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6,467 results for “process”
Data from: Using spatial capture–recapture to elucidate population processes and space-use in herpetological studies
The cryptic behavior and ecology of herpetofauna make estimating the impacts of environmental change on demography difficult; yet, the ability to measure demographic relationships is essential for elucidating mechanisms leading to the population declines reported for herpetofauna worldwide. Recently developed spatial capture–recapture (SCR) methods are well suited to standard herpetofauna monitoring approaches. Individually identifying animals and their locations allows accurate estimates of population densities and survival. Spatial capture–recapture methods also allow estimation of parameters describing space-use and movement, which generally are expensive or difficult to obtain using other methods. In this paper, we discuss the basic components of SCR models, the available software for conducting analyses, and the experimental designs based on common herpetological survey methods. We then apply SCR models to Red-backed Salamander (Plethodon cinereus), to determine differences in density, survival, dispersal, and space-use between adult male and female salamanders. By highlighting the capabilities of SCR, and its advantages compared to traditional methods, we hope to give herpetologists the resource they need to apply SCR in their own systems.
Data from: Central place foragers and moving stimuli: a hidden-state model to discriminate the processes affecting movement
1. Human activities can influence the movement of organisms, either repelling or attracting individuals depending on whether they interfere with natural behavioural patterns or enhance access to food. To discern the processes affecting such interactions, an appropriate analytical approach must reflect the motivations driving behavioural decisions at multiple scales. 2. In this study, we developed a modelling framework for the analysis of foraging trips by central place foragers. By recognising the distinction between movement phases at a larger scale and movement steps at a finer scale, our model can identify periods when animals are actively following moving attractors in their landscape. 3. We applied the framework to GPS tracking data of northern fulmars Fulmarus glacialis, paired with contemporaneous fishing boat locations, to quantify the putative scavenging activity of these seabirds on discarded fish and offal. We estimated the rate and scale of interaction between individual birds and fishing boats and the interplay with other aspects of a foraging trip. 4. The model classified periods when birds were heading out to sea, returning towards the colony or following the closest boat. The probability of switching towards a boat declined with distance and varied depending on the phase of the trip. The maximum distance at which a bird switched towards the closest boat was estimated around 35 km, suggesting the use of olfactory information to locate food. Individuals spent a quarter of a foraging trip, on average, following fishing boats, with marked heterogeneity among trips and individuals. 5. Our approach can be used to characterise interactions between central place foragers and different anthropogenic or natural stimuli. The model identifies the processes influencing central place foraging at multiple scales, which can improve our understanding of the mechanisms underlying movement behaviour and characterise individual variation in interactions with a range of human activities that may attract or repel these species. Therefore, it can be adapted to explore the movement of other species that are subject to multiple dynamic drivers.
Genetic structure in hybrids and progenitors provides insight into processes underlying an invasive cattail (Typha x glauca) hybrid zone
<p>Traditional models of hybrid zones have assumed relatively low hybrid fitness, and thus focussed more on interspecific gene flow than on hybrid dispersal. Therefore, when hybrids have high fitness and the potential for autonomous dispersal, we have limited understanding of whether hybrid dispersal or repeated local hybrid formation is more important for maintaining hybrid zones. The invasive hybrid cattail <i>Typha × glauca</i> occupies an extensive hybrid zone in northeastern North America where it is sympatric with its progenitors <i>T. latifolia</i> and <i>T. angustifolia</i>. We characterized genetic diversity and genetic structure of the three taxa across a broad spatial scale, and tested the hypothesis that the hybrid shows stronger evidence of gene flow than its progenitor species, particularly among disturbed sites (ditches) compared to established wetlands. Support for this hypothesis would suggest that dispersal, rather than repeated local formation, is more important in maintaining hybrid zones. Within each taxon, genetic differentiation among ditches was comparable to that among wetlands, although clonal richness was consistently greater in ditches suggesting more frequent seed establishment. Genetic structure across sites was more pronounced in the hybrid compared to either progenitor species. Overall, our data reflect relatively low gene flow in hybrids, and suggest that hybrids are more likely to be created <i>in situ</i> than to be introduced from other sites. Despite the high fitness of invasive <i>T. </i>× <i>glauca </i>and its potential for autonomy<i>, </i>local processes appear more important than dispersal in maintaining this hybrid zone.</p>
