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Figure 5 from: El-Sherbiny MM, Al-Harbi MA (2020) New morphological and molecular data on the little-known pontellid Calanopia media Gurney, 1927 (Crustacea, Copepoda, Calanoida) from the Red Sea, with notes on its diel vertical distribution. ZooKeys 922: 13-33. https://doi.org/10.3897/zookeys.922.46977
Figure 5 Calanopia media male from the Red Sea A habitus, dorsal view B rostrum, lateral view C enlarged rostral filaments (rudimentary rostral notch indicated by arrow) D abdomen, ventral view (knob indicated by arrow) E right antennule F enlarged segments XVIII–XXIII G leg 5, posterior view. Scale bars in mm.
Figure 1 from: El-Sherbiny MM, Al-Harbi MA (2020) New morphological and molecular data on the little-known pontellid Calanopia media Gurney, 1927 (Crustacea, Copepoda, Calanoida) from the Red Sea, with notes on its diel vertical distribution. ZooKeys 922: 13-33. https://doi.org/10.3897/zookeys.922.46977
Figure 1 Calanopia media female from the Red Sea A habitus, dorsal view B habitus, lateral view C rostrum, lateral view (rudimentary rostral notch indicated by arrow) D abdomen, ventral view E abdomen, dorsal view F–G antennule H antenna. Scale bars in mm.
Figure 4 from: El-Sherbiny MM, Al-Harbi MA (2020) New morphological and molecular data on the little-known pontellid Calanopia media Gurney, 1927 (Crustacea, Copepoda, Calanoida) from the Red Sea, with notes on its diel vertical distribution. ZooKeys 922: 13-33. https://doi.org/10.3897/zookeys.922.46977
Figure 4 Calanopia media female from the Red Sea A leg 1, anterior view B leg 2, anterior view C leg 3, anterior view D leg 4, posterior view E leg 5, posterior view. Scale bars in mm.
Figure 2 from: El-Sherbiny MM, Al-Harbi MA (2020) New morphological and molecular data on the little-known pontellid Calanopia media Gurney, 1927 (Crustacea, Copepoda, Calanoida) from the Red Sea, with notes on its diel vertical distribution. ZooKeys 922: 13-33. https://doi.org/10.3897/zookeys.922.46977
Figure 2 SEM micrographs of Calanopia media female from the Red Sea A rostrum, ventral view B abdomen, dorsal view C abdomen, ventral view D leg 5, posterior view.
The vertical distribution of soil microbial biomass carbon: A global dataset
<p>Soil microbial biomass carbon (SMBC) is important in regulating soil organic carbon (SOC) dynamics along soil profiles by mediating the decomposition and formation of SOC. The dataset is about the vertical distributions of SOC, SMBC, and soil microbial quotient (SMQ = SMBC/SOC) and their relations to environmental factors across five continents. Data are collected from literature, with a total of 289 soil profiles and 1040 observations in different soil layers compiled. The associated environment data were also collectd including climate, ecosystem types, and edaphic factors. More specifically, we develop this dataset by compiling data from 59 papers published in the Web of Sciene and the China National Knowledge Infrastructure from the year of 1970 to 2019. All the data included in this dataset meet two creteria: 1) there are at least three soil layers along a soil profile, and 2) soil MBC is measured using the fumigation extraction method. The data were obtained from tables and texts from literature directly, and the data in figures were extracted using GetData Graph digitizer software version 2.25. When climate and soil properties are not available from publications, we obtainted the data from the World Weather Information Service (https://worldweather.wmo.int/en/home.html) and SoilGrids at a spatial resolution of 250 meters (version 0.5.3, https://soilgrids.org).</p> <p>The units of all the variables are converted to the standard international units or commonly used ones and the values are converted correspondingly. For example, the value of soil organic matter (SOM) is converted to SOC using the equation (SOC = SOM × 0.58). Soil depth is calculated as the arithmetic mean value of the upper and lower boundaries for a given soil layer.</p> <p>This dataset can be used in predicting global SOC change along soil profiles using the multi-layer soil C models. It can also be used to analyse how soil microbial biomass changes with plant roots as well as the composition, structure, and functions of soil microbial communities along soil profiles at large spatial scales. This dataset offers opportunities to improve our prediction of SOC dynamics under global changes and to advance our understanding of the environmental controls.</p>
