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18,621 results for “development;”
Influence of density and salinity on larval development of salt-adapted and salt-naïve frog populations
<p>Environmental change and habitat fragmentation will affect population densities for many species. For those species that have locally adapted to persist in changed or stressful habitats, it is uncertain how density dependence will affect adaptive responses. Anurans (frogs and toads) are typically freshwater organisms, but some coastal populations of green treefrogs (<i>Hyla cinerea</i>) have adapted to brackish, coastal wetlands. Tadpoles from coastal populations metamorphose sooner and demonstrate faster growth rates than inland populations when reared solitarily. Although saltwater exposure has adaptively reduced the duration of the larval period for coastal populations, increases in densities during larval development typically increase time to metamorphosis and reduce rates of growth and survival. We test how combined stressors of density and salinity affect larval development between salt-adapted ("coastal") and non-salt adapted ("inland") populations by measuring various developmental and metamorphic phenotypes. We found that increased tadpole density strongly affected coastal and inland tadpole populations similarly. In high-density treatments, both coastal and inland populations had reduced growth rates, greater exponential decay of growth, a smaller size at metamorphosis, took longer to reach metamorphosis, and had lower survivorship at metamorphosis. Salinity only exaggerated the effects of density on the time to reach metamorphosis and exponential decay of growth. Location of origin affected length at metamorphosis, with coastal tadpoles metamorphosing slightly longer than inland tadpoles across densities and salinities. These findings confirm that density has a strong and central influence on larval development even across divergent populations and habitat types and may mitigate the expression (and therefore detection) of locally adapted phenotypes.</p>
A Case Study on the Communication of a Local Software Developer Team
<p>Raw data and scripts for the analysis of the paper "A Case Study on the Communication of a Local Software Developer Team"</p> <p>The files with the extension "list" contain the communication of the according channel. For example, "talks.list" contains all the recorded talks. The first two columns of a file contains the communication patners, the third column the date, the fourth the time of day. The sixth column contains the duration of a talk, the seventh column the rough topic, followed by the id of the event in column eight. Since often, additional developers entered the conversation, which we recorded as extra event, we have summarized the events to one conversation, denoted by the last column. That is, the last column contains the id of the conversation.</p> <p>The file analysis.Rmd contains the script that we used to analyze the data and create the plots. We used the library coronet (available at GitHub:https://github.com/ecklbarb/coronet/tree/read-data-from-company). The input data must have the folder structure as discribed in the Readme of the coronet project.</p> <p>The file analysis.Rmd must be copied in the folder of the coronet library.</p>
Extract of Local Notice to Mariners, 2018-2019, for Development of AIS Model of Texas Gulf Intracoastal Waterway Travel Times
<p>These files summarize mentions of restrictions or cautions for navigation on the Texas Gulf Intracoastal Waterway contained in Coast Guard Local Notice to Mariners files.</p>
Weekly travel times by direction and sample count for each link in Development of AIS Model of Texas Gulf Intracoastal Waterway Travel Times
<p>Excel spreadsheet containing all of the travel times and sample counts for each link (by direction).</p>
Data from: Ovary development and cold tolerance of the invasive pest Drosophila suzukii (Matsumura) in the central plains of Kansas, United States
Environmental challenges presented by temperature variation can be overcome through phenotypic plasticity in small invasive ectotherms. We tested the effect of thermal exposure to 21, 18, and 11°C throughout the whole life cycle of individuals, thermal exposure of adults reared at 25°C to 15 and 11°C for a 21-d period, and long (14:10 hr) and short (10:14 hr) photoperiod on ovary size and development in Drosophila suzukii (Matsumura) (Diptera: Drosophilidae) cultured from a recently established population in Topeka, Kansas (United States). Examination of the response to temperature and photoperiod variation in this central plains population provides insight into the role of phenotypic plasticity in a climate that is warmer than regions in North America where D. suzukii was initially established. We found both low temperature and short photoperiod resulted in reduced ovary size and level of development. In particular, reduced ovary development was observed following exposure to 15°C, indicating that ovary development in females from the central plains population is more sensitive to lower temperature compared with populations examined from the northern United States and southern Canada. We also provide evidence that D. suzukii reared at 25°C are capable of short-term hardening when exposed to −6°C following 4°C acclimation, contrary to previous reports indicating flies reared at warm temperatures do not rapidly-cold harden. Our study highlights the central role of phenotypic plasticity in response to winter-like laboratory conditions and provides an important geographic comparison to previously published assessments of ovary development and short-term hardening survival response for D. suzukii collected in cooler climates.
