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2,721 results for “Connectivity”
Marine stepping-stones: Connectivity of Mytilus edulis populations between offshore energy installations
Recent papers postulate that epifaunal organisms use artificial structures as stepping-stones to spread to areas that are too distant to reach in a single generation. With thousands of artificial structures present in the North Sea, we test the hypothesis that these structures are connected by water currents and act as an interconnected reef. Population genetic structure of the Blue mussel, Mytilus edulis was expected to follow a pattern predicted by particle tracking models (PTM). Correlation between population genetic differentiation, based on microsatellite markers, and particle exchange was tested. Specimens of M. edulis were found at each location, although the PTM indicated that locations >85 km offshore were isolated from coastal sub-populations. Fixation coefficient FST correlated with the number of arrivals in the PTM. However, the number of effective migrants per generation as inferred from coalescent simulations did not show a strong correlation with the arriving particles. Isolation by distance analysis showed no increase in isolation with increasing distance and we did not find clear structure among the populations. The marine stepping-stone effect is obviously important for the distribution of M. edulis in the North Sea and it may influence ecologically comparable species in a similar way. In the absence of artificial shallow hard substrates, M. edulis would be unlikely to survive in offshore North Sea waters. Although we found an indication that FST was lower between connected locations, isolation by distance analysis showed no increase in isolation with increasing distance. Finally, we did not find clear structure among the populations.
Data from: Detrital shadows: estuarine food web connectivity depends on fluvial influence and consumer feeding mode
We measured the influence of landscape setting on estuarine food web connectivity in five macrotidal Pacific Northwest estuaries across a gradient of freshwater influence. We used stable isotopes (δ13C, δ15N, δ34S) in combination with a Bayesian mixing model to trace primary producer contributions to suspension- and deposit-feeding bivalve consumers (Mytilus trossulus and Macoma nasuta) transplanted into three estuarine vegetation zones: emergent marsh, mudflat, Japanese eelgrass (Zostera japonica), and native eelgrass (Zostera marina). Fluvial discharge and consumer feeding mode strongly influenced the strength and spatial scale of observed food web linkages, while season played a secondary role. Mussels displayed strong cross-ecosystem connectivity in all estuaries, with decreasing marine influence in the more fluvial estuaries. Mussel diets indicated homogenization of detrital sources within the water column of each estuary. In contrast, the diets of benthic deposit-feeding clams indicated stronger compartmentalization in food web connectivity, especially in the largest river delta where clam diets were trophically disconnected from marsh sources of detritus. This suggests detritus deposition is patchy across space, and less homogenous than the suspended detritus pool. In addition to fluvial setting, other estuary-specific environmental drivers, such as marsh area or particle transport speed, influenced the degree of food web linkages across space and time, often accounting for unexpected patterns in food web connectivity. Transformations of the estuarine landscape that alter river hydrology or availability of detritus sources can thus potentially disrupt natural food web connectivity at the landscape scale, especially for sedentary organisms which cannot track their food sources through space.
