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Regeneration is a complex chain of events that restores a tissue to its original size and shape. The tissue-wide coordination of cellular dynamics that is needed for proper morphogenesis is challenged by the large dimensions of regenerating body parts. Feedback mechanisms in biochemical pathways can provide effective communication across great distances1-5, but how they might regulate growth during tissue regeneration is unresolved6,7. Here we report that rhythmic travelling waves of Erk activity control the growth of bone in time and space in regenerating zebrafish scales, millimetre-sized discs of protective body armour. We find that waves of Erk activity travel across the osteoblast population as expanding concentric rings that are broadcast from a central source, inducing ring-like patterns of tissue growth. Using a combination of theoretical and experimental analyses, we show that Erk activity propagates as excitable trigger waves that are able to traverse the entire scale in approximately two days and that the frequency of wave generation controls the rate of scale regeneration. Furthermore, the periodic induction of synchronous, tissue-wide activation of Erk in place of travelling waves impairs tissue growth, which indicates that wave-distributed Erk activation is key to regeneration. Our findings reveal trigger waves as a regulatory strategy to coordinate cell behaviour and instruct tissue form during regeneration.
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Quinasas MAP Reguladas por Señal Extracelular/metabolismo , Sistema de Señalización de MAP Quinasas , Osteoblastos/citología , Osteoblastos/metabolismo , Regeneración , Pez Cebra/fisiología , Escamas de Animales/citología , Escamas de Animales/enzimología , Escamas de Animales/crecimiento & desarrollo , Escamas de Animales/fisiología , Animales , Difusión , Femenino , Masculino , Pez Cebra/crecimiento & desarrolloRESUMEN
Since 2018, our program has utilized specific psychosocial criteria and a multidisciplinary approach to assess patients for liver transplant due to alcohol-associated liver disease (ALD), rather than the 6-month abstinence rule alone. If declined based on these criteria, specific recommendations are provided to patients and their providers regarding goals for re-referral to increase the potential for future transplant candidacy. Recommendations include engagement in treatment for alcohol use disorder, serial negative biomarker testing, and maintenance of abstinence from alcohol. In our current study, we evaluate the outcomes of patients with ALD, who were initially declined upon assessment and re-referred to our program. This is a retrospective cohort study that includes 98 patients with ALD, who were previously declined for liver transplantation and were subsequently re-referred for liver transplant assessment between May 1, 2018, and December 31, 2021. We assess the outcomes of patients who were re-referred including acceptance for transplantation following a second assessment. Of the 98 patients who were re-referred, 46 (46.9%) fulfilled the recommendations made and proceeded to further medical evaluation. Nine were eventually transplanted; others are listed and are waiting for transplant. The presence of a partner was independently associated with a higher rate of acceptance (OR 0.16, 95% CI: 0.03-0.97, p = 0.05). Most of the patients who did not proceed further (n = 52) were declined again due to ALD contraindications (n = 33, 63.4%), including ongoing drinking and lack of engagement in recommended addiction treatment. Others had medical contraindications (11.2%), clinically improved (6.1%), had adherence issues (5.1%), or lack of adequate support (2%). Patients with ALD previously declined for a liver transplant can be re-referred and successfully accepted for transplantation by fulfilling the recommendations made by the multidisciplinary team. Important factors including ongoing abstinence, engagement in addiction treatment, and social support are key for successful acceptance.
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Alcoholismo , Hepatopatías Alcohólicas , Trasplante de Hígado , Humanos , Trasplante de Hígado/efectos adversos , Estudios Retrospectivos , Hepatopatías Alcohólicas/cirugía , Hepatopatías Alcohólicas/complicaciones , Consumo de Bebidas Alcohólicas/efectos adversos , Consumo de Bebidas Alcohólicas/epidemiología , Alcoholismo/complicacionesRESUMEN
In this article, it is shown experimentally that a planar laser-generated ultrasound source with a hard reflective backing will generate higher acoustic pressures than a comparable source with an acoustically matched backing when the stress confinement condition is not met. Furthermore, while the source with an acoustically matched backing will have a broader bandwidth when the laser pulse is short enough to ensure stress confinement, the bandwidths of both source types will converge as the laser pulse duration increases beyond stress confinement. The explanation of the results is supported by numerical simulations.