Data from: Echoes of a distant time: effects of historical processes on contemporary genetic patterns in Galaxias platei in Patagonia
Interpreting the genetic structure of a metapopulation as the outcome of gene flow over a variety of timescales is essential for the proper understanding of how changes in landscape affect biological connectivity. Here we contrast historical and contemporary connectivity in two metapopulations of the freshwater fish Galaxias platei in northern and southernmost Patagonia where paleolakes existed during the Holocene and Pleistocene, respectively. Contemporary gene flow was mostly high and asymmetrical in the northern system while extremely reduced in the southernmost system. Historical migration patterns were high and symmetric in the northern system and high and largely asymmetric in the southern system. Both systems showed a moderate structure with a clear pattern of isolation by distance (IBD). Effective population sizes were smaller in populations with low contemporary gene flow. An approximate Bayesian computation (ABC) approach suggests a late Holocene colonization of the lakes in the northern system and recent divergence of the populations from refugial populations from east and west of the Andes. For the southern system, the ABC approach reveals that some of the extant G. platei populations most likely derive from an ancestral population inhabiting a large Pleistocene paleolake while the rest derive from a higher-altitude lake. Our results suggest that neither historical nor contemporary processes individually fully explain the observed structure and geneflow patterns and both are necessary for a proper understanding of the factors that affect diversity and its distribution. Our study highlights the importance of a temporal perspective on connectivity to analyse the diversity of spatially complex metapopulations.
Rupture Process of the 2020 Mw7.0 Samos earthquake and its effect on surrounding active faults
<p>Here we have archived available geodetic and strong motion data that accompany the article 'Rupture Process of the 2020 Mw7.0 Samos earthquake and its effect on surrounding active faults'.</p>
Data from: Contrasting processes drive ophiuroid phylodiversity across shallow and deep seafloors
Our knowledge of the distribution and evolution of deep-sea life is limited, impeding our ability to identify priority areas for conservation. Here we analyse, for the first time, large integrated phylogenomic and distributional datasets of seafloor fauna from sea surface to abyss and equator to pole of the Southern Hemisphere for an entire class of invertebrates (Ophiuroidea). We find that latitudinal diversity gradients are assembled through contrasting evolutionary processes for shallow (0-200 m) and deep (> 200 m) seas. The shallow-water tropical-temperate realm broadly reflects a tropical diversification-driven process but with exchange in both directions. Diversification rates are reversed for the realm containing the deep sea and Antarctica, being highest at polar and lowest at tropical latitudes, and net exchange is from high to low latitudes. The tropical upper bathyal (200-700 m deep), with its rich ancient phylodiversity, is characterised by relatively low diversification and moderate immigration rates. Conversely, the young specialised Antarctic fauna is inferred to be rebounding from regional extinction associated with the rapid cooling of polar waters over the mid-Cenozoic.
Data from: Disentangling invasion processes in a dynamic shipping - boating network
The relative importance of multiple vectors to the initial establishment, spread, and population dynamics of invasive species remains poorly understood. This study used molecular methods to clarify the roles of commercial shipping and recreational boating in the invasion by the cosmopolitan tunicate, Botryllus schlosseri. We evaluated i) single vs. multiple introduction scenarios, ii) the relative importance of shipping and boating to primary introductions, iii) the interaction between these vectors for spread (i.e., the presence of a shipping-boating network), and iv) the role of boating in determining population similarity. Tunicates were sampled from 26 populations along the Nova Scotia, Canada, coast that were exposed to either shipping (i.e., ports), or boating (i.e., marinas) activities. A total of 874 individuals (~30 per population) from 5 ports and 21 marinas was collected and analyzed using both mitochondrial cytochrome c oxidase subunit I gene (COI) and 10 nuclear microsatellite markers. The geographical location of multiple hotspot populations indicates that multiple invasions have occurred in Nova Scotia. A loss of genetic diversity from port to marina populations suggests a stronger influence of ships than recreational boats on primary coastal introductions. Population similarity analysis reveals a clear dependence of marina populations on those that had been previously established in ports and connectivity due to a boating network better explains patterns in population similarities than does natural spread. We conclude that frequent primary introductions arise by ships and that secondary spread occurs gradually thereafter around individual ports, facilitated by recreational boating.
