Human Stem Cells for Ophthalmology: Recent Advances in Diagnostic Image Analysis and Computational Modelling.

Purpose of Review: To explore the advances and future research directions in image analysis and computational modelling of human stem cells (hSCs) for ophthalmological applications. Recent Findings: hSCs hold great potential in ocular regenerative medicine due to their application in cell-based therapies and in disease modelling and drug discovery using state-of-the-art 2D and 3D organoid models. However, a deeper characterisation of their complex, multi-scale properties is required to optimise their translation to clinical practice. Image analysis combined with computational modelling is a powerful tool to explore mechanisms of hSC behaviour and aid clinical diagnosis and therapy. Summary: Many computational models draw on a variety of techniques, often blending continuum and discrete approaches, and have been used to describe cell differentiation and self-organisation. Machine learning tools are having a significant impact in model development and improving image classification processes for clinical diagnosis and treatment and will be the focus of much future research.

A mathematical modelling framework for the regulation of intra-cellular OCT4 in human pluripotent stem cells.

Human pluripotent stem cells (hPSCs) have the potential to differentiate into all cell types, a property known as pluripotency. A deeper understanding of how pluripotency is regulated is required to assist in controlling pluripotency and differentiation trajectories experimentally. Mathematical modelling provides a non-invasive tool through which to explore, characterise and replicate the regulation of pluripotency and the consequences on cell fate. Here we use experimental data of the expression of the pluripotency transcription factor OCT4 in a growing hPSC colony to develop and evaluate mathematical models for temporal pluripotency regulation. We consider fractional Brownian motion and the stochastic logistic equation and explore the effects of both additive and multiplicative noise. We illustrate the use of time-dependent carrying capacities and the introduction of Allee effects to the stochastic logistic equation to describe cell differentiation. We conclude both methods adequately capture the decline in OCT4 upon differentiation, but the Allee effect model has the advantage of allowing differentiation to occur stochastically in a sub-set of cells. This mathematical framework for describing intra-cellular OCT4 regulation can be extended to other transcription factors and developed into predictive models.

OCT4 expression in human embryonic stem cells: spatio-temporal dynamics and fate transitions.

The improved in vitro regulation of human embryonic stem cell (hESC) pluripotency and differentiation trajectories is required for their promising clinical applications. The temporal and spatial quantification of the molecular interactions controlling pluripotency is also necessary for the development of successful mathematical and computational models. Here we use time-lapse experimental data of OCT4-mCherry fluorescence intensity to quantify the temporal and spatial dynamics of the pluripotency transcription factor OCT4 in a growing hESC colony in the presence and absence of BMP4. We characterise the internal self-regulation of OCT4 using the Hurst exponent and autocorrelation analysis, quantify the intra-cellular fluctuations and consider the diffusive nature of OCT4 evolution for individual cells and pairs of their descendants. We find that OCT4 abundance in the daughter cells fluctuates sub-diffusively, showing anti-persistent self-regulation. We obtain the stationary probability distributions governing hESC transitions amongst the different cell states and establish the times at which pro-fate cells (which later give rise to pluripotent or differentiated cells) cluster in the colony. By quantifying the similarities between the OCT4 expression amongst neighbouring cells, we show that hESCs express similar OCT4 to cells within their local neighbourhood within the first two days of the experiment and before BMP4 treatment. Our framework allows us to quantify the relevant properties of proliferating hESC colonies and the procedure is widely applicable to other transcription factors and cell populations.

The recent advances in the mathematical modelling of human pluripotent stem cells.

Human pluripotent stem cells hold great promise for developments in regenerative medicine and drug design. The mathematical modelling of stem cells and their properties is necessary to understand and quantify key behaviours and develop non-invasive prognostic modelling tools to assist in the optimisation of laboratory experiments. Here, the recent advances in the mathematical modelling of hPSCs are discussed, including cell kinematics, cell proliferation and colony formation, and pluripotency and differentiation.

Seeding hESCs to achieve optimal colony clonality.