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How chromatin shapes pathways that promote genome-epigenome integrity in response to DNA damage is an issue of crucial importance. We report that human bromodomain (BRD)-containing proteins, the primary "readers" of acetylated chromatin, are vital for the DNA damage response (DDR). We discovered that more than one-third of all human BRD proteins change localization in response to DNA damage. We identified ZMYND8 (zinc finger and MYND [myeloid, Nervy, and DEAF-1] domain containing 8) as a novel DDR factor that recruits the nucleosome remodeling and histone deacetylation (NuRD) complex to damaged chromatin. Our data define a transcription-associated DDR pathway mediated by ZMYND8 and the NuRD complex that targets DNA damage, including when it occurs within transcriptionally active chromatin, to repress transcription and promote repair by homologous recombination. Thus, our data identify human BRD proteins as key chromatin modulators of the DDR and provide novel insights into how DNA damage within actively transcribed regions requires chromatin-binding proteins to orchestrate the appropriate response in concordance with the damage-associated chromatin context.
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Cromatina/metabolismo , Daño del ADN , Recombinación Homóloga/genética , Receptores de Superficie Celular/metabolismo , Autoantígenos/metabolismo , Línea Celular Tumoral , Regulación de la Expresión Génica , Silenciador del Gen , Humanos , Complejo Desacetilasa y Remodelación del Nucleosoma Mi-2/metabolismo , Unión Proteica , Transporte de Proteínas/genética , Receptores de Cinasa C Activada , Receptores de Superficie Celular/genética , Proteínas Supresoras de TumorRESUMEN
Regeneration has fascinated scientists since well before the 20th century revolutions in genetics and molecular biology. The field of regenerative biology has grown steadily over the past decade, incorporating advances in imaging, genomics and genome editing to identify key cell types and molecules involved across many model organisms. Yet for many or most tissues, it can be difficult to predict when and how findings from these studies will advance regenerative medicine. Establishing technologies to stimulate regrowth of a lost or amputated limb with a patterned replicate, as salamanders do routinely, is one of the most challenging directives of tissue regeneration research. Here, we speculate upon what research avenues the field must explore to move closer to this capstone achievement.
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Extremidades/fisiología , Regeneración/fisiología , Medicina Regenerativa/métodos , Animales , Regeneración Ósea/fisiología , Epigenómica , Humanos , Modelos Biológicos , Urodelos/fisiología , Cicatrización de Heridas/fisiologíaRESUMEN
Optical generation of ultrasound using nanosecond duration laser pulses has generated great interest both in industrial and biomedical applications. The availability of portable laser devices using semiconductor technology and optical fibres, as well as numerous source material types based on nanocomposites, has proliferated the applications of laser ultrasound. The nanocomposites can be deposited on the tip of optical fibres as well as planar hard and soft backing materials using various fabrication techniques, making devices suitable for a variety of applications. The ability to choose the acoustic material properties and the laser pulse duration gives considerable control over the ultrasound output. Here, an analytical time-domain solution is derived for the acoustic pressure waveform generated by a planar optical ultrasound source consisting of an optically absorbing layer on a backing. It is shown that by varying the optical attenuation coefficient, the thickness of the absorbing layer, the acoustic properties of the materials, and the laser pulse duration, a wide variety of pulse shapes and trains can be generated. It is shown that a source with a reflecting backing can generate pulses with higher amplitude than a source with an acoustically-matched backing in the same circumstances when stress-confinement has not been satisfied.
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Over the past decade, the range of applications in biomedical ultrasound exploiting 3D printing has rapidly expanded. For wavefront shaping specifically, 3D printing has enabled a diverse range of new, low-cost approaches for controlling acoustic fields. These methods rely on accurate knowledge of the bulk acoustic properties of the materials; however, to date, robust knowledge of these parameters is lacking for many materials that are commonly used. In this work, the acoustic properties of eight 3D-printed photopolymer materials were characterised over a frequency range from 1 to 3.5 MHz. The properties measured were the frequency-dependent phase velocity and attenuation, group velocity, signal velocity, and mass density. The materials were fabricated using two separate techniques [PolyJet and stereolithograph (SLA)], and included Agilus30, FLXA9960, FLXA9995, Formlabs Clear, RGDA8625, RGDA8630, VeroClear, and VeroWhite. The range of measured density values across all eight materials was 1120-1180 kg · m-3, while the sound speed values were between 2020 to 2630 m · s-1, and attenuation values typically in the range 3-9 dB · MHz-1· cm-1.
