System Of Hydra Research Articles

Hydra: Computer Vision for Online Data Quality Monitoring

Hydra is a system utilizing computer vision for near real-time data quality monitoring. Currently operational across all of Jefferson Lab’s experimental halls, it reduces the workload of shift takers by autonomously monitoring diagnostic plots during experiments. Hydra uses "off-the-shelf" supervised learning technologies and is supported by a comprehensive MySQL database. To simplify access, web apps have been developed to facilitate both labeling and monitoring of Hydra’s inferences. Hydra can connect with the alarm system and incorporates complete historical tracking, enabling it to identify issues that shift takers could miss. When issues are detected, a natural first question is: "Why does Hydra think there is a problem?" To answer, Hydra employs Gradient-weighted Class Activation Maps (GradCAM) to identify regions of the image that are important for the specific classification. This interpretive layer enhances transparency and trustworthiness, which is essential for integration with experiment workflows and operation. The Hydra system, results, and sociological considerations for deployment will be discussed.

A New Look at the HS Hydrae System

Abstract A growing group of stellar triple systems contains an eclipsing binary for which the depth of eclipses has been proven to change in time, a sign of evolving orbital inclination. The recent analysis of historical observations of HS Hya significantly extended the timespan over which the inclination changes are known for this system. Here we add a few more observations and reanalyze the whole data set with a single methodology. We also improve our own analytical approach to enable describing the secular evolution of the orbital architecture of hierarchical triple systems applicable to the HS Hya case. Analyzing the available photometric and spectroscopic data we obtain two main results. First, the dynamical evolution itself allows to constrain the masses of the stars in the inner binary to 1.31 ± 0.03 M ⊙ and 1.27 ± 0.03 M ⊙, and the mass of the unseen third component to 0.56 − 0.09 + 0.12 M ⊙ (all 95% confidence level results). This makes it an M- or K-type dwarf accompanying the binary. Second, the orbital planes of the inner binary and the third component are significantly noncoplanar, allowing two solutions for their mutual angle J. Either the motion of the third component is prograde, and J is most likely in the 50°–65° range, or the motion is retrograde, and J is most likely in the 120°–150° range. The precession period of both orbital planes about the total angular angular momentum is ∼700 yr (with about two centuries of uncertainty). This implies HS Hya will become eclipsing again around the year 2200.

Identification of Components of the Hippo Pathway in Hydra and Potential Role of YAP in Cell Division and Differentiation.

The Hippo signaling pathway has been shown to be involved in regulating cellular identity, cell/tissue size maintenance and mechanotransduction. The Hippo pathway consists of a kinase cascade which determines the nucleo-cytoplasmic localization of YAP in the cell. YAP is the effector protein in the Hippo pathway, which acts as a transcriptional cofactor for TEAD. Phosphorylation of YAP upon activation of the Hippo pathway prevents it from entering the nucleus and abrogates its function in the transcription of the target genes. In Cnidaria, the information on the regulatory roles of the Hippo pathway is virtually lacking. Here, we report the existence of a complete set of Hippo pathway core components in Hydra for the first time. By studying their phylogeny and domain organization, we report evolutionary conservation of the components of the Hippo pathway. Protein modelling suggested the conservation of YAP-TEAD interaction in Hydra. Further, we characterized the expression pattern of the homologs of yap, hippo, mob and sav in Hydra using whole-mount RNA in situ hybridization and report their possible role in stem cell maintenance. Immunofluorescence assay revealed that Hvul_YAP expressing cells occur in clusters in the body column and are excluded in the terminally differentiated regions. Actively proliferating cells marked by Ki67 exhibit YAP colocalization in their nuclei. Strikingly, a subset of these colocalized cells is actively recruited to the newly developing bud. Disruption of the YAP-TEAD interaction increased the budding rate indicating a critical role of YAP in regulating cell proliferation in Hydra. Collectively, we posit that the Hippo pathway is an essential signaling system in Hydra; its components are ubiquitously expressed in the Hydra body column and play a crucial role in Hydra tissue homeostasis.