GInSAR vertical surface displacements over the San Joaquin Valley, CA spanning April 2015 to October 2017
<p>A time series of vertical surface displacements over the San Joaquin Valley (SJV) spanning April 2015 to October 2017.</p> <p>Base Data: European Space Agency’s Sentinel-1A/B descending track 144; National Science Foundation Plate Boundary Observatory Global Positioning System (GPS) network; Southern California Earthquake Center’s Community Geodetic Model</p> <p>Time: 2015.04.01 – 2017.10.23, 51 acquisition times, 263 interferograms</p> <p>Processors/Software: GMTSAR, MATLAB</p> <p>Interferogram construction and unwrapping was performed in GMTSAR. GPS correction, time series inversion, and vertical projection was performed in MATLAB.</p> <p> </p> <p>This dataset was constructed following similar methods outlined in Neely et al., (2020).</p> <p>Neely, Wesley R., Adrian A. Borsa, and Francesca Silverii. “GInSAR: A CGPS Correction for Enhanced InSAR Time Series.” <em>IEEE Transactions on Geoscience and Remote Sensing</em> 58, no. 1 (January 2020): 136–46. <a href="https://doi.org/10.1109/TGRS.2019.2934118">https://doi.org/10.1109/TGRS.2019.2934118</a>.</p> <p> </p> <p>This dataset is provided as a “.mat” compatible with MATLAB. Contents include:</p> <p>TS – 3110x2940x51 matrix of the vertical surface displacements (mm) relative to April 1, 2015</p> <p>X – 3110x2940 matrix of the pixel longitudes (decimal degrees)</p> <p>Y – 3110x2940 matrix of the pixel latitudes (decimal degrees)</p> <p>rate – 3110x2940 matrix of the estimated vertical velocity (mm/yr) over April 2015 to October 2017</p> <p>time – 51x1 array of the dates for each acquisition in MATLAB data. Provided as integer day where time(1) = 736055 à April 1, 2015</p> <p> </p> <p>Example plotting in MATLAB:</p> <p>% plot the rate map</p> <p>figure</p> <p>pcolor(X,Y,rate)</p> <p>shading flat</p> <p> </p> <p>% plot the 25<sup>th</sup> time slice map of the displacement time series</p> <p>figure</p> <p>pcolor(X,Y,squeeze(TS(:,:,25))</p> <p>shading flat</p> <p> </p> <p>% plot the time series at location X(1500,1500) and Y(1500,1500)</p> <p>figure</p> <p>plot(time,squeeze(TS(1500,1500,:)))</p>
Figure 2 in Assessing high compositional differences of beetle assemblages across vertical woodland strata in the New Forest, Hampshire, England
Figure 2. Species accumulation curves created by rarefaction for each sampling method. Vertical bars = 95% confidence limits around the species richness estimate.
Figure 6 in Inter-oceanic comparison of planktonic copepod ecology (vertical distribution, abundance, community structure, population structure and body size) between the Okhotsk Sea and Oyashio region in autumn
Figure 6. Vertical distribution of the prosome length ratios of the copepods (PLOkhotsk: PLOyashio) (left) and temperature anomalies (°C: TOkhotsk – TOyashio) (right) between the Okhotsk Sea (St. OK24) and Oyashio region (St. 19) evaluated by IONESS from October to November 1996. The vertical distribution of each copepod is calculated by daily duplicate samples in the Okhotsk Sea (symbols and bars indicate the means and standard deviations of D50%, respectively). For inter-oceanic comparison, the dashed lines in each panel indicate that the positions of values of both regions are equal.
Figure 1 in Inter-oceanic comparison of planktonic copepod ecology (vertical distribution, abundance, community structure, population structure and body size) between the Okhotsk Sea and Oyashio region in autumn
Figure 1. Location of the sampling stations in the Okhotsk Sea and Oyashio region from September to December in 1996–1998. ○: closing net sampling, ●: closing net and IONESS sampling.