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In contrast to mammals, adult zebrafish have a high capacity to regenerate damaged or lost myocardium through proliferation of cardiomyocytes spared from damage. The epicardial sheet covering the heart is activated by injury and aids muscle regeneration through paracrine effects and as a multipotent cell source, and has received recent attention as a target in cardiac repair strategies. Although it is recognized that epicardium is required for muscle regeneration and itself has high regenerative potential, the extent of cellular heterogeneity within epicardial tissue is largely unexplored. Here, we performed transcriptome analysis on dozens of epicardial lineage cells purified from zebrafish harboring a transgenic reporter for the pan-epicardial gene tcf21. Hierarchical clustering analysis suggested the presence of at least three epicardial cell subsets defined by expression signatures. We validated many new pan-epicardial and epicardial markers by alternative expression assays. Additionally, we explored the function of the scaffolding protein and main component of caveolae, caveolin 1 (cav1), which was present in each epicardial subset. In BAC transgenic zebrafish, cav1 regulatory sequences drove strong expression in ostensibly all epicardial cells and in coronary vascular endothelial cells. Moreover, cav1 mutant zebrafish generated by genome editing showed grossly normal heart development and adult cardiac anatomy, but displayed profound defects in injury-induced cardiomyocyte proliferation and heart regeneration. Our study defines a new platform for the discovery of epicardial lineage markers, genetic tools, and mechanisms of heart regeneration.
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Caveolina 1/metabolismo , Corazón/fisiología , Pericardio/citología , Regeneración/fisiología , Animales , Caveolina 1/genética , Miocitos Cardíacos/citología , Pez Cebra , Proteínas de Pez Cebra/genética , Proteínas de Pez Cebra/metabolismoRESUMEN
The characterization of ultrasound fields generated by diagnostic and therapeutic equipment is an essential requirement for performance validation and to demonstrate compliance against established safety limits. This requires hydrophones calibrated to a traceable standard. Currently, the upper calibration frequency range available to the user community is limited to 60 MHz. However, high frequencies are increasingly being used for both imaging and therapy necessitating calibration frequencies up to 100 MHz. The precise calibration of hydrophones requires a source of high amplitude, broadband, quasi-planar, and stable ultrasound fields. There are challenges to using conventional piezoelectric sources, and laser generated ultrasound sources offer a promising solution. In this study, various nanocomposites consisting of a bulk polymer matrix and multi-walled carbon nanotubes were fabricated and tested using pulsed laser of a few nanoseconds for their suitability as a source for high frequency calibration of hydrophones. The pressure amplitude and bandwidths were measured using a broadband hydrophone from 27 different nanocomposite sources. The effect of nonlinear propagation of high amplitude laser generated ultrasound on bandwidth and the effect of bandlimited sensitivity response on the deconvolved pressure waveform were numerically investigated. The stability of the nanocomposite sources under sustained laser pulse excitation was also examined.
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The image reconstruction problem (or inverse problem) in photoacoustic tomography is to resolve the initial pressure distribution from detected ultrasound waves generated within an object due to an illumination by a short light pulse. Recently, a Bayesian approach to photoacoustic image reconstruction with uncertainty quantification was proposed and studied with two dimensional numerical simulations. In this paper, the approach is extended to three spatial dimensions and, in addition to numerical simulations, experimental data are considered. The solution of the inverse problem is obtained by computing point estimates, i.e., maximum a posteriori estimate and posterior covariance. These are computed iteratively in a matrix-free form using a biconjugate gradient stabilized method utilizing the adjoint of the acoustic forward operator. The results show that the Bayesian approach can produce accurate estimates of the initial pressure distribution in realistic measurement geometries and that the reliability of these estimates can be assessed.
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Procesamiento de Imagen Asistido por Computador/métodos , Imagenología Tridimensional/métodos , Técnicas Fotoacústicas/métodos , Teorema de BayesRESUMEN
Non-invasive, focal neurostimulation with ultrasound is a potentially powerful neuroscientific tool that requires effective transcranial focusing of ultrasound to develop. Time-reversal (TR) focusing using numerical simulations of transcranial ultrasound propagation can correct for the effect of the skull, but relies on accurate simulations. Here, focusing requirements for ultrasonic neurostimulation are established through a review of previously employed ultrasonic parameters, and consideration of deep brain targets. The specific limitations of finite-difference time domain (FDTD) and k-space corrected pseudospectral time domain (PSTD) schemes are tested numerically to establish the spatial points per wavelength and temporal points per period needed to achieve the desired accuracy while minimizing the computational burden. These criteria are confirmed through convergence testing of a fully simulated TR protocol using a virtual skull. The k-space PSTD scheme performed as well as, or better than, the widely used FDTD scheme across all individual error tests and in the convergence of large scale models, recommending it for use in simulated TR. Staircasing was shown to be the most serious source of error. Convergence testing indicated that higher sampling is required to achieve fine control of the pressure amplitude at the target than is needed for accurate spatial targeting.
