236 results on '"Ryan JF"'
Search Results
2. Peer Review #2 of "Diffusion tubes: a method for the mass culture of ctenophores and other pelagic marine invertebrates (v0.1)"
- Author
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Ryan, JF, additional
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- 2020
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3. Metastatic tumour in the parotid gland
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Lim, KT, Singh, D, Ryan, JF, McDonnell, L, and Lennon, F
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- 2003
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4. Ultrafast optical response of Tl2Ba2CuO6+delta
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Smith, DC, Gay, P, Stevens, CJ, Wang, DZ, Wang, JH, Ren, ZF, and Ryan, JF
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Condensed Matter::Superconductivity ,Physics::Optics - Abstract
We present the first measurements of the ultrafast optical response of Tl2Ba2CuO6+delta and show that the optical response is clearly sensitive to the electronic groundstate. In the superconducting state its decay can be interpreted as following the reformation of superconducting pairs and the dynamics of quasiparticles near the nodes in a d-mave gap.
- Published
- 2016
5. Anisotropy of the non-equilibrium quasiparticle dynamics in single crystals of YBa2Cu3O7-delta
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Stevens, CJ, Gay, P, Smith, DC, Chen, C, and Ryan, JF
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We report for the first time, measurements of ultrafast transients from YBCO in which the contributions from a- and b-axis response are separately identified using polarised light. A new signal is observed for E parallel to a which has been obscured in all previous thin film experiments. Comparing the two contributions we find the new signal to be sensitive to T-c whilst the signal for E parallel to b exhibits pseudogap behaviour.
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- 2016
6. Spin and charge density excitations and the collapse of the fractional quantum Hall state at nu=1/3
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Davies, HDM, Harris, JC, Ryan, JF, and Turberfield, AJ
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Inelastic light scattering from 2D electrons below 100 mK reveals collective charge and spin density excitations of the incompressible electron liquid at Landau level filling factor v -1/3 and provides experimental evidence for a magnetoroton minimum in the charge density dispersion curve. The temperature scale for the collapse of electron correlation in the spin-polarized electron liquid is determined by thermal excitation of long-wavelength spin waves.
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- 2016
7. Time-resolved exciton dynamics and stimulated emission from ZnCdSe/ZnSe multiple quantum well structures
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Taylor, RA, Adams, RA, Ryan, JF, and Park, RM
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Condensed Matter::Materials Science ,Condensed Matter::Other ,Condensed Matter::Mesoscopic Systems and Quantum Hall Effect - Abstract
Time-resolved luminescence has been used to investigate the dynamics of excitonic recombination and stimulated emission in ZnCdSe/ZnSe multiple quantum wells where the exciton binding energy is close to the optical phonon energy. At low excitation densities strong excitonic recombination is observed with simple exponential decay kinetics. At densities near threshold, however, bilinear recombination kinetics are found with a large rate constant (R = 1.8 x 10(-3) s(-1) cm(2)), and a dramatic reduction in the lifetime is observed. Stimulated emission occurs at an energy similar to 18 meV below the exciton absorption peak, and shifts to lower energy with increasing excitation density up to three times the threshold density. These observations are consistent with recombination in a dense exciton system, which gives way at high density to a correlated electron-hole plasma.
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- 2016
8. Role of chi((3)) anisotropy in the generation of squeezed light in semiconductors
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Dabbicco, M., A. Mark Fox, Vonplessen, G., and Ryan, Jf
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Condensed Matter::Materials Science - Abstract
We have measured the real n2 and imaginary β parts of the χ(3) nonlinear susceptibility in polycrystalline ZnS and ZnSe and its anisotropy σ in cubic ZnSe near half-band-gap using femtosecond spectroscopy. We obtain values in good agreement with recent studies. The dispersion of n2 and β in polycrystalline ZnSe is compared with two- and four-band model calculations. The dispersion of n2 and βstrongly affects the pulse transmission through thick samples, and has been included in a model that describes the pulse spectrum after self-phase modulation. The χ(3) nonlinearity allows for both self-phase modulation and cross-phase modulation, and we demonstrate that both effects can efficiently generate squeezed light in semiconductors by four-wave mixing.
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- 2016
9. Photoexcited carrier relaxation and localization in Bi2Sr2Ca1-yYyCu2O 8 and YBa2Cu3U7-δ: A study by femtosecond time-resolved spectroscopy
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Thomas, TN, Stevens, CJ, Choudhary, AJS, Ryan, JF, Mihailovic, D, Mertelj, T, Forro, L, Wagner, G, and Evetts, JE
- Abstract
Ultrafast time-resolved optical absorption has been measured as a function of doping and temperature in Bi2Sr2Ca1-yYyCu2O 8 (0
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- 2016
10. Squeezed light generation in semiconductor waveguides
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Ryan, JF, Ward, MB, and Brown, J
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- 2016
11. Role of spin excitations in the fractional quantum Hall effect at nu=1/3
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Harris, JC, Davies, HDM, Ryan, JF, and Turberfield, AJ
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We report resonant inelastic light scattering measurements of collective electronic excitations at filling factor v = 1/3 in a high mobility 2DES at temperatures between 50 mK and 3 K. In a narrow range of temperatures near 1 K the intensity of light scattering from the charge density mode, and the exchange enhancement of the energy of a collective spin excitation, fall rapidly to zero. We deduce that the electron correlation characteristic of the spin-polarized electron liquid at v = 1/3 collapses at 1 K: this collapse is triggered by thermal fluctuations of the electron spin. (C) 1998 Elsevier Science B.V. All rights reserved.
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- 2016
12. Evidence of asymmetry in cohesion and assembly of both leaflets of purple membranes
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Voitchovsky, K., Sonia Contera, Kamihira, M., Watts, A., and Ryan, Jf
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- 2016
13. Fermi-edge singularities in single modulation-doped v-groove quantum wires
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Hauert, M, Roshan, R, Maciel, AC, Kim, J, Ryan, JF, Schwarz, A, Kaluza, A, Schapers, T, and Luth, H
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Condensed Matter::Materials Science ,Physics::Optics ,Condensed Matter::Mesoscopic Systems and Quantum Hall Effect - Abstract
We report photoluminescence and photoluminescence excitation spectroscopy of the one-dimensional electron system confined in single, modulation-doped v-groove quantum wire using a variable-temperature, scanning nearfield optical microscope. This technique permits the study of 1D Fermi edge singularity in the absence of inter-wire inhomogeneous broadening.