Functional multispectral optoacoustic tomography imaging of hepatic steatosis development in mice_image analysis
<p>This dataset contains the HE staining/anti-CD31 staining/ICG fluorescence images and the image quantification data produced for publication "Functional multispectral optoacoustic tomography imaging of hepatic steatosis development in mice"</p>
Early sexual dimorphism in the developing gut microbiome of northern elephant seals
<p>The gut microbiome is an integral part of a species' ecology, but we know little about how host characteristics impact its development in wild populations. Here, we explored the role of such intrinsic factors in shaping the gut microbiome of northern elephant seals during a critical developmental window of six weeks after weaning, when the pups stay ashore without feeding. We found substantial sex-differences in the early-life gut microbiome, even though males and females could not yet be distinguished morphologically. Sex and age both explained around 15% of the variation in gut microbial beta diversity, while microbial communities sampled from the same individual showed high levels of similarity across time, explaining another 40% of the variation. Only a small proportion of the variation in beta diversity was explained by health status, assessed by full blood counts, but clinically healthy individuals had a greater microbial alpha diversity than their clinically abnormal peers. Across the post-weaning period, the northern elephant seal gut microbiome was highly dynamic. We found evidence for several colonisation and extinction events as well as a decline in <i>Bacteroides </i>and an increase in <i>Prevotella</i>, a pattern that has previously been associated with the transition from nursing to solid food. Lastly, we show that genetic relatedness was correlated with gut microbiome similarity in males but not females, again reflecting early sex-differences. Our study represents a naturally diet-controlled and longitudinal investigation of how intrinsic factors shape the early gut microbiome in a species with extreme sex differences in morphology and life history.</p>
SiEUGreen - Dataset for Baseline study including key indicators and development of a typology
<p>Dataset used for the report (D1.2) presenting the baseline study including key indicators and development of a typology. develops a theoretical and methodological framework that sustains a coherent Urban Agriculture (UA) typology that covers the specificities of the different SiEUGreen showcases. Data contains qualitative and quantitative data in an excel sheet and docx files. The purpose of the dataset is to be used to create a comprehensive conceptual framework about UA including a comparative perspective across different institutional settings and cultures. The data collection was conducted by SiEUGreen partners at Nordregio, International Research Centre for Regional Development and Planning.</p>
Functional multispectral optoacoustic tomography imaging of hepatic steatosis development in mice
<p>This dataset contains primary data produced for pulication named 'Functional multispectral optoacoustic tomography imaging of hepatic steatosis development in mice'</p>
From pup to predator; generalized hidden Markov models reveal rapid development of movement strategies in a naïve long‐lived vertebrate
<p>Rapid development of a successful foraging strategy is critical for juvenile survival, especially for naïve animals that receive no parental guidance. However, this process is poorly understood for many species. Although observation of early-life movements is increasingly possible with miniaturisation of animalborne telemetry devices, analytical limitations remain. Here, we tracked 29 recently-weaned, grey seal <em>Halichoerus grypus</em> pups from colonies in two geographically distinct regions of the United Kingdom. We analysed at-sea movements of pups throughout their initial months of nutritional independence to investigate the ontogeny of behaviour-specific (foraging and travelling) movement patterns. Using generalized hidden Markov models (HMMs), we extended the conventional HMM framework to account for temporal changes in putative foraging and travelling movement characteristics, and investigate the effects of intrinsic (sex) and extrinsic (environment) factors on this process. Putative foraging behaviour became more tortuous with time, and travelling became faster and more directed, suggesting a reduction in search scale and an increase in travel efficiency as pups shifted from exploration to an adult-like repeatable foraging strategy. Sex differences in movement characteristics were evident from colony departure, but sex-specific activity budgets were only detected in one region. We show that sex-specific behavioural strategies emerge before sexual size dimorphism in grey seals, and suggest that this phenomenon may occur in other long-lived species. Our results also indicate that environmental variation may affect the emergence of sex-specific foraging behaviour, highlighting the need to consider interacting intrinsic and extrinsic factors in shaping movement strategies of long-lived vertebrates. Moreover, comparing the behavioural state estimations to those of a conventional HMM (no variation in statespecific movement parameters) revealed differences in the amount and location of foraging activity, with implications for spatial conservation management. Overlooking intrinsic and extrinsic variation in movement processes could distort our understanding of foraging ecology, population dynamics, and conservation requirements.</p>