Data from Schmitt et al. 2021: Preattentive processing of visually guided self-motion in humans and monkeys. Progress in Neurobiology
<p><strong>Dataset associated with the following publication:</strong></p> <p>Constanze Schmitt, Jakob C.B. Schwenk, Adrian Schütz, Jan Churan, André Kaminiarz, Frank Bremmer.<br> Preattentive processing of visually guided self-motion in humans and monkeys. Progress in Neurobiology,<br> 2021,102117. https://doi.org/10.1016/j.pneurobio.2021.102117. Published 2021 July 2.</p> <p><strong>Description of dataset:</strong></p> <p>In our study we presented an optic flow stimulus simulating forward self-motion across a ground plane in an oddball EEG paradigm to 12 human participants and 2 macaque monkeys. We simulated two different headings (forward-left vs. forward-right) presented either as standard or deviant trials and tested for the occurrence of a visual mismatch negativity (vMMN) by comparing the visual-evoked potentials (VEPs). </p> <p>Human data:</p> <p>The dataset contains the preprocessed VEPs of all 12 human participants already averaged over all trials per participant. It contains data from all electrodes used for analysis (P1, P2, O1, O2, PO3, PO4, CP1, CP2) divided into data recordings in standard ('_std') or deviant ('_odd') trials. Each of these files consists of four subfiles representing the presented combinations of heading (forward to the right: '_r' or forward to the left: '_l') and attention condition (attention towards fixation target: 'fix' or attention towards the ground plane: 'plane'). The data matrices in these subfiles are sorted as [participants x time-points].</p> <p>Monkey data:</p> <p>Each .mat file contains the preprocessed VEPs from one monkey ('data'), the corresponding electrode labels ('elec') and the common time vector in seconds ('time'). The data struct contains VEPs for left- and rightwards heading in separate subfields, which again contain standard ('stan') and deviant ('odd') presentations of that heading. Within each subcondition, the actual data matrices are sorted as [electrodes x time-points x trials]. Here, the numbering of electrodes corresponds to the electrode labels contained in the 'elec' variable.</p>
FIGURES 1–8. 1. Appendicular process. a in Synopsis of lobatifrons species-group (Hymenoptera: Bethylidae, Rhabdepyris) from Neotropical region, with redefinition of the group
FIGURES 1–8. 1. Appendicular process. a. base; b. apex. 2–8. Rhabdepyris latissimus sp. nov. holotype. 2. Head and mesosoma in dorsal view; 3. Mandible in frontal view; 4. Antenna in frontal view; 5. Mesopleuron in frontal view; 6–8. Genitalia. 6. Ventral view; 7. Dorsal view; 8. Lateral view. (scale bar = 250µm).
Chimney Swift processed dataset from "Unraveling hidden interactions in complex systems with deep learning"
<p>Pre-processed dataset of chimney swift trajectory from the paper "<a href="https://www.nature.com/articles/s41598-021-91878-w">Unraveling hidden interactions in complex systems with deep learning</a>"(https://www.nature.com/articles/s41598-021-91878-w). The original data is provided by "Three-dimensional trajectories and network analyses of group behaviour within chimney swift flocks during approaches to the roost" (<a href="https://doi.org/10.1098/rspb.2016.2602">https://doi.org/10.1098/rspb.2016.2602</a>).</p> <p>Needs to be placed at "./data/Flock/system" in order to properly generate the dataset (See https://github.com/nokpil/AgentNet).</p>
Functional and morphological adaptation in DNA protocells via signal processing prompted by artificial metalloenzymes
<p>Data underlying the figures in the publication “Functional and morphological adaptation in DNA protocells via signal processing prompted by artificial metalloenzymes”, published in<em> Nat. Nanotechnol., </em><strong>2020</strong>, 15, 914–921. <a href="https://doi.org/10.1038/s41565-020-0761-y">https://doi.org/10.1038/s41565-020-0761-y</a></p> <p>Table of contents:</p> <p><strong>1. Dataset</strong>; Excel file containing the numerical data for <em>Figure 3</em>: Metathesis kinetics, mutant screenings and crowding.</p> <p><strong>2. Experimental Information</strong>; Word file containing the experimental protocols for synthesis and analysis.</p> <p> </p> <p> </p>
FIGURES 10–19 in Syvertsenia iberica (Cymatosiraceae): a new estuarine diatom genus characterized by the position of its process