Data on Vertically Transmitted Infections (VTIs) and the Spread of HIV/AIDS in Akwa Ibom State Nigeria.
<p>This data is a monthly data on the HIV Status of newborns assessed through Vertical Transmission methods. The data is collected from the Ministry of Health, Akwa Ibom state for year 2018.</p>
Matlab Algorithm for Systematic Vertical Separation Measurements of Tectonic Fault Scarps
<p>We have studied the topography along the Lost River Fault in Idaho (USA) and in particular the rupture zone generated by the strong 1983 Borah Peak earthquake (M<sub>w</sub> 6.9) almost 40 years after its occurrence. Our first reason for acquiring these data was to systematically measure vertical separation (VS) along the fault.<br> To do this we have developed and implemented a scarp analysis algorithm in MATLAB (www.mathworks.com) which enables users to measure the vertical separation from a topographic profile. The code constructs a topographic profile along the preferred trend (generally perpendicular to the fault trace) and projects the best-fit lines to each of the hanging wall and footwall flat to the fault location. The vector difference between the intersection of these lines with a vertical plane at the fault location is the vertical separation. Please see the code guide for additional detail. </p>
Cold-water coral assemblages on vertical walls: distribution patterns from the Northeast Atlantic
<p><b>Aim</b>: In this study, we assess patterns of cold-water coral assemblages observed on deep-sea vertical walls. Similar to their shallow-water counterparts, vertical and overhanging walls in the deep sea can host highly diverse communities, but because of their geometry, these habitats are generally overlooked and remain poorly known. These vertical habitats are however of particular interest, because they can protect vulnerable coral ecosystems from trawling activities. As such, it is important to understand their ecology and assess their global importance. </p> <p><b>Location</b>: Vertical walls on complex geomorphic features, in particular walls of the Rockall Bank Slope Failure Escarpment, Whittard and Explorer Canyons, Northeast Atlantic.</p> <p><b>Methods</b>: Video analysis of ROV transects carried out at five sites is used to investigate differences in species composition and diversity across walls and to compare those to nearby cold-water coral sites on flat terrain. A high-resolution photogrammetric reconstruction is further employed to examine whether wall complexity plays a role in promoting niche differentiation at very fine spatial scales. </p> <p><b>Results</b>: The investigated walls showed differences in species assemblage both across walls as well as in comparison to flat sites, with the fine-scale heterogeneity engendered by walls allowing niche differentiation between closely-related taxa. </p> <p><b>Main Conclusions</b>: Vertical walls represent an important cold-water coral habitat with differences in species composition across walls within a region, illustrating their role in driving diversity patterns. Based on publicly available bathymetric datasets and a catalogue of broad-scale terrain features, globally over 8,000 features are likely to have vertical walls and cold-water corals, which highlights the need to consider deep-sea vertical habitats in current conservation efforts.</p>
Data from: Depth and vertical hydrodynamics constrain the size–structure of a lowland streambed community
Abundance-body mass (N–M) relationships are prominent macroecological patterns and provide an integrated measurement of the structure and energy flow through natural communities. However, little is known about how N-M relationships are constrained by local environmental conditions. Here we quantify how sediment depth and direction of surface–groundwater exchange (vertical hydrodynamics), two major drivers of the streambed ecology, determine N-M scaling in a sandy lowland, European stream. Streambed assemblages included flagellates, ciliates, meiofauna and macroinvertebrates, and spanned five orders of magnitude in body mass. We detected a significant interaction of body mass with depth and vertical hydrodynamics with a sharp reduction in N–M slopes in the hyporheic zone and under upwelling conditions. These results revealed that streambed assemblages become more size–structured as environmental constraints increase with direct implications for the metabolic capacity and functioning of the system.