Connectional asymmetry of the inferior parietal lobule shapes hemispheric specialization in humans, chimpanzees, and rhesus macaques
<p>The inferior parietal lobule (IPL) is one of the most expanded cortical regions in humans relative to other primates. It is also among the most structurally and functionally asymmetric regions in the human cerebral cortex. Whether the structural and connectional asymmetries of IPL subdivisions differ across primate species and how this relates to functional asymmetries remain unclear. We identified IPL subregions that exhibited positive allometric in both hemispheres, scaling across rhesus macaque monkeys, chimpanzees, and humans. The patterns of IPL subregions asymmetry were similar in chimpanzees and humans, but no IPL asymmetries were evident in macaques. Among the comparative sample of primates, humans showed the most widespread asymmetric connections in the frontal, parietal, and temporal cortices, constituting leftward asymmetric networks that may provide an anatomical basis for language and tool use. Unique human asymmetric connectivity between the IPL and primary motor cortex might be related to handedness. These findings suggest that structural and connectional asymmetries may underlie hemispheric specialization of the human brain.</p>
Metapopulation connectivity retains genetic diversity following historical bottleneck in a federally endangered seabird
<p>Despite intensive management since the 1970s, recovery of the endangered northwestern Atlantic population of the Roseate Tern (<i>Sterna dougallii dougallii</i>) has not offset low productivity from a female-biased sex ratio, low adult survival, and habitat constriction. Now, >90% of individuals breed at three sites within 200 km from Long Island, NY to Buzzards Bay, MA (warm-water subregion). To characterize the impact of historical bottlenecks, metapopulation structure, and demographic fluctuations on genetic variation, Roseate Terns from the warm-water (1870s, 1970s, 1997, 2016) and cold-water (Nova Scotia, Canada; 2018) subregions were genotyped at 8-16 microsatellites and two-three mitochondrial regions. Diversity declined in the warm-water subregion from the 1870s (H<sub>E</sub>= 0.44, A<sub>R</sub>= 2.86) and 1970s (H<sub>E</sub> = 0.53, A<sub>R </sub>= 3.25) to 1997 (H<sub>E</sub> = 0.38, A<sub>R </sub>= 2.58). Genetic signatures of bottlenecks persisted in 1997 (<i>P</i> = 0.001 – 0.003) and 2016 (<i>P</i> = <0.001 – 0.005), but an increase in variation occurred by 2016 (H<sub>E</sub>= 0.50, A<sub>R</sub>= 2.85). Weak structure was detected between contemporary warm- and cold-water subregions (θ = 0.06) and within the warm-water subregion (θ = 0.04). Both demographic (<span><span></span></span>= 3439-3821) and genetic (<span><span></span></span>= 3040) estimates suggested effective population size stability over the last 100 years, despite large fluctuations in census size (4000 – 8662). Results suggest that 50 years of management (restoring habitat, preventing gull encroachment, controlling predators) at colony sites supported a small, stable <i>N<sub>e</sub></i> and maintained a hierarchical metapopulation that allowed gene flow to redistribute genetic variation throughout the NW Atlantic. The metapopulation remains highly vulnerable to stochastic events but harbors resiliency and redundancy through gene flow and a stable <i>Ne</i>. For long-term persistence from a genetic perspective, managers must maintain the major source colonies, increase availability of high-quality peripheral breeding sites, and protect concentrated non-breeding sites that facilitate gene flow.</p>
Immigration credit of temperate forest herbs in fragmented landscapes – implications for restoration of habitat connectivity
<p>1. In many agricultural landscapes, it is important to restore networks of forests to provide habitat and stepping stones for forest specialist taxa. More knowledge is, however, needed on how to facilitate the immigration of such taxa in restored forest patches. Here, we present the first chronosequence study to quantify the dynamics of immigration credits of forest specialist plants in post-arable forest patches.</p> <p>2. We studied the distribution of herbaceous forest specialist plant species in 54 post-arable broadleaved forest patches along gradients of age (20-140 years since forest establishment), distance from ancient forest (0-2600 m) and patch area (0.5-9.6 ha). With Linear Mixed Models we estimated the effects of these factors on species richness, patch means of four dispersal-related plant traits and with Generalized Linear Models on the occurrence of 20 individual species.