FIGURES 10–19. Syvertsenia iberica. SEM images from the holotype sample (GS1) from Guadiana Estuary, Spain. Fig. 10: General view of the interior of the process valve. Note the tubular process (white arrow) and the presence of two linearly opposed ocelluli. Fig. 11: Close up to the valve internal view. Fig. 12: Close up of the middle part of the valve. Note the areolae occlusions, tubular process (black arrowhead) and mantle expansion with an areolae (white arrow). Fig. 13: Close up of the tubular process and areolae in the mantle expansion. Fig 14: Close up to the marginal spines. Fig. 15: Close up to the valve face areolae, which present an approximated linear and equidistant distribution. Figs 16, 17: Close up to the ocellulus, external (black arrowhead, Fig. 16) and internal (white arrow, Fig. 16) showing the presence of porelli (note the presence of spines in an external view). Figs 18, 19: Close up to the opposite apex ocellulus external view, note the presence of spines within ocellulus (black arrowhead, Fig. 18). Fig. 10: Scale bar = 10 µm. Fig. 11: Scale bar = 5 µm. Figs 12, 15 and 19: Scale bar = 500 nm. Fig. 13: Scale bar = 250 nm. Fig. 14: Scale bar = 200 nm. Fig. 16: Scale bar = 2 µm. Figs 17, 18: Scale bar = 1 µm.
FIGURES 2–9 in Syvertsenia iberica (Cymatosiraceae): a new estuarine diatom genus characterized by the position of its process
FIGURES 2–9. Syvertsenia iberica. LM images. Figs 3–9: Specimens from the holotype slide. Figs 6, 7: Holotype specimen photographed in various techniques, note the presence of the tubular process on a mantle (arrow) Figs 8, 9: Same specimen photographed in various techniques. Figs 4–6 and 8: Phase contrast. Figs 7 and 9: Differential Interference Contrast. All scale bars = 10 µm.
FIGURE 1 in Syvertsenia iberica (Cymatosiraceae): a new estuarine diatom genus characterized by the position of its process
FIGURE 1. Study area: (A) Location in Iberia Peninsula, (B) Location in the lower area of the Guadiana Estuary and (C) Schematic representation of the sampling transect (elevation relative to the mean sea-level). Illustrations of Sarcocornia perennis (Miller) A. J. Scott (1977: 367) & Halimione portulacoides (L.) Aellen (1938: 126) by Tracey (2010) and Spartina maritima (Curtis) Fernald (1916: 180) by Saxby (2010).
Wall Three Fabrication Process
<p>This film contains video documentation of the demonstrator "Wall Three" fabrication</p> <p> </p> <p>This file is part of a doctoral thesis appendix:</p> <p>Scherer, A.L. (2021). "<em>CONCRETE FORM[ing]WORK: </em><em>Design, Fabrication, Simulation & Correlation of Parametric Patterned Flexible Formwork and Concrete" </em>[Doctoral Thesis, KTH Royal Institute of Technology, School of Architecture]</p>
scc-process-scheduling-instances: 2021-07-25 version
<p>Deleted excessive files</p>
Data from: Consequences of aboveground invasion by non-native plants into restored vernal pools do not prompt changes in belowground processes
<p>Given the frequent overlap between biological plant invasion and ecological restoration efforts it is important to investigate their interactions to sustain desirable plant communities and modify long-term legacies both above and belowground. To address this relationship, we used natural reference, invaded, and constructed vernal pools in the Central Valley of California to examine potential changes in direct and indirect plant effects on soils associated with biological invasion and active restoration ecosystem disturbances. Our results showed that through a shift in vegetation composition and changes in the plant community tissue chemistry, invasion by non-native plant species has the potential to transform plant inputs to soils in vernal pool systems. In particular, we found that while non-native litter decomposition was driven by seasonal and interannual variability, associated with changes in precipitation, the overall decomposition for non-native litter was drastically lower than native species. This shift has important implications for long-term alterations in plant-based inputs to soils in a negative feedback to nutrient cycling. Moreover, these results were independent of historic active restoration efforts. Despite the consistent shift in plant litter decomposition rates and community composition, we did not detect associated shifts