scholarly journals Hydrodynamic regime determines the feeding success of larval fish through the modulation of strike kinematics

2017 ◽  
Vol 284 (1853) ◽  
pp. 20170235 ◽  
Author(s):  
Victor China ◽  
Liraz Levy ◽  
Alex Liberzon ◽  
Tal Elmaliach ◽  
Roi Holzman
Keyword(s):  
High Speed ◽  
Sparus Aurata ◽  
Larval Fish ◽  
Reynolds Numbers ◽  
Early Ontogeny ◽  
Hydrodynamic Regime ◽  
Physical Growth ◽  
Larval Feeding ◽  
Feeding Success ◽  
Order Of Magnitude

Larval fishes experience extreme mortality rates, with 99% of a cohort perishing within days after starting to actively feed. While recent evidence suggests that hydrodynamic factors contribute to constraining larval feeding during early ontogeny, feeding is a complex process that involves numerous interacting behavioural and biomechanical components. How these components change throughout ontogeny and how they contribute to feeding remain unclear. Using 339 observations of larval feeding attempts, we quantified the effects of morphological and behavioural traits on feeding success of Sparus aurata larvae during early ontogeny. Feeding success was determined using high-speed videography, under both natural and increased water viscosity treatments. Successful strikes were characterized by Reynolds numbers that were an order of magnitude higher than those of failed strikes. The pattern of increasing strike success with increasing age was driven by the ontogeny of traits that facilitate the transition to higher Reynolds numbers. Hence, the physical growth of a larva plays an important role in its transition to a hydrodynamic regime of higher Reynolds numbers, in which suction feeding is more effective.

scholarly journals Suction feeding performance and prey escape response interact to determine feeding success in larval fish

2019 ◽  
Author(s):  
Noam Sommerfeld ◽  
Roi Holzman
Keyword(s):  
Early Development ◽  
Escape Response ◽  
High Speed ◽  
Sparus Aurata ◽  
Larval Fish ◽  
Reynolds Numbers ◽  
Larval Performance ◽  
Larval Feeding ◽  
Large Prey ◽  
Feeding Success

AbstractThe survival of larval marine fishes during early development is strongly dependent on their ability to capture prey. Most larval fish capture prey by expanding their mouth cavity, generating a “suction flow” that draws the prey into their mouth. Larval fish dwell in a hydrodynamic regime of low Reynolds numbers, which has been shown to impede their ability to capture non-evasive prey. However, the marine environment is characterized by an abundance of evasive prey such as Copepods. These organisms can sense the hydrodynamic disturbance created by approaching predators and perform high-acceleration escape maneuvers. Using a 3D high-speed video system, we characterized the interaction between 8-33 day post hatchingSparus auratalarvae and prey from a natural zooplankton assemblage that contained evasive prey, and assessed the factors that determine the outcome of these interactions. Larvae showed strong selectivity for large prey that was moving prior to the initialization of the strike. As previously shown in studies with non-evasive prey, larval feeding success increased with increasing Reynolds numbers. However, larval feeding success was also strongly dependent on the prey’s escape response. Feeding success was lower for larger, more evasive prey, indicating that larvae might be challenged in capturing their preferred prey. The kinematics of successful strikes resulted in shorter response time but higher hydrodynamic signature available for the prey. Thus, despite being “noisier”, successful strikes on evasive prey depended on preceding the prey’s escape response. Our results show that larval performance, rather than larval preferences, determines their diet during early development.

scholarly journals Hydrodynamic regime drives flow reversals in suction feeding larval fishes during early ontogeny

2019 ◽  
Author(s):  
Krishnamoorthy Krishnan ◽  
Asif Shahriar Nafi ◽  
Roi Gurka ◽  
Roi Holzman
Keyword(s):  
Numerical Simulations ◽  
High Speed ◽  
Prey Capture ◽  
Sparus Aurata ◽  
Larval Fish ◽  
Fish Larvae ◽  
Numerical Models ◽  
Hydrodynamic Regime ◽  
Suction Feeding ◽  
Larval Fishes

AbstractFish larvae are the smallest self-sustaining vertebrates. As such, they face multiple challenge that stem from their minute size, and from the hydrodynamic regime in which they dwell. This regime of intermediate Reynolds numbers (Re) was shown to affect the swimming of larval fish and impede their ability to capture prey. Numerical simulations indicate that the flow fields external to the mouth in younger larvae result in shallower spatial gradients, limiting the force exerted on the prey. However, observations on feeding larvae suggest that failures in prey capture can also occur during prey transport, although the mechanism causing these failures is unclear. We combine high-speed videography and numerical simulations to investigate the hydrodynamic mechanisms that impede prey transport in larval fishes. Detailed kinematics of the expanding mouth during prey capture by larval Sparus aurata were used to parameterize age-specific numerical models of the flows inside the mouth. These models reveal that, for small larvae that slowly expand their mouth, not all the fluid that enters the mouth cavity is expelled through the gills, resulting in flow reversal at the mouth orifice. This efflux at the mouth orifice was highest in the younger ages, but was also high (>8%) in slow strikes produced by larger fish. Our modeling explains the observations of “in-and-out” events in larval fish, where prey enters the mouth but is not swallowed. It further highlights the importance of prey transport as an integral part in determining suction feeding success.