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- 2016
14. OPTICAL-DETECTION OF THE INTEGER AND FRACTIONAL QUANTUM HALL-EFFECTS IN GAAS AT MILLIKELVIN TEMPERATURES
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Andrew Turberfield, Haynes, Sr, Wright, Pa, Ford, Ra, Clark, Rg, Ryan, Jf, Harris, Jj, and Foxon, Ct
- Published
- 2016
15. Relationship between growth, structure and superconductivity of single crystal YBa2Cu3O7-delta
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Chen, C, Wondre, FR, Hodby, JW, Ryan, JF, Narlikar, AV, and Samanta, SB
- Abstract
We study the crystal growth of YBa2Cu3O7-delta with additives, using ac susceptibility, X-ray diffraction and STM. One specific additive, BaF2, dramatically improves both the crystal growth and the superconducting properties. A cluster growth model is proposed to describe the function of the additive. F- reduces the Al contamination of Cu-O chains, and the orthorhombicity increases. On a nanometer scale, the roughness of the chains decreases markedly. Superconductivity is further enhanced using noncontaminating crucibles. Large single crystals with T-C = 93.7 K and Delta T-C = 0.1 K were grown in Y2O3 or BaZrO3 crucibles using the BaF2 additive.
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- 2016
16. Characterization of beta-amyloid(1-40) incorporated in model membranes: peptide conformation, acyl chain order, vesicle morphology, supported bilayer topography, and channel activity
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de Planque, MR, Contera, Sa, Gabriel Mendes, Rijkers, Dt, Ryan, Jf, and Watts, A.
- Published
- 2016
17. Exciton recombination dynamics in ZnCdSe/ZnSe quantum wells
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Taylor, RA, Adams, RA, Ryan, JF, and Park, RM
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Condensed Matter::Materials Science ,Condensed Matter::Other ,Physics::Optics ,Condensed Matter::Mesoscopic Systems and Quantum Hall Effect - Abstract
We present results of time-resolved luminescence experiments performed on Zn0.80Cd0.20Se/ZnSe quantum well laser structures as a function of carrier density and temperature. It is found that in narrow wells, where quantum confinement effects are strong, the luminescence is excitonic over all temperatures at densities up to and above threshold. For wide wells the luminescence is observed to cross over to a bimolecular decay profile at high temperature and density, which corresponds to the formation of a correlated electron-hole plasma.
- Published
- 2016
18. Reconstitution of homomeric GluA2(flop) receptors in supported lipid membranes: functional and structural properties
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Baranovic, J, Ramanujan, CS, Kasai, N, Midgett, CR, Madden, DR, Torimitsu, K, and Ryan, JF
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nervous system - Abstract
AMPA receptors (AMPARs) are glutamate-gated ion channels ubiquitous in the vertebrate central nervous system, where they mediate fast excitatory neurotransmission and act as molecular determinants of memory formation and learning. Together with detailed analyses of individual AMPAR domains, structural studies of full-length AMPARs by electron microscopy and x-ray crystallography have provided important insights into channel assembly and function. However, the correlation between the structure and functional states of the channel remains ambiguous particularly because these functional states can be assessed only with the receptor bound within an intact lipid bilayer. To provide a basis for investigating AMPAR structure in a membrane environment, we developed an optimized reconstitution protocol using a receptor whose structure has previously been characterized by electron microscopy. Single-channel recordings of reconstituted homomeric GluA2(flop) receptors recapitulate key electrophysiological parameters of the channels expressed in native cellular membranes. Atomic force microscopy studies of the reconstituted samples provide high-resolution images of membrane-embedded full-length AMPARs at densities comparable to those in postsynaptic membranes. The data demonstrate the effect of protein density on conformational flexibility and dimensions of the receptors and provide the first structural characterization of functional membrane-embedded AMPARs, thus laying the foundation for correlated structure-function analyses of the predominant mediators of excitatory synaptic signals in the brain.
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- 2016
19. Antiferrodistortive structural phase transition in the Jahn-Teller system DyKMoO. II. Magnetic field dependence
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Mihailović, D and Ryan, JF
- Abstract
We have measured the magnetic field dependence of the electronic excitations of DyKMoO, which undergoes a cooperative Jahn-Teller distortion at T=14 K. The Raman spectrum shows two modes at 2 K which split into a number of peaks with increasing field. New low-energy excitations are observed which are interpreted as arising from the splitting of the ground and excited states. The energies of these lines vary monotonically with fields up to 9 T for fields parallel to the crystallographic directions X and Y. However, for fields at intermediate directions in the x-y plane the energies are found to change abruptly at a critical value which is direction-dependent. This effect is interpreted as being due to the creation of a new form of distortion. The authors have developed a mean-field model for this field-induced ordering, which provides a satisfactory qualitative description of the experimental results. © 1987 IOP Publishing Ltd.
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- 2016
20. Time-resolved bandgap renormalization and gain in GaN epilayers
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Hess, S, Taylor, RA, Ryan, JF, Beaumont, B, Gibart, P, Cain, NJ, Roberts, V, and Roberts, JS
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Condensed Matter::Materials Science ,genetic structures ,Physics::Optics - Abstract
We present optical gain and loss spectra measured over a range of carrier densities at low temperature in hexagonal GaN epilayers. We have determined the optical loss directly to be similar to 80 cm(-1). Photoluminescence spectra show that stimulated emission in our samples arises from electron-hole plasma recombination. Time-resolved pump-probe transmission experiments have shown that there is considerable bandgap renormalization for carrier densities at which stimulated emission occurs.