</p> <p>3. Post-arable forest patch age and spatial isolation from ancient forest, but not patch size, were important predictors for species richness of forest specialists, suggesting that also small patches are valuable for habitat connectivity. Compared to species richness in ancient forest stands, the immigration credit was reduced by more than 90% after 80 years in post-arable forest patches contiguous to ancient forest compared to 40% after 80 years and 60% after 140 years in isolated patches (at least 100 m to next forest). Tall-growing species with adaptations to long-distance dispersal were faster colonizers while species with heavy diaspores and clonal growth were slower to colonize.</p> <p>4. Synthesis and applications: We show that post-arable oak plantations have a high potential for restoration of forest herb vegetation. Dispersal-related plant traits play a key role in explaining interspecific differences among forest specialists. To facilitate forest herb immigration across all functional groups in agricultural landscapes, we suggest to create clusters of relatively small new forest patches nearby older forest with source populations.</p>
Pairing functional connectivity with population dynamics to prioritize corridors for Southern California spotted owls
<p><strong>Aim:</strong> Land use change, climate change, and shifts to disturbance regimes make successful wildlife management challenging, particularly when ongoing urbanization constrains habitat and movement. Preserving and maintaining landscape connectivity is a potential strategy to support wildlife responding to these stressors. Using a novel model framework, we determined the population-level benefit of a set of identified potential corridors for spotted owl population viability.</p> <p><strong>Location:</strong> Southern California, United States.</p> <p><strong>Methods:</strong> Combining habitat suitability and dynamic metapopulation models, we compared the benefit of corridors to the Southern California spotted owl population, measured as the increase in the expected minimum abundance, both now and under a future climate. Our approach considered key corridor characteristics important to conservation decisions, namely, corridor irreplaceability and local population network benefit.</p> <p><strong>Results:</strong> We identified two corridors likely to increase Southern California spotted owl expected minimum abundance under current climate conditions. At the regional scale, of the 16 corridors evaluated, one corridor was irreplaceable (i.e. no other corridors in the network could provide a similar increase in abundance when the irreplaceable corridor was removed) and one corridor was identified as redundant (i.e. remaining corridors in the network can provide some of the increases in abundance offered by the removed corridor). Both putative corridors connected two large, populous, and similarly-sized patches. Additionally, we identified two more corridors at the local scale. We found that, under climate change, population declines may limit the benefit of connectivity for a range-restricted species like the spotted owl.</p> <p><strong>Main Conclusions:</strong> Our analytical approach highlights important criteria for corridor identification and prioritization, namely, irreplaceability versus redundancy, local versus regional benefit, and corridor impact in a changing landscape. With the capability of incorporating estimated functional connectivity into population dynamics, our modeling framework advances connectivity decision making for other species of conservation concern and archetypal taxa within ecological communities.</p>
Electrical connections of sling load platform
<p>The image describes the electrical connections of all components of the sling load platform. </p>
Lagrangian drifter output in the Southeast Indian Ocean using the Connectivity Modelling System output forced with TROPAC01
<p>This dataset contains Lagrangian drifter trajectories from the Connectivity Modelling System (CMS) in the Southeast Indian Ocean. CMS was forced with ocean velocity fields from TROPAC01 and this experiment was focused on sources of the Leeuwin Current. TROPAC01 is a high-resolution ocean general circulation model, developed by the European Drakkar cooperation [Barnier et al., 2007] it is based on the NEMO [v3.2 Madec, 2008] code. Specifically, it is a 1/10 horizontal resolution model of the tropical Indo- Pacific region (spanning the area from 73°E - 63°W to 49°S - 31°N), nested within a half-degree global ocean/ sea-ice model. More information on the model configuration used for this experiment can be found in [van Sebille et al., 2014]. Using the velocity fields from TROPAC01 we then use the Connectivity Modelling System (CMS) v1.1 [Paris et al., 2013] to integrate the virtual particles in three-dimensional time-evolving flow.</p> <p>Version v1.0 of this dataset includes ascii raw model output of CMS trajectories and the forcing file (seed file) that enables a user to calculate absolute time of a particle's location. Variables are: particle_number, time, longitude, latitude, depth, exit_code.