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1,154 results for “Pooling”
Meta-models for Software Quality and Its Evaluation: A Systematic Literature Review (Article Pool)
<p>This pdf includes all of the articles that analyzed in the study: "Meta-models for Software Quality and Its Evaluation: A Systematic Literature Review".</p>
Pooled whole genome sequencing from year 2004 and Early-Late SNP data from year 2014
<p>Speciation underlies the generation of novel biodiversity. Yet, there is much to learn about how natural selection shapes genomes during speciation. Selection is assumed to act against gene flow at barrier loci, promoting reproductive isolation. However, evidence for gene flow and selection is often indirect and we know very little about the temporal stability of barrier loci. Here we utilize haplodiploidy to identify candidate male barrier loci in hybrids between two wood ant species. As ant males are haploid they are expected to reveal recessive barrier loci, which can be masked in diploid females if heterozygous. We then test for barrier stability in a sample collected ten years later and use survival analysis to provide a direct measure of natural selection acting on candidate male barrier loci. We find multiple candidate male barrier loci scattered throughout the genome. Surprisingly, a proportion of them are not stable after ten years, natural selection apparently switching from acting against to favoring introgression in the later sample. Instability of barrier effect and natural selection for introgressed alleles could be due to environment-dependent selection, emphasizing the need to consider temporal variation in the strength of natural selection and the stability of barrier effect at putative barrier loci in future speciation work.</p>
Figure 1 in Homing behaviour of rock pool blenny Parablennius parvicornis (Pisces: Blenniidae)
Figure 1. Geographical location and spatial distribution of pools where individual of Parablennius parvicornis were caught (home pools) and displaced.
Reference allele frequencies for populations pools of Atlantic Herring (Clupea harengus)
<p>Atlantic herring is widespread in North Atlantic and adjacent waters and is one of the most abundant vertebrates on earth. This species is well suited to explore genetic adaptation due to minute genetic differentiation at selectively neutral loci. Here we report hundreds of loci underlying ecological adaptation to different geographic areas and spawning conditions. Four of these represent megabase inversions confirmed by long read sequencing. The genetic architecture underlying ecological adaptation in herring deviates from expectation under a classical infinitesimal model for complex traits because of large shifts in allele frequencies at hundreds of loci under selection.</p>
Patterns of nitrogen and phosphorus pools in terrestrial ecosystems in China
<p>Recent increases in atmospheric carbon dioxide (CO<sub>2</sub>) and temperature relieve the limitation of these two on terrestrial ecosystem productivity, while nutrient availability constrains the increasing plant photosynthesis more intensively. Nitrogen (N) and phosphorus (P) are critical for plant physiological activities and consequently regulates ecosystem productivity. Here, for the first time, we mapped N and P densities of leaves, woody stems, roots, litter and soil in forest, shrubland and grassland ecosystems across China, based on an intensive investigation in 4175 sites, covering species composition, biomass, and nutrient concentrations of different tissues of living plants, litter and soil. Forest, shrubland and grassland ecosystems in China stored 7665.62 × 10<sup>6</sup> Mg N, with 7434.53 × 10<sup>6</sup> Mg (96.99%) fixed in soil (to a depth of one metre), and 32.39 × 10<sup>6</sup> Mg (0.42%), 59.57 × 10<sup>6</sup> Mg (0.78%), 124.21 × 10<sup>6</sup> Mg (1.62%) and 14.92 × 10<sup>6</sup> Mg (0.19%) in leaves, stems, roots and litter, respectively. The forest, shrubland and grassland ecosystems in China stored 3852.66 × 10<sup>6</sup> Mg P, with 3821.64 × 10<sup>6</sup> Mg (99.19%) fixed in soil (to a depth of one metre), and 3.36 × 10<sup>6</sup> Mg (0.09%), 14.06 × 10<sup>6</sup> Mg (0.36%), 11.47 × 10<sup>6</sup> Mg (0.30%) and 2.14 × 10<sup>6</sup> Mg (0.06%) in leaves, stems, roots and litter, respectively. Our estimation showed that N pools were low in northern China except Changbai Mountains, Mount Tianshan and Mount Alta, while relatively higher values existed in eastern Qinghai-Tibetan Plateau and Yunnan. Southern China held quite small P pools, which may limit some plant-related process. P densities in plant organs were higher in the North and East China, while soil P density was higher in the South and West China. These patterns of N and P densities could potentially improve existing earth system models and large-scale researches on ecosystem nutrients.</p>
Data from: The plastoquinone pool of Nannochloropsis oceanica is not completely reduced during bright light pulses
The lipid-producing model alga Nannochloropsis oceanica has a distinct photosynthetic machinery. This organism possesses chlorophyll a as its only chlorophyll species, and has a high ratio of PSI to PSII. This high ratio of PSI to PSII may affect the redox state of the plastoquinone pool during exposure to light, and consequently may play a role in activating photoprotection mechanisms. We utilized pulse-amplitude modulated fluorometry to investigate the redox state of the plastoquinone pool during and after bright light pulses. Our data indicate that even very intense (5910 μmol photons s-1m-2 of blue light having a wavelength of 440 nm) light pulses of 0.8 second duration are not sufficient to completely reduce the plastoquinone pool in Nannochloropsis. In order to achieve extensive reduction of the plastoquinone pool by bright light pulses, anaerobic conditions or an inhibitor of the photosynthetic electron transport chain has to be utilized. The implication of this finding for the application of the widely used saturating pulse method in algae is discussed.