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- 2016
21. MEASUREMENTS OF HOT CARRIER RELAXATION AND RECOMBINATION IN GaAs QUANTUM WELLS BY PICOSECOND OPTICAL PROBING
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Ryan, JF, Taylor, RA, and Turberfield, AJ
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Condensed Matter::Materials Science ,Physics::Optics - Abstract
In this paper the authors show how picosecond time-resolved photoluminescence can be used to probe the energy relaxation of hot carriers in semiconductor structures. In addition, by measuring the variation of luminescence lifetime with carrier density one can obtain information about radiative and nonradiative decay processes. These processes are important in all photonic devices, but especially so in structures where interfaces may have a particularly strong influence.
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- 2016
22. Interpretation of the femtosecond optical response of YBa2Cu3O7-delta - Reply
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Stevens, CJ, Smith, DC, Ryan, JF, Podobnik, B, and Mihailovic, D
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- 2016
23. The late Oliver Fitzgerald
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Lim, KT, Singh, D, Ryan, JF, McDonnell, L, and Lennon, F
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- 2003
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24. Morphine-Induced Myoclonic Movements in a Pediatric Pain Patient
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de Armendi Aj, Ryan Jf, and Fahey M
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Male ,Myoclonus ,Involuntary movement ,Pain, Postoperative ,Dose-Response Relationship, Drug ,Morphine ,business.industry ,Neurological disorder ,medicine.disease ,Anesthesiology and Pain Medicine ,El Niño ,Child, Preschool ,Anesthesia ,Pediatric pain ,Humans ,Medicine ,medicine.symptom ,Infusions, Intravenous ,business ,medicine.drug - Published
- 1993
25. ZEBULON MENNELL
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Ryan Jf
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Anesthesiology and Pain Medicine ,business.industry ,Medicine ,business ,Classics - Published
- 1954
26. GROWTH OF GAINAS/INP MULTI-QUANTUM-WELL PIN PHOTODIODE STRUCTURES BY ATMOSPHERIC-PRESSURE MOVPE
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Scott, Md, Davies, Ji, Riffat, Jr, Ryan, Jf, A. Mark Fox, and Maciel, Ac
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- 1987
27. Extraction of an alpha-helical peptide from a lipid bilayer: Dynamic Force Spectroscopy and Molecular Dynamics
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Sonia Contera, Lemaitre, V., Planque, Mrr, Watts, A., and Ryan, Jf
28. EVALUATION OF GAAS/AL0.3GA0.7AS MULTIPLE-QUANTUM-WELL WAVE-GUIDES FOR PULSED SQUEEZED-LIGHT GENERATION
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A. Mark Fox, Huttner, B., Ryan, Jf, Pate, Ma, and Roberts, Js
- Abstract
We have measured the nonlinear refractive index n2 and two-photon absorption coefficient in GaAs/Al0.3Ga0.7As multiple-quantum-well waveguides in the band tail region about 45 meV below the n=1 heavy hole exciton absorption line. At 883 nm we find that =1.9×10-8 cm W-1 and that n2-1×10-12 cm2 W-1. The linear loss coefficient is measured to be 6.3 cm-1 at the same wavelength. Based on these values, we estimate that up to 4.5 dB pulsed squeezing is possible. © 1994 The American Physical Society.
29. Interactions between transmembrane beta-amyloid(1-40) and phosphatidylcholine bilayers
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Planque, Mrr, Gabriel Mendes, Contera, Sa, Rijkers, Dts, Ryan, Jf, and Watts, A.
30. Continuous Intercostal Nerve Blocks for Postoperative Pain Relief
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Haley Rw, O'Connell Ct, Ablondi Ma, and Ryan Jf
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medicine.medical_specialty ,Anesthesiology and Pain Medicine ,Postoperative pain relief ,business.industry ,Anesthesia ,medicine ,Intercostal nerves ,business ,Surgery - Published
- 1966
31. Structural and functional characterization of reconstituted alpha − amino − 3 − hydroxy − 5 − methyl − 4 − isoxazole propionic acid receptors
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Baranovic, J and Ryan, JF
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Biophysics ,Neurosciences - Abstract
This thesis describes a novel reconstitution of α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid receptors (AMPARs) for the purposes of structural characterization by atomic force microscopy (AFM) and functional characterization by electrical recordings of lipid bilayers. AMPARs are glutamate gated ion channels, ubiquitous in the vertebrate central nervous system where they mediate fast excitatory neurotransmission. In a healthy brain, AMPARs are involved in memory formation and learning and their dysfunction has been related to numerous neurological disorders such as Alzheimer's disease, epilepsy, schizophrenia and many others. AMPARs were reconstituted at high and low densities. Densely reconstituted samples contained >100 receptors per μm2, a value comparable to the AMPAR density at synapses. This allowed, for the first time, the imaging of full length tetrameric AMPARs in native-like conditions and with clearly assigned domains: the extracellular domains extended 14 nm above the membrane in agreement with electron microscopy (EM) and X-ray crystallography data. Lipid-protein interactions were studied in samples with low protein density with the receptors showing preference for lipids in the liquid crystalline phase. The activity of the reconstituted receptors was confirmed through single-channel recordings. This is the first case in which an AMPAR has been reconstituted and given (a) single-channel recordings with (b) physiologically plausible conductance levels and (c) pharmacological and no-protein controls and (d) structure. As a result, previously reported biochemistry and EM are now for the first time available in concert with AFM and single-channel recordings for a purified AMPAR of known composition.
- Published
- 2017
32. Variation in Lip Shape and Aesthetics in the Young Female Population: A Statistical Atlas Study.
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Ryan JF, Ishii LE, Dey JK, Nellis JC, Desai SC, Boahene KDO, and Ishii M
- Abstract
Background: The distribution of lip shapes in young females and how morphological variation relates to attractiveness are poorly defined. Objectives: We hypothesized that among young female lip images generated by a statistical atlas model, those with more full lips compared with those with less full lips would be perceived as more attractive as measured by anonymous survey participants. Method: A statistical atlas of lip morphology was created using photographs of 700 women aged 18-35 years. The average lip shape was determined by coregistering and averaging images. Morphological variation was analyzed using principal component analysis. The relationship between attractiveness and observed lip morphologies was assessed using publicly distributed surveys. Results: In total, 428 survey responses were obtained. We developed a statistical model of variation of lip shape in the population and its relationship to attractiveness. The most attractive lips were significantly fuller than the average shape in the population, with greater vertical height and surface area. Conclusion: A statistical atlas can provide a visual guide to variation in lip shape in the population. The most attractive lip shapes vary significantly from the population average, lending support to procedures that increase lip height and surface area.
