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25 results for “Capture regions”
Fish captures in lakes of the Arctic LTER region Toolik Field Station Alaska from 1986 to 2021.
This file contains the fish number, recap number, species, lengths, weights, sex and a list of tissues sampled of fish captured in lakes near the Toolik Lake Arctic LTER site during summers from 1986 to 2021. The file also contains information from gill-netted fish (if any), sacrificed fish, and accidentally killed fish. All dead fish are included, and if their stomachs and otoliths were taken, that is noted also.
Dataset and code: One-tenth of EU's biomethane potential combined with carbon capture and storage can shift the region's ammonia production to net-zero
<h2>Overview</h2> <p>Repository to share the data and code associated with the scientific article <strong>Istrate et al. One-tenth of EU’s biomethane potential combined with carbon capture and storage can shift the region’s ammonia production to net-zero. One Earth (2024)</strong>. The repository contains data files and code to import the life cycle inventories (LCIs), reproduce the results, and generate the figures presented in the article.</p> <div> <h2>Repository structure</h2> </div> <p>The data folder includes:</p> <ul> <li><code>inventories.xlsx</code> contains the LCI datasets for biomethane and ammonia production formatted for use with <a href="https://github.com/brightway-lca">Brightway</a>.</li> <li><code>sustainable_biomethane_potential_Europe.xlsx</code> contains data on the sustainable biomethane potential in Europe disaggregated by feedstock and country.</li> <li><code>ammonia_production_europe.xlsx</code> contains ammonia production levels in the EU in 2021.</li> <li><code>SA_methane leakage_for presample.xlsx</code> contains data to perform sensitivity analysis on the methane leakage with <a href="https://github.com/PascalLesage/presamples">presamples</a></li> <li><code>SA_upgrading technology_presamples.xlsx</code> contains data to perform sensitivity analysis on upgrading technologies with <a href="https://github.com/PascalLesage/presamples">presamples</a></li> <li><code>results</code> folder within data contains csv files with the results, which are used in <code>05_visualization.ipynb</code> for analysis and visualization purposes.</li> </ul> <p>The notebooks folder includes:</p> <ul> <li><code>01_project_setup.ipynb</code> sets up a new Brightway project and imports the ecoinvent database.</li> <li><code>02_lci.ipynb</code> imports the LCIs and regionalize some datasets (e.g., biomethane supply based on the bimethane potential).</li> <li><code>03_lcia.ipynb</code> calculates life cycle impacts and all the additional results presented in the paper (e.g., calculation of blending ratios).</li> <li><code>04_sensitivity_analysis.ipynb</code> performs the sensitivity analysis.</li> <li><code>05_visualization.ipynb</code> imports all results and generates the figures presented in the scientific article.</li> </ul> <p>The src folder contains supporting functions required to regionalize LCIs and perform the calculations.</p> <div> <h2>How to get propertary data</h2> </div> <p>Some of the LCI datasets in the <code>inventories.xlsx</code> file are partially based on data from the ecoinvent LCI database. To comply with licensing requirements, the file shared in this repository does not include these data points. If you hold a valid ecoinvent license, please contact me directly to receive the full input files containing all ecoinvent data points.</p> <h2>Contact</h2> <p>Robert Istrate: i.r.istrate@cml.leidenuniv.nl</p>
Figure 5 in Systematic analysis of leisler's bat Nyctalus leisleri (Kuhl, 1817) captured from FATA region, Pakistan
Figure 5. Peculiar to COI by Maximum parsimony method (K2P model). Numbers show percent of 1000 bootstraps replication above 50. ♦ shows the sequences of species of the present research.
Figure 4 in Systematic analysis of leisler's bat Nyctalus leisleri (Kuhl, 1817) captured from FATA region, Pakistan
Figure 4. Genus Nyctalus peculiar to COI by Maximum likelihood method. Number shows percent of 1000 bootstraps replication above 50. ♦ shows the sequences of species of the present research.
Figure 3 in Systematic analysis of leisler's bat Nyctalus leisleri (Kuhl, 1817) captured from FATA region, Pakistan
Figure 3. Genus Nyctalus peculiar to COI by Neighbour Joining method. Number shows percent of 1000 bootstraps replication above 50. ♦ shows the sequences of species of the present research.