in belowground function associated with invasion by non-native plants. Instead, soil C:N ratios and microbial biomass did not differ between invaded and reference naturally occurring pools but were reduced in the manipulated restored pools independent of invasion levels. Our results suggest that while there is an observed invasive positive feedback aboveground, this trajectory is not necessarily represented belowground and restoration legacies were still dominant ten years after practices were applied. Restoration practices that limit invasive plant feedbacks and account for soil legacy recovery, therefore offer the best solution for disturbed ephemeral ecosystems.</p>
Global process-based characterization factors of soil carbon depletion for life cycle impact assessment
<p>The dataset includes all the Life Cycle Impact Assessment (LCIA) Characterization Factors (CFs) for the Soil Organic Carbon (SOC) depletion indicator produced by Teixeira, R.F.M., Morais, T.G., Domingos, T. 2021. Global process-based characterization factors of soil carbon depletion for life cycle impact assessment.</p> <p> </p> <p>The dataset is divided by type of CF. The results (files) included in each file is:</p> <ul> <li><strong>SOC_dynamics.zip</strong>: includes all the used SOC dynamics for calculate the CFs (it includes transitions for crop, forest, grassland and urban LU classes).</li> </ul> <ul> <li><strong>Raster_Background_Occupation.zip</strong>: includes spatial data (rasters at “tif” format) for Occupation CFs per aggregated land use flow according Table 1 of the paper at country-level.</li> </ul> <p>For example, the raster “Occ_background_Agriculture.tif” has the CFs for the land use class “Agriculture”.</p> <ul> <li><strong>Raster_background_Transformation.zip</strong>: includes spatial data (rasters at “tif” format) for Transformation CFs per aggregated land use flow according Table 1 of the paper at country-level.</li> <li><strong>Table_CFs_background.xlsx</strong>: Includes, at Excel table, the Occupation and Transformation Characterization Factors that were included in “Raster_background_ Occupation.zip” and “Raster_background_Transformation.zip”</li> <li><strong>Raster_Foreground_Occupation.zip</strong>: includes spatial data (rasters at “tif” format) for Occupation CFs per unique land use flow according Table 2 of the paper at unique homogenous territorial unit (about 17,200 unique region).</li> </ul> <p>For example, the raster “Occ_foreground_Irrigated_Potatoes.tif” has the CFs for the land use class “Irrigated potatoes”.</p> <ul> <li><strong>Raster_ Foreground _Transformation.zip</strong>: includes spatial data (rasters at “tif” format) for Transformation CFs per unique land use flow according Table 2 of the paper at unique homogenous territorial unit (about 17,200 unique region).</li> <li><strong>Table_CFs_foreground.xlsx: </strong>Includes, at Excel table, the Occupation and Transformation Characterization Factors that were included in “Raster_Foreground_Occupation.zip” and “Raster_ Foreground _Transformation.zip”</li> <li><strong>LCIA_OpenLCA_file.zip</strong>: includes the Background Characterization Factors to be imported as an LCIA methods for the Product Environmental Footprint database in OpenLCA software</li> </ul>
FIGURE 3. Rafflesia mixta. A. Open male flower showing partially visible disk processes through the diaphragm aperture. B. Longitudinal section through a female flower showing ovary. C in Rafflesia mixta (Rafflesiaceae), a new species from Surigao del Norte, Mindanao, Philippines
FIGURE 3. Rafflesia mixta. A. Open male flower showing partially visible disk processes through the diaphragm aperture. B. Longitudinal section through a female flower showing ovary. C. Bud with perigone lobes removed to show the short column, blade-like processes, and ramenta. D. Disk with regularly distributed processes in two zones. E. Anthers underneath the disk. A. Barcelona 4044 with Manting, Arbolonio & Caballero. B. Arbolonio & Caballero 5. C–E. Barcelona 4043 with Manting, Arbolonio & Caballero.
Pragmatic prediction in the processing of referring expressions containing scalar quantifiers
<p>Data and analysis scripts pertaining to a study by Macuch Silva & Franke (submitted).</p>
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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.