Human embryonic stem cells (hESCs) and induced pluripotent stem cells (iPSCs) have promising clinical applications which often rely on clonally-homogeneous cell populations. To achieve this, it is important to ensure that each colony originates from a single founding cell and to avoid subsequent merging of colonies during their growth. Clonal homogeneity can be obtained with low seeding densities; however, this leads to low yield and viability. It is therefore important to quantitatively assess how seeding density affects clonality loss so that experimental protocols can be optimised to meet the required standards. Here we develop a quantitative framework for modelling the growth of hESC colonies from a given seeding density based on stochastic exponential growth. This allows us to identify the timescales for colony merges and over which colony size no longer predicts the number of founding cells. We demonstrate the success of our model by applying it to our own experiments of hESC colony growth; while this is based on a particular experimental set-up, the model can be applied more generally to other cell lines and experimental conditions to predict these important timescales.

Instability of Rotationally Tuned Dipolar Bose-Einstein Condensates.

The possibility of effectively inverting the sign of the dipole-dipole interaction, by fast rotation of the dipole polarization, is examined within a harmonically trapped dipolar Bose-Einstein condensate. Our analysis is based on the stationary states in the Thomas-Fermi limit, in the corotating frame, as well as direct numerical simulations in the Thomas-Fermi regime, explicitly accounting for the rotating polarization. The condensate is found to be inherently unstable due to the dynamical instability of collective modes. This ultimately prevents the realization of robust and long-lived rotationally tuned states. Our findings have major implications for experimentally accessing this regime.

Quantum Ferrofluid Turbulence.

We study the elementary characteristics of turbulence in a quantum ferrofluid through the context of a dipolar Bose gas condensing from a highly nonequilibrium thermal state. Our simulations reveal that the dipolar interactions drive the emergence of polarized turbulence and density corrugations. The superfluid vortex lines and density fluctuations adopt a columnar or stratified configuration, depending on the sign of the dipolar interactions, with the vortices tending to form in the low-density regions to minimize kinetic energy. When the interactions are dominantly dipolar, the decay of the vortex line length is enhanced, closely following a t^{-3/2} behavior. This system poses exciting prospects for realizing stratified quantum turbulence and new levels of generating and controlling turbulence using magnetic fields.

Correlated random walks of human embryonic stem cells in vitro.

We perform a detailed analysis of the migratory motion of human embryonic stem cells in two-dimensions, both when isolated and in close proximity to another cell, recorded with time-lapse microscopic imaging. We show that isolated cells tend to perform an unusual locally anisotropic walk, moving backwards and forwards along a preferred local direction correlated over a timescale of around 50 min and aligned with the axis of the cell elongation. Increasing elongation of the cell shape is associated with increased instantaneous migration speed. We also show that two cells in close proximity tend to move in the same direction, with the average separation of [Formula: see text]m or less and the correlation length of around 25 µm, a typical cell diameter. These results can be used as a basis for the mathematical modelling of the formation of clonal hESC colonies.

Superfluid Boundary Layer.

We model the superfluid flow of liquid helium over the rough surface of a wire (used to experimentally generate turbulence) profiled by atomic force microscopy. Numerical simulations of the Gross-Pitaevskii equation reveal that the sharpest features in the surface induce vortex nucleation both intrinsically (due to the raised local fluid velocity) and extrinsically (providing pinning sites to vortex lines aligned with the flow). Vortex interactions and reconnections contribute to form a dense turbulent layer of vortices with a nonclassical average velocity profile which continually sheds small vortex rings into the bulk. We characterize this layer for various imposed flows. As boundary layers conventionally arise from viscous forces, this result opens up new insight into the nature of superflows.

Dynamics of single human embryonic stem cells and their pairs: a quantitative analysis.

Numerous biological approaches are available to characterise the mechanisms which govern the formation of human embryonic stem cell (hESC) colonies. To understand how the kinematics of single and pairs of hESCs impact colony formation, we study their mobility characteristics using time-lapse imaging. We perform a detailed statistical analysis of their speed, survival, directionality, distance travelled and diffusivity. We confirm that single and pairs of cells migrate as a diffusive random walk for at least 7 hours of evolution. We show that the presence of Cell Tracer significantly reduces hESC mobility. Our results open the path to employ the theoretical framework of the diffusive random walk for the prognostic modelling and optimisation of the growth of hESC colonies. Indeed, we employ this random walk model to estimate the seeding density required to minimise the occurrence of hESC colonies arising from more than one founder cell and the minimal cell number needed for successful colony formation. Our prognostic model can be extended to investigate the kinematic behaviour of somatic cells emerging from hESC differentiation and to enable its wide application in phenotyping of pluripotent stem cells for large scale stem cell culture expansion and differentiation platforms.