</p> <p>These experiments were executed by Christopher Bull of the ARC Centre of Excellence for Climate System Science (ARCCSS) research program "Mechanisms and attribution of past and future ocean circulation change", as part of Christopher's PhD candidature.</p> <p> </p> <p>References:</p> <p> Code and documentation for the CMS is available at:</p> <p> https://github.com/beatrixparis/connectivity-modeling-system</p> <p>Claire B. Paris, Judith Helgers, Erik van Sebille, Ashwanth Srinivasan, 2013.<br> Connectivity Modeling System: A probabilistic modeling tool for the multi-scale tracking of biotic and abiotic variability in the ocean,<br> Environmental Modelling & Software, Volume 42, 2013, Pages 47-54, ISSN 1364-8152, https://doi.org/10.1016/j.envsoft.2012.12.006.</p> <p>van Sebille, E., Sprintall, J., Schwarzkopf, F. U., Gupta, A. S., Santoso, A., England, M. H., Biastoch, A., and Böning, C. W. (2014), Pacific-to-Indian Ocean connectivity: Tasman leakage, Indonesian Throughflow, and the role of ENSO, <em>J. Geophys. Res. Oceans</em>, 119, 1365– 1382, doi:<a href="https://doi.org/10.1002/2013JC009525">10.1002/2013JC009525</a>.</p>
IsoAnalyst: A System-Wide Stable Isotopic Labeling Aproach for Connecting Natural Products to Their Cognate Biosynthetic Gene Clusters
<p>Processed mass spectrometry data input used to develop and validate the IsoAnalyst program and the output from these analyses. The S_erythraea folder contains all MS input and output data for <em>Saccharopolyspora erythraea</em>. The Micromonospora_RL09050HVFA folder contains MS input and output data for <em>Micromonopora sp.</em> RL09050HVFA, as well as the full antiSMASH output for the <em>Micromonopora sp.</em> RL09050HVFA genome.</p> <p>Version 2 contains updated IsoAnalyst results for both organisms. </p>
Connectivity and succession of open structures as a key to sustaining light-demanding biodiversity in deciduous forests
<p>1. European forests are facing a rapid decline of light-demanding biota. This has prompted active interventions to re-establish and maintain partial habitat openness in protected areas. Managers of protected areas, however, need substantially more scientific evidence to support their decisions on where, when, and how to intervene.</p> <p>2. We investigated the importance of spatial continuity of open forest habitats in different years of succession, using six pairs of experimental clearings established in the formerly open, oak-dominated forests of the Podyji National Park (Czech Republic). In each pair, one clearing was connected to the forest edge, while the other was isolated in closed forest. We sampled butterflies (74 spp.), moths (435 spp.), saproxylic beetles (465 spp.), and vascular plants (567 spp.) on the 12 clearings during the first five years of succession. We then compared species richness, abundance, and composition of the four taxa between the two clearing types and along the succession.</p> <p>3. All studied insect groups were substantially more species-rich and more abundant in connected than in isolated clearings. Species composition of plants, moths, and butterflies differed between the clearing types.</p> <p>4. The number of species of all studied taxa generally increased from the first to the second or third year after cutting; species composition of all taxa differed among years. This suggests rapid changes in habitat quality and thus limited time for colonisation by light-demanding organisms.</p> <p>5. <i>Synthesis and applications</i>: Our results offer an evidence that spatial connectivity and rapid temporal dynamics are important habitat features for light-demanding insects. Attempts to create or restore habitats for light-demanding forest biota should take into account that: (i) Insects benefit from direct connection of new open patches to open habitats or flight corridors such as forest edges. (ii) Considering plants, the optimal solution is to connect newly created open forest habitats to existing habitats with established biota of high conservation value. (iii) Interventions should be carried out within short time intervals, i.e. within years rather than decades. (iv) A fine mosaic of interconnected<span>, open woodland patches in various successional stages is more beneficial than a single large patch with a single successional stage.</span></p>
Size, connectivity and edge effects of stream habitats explain spatiotemporal variation in brown trout (Salmo trutta) density