Text-fig. 1. Result of cumulative random counting of MN 5 localities in central Europe and the Iberian Peninsula. Ten simulations were run for each area. a. Results of the count including the average in bold, showing the clearly lower diversity in IB. b. The average lines standardized, showing similar patterns in the two areas. Note that in the simulation around thirty localities were needed to capture 80 % of the regional diversity. in Generically Speaking, A Survey On Neogene Rodent Diversity At The Genus Level In The Now Database
Text-fig. 1. Result of cumulative random counting of MN 5 localities in central Europe and the Iberian Peninsula. Ten simulations were run for each area. a. Results of the count including the average in bold, showing the clearly lower diversity in IB. b. The average lines standardized, showing similar patterns in the two areas. Note that in the simulation around thirty localities were needed to capture 80 % of the regional diversity.
Figure 2 in Systematic analysis of leisler's bat Nyctalus leisleri (Kuhl, 1817) captured from FATA region, Pakistan
Figure 2. (A) Nyctalus leisleri; (B) Head; (C) Skull lateral view; (D) Lower jaw dorsal view.
Figure 1 in Systematic analysis of leisler's bat Nyctalus leisleri (Kuhl, 1817) captured from FATA region, Pakistan
Figure 1. Localities and distribution of Nyctalus leisleri in Pakistan.
Regional Biomes outperform broader spatial units in capturing biodiversity responses to land-use change
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Matrix aggregation of species of Phyla Annelida (Polychaeta), Mollusca, Arthropoda (Decapoda, Stomatopoda, Amphipoda, and Chelicerata), and Echinodermata registered of the Caribbean Sea and Gulf of Mexico region by Ocean Biodiversity Information Systems of the research "Evaluation of the use of Autonomous Reef Monitoring Structures (ARMS) for capturing the biological diversity of two coral reefs in the Yucatán Península, México"
<p>This database consists of an aggregation matrix of species from Ocean Biodiversity Information Systems using as geographic filters the Caribbean Sea region (ID 34287) and the Gulf of Mexico region (ID 34287) nomenclature and hierarchical classification of each Phyla from World Register of Marine Species used for the calculation of average taxonomic distinction of species belonging to the Phyla Annelida (Polychaeta), Mollusca, Arthropoda (Decapoda, Stomatopoda, Amphipoda, and Chelicerata), and Echinodermata associated to Autonomous Reefs Monitoring Structures from the research “Evaluation of the use of Autonomous Reef Monitoring Structures (ARMS) to estimate cryptic diversity in two coral reefs of the Yucatan Península, México”</p> <p><strong>*Corresponding autor: </strong>edlinguerra@gmail.com</p> <p>BIS Ocean Biodiversity Information System. Available online: <a href="http://www.iobis.org/">www.iobis.org</a>.</p> <p>Horton, T.; Gofas, S.; Kroh, A.; Poore, G.C.B.; Read, G.; Rosenberg, G.; Stöhr, S.; Bailly, N.; Boury-Esnault, N.; Brandão, S.N.; et al. Improving nomenclatural consistency: A decade of experience in the World Register of Marine Species. <em>Eur. J. Taxon.</em> <strong>2017</strong>, <em>2017</em>, doi:10.5852/ejt.2017.389.</p> <p><span lang="EN-US">was produced in collaboration with the Biodiversidad Marina de Yucatán project. </span><a href="https://www.bdmy.org.mx/carteles-publicaciones/" target="_blank" rel="noopener">https://www.bdmy.org.mx/,</a> Universidad Nacional Autonoma de México and Escuela Nacional de Estudios Superiores</p>
Data from: Targeted capture of complete coding regions across divergent species
Despite continued advances in sequencing technologies, there is a need for methods that can efficiently sequence large numbers of genes from diverse species. One approach to accomplish this is targeted capture (hybrid enrichment). While these methods are well established for genome resequencing projects, cross-species capture strategies are still being developed and generally focus on the capture of conserved regions, rather than complete coding regions from specific genes of interest. The resulting data is thus useful for phylogenetic studies, but the wealth of comparative data that could be used for evolutionary and functional studies is lost. Here we design and implement a targeted capture method that enables recovery of complete coding regions across broad taxonomic scales. Capture probes were designed from multiple reference species and extensively tiled in order to facilitate cross-species capture. Using novel bioinformatics pipelines we were able to recover nearly all of the targeted genes with high completeness from species that were up to 200 myr divergent. Increased probe diversity and tiling for a subset of genes had a large positive effect on both recovery and completeness. The resulting data produced an accurate species tree, but importantly this same data can also be applied to studies of molecular evolution and function that will allow researchers to ask larger questions in broader phylogenetic contexts. Our method demonstrates the utility of cross-species approaches for the capture of full length coding sequences, and will substantially improve the ability for researchers to conduct large-scale comparative studies of molecular evolution and function.