Vortices and vortex lattices in quantum ferrofluids.

The experimental realization of quantum-degenerate Bose gases made of atoms with sizeable magnetic dipole moments has created a new type of fluid, known as a quantum ferrofluid, which combines the extraordinary properties of superfluidity and ferrofluidity. A hallmark of superfluids is that they are constrained to rotate through vortices with quantized circulation. In quantum ferrofluids the long-range dipolar interactions add new ingredients by inducing magnetostriction and instabilities, and also affect the structural properties of vortices and vortex lattices. Here we give a review of the theory of vortices in dipolar Bose-Einstein condensates, exploring the interplay of magnetism with vorticity and contrasting this with the established behaviour in non-dipolar condensates. We cover single vortex solutions, including structure, energy and stability, vortex pairs, including interactions and dynamics, and also vortex lattices. Our discussion is founded on the mean-field theory provided by the dipolar Gross-Pitaevskii equation, ranging from analytic treatments based on the Thomas-Fermi (hydrodynamic) and variational approaches to full numerical simulations. Routes for generating vortices in dipolar condensates are discussed, with particular attention paid to rotating condensates, where surface instabilities drive the nucleation of vortices, and lead to the emergence of rich and varied vortex lattice structures. We also present an outlook, including potential extensions to degenerate Fermi gases, quantum Hall physics, toroidal systems and the Berezinskii-Kosterlitz-Thouless transition.

Emergent behaviour in a chlorophenol-mineralising three-tiered microbial 'food web'.

Anaerobic digestion enables the water industry to treat wastewater as a resource for generating energy and recovering valuable by-products. The complexity of the anaerobic digestion process has motivated the development of complex models. However, this complexity makes it intractable to pin-point stability and emergent behaviour. Here, the widely used Anaerobic Digestion Model No. 1 (ADM1) has been reduced to its very backbone, a syntrophic two-tiered microbial 'food chain' and a slightly more complex three-tiered microbial 'food web', with their stability analysed as a function of the inflowing substrate concentration and dilution rate. Parameterised for phenol and chlorophenol degradation, steady-states were always stable and non-oscillatory. Low input concentrations of chlorophenol were sufficient to maintain chlorophenol- and phenol-degrading populations but resulted in poor conversion and a hydrogen flux that was too low to sustain hydrogenotrophic methanogens. The addition of hydrogen and phenol boosted the populations of all three organisms, resulting in the counterintuitive phenomena that (i) the phenol degraders were stimulated by adding hydrogen, even though hydrogen inhibits phenol degradation, and (ii) the dechlorinators indirectly benefitted from measures that stimulated their hydrogenotrophic competitors; both phenomena hint at emergent behaviour.

Anisotropic and long-range vortex interactions in two-dimensional dipolar Bose gases.

We perform a theoretical study into how dipole-dipole interactions modify the properties of superfluid vortices within the context of a two-dimensional atomic Bose gas of co-oriented dipoles. The reduced density at a vortex acts like a giant antidipole, changing the density profile and generating an effective dipolar potential centred at the vortex core whose most slowly decaying terms go as 1/ρ(2) and ln(ρ)/ρ(3). These effects modify the vortex-vortex interaction which, in particular, becomes anisotropic for dipoles polarized in the plane. Striking modifications to vortex-vortex dynamics are demonstrated, i.e., anisotropic corotation dynamics and the suppression of vortex annihilation.

Post-processing of polymer foam tissue scaffolds with high power ultrasound: a route to increased pore interconnectivity, pore size and fluid transport.

The aim of this work is to demonstrate that the structural and fluidic properties of polymer foam tissue scaffolds, post-fabrication but prior to the introduction of cells, can be engineered via exposure to high power ultrasound. Our analysis is supported by measurements of fluid uptake during insonification and imaging of the scaffold microstructure via X-ray computed tomography, scanning electron microscopy and acoustic microscopy. The ultrasonic treatment is performed with a frequency of 30 kHz, average intensities up to 80,000 Wm(-2) and exposure times up to 20 h. The treatment is found to increase the mean pore size by over 10%. More striking is the improvement in fluid uptake: for scaffolds with only 40% water uptake via standard immersion techniques, we can routinely achieve full saturation of the scaffold over approximately one hour of exposure. These desirable modifications occur with negligible loss of scaffold integrity and mass, and are optimized when the ultrasound treatment is coupled to a pre-wetting stage with ethanol. Our findings suggest that high power ultrasound is highly targeted towards flow obstructions in the scaffold architecture, thereby providing an efficient means to promote pore interconnectivity and fluid transport in thick foam tissue scaffolds.