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Simulación por Computador , Modelos Teóricos , Terapia por Ultrasonido/métodos , Ondas Ultrasónicas , Humanos , Movimiento (Física) , Análisis Numérico Asistido por Computador , Presión , Factores de TiempoRESUMEN
In this work, the use of binary amplitude holography is investigated as a mechanism to focus broadband acoustic pulses generated by high peak-power pulsed lasers. Two algorithms are described for the calculation of the binary holograms; one using ray-tracing, and one using an optimization based on direct binary search. It is shown using numerical simulations that when a binary amplitude hologram is excited by a train of laser pulses at its design frequency, the acoustic field can be focused at a pre-determined distribution of points, including single and multiple focal points, and line and square foci. The numerical results are validated by acoustic field measurements from binary amplitude holograms, excited by a high peak-power laser.
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Significance: Quantitative photoacoustic tomography (QPAT) exploits the photoacoustic effect with the aim of estimating images of clinically relevant quantities related to the tissue's optical absorption. The technique has two aspects: an acoustic part, where the initial acoustic pressure distribution is estimated from measured photoacoustic time-series, and an optical part, where the distributions of the optical parameters are estimated from the initial pressure. Aim: Our study is focused on the optical part. In particular, computational modeling of light propagation (forward problem) and numerical solution methodologies of the image reconstruction (inverse problem) are discussed. Approach: The commonly used mathematical models of how light and sound propagate in biological tissue are reviewed. A short overview of how the acoustic inverse problem is usually treated is given. The optical inverse problem and methods for its solution are reviewed. In addition, some limitations of real-life measurements and their effect on the inverse problems are discussed. Results: An overview of QPAT with a focus on the optical part was given. Computational modeling and inverse problems of QPAT were addressed, and some key challenges were discussed. Furthermore, the developments for tackling these problems were reviewed. Although modeling of light transport is well-understood and there is a well-developed framework of inverse mathematics for approaching the inverse problem of QPAT, there are still challenges in taking these methodologies to practice. Conclusions: Modeling and inverse problems of QPAT together were discussed. The scope was limited to the optical part, and the acoustic aspects were discussed only to the extent that they relate to the optical aspect.
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Algoritmos , Tomografía Computarizada por Rayos X , Tomografía Computarizada por Rayos X/métodos , Procesamiento de Imagen Asistido por Computador/métodos , Modelos Teóricos , MatemáticaRESUMEN
Real-time applications in three-dimensional photoacoustic tomography from planar sensors rely on fast reconstruction algorithms that assume the speed of sound (SoS) in the tissue is homogeneous. Moreover, the reconstruction quality depends on the correct choice for the constant SoS. In this study, we discuss the possibility of ameliorating the problem of unknown or heterogeneous SoS distributions by using learned reconstruction methods. This can be done by modelling the uncertainties in the training data. In addition, a correction term can be included in the learned reconstruction method. We investigate the influence of both and while a learned correction component can improve reconstruction quality further, we show that a careful choice of uncertainties in the training data is the primary factor to overcome unknown SoS. We support our findings with simulated and in vivo measurements in 3D.
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A new method for solving the wave equation is presented, called the learned Born series (LBS), which is derived from a convergent Born series but its components are found through training. The LBS is shown to be significantly more accurate than the convergent Born series for the same number of iterations, in the presence of high contrast scatterers, while maintaining a comparable computational complexity. The LBS is able to generate a reasonable prediction of the global pressure field with a small number of iterations, and the errors decrease with the number of learned iterations.