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- 2024
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33. An AI-generated proteome-scale dataset of predicted protein structures for the ctenophore Mnemiopsis leidyi.
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Moreland RT, Zhang S, Barreira SN, Ryan JF, and Baxevanis AD
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- Animals, Databases, Protein, Protein Conformation, Proteomics methods, Computational Biology methods, Ctenophora chemistry, Ctenophora genetics, Proteome chemistry, Proteome analysis
- Abstract
This Dataset Brief describes the computational prediction of protein structures for the ctenophore Mnemiopsis leidyi. Here, we report the proteome-scale generation of 15,333 protein structure predictions using AlphaFold, as well as an updated implementation of publicly available search, manipulation, and visualization tools for these protein structure predictions through the Mnemiopsis Genome Project Portal (https://research.nhgri.nih.gov/mnemiopsis). The utility of these predictions is demonstrated by highlighting comparisons to experimentally determined structures for the light-sensitive protein mnemiopsin 1 and the ionotropic glutamate receptor (iGluR). The application of these novel protein structure prediction methods will serve to further position non-bilaterian species such as Mnemiopsis as powerful model systems for the study of early animal evolution and human health., (© 2024 The Authors. PROTEOMICS published by Wiley‐VCH GmbH. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.)
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- 2024
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34. Functional analysis of ctenophore Shaker K + channels: N-type inactivation in the animal roots.
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Simonson BT, Jegla M, Ryan JF, and Jegla T
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- Animals, Amino Acid Sequence, Phylogeny, Oocytes metabolism, Ctenophora metabolism, Ctenophora genetics, Shaker Superfamily of Potassium Channels metabolism, Shaker Superfamily of Potassium Channels genetics, Shaker Superfamily of Potassium Channels chemistry, Ion Channel Gating
- Abstract
Here we explore the evolutionary origins of fast N-type ball-and-chain inactivation in Shaker (Kv1) K
+ channels by functionally characterizing Shaker channels from the ctenophore (comb jelly) Mnemiopsis leidyi. Ctenophores are the sister lineage to other animals and Mnemiopsis has >40 Shaker-like K+ channels, but they have not been functionally characterized. We identified three Mnemiopsis channels (MlShak3-5) with N-type inactivation ball-like sequences at their N termini and functionally expressed them in Xenopus oocytes. Two of the channels, MlShak4 and MlShak5, showed rapid inactivation similar to cnidarian and bilaterian Shakers with rapid N-type inactivation, whereas MlShak3 inactivated ∼100-fold more slowly. Fast inactivation in MlShak4 and MlShak5 required the putative N-terminal inactivation ball sequences. Furthermore, the rate of fast inactivation in these channels depended on the number of inactivation balls/channel, but the rate of recovery from inactivation did not. These findings closely match the mechanism of N-type inactivation first described for Drosophila Shaker in which 1) inactivation balls on the N termini of each subunit can independently block the pore, and 2) only one inactivation ball occupies the pore binding site at a time. These findings suggest classical N-type activation evolved in Shaker channels at the very base of the animal phylogeny in a common ancestor of ctenophores, cnidarians, and bilaterians and that fast-inactivating Shakers are therefore a fundamental type of animal K+ channel. Interestingly, we find evidence from functional co-expression experiments and molecular dynamics that MlShak4 and MlShak5 do not co-assemble, suggesting that Mnemiopsis has at least two functionally independent N-type Shaker channels., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 Biophysical Society. Published by Elsevier Inc. All rights reserved.)- Published
- 2024
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35. Morphological and dietary changes encoded in the genome of Beroe ovata , a ctenophore-eating ctenophore.
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Vargas AM, DeBiasse MB, Dykes LL, Edgar A, Hayes TD, Groso DJ, Babonis LS, Martindale MQ, and Ryan JF
- Abstract
As the sister group to all other animals, ctenophores (comb jellies) are important for understanding the emergence and diversification of numerous animal traits. Efforts to explore the evolutionary processes that promoted diversification within Ctenophora are hindered by undersampling genomic diversity within this clade. To address this gap, we present the sequence, assembly and initial annotation of the genome of Beroe ovata . Beroe possess unique morphology, behavior, ecology and development. Unlike their generalist carnivorous kin, beroid ctenophores feed exclusively on other ctenophores. Accordingly, our analyses revealed a loss of chitinase, an enzyme critical for the digestion of most non-ctenophore prey, but superfluous for ctenophorivores. Broadly, our genomic analysis revealed that extensive gene loss and changes in gene regulation have shaped the unique biology of B. ovata . Despite the gene losses in B. ovata , our phylogenetic analyses on photosensitive opsins and several early developmental regulatory genes show that these genes are conserved in B. ovata . This additional sampling contributes to a more complete reconstruction of the ctenophore ancestor and points to the need for extensive comparisons within this ancient and diverse clade of animals. To promote further exploration of these data, we present BovaDB (http://ryanlab.whitney.ufl.edu/bovadb/), a portal for the B. ovata genome., (© The Author(s) 2024. Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics.)
- Published
- 2024
- Full Text
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36. Redefining Trauma Training in Canada: A National Delphi Study on Curriculum, Educational Resources, and Training Initiatives.