A single neuron subset governs a single coactive neuron circuit in Hydra vulgaris, representing a possible ancestral feature of neural evolution

The last common ancestor of Bilateria and Cnidaria is believed to be one of the first animals to develop a nervous system over 500 million years ago. Many of the genes involved in the neural function of the advanced nervous system in Bilateria are well conserved in Cnidaria. Thus, the cnidarian Hydra vulgaris is a good model organism for the study of the putative primitive nervous system in its last common ancestor. The diffuse nervous system of Hydra consists of several peptidergic neuron subsets. However, the specific functions of these subsets remain unclear. Using calcium imaging, here we show that the neuron subsets that express neuropeptide, Hym-176, function as motor circuits to evoke longitudinal contraction. We found that all neurons in a subset defined by the Hym-176 gene (Hym-176A) or its paralogs (Hym-176B) expression are excited simultaneously, followed by longitudinal contraction. This indicates not only that these neuron subsets have a motor function but also that a single molecularly defined neuron subset forms a single coactive circuit. This is in contrast with the bilaterian nervous system, where a single molecularly defined neuron subset harbors multiple coactive circuits, showing a mixture of neurons firing with different timings. Furthermore, we found that the two motor circuits, one expressing Hym-176B in the body column and the other expressing Hym-176A in the foot, are coordinately regulated to exert region-specific contraction. Our results demonstrate that one neuron subset is likely to form a monofunctional circuit as a minimum functional unit to build a more complex behavior in Hydra. This simple feature (one subset, one circuit, one function) found in Hydra may represent the simple ancestral condition of neural evolution.

HyDRa: discrete polishing

New hydrodynamic improvements have been developed in order to enable pulsed polishing with the HyDRa system. The operational parameters of the tool are not affected by these modifications, i.e., tool bias and the tool’s floating capability are not lost, and a linear erosion function is produced. The minimum removal is no longer ruled by maximum computer numerical control speed, allowing for high-precision removal that can be taken from zero to the maximum attainable of the tool, in minimum increments of 3.5 nm / ms. This modification also improves the convergence rate of the polishing process toward the desired surface. This development guarantees a high-speed, pulsed operation that enables the tool to be used in a variety of polishing modes, ranging from discrete pixel to continuous pulse width modulation (PWM) polishing. This new capability opens a wide range of applications that can now be tackled with the system, such as zonal and tessellated polishing. PWM capability also allows for simultaneous, multi-head polishing of large optical surfaces.

G protein-coupled receptor signal transduction and Ca2+ signaling pathways of the allatotropin/orexin system in Hydra

Allatotropin is a pleiotropic peptide originally characterized in insects. The existence of AT neuropeptide signaling was proposed in other invertebrates. In fact, we previously proposed the presence of an AT-like system regulating feeding behavior in Hydra sp. Even in insects, the information about the AT signaling pathway is incomplete. The aim of this study is to analyze the signaling cascade activated by AT in Hydra plagiodesmica using a pharmacological approach. The results show the involvement of Ca2+ and IP3 signaling in the transduction pathway of the peptide. Furthermore, we confirm the existence of a GPCR system involved in this pathway, that would be coupled to a Gq subfamily of Gα protein, which activates a PLC, inducing an increase in IP3 and cytosolic Ca2+. To the best of our knowledge, this work represents the first in vivo approach to study the overall signaling pathway and intracellular events involved in the myoregulatory effect of AT in Hydra sp.

Comparative Aspects of Structure and Function of Cnidarian Neuropeptides.

Cnidarians are early-branching animals in the eukaryotic tree of life. The phylum Cnidaria are divided into five classes: Scyphozoa (true jellyfish), Cubozoa (box jellyfish), Hydrozoa (species, Hydra and Hydractinia), Anthozoa (sea anemone, corals, and sea pen), and Staurozoa (stalked jellyfish). Peptides play important roles as signaling molecules in development and differentiation in cnidaria. For example, cnidaria use peptides for cell-to cell communication. Recent discoveries show that Hydra neuropeptides control several biological processes including muscle contraction, neuron differentiation, and metamorphosis. Here, I describe the structure and functions of neuropeptides in Hydra and other cnidarian species. I also discuss that so-called primitive nervous system of Hydra is in more complex than generally believed. I also discuss how cnidaria use peptides for communication among cells rather than in higher animals.