scholarly journals The Expression of agrp1, A Hypothalamic Appetite-Stimulating Neuropeptide, Reveals Hydrodynamic-Induced Starvation in a Larval Fish

2018 ◽  
Vol 1 (1) ◽  
Author(s):  
L Koch ◽  
I Shainer ◽  
T Gurevich ◽  
R Holzman
Keyword(s):  
Sparus Aurata ◽  
Larval Fish ◽  
Mechanistic Explanation ◽  
Early Ontogeny ◽  
Larval Feeding ◽  
Feeding Rates ◽  
Fluid Forces ◽  
Water Viscosity ◽  
Hydrodynamic Environment

Abstract Larval fish suffer dramatic mortality in the days following transition to autonomous feeding, with over 90% of larvae being eliminated within a period of few weeks. Recent work has shown that the hydrodynamic environment experienced by recently-hatched larvae impedes their feeding rates even under high prey densities. Here, we quantified starvation through early ontogeny in Sparus aurata larvae (8–18 days post-hatching; DPH) and tested whether the emerging ontogenetic pattern is consistent with that expected one based on the hydrodynamic environment that these larvae experience. We screened three candidate genes agrp1, npy, and hsp70, whose expression was previously shown to respond to starvation in fish. Of the three genes, agrp1 was identified as a suitable indicator for starvation. Localization of agrp1 mRNA by whole-mount in-situ hybridization confirmed that, in S. aurata larvae, agrp1 is expressed only in the hypothalamus. Quantification of agrp1 mRNA using real-time PCR revealed that the expression of this gene is elevated in starved compared to fed larvae, and in younger (8 DPH) compared to older larvae (18 DPH). Manipulating the water viscosity to simulate the hydrodynamic conditions during the onset of the critical period led to increased agrp1 expression. These findings suggest that the hydrodynamic constraints on larval feeding lead to the starvation of small larvae. Further, they provide a mechanistic explanation for the “safe harbor” hypothesis, which postulates that larvae should allocate resources toward rapid linear growth to escape detrimental effects of dwelling in an environment where viscous fluid forces dominate.

scholarly journals Are Microplastics Impairing Marine Fish Larviculture?—Preliminary Results with Argyrosomus regius

Water ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 104
Author(s):  
Diana Campos ◽  
Andreia C. M. Rodrigues ◽  
Rui J. M. Rocha ◽  
Roberto Martins ◽  
Ana Candeias-Mendes ◽  
...  
Keyword(s):  
Oxidative Damage ◽  
Fish Larvae ◽  
Feeding Activity ◽  
Early Ontogeny ◽  
Antioxidant Defenses ◽  
Nutritional Requirements ◽  
Larval Feeding ◽  
Argyrosomus Regius ◽  
And Performance ◽  
Aquaculture Facilities

The presence of small-sized (<300 µm) microplastics (MPs) in aquaculture facilities may threaten finfish hatchery, as their (in)voluntary ingestion by fish larvae may compromise nutritional requirements during early ontogeny, and consequently larval health and performance. Thus, we addressed the short-term effects (7 h) of polyethylene microplastics (0.1, 1.0, 10 mg/L, PE-MPs) in meagre larvae Argyrosomus regius (15 dph) in the presence/absence of food. Larval feeding behavior, oxidative stress status, neurotoxicity, and metabolic requirements were evaluated. Results showed that meagre larvae ingested PE-MPs regardless of their concentration, decreasing in the presence of food (Artemia metanauplii). The presence of PE-MPs compromised larval feeding activity at the highest concentration. Under starvation, exposed larvae activated the antioxidant defenses by increasing the total glutathione levels and inhibiting catalase activity, which seemed efficient to prevent oxidative damage. Such larvae also presented increased energy consumption potentially related to oxidative damage prevention and decreased neurotransmission. Biochemical responses of fed larvae showed a similar trend, except for LPO, which remained unaffected, except at 0.1 mg/PE-MPs/L. Our results suggest that small-sized MPs in finfish hatcheries may compromise larvae nutritional requirements, but at considerably higher levels than those reported in marine environments. Nevertheless, cumulative adverse effects due to lower MPs concentrations may occur.