Longitudinal acoustic properties of poly(lactic acid) and poly(lactic-co-glycolic acid).

Acoustics offers rich possibilities for characterizing and monitoring the biopolymer structures being employed in the field of biomedical engineering. Here we explore the rudimentary acoustic properties of two common biodegradable polymers: poly(lactic acid) and poly(lactic-co-glycolic acid). A pulse-echo technique is developed to reveal the bulk speed of sound, acoustic impedance and acoustic attenuation of small samples of the polymer across a pertinent temperature range of 0-70 °C. The glass transition appears markedly as both a discontinuity in the first derivative of the speed of sound and a sharp increase in the acoustic attenuation. We further extend our analysis to consider the role of ethanol, whose presence is observed to dramatically modify the acoustic properties and reduce the glass transition temperature of the polymers. Our results highlight the sensitivity of acoustic properties to a range of bulk properties, including visco-elasticity, molecular weight, co-polymer ratio, crystallinity and the presence of plasticizers.

Dynamical instability of a rotating dipolar Bose-Einstein condensate.

We analyze the hydrodynamic solutions for a dilute Bose-Einstein condensate with long-range dipolar interactions in a rotating, elliptical harmonic trap. The static solutions and their regimes of dynamical instability vary nontrivially with the strength of the dipolar interactions. We comprehensively map out this behavior, and, in particular, examine the experimental routes toward unstable dynamics, which, in analogy to conventional condensates, may lead to vortex lattice formation.

Emergence and decay of turbulence in stirred atomic Bose-Einstein condensates.

We show that "weak" elliptical deformation of an atomic Bose-Einstein condensate rotating at close to the quadrupole instability frequency leads to turbulence with a Kolmogorov energy spectrum. The turbulent state is produced by energy transfer to condensate fragments that are ejected by the quadrupole instability. This energy transfer is driven by breaking the twofold rotational symmetry of the condensate. Subsequently, vortex-sound interactions damp the turbulent state leading to the crystallization of a vortex lattice.

Parametric driving of dark solitons in atomic Bose-Einstein condensates.

A dark soliton oscillating in an elongated harmonically confined atomic Bose-Einstein condensate continuously exchanges energy with the sound field. Periodic optical paddles are employed to controllably enhance the sound density and transfer energy to the soliton, analogous to parametric driving. In the absence of damping, the amplitude of the soliton oscillations can be dramatically reduced, whereas with damping, a driven soliton equilibrates as a stable soliton with lower energy, thereby extending the soliton lifetime up to the lifetime of the condensate.

Controlled vortex-sound interactions in atomic Bose-Einstein condensates.

The low temperature dynamics of a vortex in a trapped quasi-two-dimensional Bose-Einstein condensate are studied quantitatively. Precession of an off-centered vortex in a dimple trap, embedded in a weaker harmonic trap, leads to the emission of sound in a dipolar radiation pattern. Sound emission and reabsorption can be controlled by varying the depth of the dimple. In a shallow dimple, the power emitted is proportional to the vortex acceleration-squared over the precession frequency, whereas for a deep dimple, periodic sound reabsorption stabilizes the vortex against radiation-induced decay.

Soliton-sound interactions in quasi-one-dimensional Bose-Einstein condensates.

Longitudinal confinement of dark solitons in quasi-one-dimensional Bose-Einstein condensates leads to sound emission and reabsorption. We perform quantitative studies of the dynamics of a soliton oscillating in a tight dimple trap, embedded in a weaker harmonic trap. The dimple depth provides a sensitive handle to control the soliton-sound interaction. In the limit of no reabsorption, the power radiated is found to be proportional to the soliton acceleration squared. An experiment is proposed to detect sound emission as a change in amplitude and frequency of soliton oscillations.