Effect of Valproic Acid on Morphology and Behavior of Hydra viridissima : Possibility of using Hydra for Screening Neuromodulators

Nervous system of Hydra responds to mechanical, chemical, light and temperature stimuli, despite lack of organizational complexities like ganglion or sense organs. Nerve net of Hydra shows remarkable similarities with vertebrates at cellular and molecular level. Chemical and electrical synapses of Hydra modulate array of behavioral responses exhibited by Hydra . We have assayed toxicity and tested effect of Valproic Acid (VPA), an anti-epileptic drug on Hydra . We have performed whole animal toxicity testing, cytological staining using toluidine blue and assayed feeding behavior post VPA treatment. We conclude mild toxicity and loss of cell organization pattern in tentacles of Hydra upon prolonged VPA exposure. Our results indicate the possibility of using invertebrates like Hydra for screening of chemical modulators of molecular pathways.

Regionalized nervous system in Hydra and the mechanism of its development

The last common ancestor of Bilateria and Cnidaria is considered to develop a nervous system over 500 million years ago. Despite the long course of evolution, many of the neuron-related genes, which are active in Bilateria, are also found in the cnidarian Hydra. Thus, Hydra is a good model to study the putative primitive nervous system in the last common ancestor that had the great potential to evolve to a more advanced one. Regionalization of the nervous system is one of the advanced features of bilaterian nervous system. Although a regionalized nervous system is already known to be present in Hydra, its developmental mechanisms are poorly understood. In this study we show how it is formed and maintained, focusing on the neuropeptide Hym-176 gene and its paralogs. First, we demonstrate that four axially localized neuron subsets that express different combination of the neuropeptide Hym-176 gene and its paralogs cover almost an entire body, forming a regionalized nervous system in Hydra. Second, we show that positional information governed by the Wnt signaling pathway plays a key role in determining the regional specificity of the neuron subsets as is the case in bilaterians. Finally, we demonstrated two basic mechanisms, regionally restricted new differentiation and phenotypic conversion, both of which are in part conserved in bilaterians, are involved in maintaining boundaries between the neuron subsets. Therefore, this study is the first comprehensive analysis of the anatomy and developmental regulation of the divergently evolved and axially regionalized peptidergic nervous system in Hydra, implicating an ancestral origin of neural regionalization.

Rethinking the Role of the Nervous System: Lessons From the Hydra Holobiont

Here we evaluate our current understanding of the function of the nervous system in Hydra, a non-bilaterian animal which is among the first metazoans that contain neurons. We highlight growing evidence that the nervous system, with its rich repertoire of neuropeptides, is involved in controlling resident beneficial microbes. We also review observations that indicate that microbes affect the animal's behavior by directly interfering with neuronal receptors. These findings provide new insight into the original role of the nervous system, and suggest that it emerged to orchestrate multiple functions including host-microbiome interactions. The excitement of future research in the Hydra model now relies on uncovering the common rules and principles that govern the interaction between neurons and microbes and the extent to which such laws might apply to other and more complex organisms.

Features of the accretion in the EX Hydrae system: Results of numerical simulation

A two dimensional numerical model in the axisymmetric approximation that describes the flow structure in the magnetosphere of the white dwarf in the EX Hya system has been developed. Results of simulations show that the accretion in EX Hya proceeds via accretion columns, that are not closed and have curtain-like shapes. The thickness of the accretion curtains depends only weakly on the thickness of the accretion disk. This thickness developed in the simulations does not agree with observations. It is concluded that the main reason for the formation of thick accretion curtains in the used model is the assumption that the magnetic field penetrates fully into the plasma of the disk. An analysis based on simple estimates shows that a diamagnetic disk that fully or partially shields the magnetic field of the star may be a more attractive explanation for the observed features of the accretion in EX Hya.