<p>Ecological theory postulates that size and isolation of habitat patches impact the colonization/extinction dynamics that determine community species richness and population persistence. Given the key role of lotic habitats for life history completion in rheophilic fish, evaluating how the distribution of swift-flowing habitats affects the abundance and dynamics of subpopulations is essential. Using extensive electrofishing data, we show that merging island biogeography with meta-population theory, where lotic habitats are considered as islands in a lentic matrix, can explain spatiotemporal variation in occurrence and density of brown trout (Salmo trutta). Subpopulations in larger and less isolated habitat patches had higher average densities and smaller between-year density fluctuations. Larger habitat patches also had lower predicted risk of excessive zero catches, indicative of lower extinction risk. Trout density further increased with distance from the edge of adjacent lentic habitats with predator (Esox lucius) presence, suggesting that edge- and matrix-related mortality contributes to the observed patterns. These results can help reduce the negative impacts that habitat loss and fragmentation have on biodiversity, by stressing the importance of suitable habitat size and connectivity, and aid in prioritization of habitat restoration, dam removal and reintroduction programs aimed at vitalizing declining and locally extinct riverine fish populations.</p>
SEED-G: Simulated EEG Data Generator for testing connectivity algorithms
<p>SEED-G toolbox was developed in MATLAB environment (tested on version R2017a and R2020b) and released on the GitHub page <a href="https://github.com/aanzolin/SEED-G-toolbox">https://github.com/aanzolin/SEED-G-toolbox</a> (accessed date 12 April 2021). It is organized in the following subfolders:</p> <ul> <li> <p><strong>main</strong>: it is the core of the toolbox and contains all the functions for the generation of EEG data according to a predefined ground-truth network.</p> </li> <li> <p><strong>dependencies</strong>: containing parts of other toolboxes required to successfully run SEED-G functions. The links to the full packages can be found in the documentation on the GitHub page. The additional packages are Brain Connectivity Toolbox (BCT) [<a href="https://www.mdpi.com/1424-8220/21/11/3632/htm#B40-sensors-21-03632">40</a>], FieldTrip [<a href="https://www.mdpi.com/1424-8220/21/11/3632/htm#B41-sensors-21-03632">41</a>], Multivariate Granger Causality Toolbox (MVGC) [<a href="https://www.mdpi.com/1424-8220/21/11/3632/htm#B24-sensors-21-03632">24</a>], and AsympPDC Package (PDC_AsympSt) [<a href="https://www.mdpi.com/1424-8220/21/11/3632/htm#B42-sensors-21-03632">42</a>,<a href="https://www.mdpi.com/1424-8220/21/11/3632/htm#B43-sensors-21-03632">43</a>]. Additionally, the implemented forward model is solved according to the New York Head (NYH) model, whose parameters are contained in the structure available on the ICBM-NY platform [<a href="https://www.mdpi.com/1424-8220/21/11/3632/htm#B28-sensors-21-03632">28</a>].</p> </li> <li> <p><strong>real data</strong>: containing real EEG data acquired from one healthy subject during resting state at scalp level (‘EEG_real_sources.mat’) and its reconstructed version in source domain (‘sLOR_cortical_sources.mat’). These signals can be employed to extract the AR components to be included in the model to generate data with the same spectral properties of the real ones.</p> </li> <li> <p><strong>demo</strong>: containing examples of MATLAB scripts to be used to learn the different functionalities of the toolbox. For example, the code ‘run_generation.m’ allows to specify the directory containing the real sources and each specific input of the function ‘simulatedData_generation.m’.</p> </li> <li> <p><strong>auxiliary functions</strong>: containing either original MATLAB functions or modified version of free available functions.</p> </li> </ul>
Brain functional connectivity in chronic tic disorders and Gilles de la Tourette syndrome
<p>The pathophysiology of chronic tic disorder (cTD) and Gilles de la Tourette syndrome (GTS) is characterized by the dysfunction of both motor and non - motor cortico - striatal - thalamo - cortical (CSTC) circuitries, which leads to tic release and comorbids. A role of fronto - parietal network (FPN) connectivity breakdown has been postulated for tic pathogenesis, given that the FPN entertain connections with limbic, paralimbic, and CSTC networks. Our study was aimed at characterizing the FPN functional connectivity in cTD and GTS in order to assess the role of its deterioration in tic severity and the degree of comorbids. We recorded scalp EEG during resting state in patients with cTD and GTS. The eLORETA current source densities were analyzed, and the lagged phase synchronization (LPS) was calculated to estimate nonlinear functional connectivity between cortical areas. We found that the FPN functional connectivity in delta band was more detrimental in more severe GTS patients. Also, the sensorimotor functional connectivity in beta2 band was stronger in more severe cTD and GTS patients. FPN functional connectivity deterioration correlated with comorbids presence and severity in patients with GTS. Our data suggest that a FPN disconnection may contribute to the motoric symptomatology and comorbid severity in GTS, whereas sensorimotor disconnection may contribute to tic severity in cTD and GTS. Although preliminary, our study points out a differently disturbed brain connectivity between patients with cTD and GTS. This may serve as diagnostic marker and potentially interesting base to develop pharmacological and noninvasive neuromodulation trials aimed at reducing tic symptomatology.</p>