Data from: Targeted sequence capture and resequencing implies a predominant role of regulatory regions in the divergence of a sympatric lake whitefish species pair (Coregonus clupeaformis)
Latest technological developments in evolutionary biology bring new challenges in documenting the intricate genetic architecture of species in the process of divergence. Sympatric populations of lake whitefish represent one of the key systems to investigate this issue. Despite the value of random genotype-by-sequencing methods and decreasing cost of sequencing technologies, it remains challenging to investigate variation in coding regions, especially in the case of recently duplicated genomes as in salmonids, as this greatly complicates whole genome resequencing. We thus designed a sequence capture array targeting 2773 annotated genes to document the nature and the extent of genomic divergence between sympatric dwarf and normal whitefish. Among the 2728 genes successfully captured, a total of 2182 coding and 10 415 noncoding putative single-nucleotide polymorphisms (SNPs) were identified after applying a first set of basic filters. A genome scan with a quality-refined selection of 2203 SNPs identified 267 outlier SNPs in 210 candidate genes located in genomic regions potentially involved in whitefish divergence and reproductive isolation. We found highly heterogeneous FST estimates among SNP loci. There was an overall low level of coding polymorphism, with a predominance of noncoding mutations among outliers. The heterogeneous patterns of divergence among loci confirm the porous nature of genomes during speciation with gene flow. Considering that few protein-coding mutations were identified as highly divergent, our results, along with previous transcriptomic studies, imply that changes in regulatory regions most likely had a greater role in the process of whitefish population divergence than protein-coding mutations. This study is the first to demonstrate the efficiency of large-scale targeted resequencing for a nonmodel species with such a large and unsequenced genome.
Data from: Targeted sequence capture and resequencing implies a predominant role of regulatory regions in the divergence of a sympatric lake whitefish species pair (Coregonus clupeaformis)
Open the record for dataset details and reuse information.
Data from: Targeted capture of complete coding regions across divergent species
Open the record for dataset details and reuse information.
Transcript Profiling of Common Bean Embryo Regions at Globular Stage Using Laser Capture Microdissection Coupled with RNA-Seq
GEO Series GSE57535. Phaseolus vulgaris. 4 samples. Type: Expression profiling by high throughput sequencing.
A map of enhancer regions in primary human neural progenitor cells using capture STARR-seq
GEO Series GSE281139. Homo sapiens. 11 samples. Type: Other.
Transcript Profiling of Scarlet Runner Bean Embryo Regions at Globular Stage Using Laser Capture Microdissection Coupled with RNA-Seq
GEO Series GSE57536. Phaseolus coccineus. 4 samples. Type: Expression profiling by high throughput sequencing.
Transcript Profiling of Phaseolus coccineus and Phaseolus vulgaris Embryo Regions at Globular Stage Using Laser Capture Microdissection Coupled with RNA-Seq
GEO Series GSE57537. Phaseolus vulgaris; Phaseolus coccineus. 8 samples. Type: Expression profiling by high throughput sequencing.
Estradiol-dependent 3D chromatin structure changes in MCF7 cells assessed by Capture-C, covering GREB1 and NRIP1 gene and enhancer regions
GEO Series GSE225617. Homo sapiens. 46 samples. Type: Other.
Capture-C in MGE, CGE, LGE and cortical regions from mouse embryonic forebrain
GEO Series GSE201317. Mus musculus. 10 samples. Type: Other.
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
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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.