Non-overlapping Neural Networks in Hydra vulgaris

To understand the emergent properties of neural circuits, it would be ideal to record the activity of every neuron in a behaving animal and decode how it relates to behavior. We have achieved this with the cnidarian Hydra vulgaris, using calcium imaging of genetically engineered animals to measure the activity of essentially all of its neurons. Although the nervous system of Hydra is traditionally described as a simple nerve net, we surprisingly find instead a series of functional networks that are anatomically non-overlapping and are associated with specific behaviors. Three major functional networks extend through the entire animal and are activated selectively during longitudinal contractions, elongations in response to light, and radial contractions, whereas an additional network is located near the hypostome and is active during nodding. These results demonstrate the functional sophistication of apparently simple nerve nets, and the potential of Hydra and other basal metazoans as a model system for neural circuit studies.

THE EFFECTS OF SELF-SHADOWING BY A PUFFED-UP INNER RIM IN SCATTERED LIGHT IMAGES OF PROTOPLANETARY DISKS

We explore whether protoplanetary disks with self-shadowing from puffed-up inner rims exhibit observable features in scattered light images. We use both self-consistent hydrostatic equilibrium calculations and parameterized models to produce the vertically puffed-up inner rims. We find that, in general, the transition between the shadowed and flared regions occurs in a smooth manner over a broad radius range, and no sudden jump exists at the outer edge of the shadow in either the disk temperature or density structures. As a result, a puffed-up rim cannot create sharp ring/arc/spiral-arm-like features in the outer disk as have been detected in recent direct near-infrared imaging of disks. On the other hand, if the puffed-up rim has a sharp edge in the vertical direction, the shadowing effect can produce a distinct three-stage broken power law in the radial intensity profile of the scattered light, with two steep surface brightness radial profiles in the inner and outer disk joined by a shallow transition region around the shadow edge. These types of scattered light profiles may have already been observed, such as in the recent Subaru direct imaging of the TW Hydrae system.

MP23-08 INITIAL VALIDATION DURING DEVELOPMENT OF LOW COST ALTERNATIVE TO THE DV-TRAINER USING THE HYDRA SYSTEM

You have accessJournal of UrologyTechnology & Instruments: Surgical Education & Skills Assessment II1 Apr 2015MP23-08 INITIAL VALIDATION DURING DEVELOPMENT OF LOW COST ALTERNATIVE TO THE DV-TRAINER USING THE HYDRA SYSTEM Swar Shah, Eric Hwang, Inderbir Gill, and Andrew Hung Swar ShahSwar Shah More articles by this author , Eric HwangEric Hwang More articles by this author , Inderbir GillInderbir Gill More articles by this author , and Andrew HungAndrew Hung More articles by this author View All Author Informationhttps://doi.org/10.1016/j.juro.2015.02.1251AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookTwitterLinked InEmail INTRODUCTION AND OBJECTIVES Robotic simulation is a popular training modality. However, simulators are costly, driving a push for lower cost options to improve access to training. Herein, we evaluate the face, content, and construct validity of a proof-of-concept simulation platform developed by Mimic Technologies, Inc. using third party, off-the-shelf gaming controllers (Hydra System) on existing virtual (VR) and procedure-specific augmented reality (AR) and procedure-specific VR (PS VR) exercises previously validated on the dV-Trainer (dVT). METHODS Participants were classified as novice (no robot experience, n=21) or expert (≥30 console cases, n=9) and prospectively assessed on a VR suturing task, robotic partial nephrectomy procedure-specific AR module, and PS VR suturing task on both the Hydra and dVT platforms. Post exercise and post study questionnaires assessed realism of simulation (face validity) and utility for training (content validity), as well as user feedback for each system via Likert scale. Integrated tasks and questions in the AR module were assessed. Questionnaire responses, as well as novice and expert performance data, were compared using t tests to establish face, content, and construct validity. RESULTS Face Validity: Experts rated Hydra “very realistic” on the AR module (4/5 (2-5)), but less so for VR and PS VR tasks. VR on Hydra was significantly less realistic than dVT (p=0.02), with no difference in PS VR and AR. Content Validity: On the AR module, Hydra had content validity for training residents, and teaching anatomy and operation steps (4-5/5). The Hydra VR and PS VR tasks had lower content validity, with the VR task rating significantly less for training residents and teaching technical skills (p=0.01 and 0.005, respectively). Construct Validity: For the VR task construct validity was seen in 4 of 7 metrics (p ≤ 0.03) on Hydra and 6 of 7 metrics (p ≤0.04) on dVT. Hydra did not show construct validity in the AR module and PS VR task. User Feedback: Hydra was rated “moderately” easy, comfortable, and smooth to use (3/5 (1-4) each). The interface was rated “fair” (2/5 (1-3)), versus “very good” for dVT (4/5 (3-5), p= <0.0001). CONCLUSIONS This proof-of-concept, low-cost prototype based on the Hydra System for robotic simulation demonstrates face and content validity in an AR module for teaching residents cognitive content (anatomy and steps). The prototype has construct validity presently limited to VR basic skills tasks. This data is valuable for defining platform refinements, and highlights the role of early validation during simulation development. © 2015 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 193Issue 4SApril 2015Page: e270 Advertisement Copyright & Permissions© 2015 by American Urological Association Education and Research, Inc.MetricsAuthor Information Swar Shah More articles by this author Eric Hwang More articles by this author Inderbir Gill More articles by this author Andrew Hung More articles by this author Expand All Advertisement Advertisement PDF DownloadLoading ...

