Computing Interpretable Representations of Cell Morphodynamics

Shape changes (morphodynamics) are one of the principal ways cells interact with their environments and perform key intrinsic behaviours like division. These dynamics arise from a myriad of complex signalling pathways that often organise with emergent simplicity to carry out critical functions including predation, collaboration and migration. A powerful method for analysis can therefore be to quantify this emergent structure, bypassing the low-level complexity. Enormous image datasets are now available to mine. However, it can be difficult to uncover interpretable representations of the global organisation of these heterogeneous dynamic processes. Here, such representations were developed for interpreting morphodynamics in two key areas: mode of action (MoA) comparison for drug discovery (developed using the economically devastating Asian soybean rust crop pathogen) and 3D migration of immune system T cells through extracellular matrices (ECMs). For MoA comparison, population development over a 2D space of shapes (morphospace) was described using two models with condition-dependent parameters: a top-down model of diffusive development over Waddington-type landscapes, and a bottom-up model of tip growth. A variety of landscapes were discovered, describing phenotype transitions during growth, and possible perturbations in the tip growth machinery that cause this variation were identified. For interpreting T cell migration, a new 3D shape descriptor that incorporates key polarisation information was developed, revealing low-dimensionality of shape, and the distinct morphodynamics of run-and-stop modes that emerge at minute timescales were mapped. Periodically oscillating morphodynamics that include retrograde deformation flows were found to underlie active translocation (run mode). Overall, it was found that highly interpretable representations could be uncovered while still leveraging the enormous discovery power of deep learning algorithms. The results show that whole-cell morphodynamics can be a convenient and powerful place to search for structure, with potentially life-saving applications in medicine and biocide discovery as well as immunotherapeutics.Open Acces

Contributions to fuzzy polynomial techniques for stability analysis and control

The present thesis employs fuzzy-polynomial control techniques in order to improve the stability analysis and control of nonlinear systems. Initially, it reviews the more extended techniques in the field of Takagi-Sugeno fuzzy systems, such as the more relevant results about polynomial and fuzzy polynomial systems. The basic framework uses fuzzy polynomial models by Taylor series and sum-of-squares techniques (semidefinite programming) in order to obtain stability guarantees. The contributions of the thesis are: ¿ Improved domain of attraction estimation of nonlinear systems for both continuous-time and discrete-time cases. An iterative methodology based on invariant-set results is presented for obtaining polynomial boundaries of such domain of attraction. ¿ Extension of the above problem to the case with bounded persistent disturbances acting. Different characterizations of inescapable sets with polynomial boundaries are determined. ¿ State estimation: extension of the previous results in literature to the case of fuzzy observers with polynomial gains, guaranteeing stability of the estimation error and inescapability in a subset of the zone where the model is valid. ¿ Proposal of a polynomial Lyapunov function with discrete delay in order to improve some polynomial control designs from literature. Preliminary extension to the fuzzy polynomial case. Last chapters present a preliminary experimental work in order to check and validate the theoretical results on real platforms in the future.Pitarch Pérez, JL. (2013). Contributions to fuzzy polynomial techniques for stability analysis and control [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/34773TESI

Book of Abstracts 15th International Symposium on Computer Methods in Biomechanics and Biomedical Engineering and 3rd Conference on Imaging and Visualization

In this edition, the two events will run together as a single conference, highlighting the strong connection with the Taylor & Francis journals: Computer Methods in Biomechanics and Biomedical Engineering (John Middleton and Christopher Jacobs, Eds.) and Computer Methods in Biomechanics and Biomedical Engineering: Imaging and Visualization (JoãoManuel R.S. Tavares, Ed.). The conference has become a major international meeting on computational biomechanics, imaging andvisualization. In this edition, the main program includes 212 presentations. In addition, sixteen renowned researchers will give plenary keynotes, addressing current challenges in computational biomechanics and biomedical imaging. In Lisbon, for the first time, a session dedicated to award the winner of the Best Paper in CMBBE Journal will take place. We believe that CMBBE2018 will have a strong impact on the development of computational biomechanics and biomedical imaging and visualization, identifying emerging areas of research and promoting the collaboration and networking between participants. This impact is evidenced through the well-known research groups, commercial companies and scientific organizations, who continue to support and sponsor the CMBBE meeting series. In fact, the conference is enriched with five workshops on specific scientific topics and commercial software.info:eu-repo/semantics/draf

Virtual Morphology and Evolutionary Morphometrics in the new millenium.