Data from: Experimental amelioration of harsh weather speeds growth and development in a tropical montane songbird
<p>Organisms living at high elevations generally grow and develop slower than those at lower elevations. Slow montane ontogeny is thought to be an evolved adaptation to harsh environments that improve juvenile quality via physiological tradeoffs. However, slower montane ontogeny may also reflect proximate influences of harsh weather on parental care and offspring development. We experimentally heated and protected nests from rain to ameliorate harsh montane weather conditions for Mountain Blackeyes (<i>Chlorocharis emiliae</i>), a montane songbird living at ca. 3200 m asl in Malaysian Borneo. This experiment was designed to test if cold and wet montane conditions contribute to parental care and post-natal growth and development rates at high elevations. We found that parents increased provisioning and reduced time spent warming offspring, which grew faster and departed the nest earlier compared to unmanipulated nests. Earlier departure reduces time-dependent predation risk, benefitting parents and offspring. These plastic responses highlight the importance of proximate weather contributions to broad patterns of montane ontogeny and parental care.</p>
Anuran limbs reflect microhabitat and distal, later-developing bones are more evolutionarily labile
Tetrapod limbs have been used as a model system to investigate how selective pressures and constraints shape morphological evolution. Anurans have had many independent transitions to various microhabitats, allowing us to dissect how these factors influence limb morphology. Furthermore, anurans provide a unique system to test the generality of developmental constraints proposed in mammals, namely that later-developing limb bones are under less constraint and show more variation. We used micro-computed tomography scans of 236 species from 52 of 55 families, geometric morphometrics, and modern phylogenetic comparative methods to examine how limb bones are related to microhabitat, phylogeny, allometry, and developmental timing. Although there was significant phylogenetic signal, anuran limb shape showed a relationship with microhabitat and to a lesser extent, body size. We found that distal bones had higher evolutionary rates than proximal bones, providing evidence that developmental constraints are reduced in later-developing bones. Distal bones also showed increased selection related to allometry and microhabitat, providing an additional explanation for higher evolutionary rates. By looking at the evolution of limb shape across a diverse clade, we demonstrated that multiple factors have shaped anuran limbs and that greater evolutionary lability in later-developing limb bones is likely a general trend among tetrapods.
Evolution and development at the origin of a phylum
<p class="AbstractSummary">Quantifying morphological evolution is key to determining the patterns and processes underlying the origin of phyla. We constructed a hierarchical morphological character matrix to characterize the radiation and establishment of echinoderm body plans during the early Paleozoic. This showed that subphylum-level clades diverged gradually through the Cambrian, and the distinctiveness of the resulting body plans was amplified by the extinction of transitional forms and obscured by convergent evolution during the Ordovician. Higher-order characters that define these body plans were not fixed at the origin of the phylum, countering hypotheses regarding developmental processes governing the early evolution of animals. Instead, these burdened characters were flexible enabling continued evolutionary innovation throughout the clades' history.</p>
Data from: Developmental Dieldrin exposure alters DNA methylation at genes related to dopaminergic neuron development and Parkinson's disease in mouse midbrain
Human and animal studies have shown that exposure to the organochlorine pesticide dieldrin is associated with increased risk of Parkinson's disease (PD). Despite previous work showing a link between developmental dieldrin exposure and increased neuronal susceptibility to MPTP toxicity in male C57BL/6 mice, the mechanism mediating this effect has not been identified. Here, we tested the hypothesis that developmental exposure to dieldrin increases neuronal susceptibility via genome-wide changes in DNA methylation. Starting at 8 weeks of age and prior to mating, female C57BL/6 mice were exposed to 0.3 mg/kg dieldrin by feeding (every 3 days) throughout breeding, gestation, and lactation. At 12 weeks of age, pups were sacrificed and ventral mesencephalon, containing primarily substantia nigra, were microdissected. DNA was isolated and dieldrin-related changes in DNA methylation were assessed via reduced representation bisulfite sequencing (RRBS). We identified significant, sex-specific differentially methylated CpGs (DMCs) and regions (DMRs) by developmental dieldrin exposure (FDRNr4a2 and Lmx1b genes, which are involved in dopaminergic neuron development and maintenance. Developmental dieldrin exposure had distinct effects on the male and female epigenome. Together, our data suggest that developmental dieldrin exposure establishes sex-specific poised epigenetic states early in life. These poised epigenomes may mediate sensitivity to subsequent toxic stimuli and contribute to the development of late-life neurodegenerative disease, including PD.