How hydrological connectivity regulates the plant recovery process in salt marshes
<p>1. Designing effective restoration strategies is a priority in recovering salt marsh plants. As a main driver underpinning the success of plant recovery process, hydrological connectivity can regulate life history process-based restoration strategies, but the relations are not clear.</p> <p>2. Plant recovering needs to go through a whole life history process, from seed to adult. Common restoration strategies are seed addition (SA) or seedling transplantation (ST), which start from seed germination and seedling growth stage. Besides these two strategies, another strategy starting from seed retention stage, microtopographic adjustment (MA), were designed to study the relationship with hydrological connectivity. And a framework was construct to assess a gradient of hydrological connectivity between marsh plain and sea and conducted several field experiments to test their relationships.</p> <p>3. The composite measurement of hydrological connectivity with five geomorphic variables can well represent the variation of environmental factors. Soil moisture, inundation frequency and sediment deposition were positive correlated, while soil salinity and hardness were negative correlated with hydrological connectivity.</p> <p>4. The success of different restoration strategies varied with hydrological connectivity. MA showed a monotone decreasing trend, while SA and ST showed unimodal trend with the increasing of hydrological connectivity. The important is, each strategy occupies a non-overlapping optimum range along hydrological connectivity gradient, they are low hydrological connectivity for MA (0 – 0.28), middle hydrological connectivity for SA (0.28 – 0.55) and high hydrological connectivity for ST (0.55 – 1).</p> <p>5. Synthesis and applications. Our findings expand the quantification of the hydrological environment beyond elevation or distance or other single index to include a range of elements of hydrological connectivity, and illustrate the underlying mechanisms of hydrological connectivity regulating restoration strategies based on different life stages. The results not only provide a reliable framework to assess hydrological connectivity, but also the guidance to select optimum restoration strategy under different hydrological connectivities, or to regulate the hydrological connectivity variables (topography on marsh plain and morphology of tidal creeks) to relief stresses. These findings will benefit ecological restoration and coastal management a lot.</p>
Going against the flow: barriers to gene flow impact patterns of connectivity in cryptic coral reef gobies throughout the western Atlantic
<p class="CxSpFirst"><b>Aim</b>: Complex oceanographic features have historically caused difficulty in understanding gene flow in marine taxa. Here, we evaluate the impact of potential phylogeographic barriers to gene flow and assess demography and evolutionary history of a coral reef goby species complex. Specifically, we test how the Amazon River outflow and ocean currents impact gene flow.</p> <p class="CxSpMiddle"><b>Location</b>: Western Atlantic.</p> <p class="CxSpMiddle"><b>Taxon</b>: The bridled goby (<i>Coryphopterus glaucofraenum</i>) and sand-canyon goby (<i>C. venezuelae</i>) species complex.</p> <p class="CxSpMiddle"><b>Methods</b>: We used mitochondrial DNA and 2401 genomic SNPs to investigate evolutionary history and test hypotheses of how major barriers impact species-level differentiation. We used clustering algorithms and pairwise <i>F</i><sub>ST</sub> to assess population differentiation caused by minor barriers within and among regions. Finally, we tested alternate hypotheses of demographic history via coalescent simulations to determine the most plausible spread across the Western Atlantic.</p> <p class="CxSpMiddle"><b>Results</b>: We found two unique clades of <i>C. glaucofraenum</i> along the Brazilian coast and Atol das Rocas (AR) that are more closely related to <i>C. venzuelae</i>. Further genetic structure within the Caribbean and separately along the Brazilian coast led to at least two distinct populations in each location. Coalescent simulations indicated that an ancestral population of <i>C. venezuelae</i> split from <i>C. glaucofraenum</i> in the Caribbean, dispersed to Brazil, then spread to AR.</p> <p class="CxSpMiddle"><b>Main Conclusions</b>: Species-level genetic differentiation has resulted from the Amazon River outflow and isolation of AR. Population differentiation within the Caribbean matched previous studies indicating an east-west pattern of divergence. Brazilian population differentiation was impacted by the cold-water upwelling at Cabo Frio. Overall, this research highlights how barriers to gene flow impact speciation and genetic structure within western Atlantic gobies and provides insight into the role oceanographic features have in the speciation process of fishes.</p>