MP23-09 A NOVEL TECHNIQUE FOR SIMULATED SURGICAL PROCEDURES USING 3D PRINTING TECHNOLOGY

INTRODUCTION AND OBJECTIVES: Robotic simulation is a popular training modality. However, simulators are costly, driving a push for lower cost options to improve access to training. Herein, we evaluate the face, content, and construct validity of a proof-of-concept simulation platform developed by Mimic Technologies, Inc. using third party, off-the-shelf gaming controllers (Hydra System) on existing virtual (VR) and procedure-specific augmented reality (AR) and procedure-specific VR (PS VR) exercises previously validated on the dV-Trainer (dVT). METHODS: Participants were classified as novice (no robot experience, n1⁄421) or expert ( 30 console cases, n1⁄49) and prospectively assessed on a VR suturing task, robotic partial nephrectomy procedure-specific AR module, and PS VR suturing task on both the Hydra and dVT platforms. Post exercise and post study questionnaires assessed realism of simulation (face validity) and utility for training (content validity), as well as user feedback for each system via Likert scale. Integrated tasks and questions in the AR module were assessed. Questionnaire responses, as well as novice and expert performance data, were compared using t tests to establish face, content, and construct validity. RESULTS: Face Validity: Experts rated Hydra “very realistic” on the AR module (4/5 (2-5)), but less so for VR and PS VR tasks. VR on Hydra was significantly less realistic than dVT (p1⁄40.02), with no difference in PS VR and AR. Content Validity: On the AR module, Hydra had content validity for training residents, and teaching anatomy and operation steps (4-5/5). The Hydra VR and PS VR tasks had lower content validity, with the VR task rating significantly less for training residents and teaching technical skills (p1⁄40.01 and 0.005, respectively). Construct Validity: For the VR task construct validity was seen in 4 of 7 metrics (p 0.03) on Hydra and 6 of 7 metrics (p 0.04) on dVT. Hydra did not show construct validity in the AR module and PS VR task. User Feedback: Hydra was rated “moderately” easy, comfortable, and smooth to use (3/5 (1-4) each). The interface was rated “fair” (2/5 (1-3)), versus “very good” for dVT (4/5 (3-5), p1⁄4 <0.0001). CONCLUSIONS: This proof-of-concept, low-cost prototype based on the Hydra System for robotic simulation demonstrates face and content validity in an AR module for teaching residents cognitive content (anatomy and steps). The prototype has construct validity presently limited to VR basic skills tasks. This data is valuable for defining platform refinements, and highlights the role of early validation during simulation development.

