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1,037 results for “large-scale”
Figure 6 from: Avila-Poveda OH (2020) Large-scale project 'Chiton of the Mexican Tropical Pacific': Chiton articulatus (Mollusca: Polyplacophora). Research Ideas and Outcomes 6: e60446. https://doi.org/10.3897/rio.6.e60446
Figure 6 Locations of Chiton articulatus collection. The star indicates the local headquarters of this project. The base map was taken from Instituto Nacional de Estadística, Geografía e Informática (INEGI). https://www.inegi.org.mx/
Figure 3 from: Avila-Poveda OH (2020) Large-scale project 'Chiton of the Mexican Tropical Pacific': Chiton articulatus (Mollusca: Polyplacophora). Research Ideas and Outcomes 6: e60446. https://doi.org/10.3897/rio.6.e60446
Figure 3 The food menu of some restaurants in Acapulco, Guerrero, including a dish with chiton, common name "Cucaracha/cockroach".
Figure 2 from: Avila-Poveda OH (2020) Large-scale project 'Chiton of the Mexican Tropical Pacific': Chiton articulatus (Mollusca: Polyplacophora). Research Ideas and Outcomes 6: e60446. https://doi.org/10.3897/rio.6.e60446
Figure 2 Example of sale and consumption of meat (foot, in colloquial Spanish "Lengua") of Chiton articulatus. Sale of chitons in beaches of Acapulco (left upper). Sale of chitons in streets of Pochutla, Oaxaca, close to Huatulco (left lower). Dish (Lengua a la Mexicana) in a restaurant in Huatulco (right upper). Artisanal fishing of chitons for a family weekend reunion at Puerto Angel, Oaxaca close to Huatulco (right lower).
Figure 9 from: Avila-Poveda OH (2020) Large-scale project 'Chiton of the Mexican Tropical Pacific': Chiton articulatus (Mollusca: Polyplacophora). Research Ideas and Outcomes 6: e60446. https://doi.org/10.3897/rio.6.e60446
Figure 9 Collage (application letters) of the procedure to request the recognition and incorporation of this Chiton articulatus mollusc into the National Fisheries Chart.
Reproducible results for: pmparser and PMDB: resources for large-scale, open studies of the biomedical literature
<p>The zip file contains all code and results. See the included readme.</p>
Data from: Large-scale functional networks identified from resting-state EEG using spatial ICA
Several methods have been applied to EEG or MEG signals to detect functional networks. In recent works using MEG/EEG and fMRI data, temporal ICA analysis has been used to extract spatial maps of resting-state networks with or without an atlas-based parcellation of the cortex. Since the links between the fMRI signal and the electromagnetic signals are not fully established, and to avoid any bias, we examined whether EEG alone was able to derive the spatial distribution and temporal characteristics of functional networks. To do so, we propose a two-step original method: 1) An individual multi-frequency data analysis including EEG-based source localisation and spatial independent component analysis, which allowed us to characterize the resting-state networks. 2) A group-level analysis involving a hierarchical clustering procedure to identify reproducible large-scale networks across the population. Compared with large-scale resting-state networks obtained with fMRI, the proposed EEG-based analysis revealed smaller independent networks thanks to the high temporal resolution of EEG, hence hierarchical organization of networks. The comparison showed a substantial overlap between EEG and fMRI networks in motor, premotor, sensory, frontal, and parietal areas. However, there were mismatches between EEG-based and fMRI-based networks in temporal areas, presumably resulting from a poor sensitivity of fMRI in these regions or artefacts in the EEG signals. The proposed method opens the way for studying the high temporal dynamics of networks at the source level thanks to the high temporal resolution of EEG. It would then become possible to study detailed measures of the dynamics of connectivity.