High-speed videos for the paper "Upward bipolar lightning flashes originated from the connection of recoil leaders with intracloud lightning"
<p>This page contains high-speed video files as .cine files, that can be watched frame by frame to reproduce the analysis done in the paper titled "Upward bipolar lightning flashes originated from the connection of recoil leaders with intracloud lightning", submitted for publication in Geophysical Research Letters.</p> <p><em>Instructions to watch the videos</em>: <strong>UP 44.cine </strong>and<strong> UP 76.cine:</strong></p> <p>Download and use the software Phantom Camera Control (PCC) available at:</p> <p><a href="https://www.phantomhighspeed.com/resourcesandsupport/phantomresources/pccsoftware">https://www.phantomhighspeed.com/resourcesandsupport/phantomresources/pccsoftware</a></p> <p>The Phantom Camera Control (PCC) software is compatible with Windows 7 Pro and Windows 8.1 and Windows 10, for both 32 and 64-bit operating systems.</p>
Helminth-associated changes in host immune phenotype connect top-down and bottom-up interactions during co-infection
<p>Within-host parasite interactions can be mediated by the host and changes in host phenotypes often serve as indicators of the presence or intensity of parasite interactions.</p> <p>Parasites like helminths induce a range of physiological, morphological, and immunological changes in hosts that can drive bottom-up (resource-mediated) or top-down (immune-mediated) interactions with co-infecting parasites. Although top-down and bottom-up interactions are typically studied in isolation, the diverse phenotypic changes induced by parasite infection may serve as a useful tool for understanding if, and when, these processes act in concert.</p> <p>Using an anthelmintic treatment study of African buffalo (Syncerus caffer), we tracked changes in host immunological and morphological phenotypes during helminth-coccidia co-infection to investigate their role in driving independent and combinatorial bottom-up and top-down parasite interactions. We also examined repercussions for host fitness.</p> <p>Clearance of a blood-sucking helminth, Haemonchus, from the host gastrointestinal tract induced a systemic Th2 immune phenotype, while clearance of a tissue-feeding helminth, Cooperia, induced a systemic Th1 phenotype. Furthermore, the Haemonchus-associated systemic Th2 immune phenotype drove simultaneous top-down and bottom-up effects that increased coccidia shedding by changing the immunological and morphological landscapes of the intestine.</p> <p>Higher coccidia shedding was associated with lower host body condition, a lower chance of pregnancy, and older age at first pregnancy, suggesting that coccidia infection imposed significant condition and reproductive costs on the host.</p> <p>Our findings suggest that top-down and bottom-up interactions may commonly co-occur and that tracking key host phenotypes that change in response to infection can help uncover complex pathways by which parasites interact.</p>
Biophysical larval dispersal models of observed bonefish (Albula vulpes) spawning events in Abaco, The Bahamas: An assessment of population connectivity and ocean dynamics
<p>Biophysical models are a powerful tool for assessing population connectivity of marine organisms that broadcast spawn. <em>Albula</em> <em>vulpes</em> is a species of bonefish that is an economically and culturally important sportfish found throughout the Caribbean and that exhibits genetic connectivity among geographically distant populations. We created ontogenetically relevant biophysical models for bonefish larval dispersal based upon multiple observed spawning events in Abaco, The Bahamas in 2013, 2018, and 2019. Biological parameterizations were informed through active acoustic telemetry, CTD casts, captive larval rearing, and field collections of related albulids and anguillids. Ocean conditions were derived from the Regional Navy Coastal Ocean Model American Seas dataset. Each spawning event was simulated 100 times using the program Ichthyop. Ten thousand particles were released at observed and putative spawning locations and were allowed to disperse for the full 71-day pelagic larval duration for <em>A</em>. <em>vulpes</em>. Settlement densities in defined settlement zones were assessed along with interactions with oceanographic features. The prevailing Northern dispersal paradigm exhibited strong connectivity with Grand Bahama, the Berry Islands, Andros, and self-recruitment to lower and upper Abaco. Ephemeral gyres and flow direction within Northwest and Northeast Providence Channels were shown to have important roles in larval retention to the Bahamian Archipelago. Larval development environments for larvae settling upon different islands showed few differences and dispersal was closely associated with the thermocline. Settlement patterns informed the suggestion for expansion of conservation parks in Grand Bahama, Abaco, and Andros, and the creation of a park in Eleuthera and the Berry Islands to protect fisheries. Further observation of spawning events and the creation of biophysical models will help to maximize protection for bonefish spawning locations and nursery habitat, and may help to predict year-class strength for bonefish stocks throughout the Greater Caribbean.</p>