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Ryan JF, Engels PT, Vogt KN, Minor S, and Mador BD
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- Humans, Delphi Technique, Canada, Needs Assessment, Clinical Competence, Curriculum, Internship and Residency
- Abstract
Objective: This study aims to develop a set of curriculum recommendations to support trauma training in Canadian general surgery residency programs., Design: A modified Delphi study was conducted with a panel of trauma and surgical education experts. Proposed curriculum components were developed from Canadian trauma surgery exposure and educational needs assessment data. Panelists were asked to rate each potential curriculum component for inclusion (mandatory or exemplary) or exclusion in the ideal and feasible trauma training curriculum., Setting: This national Delphi study was conducted in the Canadian trauma education context., Participants: A panel of trauma experts and surgeons holding leadership positions in training programs and professional societies across Canada were invited to participate., Results: Nineteen panelists representing all geographic regions of Canada achieved consensus on a set of curriculum components. The panel was largely in agreement with the RCPSC trauma competencies. At the end of the study, 71 items were considered mandatory for all programs (such as dedicated trauma rotations, trauma resuscitation and operative skills courses, structured trauma teaching within academic half day, and simulation experiences), and 21 items were considered exemplary (such as program funding for trauma courses, and opportunities to participate in trauma research and quality improvement projects)., Conclusions: This study suggests a framework of education components for curricular reform for trauma training in Canadian general surgery residency programs. Such recommendations include rotations, formal courses and certifications, education resources, and simulation experiences to supplement limited clinical exposure., (Copyright © 2023 Association of Program Directors in Surgery. Published by Elsevier Inc. All rights reserved.)
- Published
- 2024
- Full Text
- View/download PDF
37. The ctenophore Mnemiopsis leidyi deploys a rapid injury response dating back to the last common animal ancestor.
- Author
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Mitchell DG, Edgar A, Mateu JR, Ryan JF, and Martindale MQ
- Subjects
- Animals, Wound Healing, Transcription Factors, Ctenophora genetics
- Abstract
Regenerative potential is widespread but unevenly distributed across animals. However, our understanding of the molecular mechanisms underlying regenerative processes is limited to a handful of model organisms, restricting robust comparative analyses. Here, we conduct a time course of RNA-seq during whole body regeneration in Mnemiopsis leidyi (Ctenophora) to uncover gene expression changes that correspond with key events during the regenerative timeline of this species. We identified several genes highly enriched in this dataset beginning as early as 10 minutes after surgical bisection including transcription factors in the early timepoints, peptidases in the middle timepoints, and cytoskeletal genes in the later timepoints. We validated the expression of early response transcription factors by whole mount in situ hybridization, showing that these genes exhibited high expression in tissues surrounding the wound site. These genes exhibit a pattern of transient upregulation as seen in a variety of other organisms, suggesting that they may be initiators of an ancient gene regulatory network linking wound healing to the initiation of a regenerative response., (© 2024. The Author(s).)
- Published
- 2024
- Full Text
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38. Building Affordable, Durable, Medium-fidelity Ballistic Gel Phantoms for Ultrasound-guided Nerve Block Training.
- Author
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Marsh-Armstrong BP, Ryan JF, Mariano DJ, Suresh PJ, and Supat B
- Subjects
- Humans, Phantoms, Imaging, Ultrasonography, Silicones, Ultrasonography, Interventional, Nerve Block
- Abstract
Ultrasound phantoms - alternatives to live human tissue - give learners the opportunity to practice ultrasound-guided regional anesthesia without introducing undue risk to patients. Gelatin-based phantoms provide educators with durable and reusable task trainers; however, commercially available gel-based phantoms are expensive. Here, we investigate the production of durable, low-cost, ballistic gel-based ultrasound phantoms for median, femoral, suprainguinal fascia iliaca plane, and serratus anterior plane nerve blocks, as well as a methodology for producing a phantom for any ultrasound-guided nerve block procedure. Computer-aided design (CAD) software was utilized to design four phantoms replicating the anatomy of median, femoral, suprainguinal fascia iliaca plane, and serratus anterior plane nerve blocks, including relevant landmarks and tissue planes. Plastic models of the desired tissue planes were 3D printed and used to create silicone molds. Ballistic gel was melted and mixed with flour and dye to create a liquid, echogenic ballistic gel, which was poured into the silicone molds. Vessels were simulated by creating negative space in the ballistic gel using metal rods. Nerves were simulated using yarn submerged in ultrasound gel. Simulated bones were designed using CAD and 3D printed. Ballistic gel is a versatile, durable medium that can be used to simulate a variety of tissues and can be melted and molded into any shape. Under ultrasound, these phantoms provide realistic tissue planes that represent the borders between different layers of skin, muscle, and fascia. The echogenicity of the muscle tissue layers, nerves, vessels, and bones is realistic, and bones have significant posterior shadowing as would be observed in a human subject. These phantoms cost $200 each for the first phantom and $60 for each subsequent phantom. These phantoms require some technical skill to design, but they can be built for just 4% of the cost of their commercial counterparts.
- Published
- 2024
- Full Text
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39. Validity Evidence for Procedure-specific Competence Assessment Tools in Orthopaedic Surgery: A Scoping Review.
- Author
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Li Y, Chan R, Menon MRG, Ryan JF, Mador B, Campbell SM, and Turner SR
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- Educational Measurement methods, Orthopedics, Clinical Competence, Orthopedic Procedures
- Abstract
Introduction: Competency-based training requires frequent assessment of residents' skills to determine clinical competence. This study reviews existing literature on procedure-specific competence assessment tools in orthopaedic surgery., Methods: A systematic search of eight databases up to May 2023 was conducted. Two reviewers independently assessed validity evidence and educational utility of each assessment tool and evaluated studies' methodological quality., Results: Database searching identified 2,556 unique studies for title and abstract screening. Full texts of 290 studies were reviewed; 17 studies met the inclusion criteria. Bibliography review identified another five studies, totaling 22 studies examining 24 assessment tools included in the analysis. These tools assessed various orthopaedic surgery procedures within trauma, sports medicine, spine, and upper extremity. Overall validity evidence was low across all studies, and was lowest for consequences and highest for content. Methodological quality of studies was moderate. Educational utility assessment was not explicitly done for most tools., Discussion: The paucity of current procedure-specific assessment tools in orthopaedic surgery lacks the validity evidence required to be used reliably in high-stake summative assessments. Study strengths include robust methodology and use of an evidence-based validity evidence framework. Poor-quality existing evidence is a limitation and highlights the need for evidence-based tools across more subspecialties., (Copyright © 2024 The Authors. Published by Wolters Kluwer Health, Inc. on behalf of the American Academy of Orthopaedic Surgeons.)