Data from: Large-scale proteomics of the cassava storage root and identification of a target gene to reduce post-harvest deterioration
Cassava (Manihot esculenta) is the most important root crop in the tropics, but rapid postharvest physiological deterioration (PPD) of the root is a major constraint to commercial cassava production. We established a reliable method for image-based PPD symptom quantification and used label-free quantitative proteomics to generate an extensive cassava root and PPD proteome. Over 2600 unique proteins were identified in the cassava root, and nearly 300 proteins showed significant abundance regulation during PPD. We identified protein abundance modulation in pathways associated with oxidative stress, phenylpropanoid biosynthesis (including scopoletin), the glutathione cycle, fatty acid α-oxidation, folate transformation, and the sulfate reduction II pathway. Increasing protein abundances and enzymatic activities of glutathione-associated enzymes, including glutathione reductases, glutaredoxins, and glutathione S-transferases, indicated a key role for ascorbate/glutathione cycles. Based on combined proteomics data, enzymatic activities, and lipid peroxidation assays, we identified glutathione peroxidase as a candidate for reducing PPD. Transgenic cassava overexpressing a cytosolic glutathione peroxidase in storage roots showed delayed PPD and reduced lipid peroxidation as well as decreased H2O2 accumulation. Quantitative proteomics data from ethene and phenylpropanoid pathways indicate additional gene candidates to further delay PPD. Cassava root proteomics data are available at www.pep2pro.ethz.ch for easy access and comparison with other proteomics data.
Data from: Large-scale natural disturbance alters genetic population structure of the sailfin molly, Poecilia latipinna
Many inferences about contemporary rates of gene flow are based on the assumption that the observed genetic structure among populations is stable. Recent studies have uncovered several cases in which this assumption is tenuous. Most of those studies have focused on the effects that regular environmental fluctuations can have on genetic structure and gene flow patterns. Occasional catastrophic disturbances could also alter either the distribution of habitat or the spatial distribution of organisms in a way that affects population structure. However, evidence of such effects is sparse in the literature because it is difficult to obtain. Hurricanes, in particular, have the potential to exert dramatic effects on population structure of organisms found on islands or coral reefs or in near shore and coastal habitats. Here we draw on a historic genetic data set and new data to suggest that the genetic structure of sailfin molly (Poecilia latipinna) populations in north Florida was altered dramatically by an unusually large and uncommon type of storm surge associated with Hurricane Dennis in 2005. We compare the spatial pattern of genetic variation in these populations after Hurricane Dennis to the patterns described in an earlier study in this same area. We use comparable genetic data from another region of Florida, collected in the same two periods, to estimate the amount of change expected from typical temporal variation in population structure. The comparative natural history of sailfin mollies in these two regions indicates that the change in population structure produced by the storm surge is not the result of many local extinctions with recolonization from a few refugia but emerged from a pattern of mixing and redistribution.
Data from: Large-scale genotyping of highly polymorphic loci by next generation sequencing: how to overcome the challenges to reliably genotype individuals?
Studying the different roles of adaptive genes is still a challenge in evolutionary ecology and requires reliable genotyping of large numbers of individuals. Next-generation sequencing (NGS) techniques enable such large-scale sequencing, but stringent data processing is required. Here, we develop an easy to use methodology to process amplicon-based NGS data and we apply this methodology to reliably genotype four major histocompatibility complex (MHC) loci belonging to MHC class I and II of Alpine marmots (Marmota marmota). Our post-processing methodology allowed us to increase the number of retained reads. The quality of genotype assignment was further assessed using three independent validation procedures. A total of 3069 high-quality MHC genotypes were obtained at four MHC loci for 863 Alpine marmots with a genotype assignment error rate estimated as 0.21%. The proposed methodology could be applied to any genetic system and any organism, except when extensive copy-number variation occurs (that is, genes with a variable number of copies in the genotype of an individual). Our results highlight the potential of amplicon-based NGS techniques combined with adequate post-processing to obtain the large-scale highly reliable genotypes needed to understand the evolution of highly polymorphic functional genes.
Data from: Crowdsourced geometric morphometrics enable rapid large-scale collection and analysis of phenotypic data
1. Advances in genomics and informatics have enabled the production of large phylogenetic trees. However, the ability to collect large phenotypic datasets has not kept pace. 2. Here, we present a method to quickly and accurately gather morphometric data using crowdsourced image-based landmarking. 3. We find that crowdsourced workers perform similarly to experienced morphologists on the same digitization tasks. We also demonstrate the speed and accuracy of our method on seven families of ray-finned fishes (Actinopterygii). 4. Crowdsourcing will enable the collection of morphological data across vast radiations of organisms, and can facilitate richer inference on the macroevolutionary processes that shape phenotypic diversity across the tree of life.