Data from: A well-defined readily releasable pool with fixed capacity for storing vesicles at calyx of held
The readily releasable pool (RRP) of vesicles is a core concept in studies of presynaptic function. However, operating principles lack consensus definition and the utility for quantitative analysis has been questioned. Here we confirm that RRPs at calyces of Held from 14 to 21 day old mice have a fixed capacity for storing vesicles that is not modulated by Ca2+. Discrepancies with previous studies are explained by a dynamic flow-through pool, established during heavy use, containing vesicles that are released with low probability despite being immediately releasable. Quantitative analysis ruled out a posteriori explanations for the vesicles with low release probability, such as Ca2+-channel inactivation, and established unexpected boundary conditions for remaining alternatives. Vesicles in the flow-through pool could be incompletely primed, in which case the full sequence of priming steps downstream of recruitment to the RRP would have an average unitary rate of at least 9/s during heavy use. Alternatively, vesicles with low and high release probability could be recruited to distinct types of release sites; in this case the timing of recruitment would be similar at the two types, and the downstream transition from recruited to fully primed would be much faster. In either case, further analysis showed that activity accelerates the upstream step where vesicles are initially recruited to the RRP. Overall, our results show that the RRP can be well defined in the mathematical sense, and support the concept that the defining mechanism is a stable group of autonomous release sites.
Data from: Removal of an apex predator initiates a trophic cascade that extends from herbivores to vegetation and the soil nutrient pool
It is widely assumed that organisms at low trophic levels, particularly microbes and plants, are essential to basic services in ecosystems, such as nutrient cycling. In theory, apex predators' effects on ecosystems could extend to nutrient cycling and the soil nutrient pool by influencing the intensity and spatial organization of herbivory. Here, we take advantage of a long-term manipulation of dingo abundance across Australia's dingo-proof fence in the Strzelecki Desert to investigate the effects that removal of an apex predator has on herbivore abundance, vegetation and the soil nutrient pool. Results showed that kangaroos were more abundant where dingoes were rare, and effects of kangaroo exclusion on vegetation, and total carbon, total nitrogen and available phosphorus in the soil were marked where dingoes were rare, but negligible where dingoes were common. By showing that a trophic cascade resulting from an apex predator's lethal effects on herbivores extends to the soil nutrient pool, we demonstrate a hitherto unappreciated pathway via which predators can influence nutrient dynamics. A key implication of our study is the vast spatial scale across which apex predators' effects on herbivore populations operate and, in turn, effects on the soil nutrient pool and ecosystem productivity could become manifest.