Data from: Laying sequence interacts with incubation temperature to influence rate of embryonic development and hatching synchrony in a precocial bird
Incubation starts during egg laying for many bird species and causes developmental asynchrony within clutches. Faster development of late-laid eggs can help reduce developmental differences and synchronize hatching, which is important for precocial species whose young must leave the nest soon after hatching. In this study, we examined the effect of egg laying sequence on length of the incubation period in Wood Ducks (Aix sponsa). Because incubation temperature strongly influences embryonic development rates, we tested the interactive effects of laying sequence and incubation temperature on the ability of late-laid eggs to accelerate development and synchronize hatching. We also examined the potential cost of faster development on duckling body condition. Fresh eggs were collected and incubated at three biologically relevant temperatures (Low: 34.9°C, Medium: 35.8°C, and High: 37.6°C), and egg laying sequences from 1 to 12 were used. Length of the incubation period declined linearly as laying sequence advanced, but the relationship was strongest at medium temperatures followed by low temperatures and high temperatures. There was little support for including fresh egg mass in models of incubation period. Estimated differences in length of the incubation period between eggs 1 and 12 were 2.7 d, 1.2 d, and 0.7 d at medium, low and high temperatures, respectively. Only at intermediate incubation temperatures did development rates of late-laid eggs increase sufficiently to completely compensate for natural levels of developmental asynchrony that have been reported in Wood Duck clutches at the start of full incubation. Body condition of ducklings was strongly affected by fresh egg mass and incubation temperature but declined only slightly as laying sequence progressed. Our findings show that laying sequence and incubation temperature play important roles in helping to shape embryo development and hatching synchrony in a precocial bird.
Data from: Individual and population fitness consequences associated with large carnivore use of residential development
<p><span>Large carnivores are negotiating increasingly developed landscapes, but little is known about how such behavioral plasticity influences their demographic rates and population trends. Some investigators have suggested that the ability of carnivores to behaviorally adapt to human development will enable their persistence, and yet, others have suggested that such landscapes are likely to serve as population sinks or ecological traps. To understand how plasticity in black bear (<i>Ursus americanus</i>) use of residential development influences their population dynamics, we conducted a 6 year study near Durango, Colorado, USA. </span>Using space-use data on individual bears, we examined the influence of use of residential development on annual measures of bear body fat, cub productivity, cub survival and adult female survival, after accounting for variation in natural food availability and individual attributes (e.g., age). We then used our field-based vital rate estimates to parameterize a matrix model that simulated asymptotic population growth for bears using residential development to different degrees. We found that bear use of residential development was highly variable within and across years, with bears increasing their foraging within development when natural foods were scarce. Increased bear use of development was associated with increased body fat and cub productivity, but reduced cub and adult survival.<span> When these effects were simultaneously incorporated into a matrix model </span>we found that the population was projected to decline as bear use of development increased, given that the costs of reduced survival outweighed the benefits of enhanced productivity. Our results provide a mechanistic understanding of how black bear use of residential development exerts opposing effects on different bear fitness traits and a negative effect on population growth, with the magnitude of those effects mediated by variation in environmental conditions. They also highlight the importance of monitoring bear population dynamics, particularly as shifts in bear behavior are likely to drive increases in human-bear conflicts and the perception of growing bear populations. Finally, our work emphasizes the need to consider the demographic viability of large carnivore populations when promoting the coexistence of people and carnivores on shared landscapes.</p>
Data from: Vocal state change through laryngeal development
<p>Across vertebrates, progressive changes in vocal behavior during postnatal development are typically attributed solely to developing neural circuits. How the changing body influences vocal development remains unknown. Here we show that state changes in the contact vocalizations of infant marmoset monkey<span class="oxeins_1">s</span>, which transition from noisy, low frequency cries to tonal, higher pitched vocalizations in adults, are caused partially by laryngeal development. Combining analyses of natural vocalizations, motorized excised larynx experiments, tensile material tests and high-speed imaging, we show that vocal state transition occurs via a sound source switch from vocal folds to apical vocal membranes, producing louder vocalizations with higher efficiency. We show with an empirically-based model of descending motor control how neural circuits could interact with changing laryngeal dynamics, leading to adaptive vocal development. Our results emphasize the importance of embodied approaches to vocal development, where exploiting biomechanical consequences of changing material properties can simplify motor control, reducing the computational load on the developing brain.</p>