Data from: Large-scale fungal diversity assessment in the Andean Yungas forests reveals strong community turnover among forest types along an altitudinal gradient
The Yungas, a system of tropical and subtropical montane forests on the eastern slopes of the Andes, are extremely diverse and severely threatened by anthropogenic pressure and climate change. Previous mycological works focused on macrofungi (e.g., agarics, polypores) and mycorrhizae in Alnus acuminata forests, while fungal diversity in other parts of the Yungas has remained mostly unexplored. We carried out Ion Torrent sequencing of ITS2 rDNA from soil samples taken at 24 sites along the entire latitudinal extent of the Yungas in Argentina. The sampled sites represent the three altitudinal forest types: the piedmont (400–700 masl), montane (700–1500 masl), and montane cloud (1500–3000 masl) forests. The deep sequence data presented here (i.e. 4 108 126 quality-filtered sequences) indicate that fungal community composition correlates most strongly with elevation, with many fungi showing preference for a certain altitudinal forest type. For example, ectomycorrhizal and root endophytic fungi were most diverse in the montane cloud forests, particularly at sites dominated by Alnus acuminata, while the diversity values of various saprobic groups were highest at lower elevations. Despite the strong altitudinal community turnover, fungal diversity was comparable across the different zonal forest types. Besides elevation, soil pH, N, P, and organic matter contents correlated with fungal community structure as well, although most of these variables were co-correlated with elevation. Our data provide an unprecedented insight into the high diversity and spatial distribution of fungi in the Yungas forests.
Data from: Building the avian tree of life using a large-scale, sparse supermatrix
Birds are the most diverse tetrapod class, with about 10,000 extant species that represent a remarkable evolutionary radiation in which most taxa arose during a short period of time. There has been a tremendous increase in the amount of molecular data available from birds, and more than two-thirds of these species have some sequence data available. Here we assembled these available sequence data from birds to estimate a large-scale avian phylogeny. We performed an unconstrained maximum likelihood analysis of a sparse supermatrix comprising 22 nuclear loci and seven mitochondrial regions from 6714 species. We inferred a phylogeny with a backbone remarkably similar to that obtained by detailed analyses of multigene datasets, yet with the addition of thousands of more taxa. All orders were monophyletic with generally high support. While most families and genera were well supported, a number of them, especially within the oscine passerines, had little or no support. This likely reflects problems with the circumscription of these genera and families. Our results indicate that the amount of sequence data currently available is sufficient to produce a robust estimate of the avian tree of life using current methods of inference. The availability of a tree that is unconstrained by prior information, with branch lengths that have a direct connection to the underlying data, should be useful for comparative methods, taxonomic revisions, and prioritizing taxa that should be targeted for additional data collection.
FIGURE 8. Pseudotomias kisarawe n in The Eastern Arc Mountains and coastal forests of East Africa—an archive to understand large-scale biogeographical patterns: Pseudotomias, a new genus of African Pseudophyllinae (Orthoptera: Tettigoniidae)
FIGURE 8. Pseudotomias kisarawe n. sp. male mounting female showing sexual size dimorphism.
FIGURE 6 in The Eastern Arc Mountains and coastal forests of East Africa—an archive to understand large-scale biogeographical patterns: Pseudotomias, a new genus of African Pseudophyllinae (Orthoptera: Tettigoniidae)
FIGURE 6. Last instar of female Pseudotomias usambaricus n. sp.
FIGURE 7. Pseudotomias kisarawe n in The Eastern Arc Mountains and coastal forests of East Africa—an archive to understand large-scale biogeographical patterns: Pseudotomias, a new genus of African Pseudophyllinae (Orthoptera: Tettigoniidae)
FIGURE 7. Pseudotomias kisarawe n. sp., male (A) and female (B).