Data from: Validation of perfusion quantification with 3D gradient echo dynamic contrast-enhanced magnetic resonance imaging using a blood pool contrast agent in skeletal swine muscle
The purpose of our study was to validate perfusion quantification in a low-perfused tissue by dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) with shared k-space sampling using a blood pool contrast agent. Perfusion measurements were performed in a total of seven female pigs. An ultrasonic Doppler probe was attached to the right femoral artery to determine total flow in the hind leg musculature. The femoral artery was catheterized for continuous local administration of adenosine to increase blood flow up to four times the baseline level. Three different stable perfusion levels were induced. The MR protocol included a 3D gradient-echo sequence with a temporal resolution of approximately 1.5 seconds. Before each dynamic sequence, static MR images were acquired with flip angles of 5°, 10°, 20°, and 30°. Both static and dynamic images were used to generate relaxation rate and baseline magnetization maps with a flip angle method. 0.1 mL/kg body weight of blood pool contrast medium was injected via a central venous catheter at a flow rate of 5 mL/s. The right hind leg was segmented in 3D into medial, cranial, lateral, and pelvic thigh muscles, lower leg, bones, skin, and fat. The arterial input function (AIF) was measured in the aorta. Perfusion of the different anatomic regions was calculated using a one- and a two-compartment model with delay- and dispersion-corrected AIFs. The F-test for model comparison was used to decide whether to use the results of the one- or two-compartment model fit. Total flow was calculated by integrating volume-weighted perfusion values over the whole measured region. The resulting values of delay, dispersion, blood volume, mean transit time, and flow were all in physiologically and physically reasonable ranges. In 107 of 160 ROIs, the blood signal was separated, using a two-compartment model, into a capillary and an arteriolar signal contribution, decided by the F-test. Overall flow in hind leg muscles, as measured by the ultrasound probe, highly correlated with total flow determined by MRI, R = 0.89 and P = 10−7. Linear regression yielded a slope of 1.2 and a y-axis intercept of 259 mL/min. The mean total volume of the investigated muscle tissue corresponds to an offset perfusion of 4.7mL/(min ⋅ 100cm3). The DCE-MRI technique presented here uses a blood pool contrast medium in combination with a two-compartment tracer kinetic model and allows absolute quantification of low-perfused non-cerebral organs such as muscles.
Data from: Process-based species pools reveal the hidden signature of biotic interactions amid the influence of temperature filtering
A persistent challenge in ecology is to tease apart the influence of multiple processes acting simultaneously and interacting in complex ways to shape the structure of species assemblages. We implement a heuristic approach that relies on explicitly defining species pools and permits assessment of the relative influence of the main processes thought to shape assemblage structure: environmental filtering, dispersal limitations and biotic interactions. We illustrate our approach using data on the assemblage composition and geographic distribution of hummingbirds, a comprehensive phylogeny and morphological traits. The implementation of several process-based species pool definitions in null models suggests that temperature, but not precipitation or dispersal limitation, acts as the main regional filter of assemblage structure. Incorporating this environmental filter directly into the definition of assemblage-specific species pools revealed an otherwise hidden pattern of phylogenetic evenness, indicating that biotic interactions might further influence hummingbird assemblage structure. Such hidden patterns of assemblage structure call for a reexamination of a multitude of phylogenetic- and trait-based studies that did not explicitly consider potentially important processes in their definition of the species pool. Our heuristic approach provides a transparent way to explore patterns and refine interpretations of the underlying causes of assemblage structure.
Data from: Female collared flycatchers choose neighbouring and older extra-pair partners from the pool of males around their nests
Extra-pair copulation is common among passerine birds. Females might engage in this behavior to obtain direct or indirect benefits. They may choose extra-pair males with larger ornaments, especially if they are costly to produce. Here we studied extra-pair paternity in the collared flycatcher. Genetic analysis allowed us to identify the presence or absence of extra-pair young in the focal nests, and to identify extra-pair fathers. We also identified potential males available as extra-pair sires around the nests of females who had extra-pair young. First, we tested the relationship between paternity in own nest and ornament size (wing patch and/or forehead patch), morphological traits and age of social males and females. Second, we compared the same suite of traits among social mates, extra-pair males and all potential extra-pair mates. Finally, we investigated the effect of the size of ornaments on the distance between the social nest and that of nest the extra-pair father. Contrary to our prediction, males with larger ornaments and longer wings lost more paternity in their nests. We also found that early breeders lost less paternity in their nests. Extra-pair males were older and had longer wings than social and potential extra-pair males. Females mainly obtained extra-pair mates near their nests but the distance did not vary according to ornamentation. These results could potentially be explained by differences in mate guarding strategy as older males may be more experienced in guarding their mate and attract other females more easily. More data about mate guarding and prospecting are needed to increase our understanding of mechanisms underlying the extra-pair paternity in birds.