- Published
- 2024
- Full Text
- View/download PDF
40. Erector spinae plane blocks for analgesia after percutaneous nephrolithotomy A pathway to reduce opioids.
- Author
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Berger JH, Abdou W, Roberts JL, Leach M, Ryan JF, Attaluri SV, Finneran JJ, Sur RL, Monga M, and Bechis SK
- Abstract
Introduction: Despite its minimally invasive nature, percutaneous nephrolithotomy (PCNL ) may be associated with significant pain. Challenges in pain control may prevent timely discharge (and expose patients to adverse effects of opioid use). We sought to evaluate whether our patients who underwent erector spinae plane (ESP) regional blocks experienced improved postoperative pain control and decreased opioid use after PCNL (compared with those who did not receive blocks)., Methods: We retrospectively reviewed consecutive PCNL cases on patients admitted for greater than 24 hours without pre-existing opioid regimens for chronic pain. Cases were completed by a single high-volume surgeon. Patients who accepted an ESP block were compared to those who did not receive a block. Patients received either a single injection or a disposable pump delivering intermittent boluses of ropivacaine 0.2%. Demographic and perioperative data were analyzed. The primary outcomes were opioid use measured in morphine milligram equivalent (MME ) and patient-reported pain scores during the first 24 hours of hospitalization., Results: From March 2019 to August 2021, 44 patients were identified who met criteria - 28 of whom received an ESP block (including 14 continuous blocks). The patients who received blocks had significantly decreased opioid use (18.3 vs. 81.3 MME, p=0.004) and a longer mean time to first non-zero pain score (p=0.004). Continuous blocks had similar opioid use to single shot blocks (21.0 vs. 15.6 MME, p=0.952)., Conclusions: ESP regional blocks appear to offer an effective adjunct method for pain control after PCNL and may reduce post-PCNL opioid use while maintaining adequate patient analgesia.
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- 2023
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41. Surgeon Factors Influencing Breast Surgery Outcomes: A Scoping Review to Define the Modern Breast Surgical Oncologist.
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Ryan JF, Lesniak DM, Cordeiro E, Campbell SM, and Rajaee AN
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- Female, Humans, Breast pathology, Mastectomy methods, Mastectomy, Segmental methods, Breast Neoplasms surgery, Breast Neoplasms pathology, Oncologists, Surgeons
- Abstract
Background: Modern breast surgical oncology incorporates many aspects of care including preoperative workup, surgical management, and multidisciplinary collaboration to achieve favorable oncologic outcomes and high patient satisfaction. However, there is variability in surgical practice and outcomes. This review aims to identify modifiable surgeon factors influencing breast surgery outcomes and provide a definition of the modern breast surgical oncologist., Methods: A systematic literature search with additional backward citation searching was conducted. Studies describing modifiable surgeon factors with associated breast surgery outcomes such as rates of breast conservation, sentinel node biopsy, re-excision, complications, acceptable esthetic outcome, and disease-free and overall survival were included. Surgeon factors were categorized for qualitative analysis., Results: A total of 91 studies met inclusion criteria describing both modifiable surgeon factor and outcome data. Four key surgeon factors associated with improved breast surgery outcomes were identified: surgical volume (45 studies), use of oncoplastic techniques (41 studies), sub-specialization in breast surgery or surgical oncology (9 studies), and participation in professional development activities (5 studies)., Conclusions: On the basis of the literature review, the modern breast surgical oncologist has a moderate- to high-volume breast surgery practice, understands the use and application of oncoplastic breast surgery, engages in additional training opportunities, maintains memberships in relevant societies, and remains up to date on key literature. Surgeons practicing in breast surgical oncology can target these modifiable factors for professional development and quality improvement., (© 2023. Society of Surgical Oncology.)
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- 2023
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42. Cytoplasmic Polyadenylation Is an Ancestral Hallmark of Early Development in Animals.
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Rouhana L, Edgar A, Hugosson F, Dountcheva V, Martindale MQ, and Ryan JF
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- Animals, Phylogeny, Polyadenylation, Ctenophora genetics, Sea Anemones genetics
- Abstract
Differential regulation of gene expression has produced the astonishing diversity of life on Earth. Understanding the origin and evolution of mechanistic innovations for control of gene expression is therefore integral to evolutionary and developmental biology. Cytoplasmic polyadenylation is the biochemical extension of polyadenosine at the 3'-end of cytoplasmic mRNAs. This process regulates the translation of specific maternal transcripts and is mediated by the Cytoplasmic Polyadenylation Element-Binding Protein family (CPEBs). Genes that code for CPEBs are amongst a very few that are present in animals but missing in nonanimal lineages. Whether cytoplasmic polyadenylation is present in non-bilaterian animals (i.e., sponges, ctenophores, placozoans, and cnidarians) remains unknown. We have conducted phylogenetic analyses of CPEBs, and our results show that CPEB1 and CPEB2 subfamilies originated in the animal stem lineage. Our assessment of expression in the sea anemone, Nematostella vectensis (Cnidaria), and the comb jelly, Mnemiopsis leidyi (Ctenophora), demonstrates that maternal expression of CPEB1 and the catalytic subunit of the cytoplasmic polyadenylation machinery (GLD2) is an ancient feature that is conserved across animals. Furthermore, our measurements of poly(A)-tail elongation reveal that key targets of cytoplasmic polyadenylation are shared between vertebrates, cnidarians, and ctenophores, indicating that this mechanism orchestrates a regulatory network that is conserved throughout animal evolution. We postulate that cytoplasmic polyadenylation through CPEBs was a fundamental innovation that contributed to animal evolution from unicellular life., (© The Author(s) 2023. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)
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- 2023
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43. Genome-Scale Analysis Reveals Extensive Diversification of Voltage-Gated K+ Channels in Stem Cnidarians.