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The use of a planar detection geometry in photoacoustic tomography results in the so- called limited-view problem due to the finite extent of the acoustic detection aperture. When images are reconstructed using one-step reconstruction algorithms, image quality is compromised by the presence of streaking artefacts, reduced contrast, image distortion and reduced signal-to-noise ratio. To mitigate this, model-based iterative reconstruction approaches based on least squares minimisation with and without total variation regularization were evaluated using in-silico, experimental phantom, ex vivo and in vivo data. Compared to one-step reconstruction methods, it has been shown that iterative methods provide better image quality in terms of enhanced signal-to-artefact ratio, signal-to-noise ratio, amplitude accuracy and spatial fidelity. For the total variation approaches, the impact of the regularization parameter on image feature scale and amplitude distribution was evaluated. In addition, the extent to which the use of Bregman iterations can compensate for the systematic amplitude bias introduced by total variation was studied. This investigation is expected to inform the practical application of model-based iterative image reconstruction approaches for improving photoacoustic image quality when using finite aperture planar detection geometries.
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Algoritmos , Tomografía Computarizada por Rayos X , Tomografía Computarizada por Rayos X/métodos , Fantasmas de Imagen , Artefactos , Análisis de los Mínimos Cuadrados , Procesamiento de Imagen Asistido por Computador/métodosRESUMEN
Fast imaging methods are needed to promote clinical adoption of ultrasound tomography (UST), and more widely available UST hardware could support the experimental validation of new measurement configurations. In this work, an open-source 256-element transducer ring array was developed (morganjroberts.github. io/open-UST) and manufactured using rapid prototyping, for only £2k. Novel manufacturing techniques were used, resulting in a 1.17° mean beam axis skew angle, a [Formula: see text] mean element position error, and a [Formula: see text] deviation in matching layer thickness. The nominal acoustic performance was measured using hydrophone scans and watershot data, and the 61.2 dB signal-to-noise ratio (SNR), 55.4° opening angle, 10.2 mm beamwidth, and 54% transmit-receive bandwidth (-12 dB) were found to be similar to existing systems and compatible with state-of-the-art full-waveform-inversion image reconstruction methods. The interelement variation in acoustic performance was typically < 10% without using normalization, meaning that the elements can be modeled identically during image reconstruction, removing the need for individual source definitions based on hydrophone measurements. Finally, data from a phantom experiment were successfully reconstructed. These results demonstrate that the open-UST system is accessible for users and is suitable for UST imaging research.
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Tomografía Computarizada por Rayos X , Tomografía , Ultrasonografía/métodos , Procesamiento de Imagen Asistido por Computador , Fantasmas de Imagen , TransductoresRESUMEN
The small freshwater cnidarian polyp Hydra vulgaris uses adult stem cells (interstitial stem cells) to continually replace neurons throughout its life. This feature, combined with the ability to image the entire nervous system (Badhiwala et al., 2021; Dupre & Yuste, 2017) and availability of gene knockdown techniques (Juliano, Reich, et al., 2014; Lohmann et al., 1999; Vogg et al., 2022), makes Hydra a tractable model for studying nervous system development and regeneration at the whole-organism level. In this study, we use single-cell RNA sequencing and trajectory inference to provide a comprehensive molecular description of the adult nervous system. This includes the most detailed transcriptional characterization of the adult Hydra nervous system to date. We identified eleven unique neuron subtypes together with the transcriptional changes that occur as the interstitial stem cells differentiate into each subtype. Towards the goal of building gene regulatory networks to describe Hydra neuron differentiation, we identified 48 transcription factors expressed specifically in the Hydra nervous system, including many that are conserved regulators of neurogenesis in bilaterians. We also performed ATAC-seq on sorted neurons to uncover previously unidentified putative regulatory regions near neuron-specific genes. Finally, we provide evidence to support the existence of transdifferentiation between mature neuron subtypes and we identify previously unknown transition states in these pathways. All together, we provide a comprehensive transcriptional description of an entire adult nervous system, including differentiation and transdifferentiation pathways, which provides a significant advance towards understanding mechanisms that underlie nervous system regeneration.
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Photoacoustic imaging (PAI), also referred to as optoacoustic imaging, has shown promise in early-stage clinical trials in a range of applications from inflammatory diseases to cancer. While the first PAI systems have recently received regulatory approvals, successful adoption of PAI technology into healthcare systems for clinical decision making must still overcome a range of barriers, from education and training to data acquisition and interpretation. The International Photoacoustic Standardisation Consortium (IPASC) undertook an community exercise in 2022 to identify and understand these barriers, then develop a roadmap of strategic plans to address them. Here, we outline the nature and scope of the barriers that were identified, along with short-, medium- and long-term community efforts required to overcome them, both within and beyond the IPASC group.