Data from: Seasonally sympatric but allochronic: differential expression of hypothalamic genes in a songbird during gonadal development
Allochrony, the mismatch of reproductive schedules, is one mechanism that can mediate sympatric speciation and diversification. In songbirds, the transition into breeding condition and gonadal growth is regulated by the hypothalamic-pituitary-gonadal (HPG) axis at multiple levels. We investigated whether the difference in reproductive timing between two, seasonally sympatric subspecies of dark-eyed juncos (Junco hyemalis) was related to gene expression along the HPG axis. During the sympatric pre-breeding stage, we measured hypothalamic and testicular mRNA expression of candidate genes via qPCR in captive male juncos. For hypothalamic mRNA, we found our earlier breeding subspecies had increased expression of gonadotropin-releasing hormone (GnRH) and decreased expression of androgen receptor, estrogen receptor alpha, and mineralocorticoid receptor (MR). Subspecies did not differ in expression of hypothalamic gonadotropin-inhibitory hormone (GnIH) and glucocorticoid receptor (GR). While our earlier breeding subspecies had higher mRNA expression of testicular GR, subspecies did not differ in testicular luteinizing hormone receptor, follicle-stimulating hormone receptor, or MR mRNA expression levels. Our findings indicate increased GnRH production and decreased hypothalamic sensitivity to sex steroid negative feedback as factors promoting differences in the timing of gonadal recrudescence between recently diverged populations. Differential gene expression along the HPG axis may facilitate species diversification under seasonal sympatry.
Data from: An exotic species alters patterns of marine community development
Predictions of ecological patterns can be strengthened through replication of foundational studies under different environmental conditions to evaluate the consistency in their underlying processes. In this study, we replicated Sutherland and Karlson's 1977 classic ecology study that tested terrestrial paradigms of community development in a marine fouling community. The abundance patterns of marine fouling species were quantified on sequentially submerged settlement plates to investigate the effects of disturbance date on short- and long-term patterns of community development, and the original study's datasets were re-analyzed for comparison. In both studies, community structure was initially shaped by disturbance date due to monthly and annual variation in larval recruitment; however, the influence of disturbance date diminished over time. Despite these similarities, the underlying drivers of long-term patterns of community development have shifted substantially since the 1970′s. During the present study, an exotic tunicate, Clavelina oblonga, dominated plates over time and its dominance was associated with significant declines in species diversity. In contrast, the 1970s long-term community was characterized by a heterogeneous mixture of species that varied inter-annually, yielding increased species diversity over time. Continued observations of our settlement plates (2 years total) indicated that C. oblonga remains the dominant species in this community, suggesting that these findings are not the result of a single, novel recruitment event. These results highlight how an exotic species can alter patterns of community development and biodiversity. Moreover, this study demonstrates the need to replicate foundational ecological studies to evaluate community dynamics and underlying processes in light of ongoing ecosystem change.
Data from: Development of a sustainability assessment algorithm and its validation using case studies on cryogenic machining
This work presents a comprehensive structure for evaluating the sustainability of machining processes. Industries can contribute towards developing a sustainable future by using algorithms that evaluate the sustainability of their processes. Inspired by the literature, the proposed model involves a set of metrics that are critical in evaluating the impact of a process on society, environment, and economy. The flexibility of this model allows decision-makers to use the available responses to identify the most favorable process. The entropy weight method was suggested for objectively calculating the weights of each indicator. A multi-criteria decision-making method i.e., Technique for Order Preference based on Similarity to Ideal Solution (TOPSIS), was used to rank processes in the decreasing order of their sustainability. The proposed algorithm was successfully validated with case studies from the published literature. A MATLAB code was also created so that industries may expeditiously apply this method to evaluate the sustainability of machining processes.
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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.