Data from: Vertically transmitted symbiont reduces host fitness along temperature gradient
Parasites with exclusive vertical transmission from host parent to offspring are an evolutionary puzzle. With parasite fitness entirely linked to host reproduction, any fitness cost for infected hosts risks their selective elimination. Environmental conditions likely influence parasite impact, and thereby the success of purely vertical transmission strategies. We tested for temperature-dependent virulence of Caedibacter taeniospiralis, a vertically transmitted bacterial symbiont of the protozoan Paramecium tetraurelia. We compared growth of infected and cured host populations at five temperatures (16-32°C). Infection reduced host density at all temperatures, with a peak at 28°C. These patterns were largely consistent across five infected Paramecium strains. Similar to Wolbachia symbionts, C. taeniospiralis may compensate fitness costs by conferring to the host a 'killer trait', targeting uninfected competitors. Considerable loss of infection at 32°C suggests that killer efficacy is not universal and that limited heat tolerance restricts the conditions for persistence of C. taeniospiralis.
Data from: Vertical partitioning between sister species of Rhizopogon fungi on mesic and xeric sites in an interior Douglas-fir forest
Understanding ectomycorrhizal fungal (EMF) community structure is limited by a lack of taxonomic resolution and autecological information. Rhizopogon vesiculosus and R. vinicolor (Basidiomycota) are morphologically and genetically related species. They are dominant members of interior Douglas-fir (Pseudotsuga menziesii var. glauca) EMF communities, but mechanisms leading to their coexistence are unknown. We investigated the microsite associations and foraging strategy of individual R. vesiculosus and R. vinicolor genets. Mycelia spatial patterns, pervasiveness and root colonization patterns of fungal genets were compared between Rhizopogon species and between xeric and mesic soil moisture regimes. Rhizopogon spp. mycelia were systematically excavated from the soil and identified using microsatellite DNA markers. Rhizopogon vesiculosus mycelia occurred at greater depth, were more spatially pervasive, and colonized more tree roots than R. vinicolor mycelia. Both species were frequently encountered in organic layers and between the interface of organic and mineral horizons. They were particularly abundant within microsites associated with soil moisture retention. The occurrence of R. vesiculosus shifted in the presence of R. vinicolor towards mineral soil horizons, where R. vinicolor was mostly absent. This suggests that competition and foraging strategy may contribute towards the vertical partitioning observed between these species. R. vesiculosus and R. vinicolor mycelia systems occurred at greater mean depths and were more pervasive in mesic plots compared to xeric plots. The spatial continuity and number of trees colonized by genets of each species did not significantly differ between soil moisture regimes.
Data from: Improving short-term information spreading efficiency in scale-free networks by specifying top large-degree vertices as the initial spreaders.
The positive function of initially influential vertices could be exploited to improve spreading efficiency for short-term spreading in scale-free networks. However, the selection of initial spreaders depends on the specific scenes. The selection of initial spreaders needs to offer low complexity and low power consumption for short-term spreading. In this paper, we propose a selection strategy for efficiently spreading information by specifying a set of top large-degree vertices as the initially informed vertices. The essential idea behind the proposed selection strategy is to exploit the significant diffusion of the top large-degree vertices at the beginning of spreading. To evaluate the positive impact of initially influential vertices, we first build an information spreading model in the Barabási-Albert (BA) scale-free network; next, we design 54 comparative Monte Carlo experiments based on a benchmark strategy and the proposed selection strategy in different BA scale-free network structures. Experimental results indicate that (1) the proposed selection strategy significantly can improve spreading efficiency in the short-term spreading and (2) both network size and number of hubs have a strong impact on spreading efficiency, while the number of initially informed vertices has a weak impact. The proposed selection strategy can be employed in short-term spreading, such as sending warnings or crisis information spreading or information spreading in emergency training or realistic emergency scenes.
Data from: 5α-cyprinol sulfate, a bile salt from fish, induces diel vertical migration in Daphnia
Prey are under selection to minimize predation losses. In aquatic environments many prey use chemical cues released by predators, which initiate predator-avoidance. A prominent example of behavioural predator-avoidance constitutes diel vertical migration (DVM) in the freshwater microcrustacean Daphnia spp., which is induced by chemical cues (kairomones) released by planktivorous fish. In a bioassay-guided approach using liquid chromatography and mass spectrometry we isolated the kairomone from fish incubation water and identified it as 5α-cyprinol sulfate inducing DVM in Daphnia at picomolar concentrations. The role of 5α-cyprinol sulfate in lipid digestion in fish explains why from an evolutionary perspective fish has not stopped releasing 5α-cyprinol sulfate despite the disadvantages for the releaser. The identification of the DVM-inducing kairomone enables investigating its spatial and temporal distribution and the underlying molecular mechanism of its perception. Furthermore, it allows to test if fish-mediated inducible defenses in other aquatic invertebrates are triggered by the same compound.
