing, are limited to using very high-quality source materials, which are often unavailable from a large proportion of biologically important insect samples. Recent research suggests that DNA-based target enrichment of conserved genomic elements offers another path to collecting phylogenomic data across insect taxa, provided that conserved elements are present in and can be collected from insect genomes. Here, we identify a large set (n = 1510) of ultraconserved elements (UCEs) shared among the insect order Hymenoptera. We used in silico analyses to show that these loci accurately reconstruct relationships among genome-enabled hymenoptera, and we designed a set of RNA baits (n = 2749) for enriching these loci that researchers can use with DNA templates extracted from a variety of sources. We used our UCE bait set to enrich an average of 721 UCE loci from 30 hymenopteran taxa, and we used these UCE loci to reconstruct phylogenetic relationships spanning very old (≥220 Ma) to very young (≤1 Ma) divergences among hymenopteran lineages. In contrast to a recent study addressing hymenopteran phylogeny using transcriptome data, we found ants to be sister to all remaining aculeate lineages with complete support, although this result could be explained by factors such as taxon sampling. We discuss this approach and our results in the context of elucidating the evolutionary history of one of the most diverse and speciose animal orders.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.