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Lara A, Simonson BT, Ryan JF, and Jegla T
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- Animals, Humans, Phylogeny, Genome, Signal Transduction, Cnidaria genetics, Potassium Channels, Voltage-Gated genetics, Sea Anemones genetics
- Abstract
Ion channels are highly diverse in the cnidarian model organism Nematostella vectensis (Anthozoa), but little is known about the evolutionary origins of this channel diversity and its conservation across Cnidaria. Here, we examined the evolution of voltage-gated K+ channels in Cnidaria by comparing genomes and transcriptomes of diverse cnidarian species from Anthozoa and Medusozoa. We found an average of over 40 voltage-gated K+ channel genes per species, and a phylogenetic reconstruction of the Kv, KCNQ, and Ether-a-go-go (EAG) gene families identified 28 voltage-gated K+ channels present in the last common ancestor of Anthozoa and Medusozoa (23 Kv, 1 KCNQ, and 4 EAG). Thus, much of the diversification of these channels took place in the stem cnidarian lineage prior to the emergence of modern cnidarian classes. In contrast, the stem bilaterian lineage, from which humans evolved, contained no more than nine voltage-gated K+ channels. These results hint at a complexity to electrical signaling in all cnidarians that contrasts with the perceived anatomical simplicity of their neuromuscular systems. These data provide a foundation from which the function of these cnidarian channels can be investigated, which will undoubtedly provide important insights into cnidarian physiology., (© The Author(s) 2023. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)
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- 2023
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44. Reconstruction in open anterior skull base surgery: A review and algorithmic approach.
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Ryan JF, Tanavde VA, Gallia GL, Boahene KDO, London NR Jr, and Desai SC
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- Humans, Surgical Flaps, Nose surgery, Skull Base surgery, Retrospective Studies, Plastic Surgery Procedures, Skull Base Neoplasms surgery
- Abstract
Purpose: Defects resulting from open resection of anterior skull base neoplasms are difficult to reconstruct. Our objective was to review the literature and describe an evidence-based algorithm that can guide surgeons reconstructing anterior skull base defects., Methods: A research librarian designed database search strategies. Two investigators independently reviewed the resulting abstracts and full text articles. Studies on reconstruction after open anterior skull base resection were included. Studies of lateral and posterior skull base reconstruction, endoscopic endonasal surgery, traumatic and congenital reconstruction were excluded. Based on the review, a reconstructive algorithm was proposed., Results: The search strategy identified 603 unique abstracts. 53 articles were included. Adjacent subsites resected, defect size, radiotherapy history, and contraindications to free tissue transfer were identified as key factors influencing decision making and were used to develop the algorithm. Discussion of the reconstructive ladder as it applies to skull base reconstruction and consideration of patient specific factors are reviewed. Patients with a prior history of radiotherapy or with simultaneous resection of multiple anatomic subsites adjacent to the anterior skull base will likely benefit from free tissue transfer., Conclusions: Reconstruction of anterior skull base defects requires knowledge of the available reconstructive techniques and consideration of defect-specific and patient-specific factors., Competing Interests: Declaration of competing interest No competing financial interests exist., (Copyright © 2022 Elsevier Inc. All rights reserved.)
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- 2023
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45. Single-cell atavism reveals an ancient mechanism of cell type diversification in a sea anemone.
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Babonis LS, Enjolras C, Reft AJ, Foster BM, Hugosson F, Ryan JF, Daly M, and Martindale MQ
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- Animals, Biological Evolution, Gene Expression Regulation, Transcription Factors metabolism, Cell Differentiation, Sea Anemones metabolism
- Abstract
Cnidocytes are the explosive stinging cells unique to cnidarians (corals, jellyfish, etc). Specialized for prey capture and defense, cnidocytes comprise a group of over 30 morphologically and functionally distinct cell types. These unusual cells are iconic examples of biological novelty but the developmental mechanisms driving diversity of the stinging apparatus are poorly characterized, making it challenging to understand the evolutionary history of stinging cells. Using CRISPR/Cas9-mediated genome editing in the sea anemone Nematostella vectensis, we show that a single transcription factor (NvSox2) acts as a binary switch between two alternative stinging cell fates. Knockout of NvSox2 causes a transformation of piercing cells into ensnaring cells, which are common in other species of sea anemone but appear to have been silenced in N. vectensis. These results reveal an unusual case of single-cell atavism and expand our understanding of the diversification of cell type identity., (© 2023. The Author(s).)
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- 2023
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46. Independent Innexin Radiation Shaped Signaling in Ctenophores.
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Ortiz J, Bobkov YV, DeBiasse MB, Mitchell DG, Edgar A, Martindale MQ, Moss AG, Babonis LS, and Ryan JF
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- Animals, Phylogeny, Signal Transduction, Genome, Cell Communication physiology, Ctenophora genetics
- Abstract
Innexins facilitate cell-cell communication by forming gap junctions or nonjunctional hemichannels, which play important roles in metabolic, chemical, ionic, and electrical coupling. The lack of knowledge regarding the evolution and role of these channels in ctenophores (comb jellies), the likely sister group to the rest of animals, represents a substantial gap in our understanding of the evolution of intercellular communication in animals. Here, we identify and phylogenetically characterize the complete set of innexins of four ctenophores: Mnemiopsis leidyi, Hormiphora californensis, Pleurobrachia bachei, and Beroe ovata. Our phylogenetic analyses suggest that ctenophore innexins diversified independently from those of other animals and were established early in the emergence of ctenophores. We identified a four-innexin genomic cluster, which was present in the last common ancestor of these four species and has been largely maintained in these lineages. Evidence from correlated spatial and temporal gene expression of the M. leidyi innexin cluster suggests that this cluster has been maintained due to constraints related to gene regulation. We describe the basic electrophysiological properties of putative ctenophore hemichannels from muscle cells using intracellular recording techniques, showing substantial overlap with the properties of bilaterian innexin channels. Together, our results suggest that the last common ancestor of animals had gap junctional channels also capable of forming functional innexin hemichannels, and that innexin genes have independently evolved in major lineages throughout Metazoa., (© The Author(s) 2023. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)
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- 2023
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47. Gene Loss may have Shaped the Cnidarian and Bilaterian Hox and ParaHox Complement.