FIGURE 2 in The Eastern Arc Mountains and coastal forests of East Africa—an archive to understand large-scale biogeographical patterns: Pseudotomias, a new genus of African Pseudophyllinae (Orthoptera: Tettigoniidae)
FIGURE 2. Male holotype of Pseudotomias usambaricus n. sp., Sigi Trail, East Usambara Mountains.
Dataset to reproduce the figures in "Parameterizing the Impact of Unresolved Temperature Variability on the Large-Scale Density Field: Part 2. Modeling." in Journal of Advances in Modeling Earth Systems (JAMES)
Ocean circulation models have systematic errors in large-scale horizontal density gradients due to estimating the grid-cell-mean density by applying the nonlinear seawater equation of state to the grid-cell-mean water properties. In frontal regions where unresolved subgrid-scale (SGS) fluctuations are significant, dynamically relevant errors in the representation of current systems can result. A previous study developed a novel and computationally efficient parameterization of the unresolved SGS temperature variance andresulting density correction. This parameterization was empirically validated but not tested in an ocean model. In this study, we implement deterministic and stochastic variants of this parameterization in the pressure-gradient force term of a coupled ocean-sea ice configuration of CESM-MOM6 and perform a suite of hindcast sensitivity experiments to investigate the ocean response. The parameterization leads to coherent changes in the large-scale ocean circulation and hydrography, particularly in the Nordic Seas and Labrador Sea, which are attributable in large part to changes in the seasonally varying upper-ocean exchange through Denmark Strait. In addition, the separated Gulf Stream strengthens and shifts equatorward, reducing a common bias in coarse-resolution ocean models. The ocean response to the deterministic and stochastic variants of the parameterization is qualitatively, albeit not quantitatively, similar, yet qualitative differences are found in various regions.
Coupling a large-scale glacier and hydrological model (OGGM v1.5.3 and CWatM V1.08) - Data Set
<p>GENERAL INFORMATION</p> <p>The data and scripts used for the analysis of the paper "Coupling a large-scale glacier and hydrological model (OGGM v1.5.3 and CWatM V1.08) – Towards an improved representation of mountain water resources in global assessments"</p> <p><strong>When using this dataset, please refer to the original publication in addition to this Zenodo repository.</strong></p> <p><strong>Hanus, S., Schuster, L., Burek, P., Maussion, F., Wada, Y., and Viviroli, D.: Coupling a large-scale glacier and hydrological model (OGGM v1.5.3 and CWatM V1.08) – towards an improved representation of mountain water resources in global assessments, Geosci. Model Dev., 17, 5123–5144, https://doi.org/10.5194/gmd-17-5123-2024, 2024.</strong></p> <p>DATA & FILE OVERVIEW</p> <p>please have a look at readme.txt </p> <p>Don't hesitate to contact us in case of any questions (sarah.hanus@geo.uzh.ch)</p>
Data set for "A large-scale integrated vector–matrix multiplication processor based on monolayer molybdenum disulfide memories"
<p>Data accompanying the paper "A large-scale integrated vector–matrix multiplication processor based on monolayer molybdenum disulfide memories" </p>
LIVECell A large-scale dataset for label-free live cell segmentation - organised by cell type
<p>This data was originally published in </p><p><a href="https://doi.org/10.1038/s41592-021-01249-6">Edlund, C., Jackson, T.R., Khalid, N. <i>et al.</i> LIVECell—A large-scale dataset for label-free live cell segmentation. <i>Nat Methods</i> <strong>18</strong>, 1038–1045 (2021). https://doi.org/10.1038/s41592-021-01249-6</a></p><p>The instance segmentation annotation data has been downloaded and organised in folders for each cell type to ease its use in demos and courses. Please, refer to the original publication and <a href="https://sartorius-research.github.io/LIVECell/">original data source</a> for further research studies. </p><p><strong>IF YOU USE THIS DATASET, PLEASE ACKNOWLEDGE THE ORIGINAL AUTHORS (Edlund et al., Nat Methods 2021)</strong></p>
ScienceDex guides
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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.