Vertical transmission of a nematode from female lizards to the brains of their offspring
Parasites have evolved a diversity of life styles that exploit the biology of their hosts. Some nematodes that parasitize mammals pass via the placenta or milk from one host to another. Similar cases of vertical transmission have never been reported in avian and non-avian reptiles, suggesting that egg laying may constrain themeans of parasite transmission. However, here we report the first incidence of transovarial transmission of a previously undescribed nematode in an egg-laying amniote, the common wall lizard, Podarcis muralis . Nematodes enter the developing brain from the female ovary early in embryonic development. Infected lizard embryos develop normally and hatch with nematodes residing in their braincase. We present a morphological and molecular phylogenetic characterization of the nematode and suggest that particular features of lizard biology that are absent from birds and turtles facilitated the evolutionary origin of this novel life history.
Data from: Environmental influences and ontogenetic differences in vertical habitat use of black marlin (Istiompax indica) in the southwestern Pacific
The black marlin (Istiompax indica) is a highly migratory billfish that occupies waters throughout the tropical and subtropical Indo-Pacific. To characterize the vertical habitat use of I. indica, we examined the temperature-depth profiles collected using 102 pop-up satellite archival tags deployed off the east coast of Australia. Modelling of environmental variables revealed location, sea-surface height deviation, mixed layer depth and dissolved oxygen to all be significant predictors of vertical habitat use. Distinct differences in diel movements were observed between the size classes, with larger size classes of marlin (greater than 50 kg) undertaking predictable bounce-diving activity during daylight hours, while diving behaviour of the smallest size class occurred randomly during both day and night. Overall, larger size classes of I. indica were found to use an increased thermal range and spend more time in waters below 150 m than fish of smaller size classes. The differences in the diving behaviour among size classes were suggested to reflect ontogenetic differences in foraging behaviour or physiology. The findings of this study demonstrate, for the first time to our knowledge, ontogenetic differences in vertical habitat in a species of billfish, and further the understanding of pelagic fish ecophysiology in the presence of global environmental change.
Data from: Landing maneuvers of houseflies on vertical and inverted surfaces
Landing maneuvers of flies are complex behaviors which can be conceptually decomposed into sequences of modular actions, including body-deceleration, leg-extension, and body rotations. These behavioral 'modules' must be coordinated to ensure well-controlled landing. The composite nature of these behaviors induces kinematic variability, making it difficult to identify the central rules that govern landing. Many previous studies have relied on tethered preparations to study landing behaviors, but tethering induces experimental artefacts by forcing some behaviors to operate in open-feedback control loop while others remain closed-loop. On the other hand, freely-flying insects are harder to precisely control, and hence inherently prone to behavioral variability. One approach towards understanding general mechanisms of landing is to determine the common elements of their kinematics on surfaces of different orientations. We conducted a series of experiments in which the houseflies, Musca domestica, were lured to land on vertical (vertical landings) or inverted (inverted landings) substrates, while their flight was recorded with multiple high-speed cameras. We observed that, in both cases, well-controlled landings occurred when the distance at which flies initiated deceleration was proportional to flight velocity component in the direction of substrate. The ratio of substrate distance and velocity at onset of deceleration (tau) was conserved, despite substantial differences in mechanics of vertical vs. inverted landings. When these conditions were not satisfied, their landing performance was compromised, causing their heads to collide into the substrate. Unlike body-deceleration, leg-extension in flies was independent of substrate distance or approach velocity. Thus, the robust reflexive visual initiation of deceleration is independent of substrate orientation, and combines with a more variable initiation of leg-extension which depends on surface orientation. Together, these combinations of behaviors enable flies to land in a versatile manner on substrates of various orientations.
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.