Hydra, a candidate for an alternative model in environmental genomics

The need for nonmammalian and nonvertebrate experimental systems for toxicology is increasing because of growing concern about animal welfare. Hydra, a genus of freshwater cnidarian, has been used in classical toxicology for more than 40 years and has been recommended as a standard model for ecotoxicology. Functional assays using Hydra homologues of the signal molecules and transcription factors of other metazoans have demonstrated that Hydra shares the common molecular mechanisms for pattern formation with bilaterian animals. The availability of the Hydra genome and mRNA information has meant that it can be used as a model organism in biological sciences. The purpose of this review is to explore recent developments in our understanding of the molecular aspects of axis formation, bud formation, regeneration, and the nervous system in Hydra and to introduce Hydra as an alternative animal model in environmental toxicogenomics for predicting the toxicity of environmental pollutants at the molecular level.

Automatic Real-Time River Traffic Monitoring Based on Artificial Vision Techniques

Artificial vision techniques derived from computer vision and autonomous robotic systems have been successfully employed for river traffic monitoring and management. For this purpose, ARGOS and HYDRA systems have been developed by Achimedes Logica in collaboration with Sapienza University of Rome under the EU initiatives URBAN and MOBILIS for the monitoring of the boat traffic in Venice on the Gran Canal and the harbour area. These advanced systems provide an efficient automatic traffic monitoring to guarantee navigation safety and regular flow while producing and distributing information about the traffic. The systems are based on the processing of digital images that are gathered by survey cell stations distributed throughout the supervised area providing a visual platform on which the system displays recent and live traffic conditions in a synthetic way similar to radar view. ARGOS and HYDRA systems are programmed to automatically recognize and notice situations of great interest in whatever sea or land-targeted security applications including environmental, perimeter, and security control. This article describes the wide spectrum of applications of these two systems, that is, monitoring traffic and automatically tracking position, speed and direction of all vehicles.

Molecular characterization of Hydra acetylcholinesterase and its catalytic activity

A full-length cDNA encoding an acetylcholinesterase (AChE) from Hydra magnipapillata was isolated. All of the important aromatic residues that line a catalytic gorge in cholinesterases of other species were conserved, but the sequences of peripheral anionic and choline binding sites were not. Hydra AChE, expressed in Xenopus oocytes, showed AChE activity. The gene was expressed in both ectodermal and endodermal epithelial cells except for the tentacles and basal disk. AChE gene expression was not detected in the regenerating tips in either the head or the foot, indicating that regeneration is controlled by the non-neuronal cholinergic system in Hydra.

Uncovering the evolutionary history of innate immunity: The simple metazoan Hydra uses epithelial cells for host defence

Although many properties of the innate immune system are shared among multicellular animals, the evolutionary origin remains poorly understood. Here we characterize the innate immune system in Hydra, one of the simplest multicellular animals known. In the complete absence of both protective mechanical barriers and mobile phagocytes, Hydra ’s epithelium is remarkably well equipped with potent antimicrobial peptides to prevent pathogen infection. Induction of antimicrobial peptide production is mediated by the interaction of a leucine-rich repeats (LRRs) domain containing protein with a TIR-domain containing protein lacking LRRs. Conventional Toll-like receptors (TLRs) are absent in the Hydra genome. Our findings support the hypothesis that the epithelium represents the ancient system of host defence.

Neuropeptides and their functions inHydra

In order to identify novel peptide signaling molecules involved in the regulation of developmental and physiological processes in the freshwater cnidarian, Hydra magnipapillata, we initiated a systematic peptide screening project, the Hydra Peptide Project. In the project, twelve neuropeptides were identified so far. The LWamide family is composed of seven members, which share a GLWamide motif at their C-termini. All the peptides have an ability to induce metamorphosis of Hydractinia serrata planula larvae into polyps. In Hydra, LWamides induce detachment of the bud from a parental polyp. A neuropeptide, Hym-355, enhances neuronal differentiation by inducing the multipotent interstitial stem cells to enter the neuron differentiation pathway. A myoactive neutopeptide, Hym-176, specifically and reversibly induces contraction of the ectodermal muscle of the body column, in particularly in the peduncle region of epithelial Hydra that totally lack nerve cells. Two members of a novel neuropeptide family (FRamides) were contained in the same precursor. However, they have opposite myoactive functions in epithelial hydra. From these results, it seems fair to say reasonable to conclude that the so-called 'primitive' nervous system of Hydra is in reality more complex than generally believed.