scholarly journals LiDAR Point Cloud Recognition and Visualization with Deep Learning for Overhead Contact Inspection

Sensors ◽  
2020 ◽  
Vol 20 (21) ◽  
pp. 6387 ◽  
Author(s):  
Xiaohan Tu ◽  
Cheng Xu ◽  
Siping Liu ◽  
Shuai Lin ◽  
Lipei Chen ◽  
...  
Keyword(s):  
Deep Learning ◽  
Computational Complexity ◽  
Point Cloud ◽  
High Speed ◽  
Point Cloud Data ◽  
Embedded Devices ◽  
Cloud Data ◽  
Manual Inspection ◽  
Order Of Magnitude ◽  
Supply Systems

As overhead contact (OC) is an essential part of power supply systems in high-speed railways, it is necessary to regularly inspect and repair abnormal OC components. Relative to manual inspection, applying LiDAR (light detection and ranging) to OC inspection can improve efficiency, accuracy, and safety, but it faces challenges to efficiently and effectively segment LiDAR point cloud data and identify catenary components. Recent deep learning-based recognition methods are rarely employed to recognize OC components, because they have high computational complexity, while their accuracy needs to be improved. To track these problems, we first propose a lightweight model, RobotNet, with depthwise and pointwise convolutions and an attention module to recognize the point cloud. Second, we optimize RobotNet to accelerate its recognition speed on embedded devices using an existing compilation tool. Third, we design software to facilitate the visualization of point cloud data. Our software can not only display a large amount of point cloud data, but also visualize the details of OC components. Extensive experiments demonstrate that RobotNet recognizes OC components more accurately and efficiently than others. The inference speed of the optimized RobotNet increases by an order of magnitude. RobotNet has lower computational complexity than other studies. The visualization results also show that our recognition method is effective.

scholarly journals Fish larvae exploit edge vortices along their dorsal and ventral fin folds to propel themselves

2016 ◽  
Vol 13 (116) ◽  
pp. 20160068 ◽  
Author(s):  
Gen Li ◽  
Ulrike K. Müller ◽  
Johan L. van Leeuwen ◽  
Hao Liu
Keyword(s):  
Larval Fish ◽  
Fish Larvae ◽  
Fluid Dynamic ◽  
Three Dimensional ◽  
Reynolds Numbers ◽  
Bony Fish ◽  
The Body ◽  
Functional Explanation ◽  
Image Velocimetry ◽  
Median Fins

Larvae of bony fish swim in the intermediate Reynolds number ( Re ) regime, using body- and caudal-fin undulation to propel themselves. They share a median fin fold that transforms into separate median fins as they grow into juveniles. The fin fold was suggested to be an adaption for locomotion in the intermediate Reynolds regime, but its fluid-dynamic role is still enigmatic. Using three-dimensional fluid-dynamic computations, we quantified the swimming trajectory from body-shape changes during cyclic swimming of larval fish. We predicted unsteady vortices around the upper and lower edges of the fin fold, and identified similar vortices around real larvae with particle image velocimetry. We show that thrust contributions on the body peak adjacent to the upper and lower edges of the fin fold where large left–right pressure differences occur in concert with the periodical generation and shedding of edge vortices. The fin fold enhances effective flow separation and drag-based thrust. Along the body, net thrust is generated in multiple zones posterior to the centre of mass. Counterfactual simulations exploring the effect of having a fin fold across a range of Reynolds numbers show that the fin fold helps larvae achieve high swimming speeds, yet requires high power. We conclude that propulsion in larval fish partly relies on unsteady high-intensity vortices along the upper and lower edges of the fin fold, providing a functional explanation for the omnipresence of the fin fold in bony-fish larvae.

scholarly journals A faster escape does not enhance survival in zebrafish larvae

2017 ◽  
Vol 284 (1852) ◽  
pp. 20170359 ◽  
Author(s):  
Arjun Nair ◽  
Christy Nguyen ◽  
Matthew J. McHenry
Keyword(s):  
High Speed ◽  
Larval Fish ◽  
Body Position ◽  
Three Dimensional ◽  
Limited Range ◽  
The Body ◽  
Model Parameters ◽  
Fish Prey ◽  
Zebrafish Larvae ◽  
Fish Predators