Country‐wide genetic monitoring over 21 years reveals lag in genetic recovery despite spatial connectivity in an expanding carnivore (Eurasian otter, Lutra lutra) population
<p>Numerous terrestrial mammal species have experienced extensive population declines during past centuries, due largely to anthropogenic pressures. For some species, including the Eurasian otter (<em>Lutra lutra</em>), environmental and legal protection has more recently led to population growth and recolonisation of parts of their historic ranges. While heralded as conservation successes, only a few such recoveries have been examined from a genetic perspective, i.e. whether genetic variability and connectivity have been restored. We here use large-scale and long-term genetic monitoring data from UK otters, whose population underwent a well-documented population decline between the 1950s to 1970s, to explore the dynamics of a population re-expansion over a 21-year period. We genotyped otters from across Wales and England at five time points between 1994 and 2014 using 15 microsatellite loci. We used this combination of long-term temporal and large-scale spatial sampling to evaluate 3 hypotheses relating to genetic recovery; that (i) gene flow between sub-populations would increase over time, (ii) genetic diversity of previously isolated populations would increase, and that (iii) genetic structuring would weaken over time. Although we found an increase in inter-regional gene flow and admixture levels among subpopulations, there was no significant temporal change in either heterozygosity or allelic richness. Genetic structuring among the main sub-populations hence remained strong and showed a clear historical continuity. These findings highlight an underappreciated aspect of population recovery of endangered species, that genetic recovery may often lag behind the processes of spatial and demographic recovery. In other words, the restoration of physical connectivity of populations does not necessarily lead to genetic connectivity. Our findings emphasise the need for genetic data as an integral part of conservation monitoring, to enable the potential vulnerability of populations to be evaluated.</p>
Examining local and regional ecological connectivity throughout North America
<p>Output from 12 Omniscape model runs using three resistance surfaces and four moving window sizes (Belote et al. 2022, Landscape Ecology). Resistance surfaces were created through alternative transformations (varying c) of the 2015 estimates of human modification from Theobald et al. (2020). The radius of the circular moving windows were 30-km, 150-km, 300-km, or 700-km. Descriptions of directories are in the csv file called “folder descriptions.” There are three outputs within each of the 12 folders: cum_currmap, flow_potential, and normalized_cum_currmap. These are, respectively:</p> <p>1. Cumulative current flow: the total current flowing through the landscape – the result of the Omniscape algorithm described above.<br> 2. Flow potential (optional): current flow under "null" resistance conditions. Flow potential demonstrates what movement/flow would look like when movement is unconstrained by resistance and barriers. Flow potential is calculated exactly as cumulative current flow is, but with resistance set to 1 for the entire landscape.<br> 3. Normalized current flow (optional): calculated as cumulative current flow divided by flow potential. Normalized current helps identify areas where current is impeded or channelized (e.g. more or less current than expected under null resistance conditions). High values mean current flow is channelized, low values mean current is impeded.</p> <p>Descriptions of outputs above are quoted directly from https://docs.juliahub.com/Omniscape/uqaJf/0.4.3/.</p> <p><br> References:</p> <p>Belote, RT, Barnett K, Zeller K, Brennan A, and Gage J (2022) Examining local and regional ecological connectivity throughout North America. Landscape Ecology</p> <p>Theobald DM, Kennedy C, Chen B, et al (2020) Earth transformed: Detailed mapping of global human modification from 1990 to 2017. Earth System Science Data 12:1953–1972. https://doi.org/10.5194/essd-12-1953-2020</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.