Data from: The impact of library preparation protocols on the accuracy of allele frequency estimates in Pool-Seq data
Sequencing pools of individuals (Pool-Seq) is a cost-effective method to determine genome-wide allele frequency estimates. Given the importance of meta-analyses combining data sets, we determined the influence of different genomic library preparation protocols on the consistency of allele frequency estimates. We found that typically no more than 1% of the variation in allele frequency estimates could be attributed to differences in library preparation. Also read length had only a minor effect on the consistency of allele frequency estimates. By far, the most pronounced influence could be attributed to sequence coverage. Increasing the coverage from 30- to 50-fold improved the consistency of allele frequency estimates by at least 27%. We conclude that Pool-Seq data can be easily combined across different library preparation methods, but sufficient sequence coverage is key to reliable results.
FIGURE 9 in " Microturbellarian " flatworms (Platyhelminthes) from freshwater pools: New species and records from Israel
FIGURE 9: Strongylostoma elongatum elongatum Hofsten, 1907. Habitus; lightly squashed.
FIGURE 1 in On Amphibolocypris arida sp. nov. (Crustacea, Ostracoda), from rock pools in Botswana (southern Africa)
FIGURE 1. Map of the type locality of Amphibolocypris arida sp.nov. (after Jocque et al. 2006).
FIGURE 1 in Microdrile Oligochaeta in bromeliad pools of a Honduran cloud forest
FIGURE 1. Map to show the location of the study site.
CALCULATION OF THERMAL-TECHNICAL PARAMETERS OF THE SOLAR POND HEATING SYSTEM OF INDOOR SWIMMING POOLS
Open the record for dataset details and reuse information.
Dehydrated males are less likely to dive into the mating pool
<p>The hydration state of animals vying for reproductive success may have implications for the tempo and mode of sexual selection, which may be salient in populations that experience increasing environmental fluctuations in water availability. Using red-sided garter snakes as a model system, we tested the effect of water supplementation on courtship, mating behavior, and copulatory plug (CP) production during a drought year. Over three days of mating trials, water-supplemented males (WET males, n = 45) outperformed a control group that was not supplemented with water (DRY males, n = 45). Over 70% of WET males mated but just 33% of DRY males did so. As a group, WET males mated 79 times vs 28 times by DRY males. On the last day of mating trials, over 70% of WET males were still courting, with 19 of them mating, whereas less than 25% of DRY males were courting and only one mated. CP deposition accounted for 4-6% of the mass lost by mating males, but hydration did not affect CP mass or water content. These findings suggest that, in years of low water availability, the number of courting males and the intensity of their courtship declines, thereby affecting sexual selection and conflict, at least within that year.</p>
Supplementary material 2 from: Van den Bulcke L, De Backer A, Ampe B, Maes S, Wittoeck J, Waegeman W, Hostens K, Derycke S (2021) Towards harmonization of DNA metabarcoding for monitoring marine macrobenthos: the effect of technical replicates and pooled DNA extractions on species detection. Metabarcoding and Metagenomics 5: e71107. https://doi.org/10.3897/mbmg.5.71107
Tables S1–S8
Supplementary material 1 from: Van den Bulcke L, De Backer A, Ampe B, Maes S, Wittoeck J, Waegeman W, Hostens K, Derycke S (2021) Towards harmonization of DNA metabarcoding for monitoring marine macrobenthos: the effect of technical replicates and pooled DNA extractions on species detection. Metabarcoding and Metagenomics 5: e71107. https://doi.org/10.3897/mbmg.5.71107
Figures S1–S14
Doryteuthis pealeii embyronic transcriptome individual stages 16-27 pooled and annotation
<p>Photoreception is a ubiquitous sensory ability found across the Metazoa, and photoreceptive organs are intricate and diverse in their structure. Although the morphology of the compound eye in Drosophila and the single-chambered eye in vertebrates have elaborated independently, the amount of conservation within the 'eye' gene regulatory network remains controversial, with few taxa studied. To better understand the evolution of photoreceptive organs, we established the cephalopod Doryteuthis pealeii as a lophotrochozoan model for eye development. Utilizing histological, transcriptomic and molecular assays, we characterize eye formation in Doryteuthis pealeii Through lineage tracing and gene expression analyses, we demonstrate that cells expressing Pax and Six genes incorporate into the lens, cornea and iris, and the eye placode is the sole source of retinal tissue. Functional assays demonstrate that Notch signaling is required for photoreceptor cell differentiation and retinal organization. This comparative approach places the canon of eye research in traditional models into perspective, highlighting complexity as a result of both conserved and convergent mechanisms.</p>
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Allen Brain Atlas
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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.
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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.
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