An escape response is a rapid manoeuvre used by prey to evade predators. Performing this manoeuvre at greater speed, in a favourable direction, or from a longer distance have been hypothesized to enhance the survival of prey, but these ideas are difficult to test experimentally. We examined how prey survival depends on escape kinematics through a novel combination of experimentation and mathematical modelling. This approach focused on zebrafish ( Danio rerio ) larvae under predation by adults and juveniles of the same species. High-speed three-dimensional kinematics were used to track the body position of prey and predator and to determine the probability of behavioural actions by both fish. These measurements provided the basis for an agent-based probabilistic model that simulated the trajectories of the animals. Predictions of survivorship by this model were found by Monte Carlo simulations to agree with our observations and we examined how these predictions varied by changing individual model parameters. Contrary to expectation, we found that survival may not be improved by increasing the speed or altering the direction of the escape. Rather, zebrafish larvae operate with sufficiently high locomotor performance due to the relatively slow approach and limited range of suction feeding by fish predators. We did find that survival was enhanced when prey responded from a greater distance. This is an ability that depends on the capacity of the visual and lateral line systems to detect a looming threat. Therefore, performance in sensing, and not locomotion, is decisive for improving the survival of larval fish prey. These results offer a framework for understanding the evolution of predator–prey strategy that may inform prey survival in a broad diversity of animals.

Development of an Inverse Plume Model for Mass Eruption Rate in Unsteady Conditions

2021 ◽  
Author(s):  
Stephen A Solovitz
Keyword(s):  
Laboratory Data ◽  
Model Performance ◽  
Volcanic Eruptions ◽  
Reynolds Numbers ◽  
Model Parameters ◽  
Plume Height ◽  
Eruption Rate ◽  
Mass Eruption Rate ◽  
Downstream Effects ◽  
Order Of Magnitude

Abstract Following volcanic eruptions, forecasters need accurate estimates of mass eruption rate (MER) to appropriately predict the downstream effects. Most analyses use simple correlations or models based on large eruptions at steady conditions, even though many volcanoes feature significant unsteadiness. To address this, a superposition model is developed based on a technique used for spray injection applications, which predicts plume height as a function of the time-varying exit velocity. This model can be inverted, providing estimates of MER using field observations of a plume. The model parameters are optimized using laboratory data for plumes with physically-relevant exit profiles and Reynolds numbers, resulting in predictions that agree to within 10% of measured exit velocities. The model performance is examined using a historic eruption from Stromboli with well-documented unsteadiness, again providing MER estimates of the correct order of magnitude. This method can provide a rapid alternative for real-time forecasting of small, unsteady eruptions.

scholarly journals Workstation benchmark of Spark Capable Genome Analysis ToolKit 4 Variant Calling

2020 ◽  
Author(s):  
Marcus H. Hansen ◽  
Anita T. Simonsen ◽  
Hans B. Ommen ◽  
Charlotte G. Nyvold
Keyword(s):  
Dna Sequencing ◽  
Genome Analysis ◽  
High Speed ◽  
High Performance ◽  
Variant Calling ◽  
Amplicon Sequencing ◽  
Targeted Sequencing ◽  
Sequencing Analysis ◽  
Genome Analysis Toolkit ◽  
Order Of Magnitude

AbstractBackgroundRapid and practical DNA-sequencing processing has become essential for modern biomedical laboratories, especially in the field of cancer, pathology and genetics. While sequencing turn-over time has been, and still is, a bottleneck in research and diagnostics, the field of bioinformatics is moving at a rapid pace – both in terms of hardware and software development. Here, we benchmarked the local performance of three of the most important Spark-enabled Genome analysis toolkit 4 (GATK4) tools in a targeted sequencing workflow: Duplicate marking, base quality score recalibration (BQSR) and variant calling on targeted DNA sequencing using a modest hyperthreading 12-core single CPU and a high-speed PCI express solid-state drive.ResultsCompared to the previous GATK version the performance of Spark-enabled BQSR and HaplotypeCaller is shifted towards a more efficient usage of the available cores on CPU and outperforms the earlier GATK3.8 version with an order of magnitude reduction in processing time to analysis ready variants, whereas MarkDuplicateSpark was found to be thrice as fast. Furthermore, HaploTypeCallerSpark and BQSRPipelineSpark were significantly faster than the equivalent GATK4 standard tools with a combined ∼86% reduction in execution time, reaching a median rate of ten million processed bases per second, and duplicate marking was reduced ∼42%. The called variants were found to be in close agreement between the Spark and non-Spark versions, with an overall concordance of 98%. In this setup, the tools were also highly efficient when compared execution on a small 72 virtual CPU/18-node Google Cloud cluster.ConclusionIn conclusion, GATK4 offers practical parallelization possibilities for DNA sequence processing, and the Spark-enabled tools optimize performance and utilization of local CPUs. Spark utilizing GATK variant calling is several times faster than previous GATK3.8 multithreading with the same multi-core, single CPU, configuration. The improved opportunities for parallel computations not only hold implications for high-performance cluster, but also for modest laboratory or research workstations for targeted sequencing analysis, such as exome, panel or amplicon sequencing.

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