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Steinworth BM, Martindale MQ, and Ryan JF
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- Animals, Phylogeny, Genes, Homeobox, Evolution, Molecular, Cnidaria genetics, Anthozoa genetics
- Abstract
Hox and ParaHox transcription factors are important for specifying cell fates along the primary body axes during the development of most animals. Within Cnidaria, much of the research on Hox/ParaHox genes has focused on Anthozoa (anemones and corals) and Hydrozoa (hydroids) and has concentrated on the evolution and function of cnidarian Hox genes in relation to their bilaterian counterparts. Here we analyze together the full complement of Hox and ParaHox genes from species representing all four medusozoan classes (Staurozoa, Cubozoa, Hydrozoa, and Scyphozoa) and both anthozoan classes (Octocorallia and Hexacorallia). Our results show that Hox genes involved in patterning the directive axes of anthozoan polyps are absent in the stem leading to Medusozoa. For the first time, we show spatial and temporal expression patterns of Hox and ParaHox genes in the upside-down jellyfish Cassiopea xamachana (Scyphozoa), which are consistent with diversification of medusozoan Hox genes both from anthozoans and within medusozoa. Despite unprecedented taxon sampling, our phylogenetic analyses, like previous studies, are characterized by a lack of clear homology between most cnidarian and bilaterian Hox and Hox-related genes. Unlike previous studies, we propose the hypothesis that the cnidarian-bilaterian ancestor possessed a remarkably large Hox complement and that extensive loss of Hox genes was experienced by both cnidarian and bilaterian lineages., (© The Author(s) 2022. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)
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- 2023
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48. Visual Attention to Facial Defects Predicts Willingness to Pay for Reconstructive Surgery.
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Ryan JF, Ishii LE, Dey JK, Boahene KDO, Byrne PJ, and Ishii M
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- Humans, Postoperative Period, Face, Plastic Surgery Procedures methods
- Abstract
Background: The relationship between the value of reconstructive surgery and the visual attention drawn by facial deformity has not been studied. Objectives: We hypothesized that willingness to pay (WTP) for reconstructive surgery would increase as visual attention to deformity increased in a Mohs defect eye-tracking model. Methods: We conducted a randomized observational study. Eighty casual observers participated in timed eye-tracking trials utilizing preoperative and postoperative photographs from 32 patients with facial Mohs defects. Fixation on each defect was quantified in milliseconds. For each photograph, casual observers reported how much they would be willing to pay for a perfect reconstruction and rated defect severity and patient attractiveness. The associations between defect fixation time and WTP, attractiveness, and severity were modeled using a multivariate mixed-effects model. Results: Increased defect fixation time was associated with increased WTP (regression coefficient = 0.332651, p < 0.001), decreased attractiveness (regression coefficient = -0.221779, p < 0.001), and increased severity (regression coefficient = 0.363111, p < 0.001). As defect fixation time increased, WTP increased exponentially. Conclusions: Observer WTP for facial reconstruction increases exponentially as defects become more distracting. These findings justify the dedication of health care resources to reconstructive procedures that decrease attentional distraction to the greatest extent possible.
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- 2022
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49. Do Attending and Trainee Surgeons Agree on What Happens in the Operating Room During Septoplasty?
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Ryan JF, Malpani A, Naz H, Boahene KDO, Papel ID, Kontis TC, Maxwell JH, Creighton FX, Byrne PJ, Wanamaker JR, Hager GD, Vedula SS, Malekzadeh S, Ishii LE, and Ishii M
- Subjects
- Humans, Operating Rooms, Clinical Competence, Surgeons, Rhinoplasty, Otolaryngology
- Abstract
Background: Surgeons must select cases whose complexity aligns with their skill set. Objectives: To determine how accurately trainees report involvement in procedures, judge case complexity, and assess their own skills. Methods: We recruited attendings and trainees from two otolaryngology departments. After performing septoplasty, they completed identical surveys regarding case complexity, achievement of goals, who performed which steps, and trainee skill using the septoplasty global assessment tool (SGAT) and visual analog scale (VAS). Agreement regarding which steps were performed by the trainee was assessed with Cohen's kappa coefficients ( κ ). Correlations between trainee and attending responses were measured with Spearman's correlation coefficients (rho). Results: Seven attendings and 42 trainees completed 181 paired surveys. Trainees and attendings sometimes disagreed about which steps were performed by trainees (range of κ = 0.743-0.846). Correlation between attending and trainee responses was low for VAS skill ratings (range of rho = 0.12-0.34), SGAT questions (range of rho = 0.03-0.53), and evaluation of case complexity (range of rho = 0.24-0.48). Conclusion: Trainees sometimes disagree with attendings about which septoplasty steps they perform and are limited in their ability to judge complexity, goals, and their skill.
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- 2022
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50. A Chromosome-level Genome Assembly of the Highly Heterozygous Sea Urchin Echinometra sp. EZ Reveals Adaptation in the Regulatory Regions of Stress Response Genes.
- Author
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Ketchum RN, Davidson PL, Smith EG, Wray GA, Burt JA, Ryan JF, and Reitzel AM
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- Animals, Molecular Sequence Annotation, Regulatory Sequences, Nucleic Acid, Transcription Factors genetics, Chromosomes genetics, Sea Urchins genetics
- Abstract
Echinometra is the most widespread genus of sea urchin and has been the focus of a wide range of studies in ecology, speciation, and reproduction. However, available genetic data for this genus are generally limited to a few select loci. Here, we present a chromosome-level genome assembly based on 10x Genomics, PacBio, and Hi-C sequencing for Echinometra sp. EZ from the Persian/Arabian Gulf. The genome is assembled into 210 scaffolds totaling 817.8 Mb with an N50 of 39.5 Mb. From this assembly, we determined that the E. sp. EZ genome consists of 2n = 42 chromosomes. BUSCO analysis showed that 95.3% of BUSCO genes were complete. Ab initio and transcript-informed gene modeling and annotation identified 29,405 genes, including a conserved Hox cluster. E. sp. EZ can be found in high-temperature and high-salinity environments, and we therefore compared E. sp. EZ gene families and transcription factors associated with environmental stress response ("defensome") with other echinoid species with similar high-quality genomic resources. While the number of defensome genes was broadly similar for all species, we identified strong signatures of positive selection in E. sp. EZ noncoding elements near genes involved in environmental response pathways as well as losses of transcription factors important for environmental response. These data provide key insights into the biology of E. sp. EZ as well as the diversification of Echinometra more widely and will serve as a useful tool for the community to explore questions in this taxonomic group and beyond., (© The Author(s) 2022. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)
- Published
- 2022
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