EDITED VOLUME; abstract N/

The isolation, identification and exploration of the biophysiological significance of plasma biliverdin in the ballan wrasse (Labrus bergylta)

Labrus bergylta (ballan wrasse) have recently emerged as a key resource to aquaculture through proven efficacy in controlling infestations of sea lice (Leclercq et al., 2014a). However, due to complex ecology, and a complete lack of sexual dimorphism gender identification endures as a key restriction to optimising broodstock management therefore male selection and establishing optimal sex ratios is difficult (Talbot et al., 2012). L. bergylta, are noted to demonstrate unusually coloured plasma ranging in hue from green to blue with the haem catabolite biliverdin established as the causal pigment in the majority of cases (Abolins, 1961). As most vertebrates excrete biliverdin, or rapidly metabolise it to prevent toxicity, accumulation to such excess is a phenomenon which merits attention. Notably, correlation between plasma biliverdin and gender has been reported in some Labridae. Although patterns vary between species, the abundance or characteristics were such that sexual identity could be established (Gagnon, 2006). Pigment analysis was therefore proposed as a potential sex-marker in L. bergylta. In the initial experimental phase (Chapter 3), the ultimate aim was to isolate and identify the blue pigment from L. bergylta plasma, and to develop a method of quantification. The initial phase confirmed the target pigment was biliverdin IXα by visible spectroscopy, TLC, HPLC, MSMS, and a series of reactions. Following this, a protocol was developed (Chapter 2) to quantify the pigment. This method was applied accross plasma sampled from four geographically distinct wild populations with established biometrics including age, mass, length, gender and external phenotype. Subsequent analysis revealed that although pigment abundance did not vary relative to ontogeny, and there was no difference in concentration between the binary genders, plasma biliverdin was depleted in individuals undergoing sex change. Although this conclusion was complicated by significant biliverdin variation relative to origin and phenotype, which were interrelated based on relative distributions across populations, further analysis of plasma pigment in related species identified that biliverdin accumulation was associated with protogynous species. Considering the anti-oxidant capacity of biliverdin and other potentially relevant functions, this was indicative of association with the tissue remodelling processes which accompany inversion. During Chapter 3 it was noted that the biliverdin appeared tightly bound to a protein moiety. Based on the hypothesis that the pigment was actively managed and accumulated in L. bergylta plasma by this association, the next phase of experiments (Chapter 4) was an exploration of biliverdin and its binding protein in L. bergylta. The experiments revealed plasma biliverdin comigrated with the protein such that it was depleted from solution at the same rate indicating that all of the pigment was associated. Subsequent electrophoretic experiments using the fractionation products supported this, and UV fluourescence identified fragments of interest in the 25-28 kDa region. To confirm observations from the previous cross species comparison, the study was similarly expanded to include other Labrini. This revealed that although the 25 kDa band was common to all species, and genders, the 28 kDa band was collocated with the protogynous, and as such hyperbiliverdinaemic species. The 28 kDa band was sequenced using MSMS, and was identified as similar to the lipocalin Apolipoprotein A1. In combination with the properties of biliverdin, and considering that ApoA1 is analogous to serum albumin in many telesots, this supported the chromoprotein association as the main mechanism of biliverdin accumulation in such species. Further to the proposed function of biliverdin with inversion processes, and considering relevant literature, the active properties of ApoA1 suggested additional associations with prolonged altered states of metabolism which considering the ecology of L. bergylta would include gender transition, overwintering torpor and prolonged micronutrient limitation, all of which occur simultaneously. Other potential roles include modulating inflammatory responses, inhibiting pathogenic incursions and acting as an external point of contact innate immune response. From this, it was concluded that the data fully supported the previous assertions of biliverdins relevance in protogynous species, and identified a number of properties which could be of great interest to the industry in terms of welfare. The final experimental phase (Chapter 5) had two main aims. The first was to establish whether protogynous inversion could be artificially induced in L. bergylta as a means of generating male fish, and whether size had any effect on the process. The second was then to utilise controlled induction for tracking biliverdin mobilisation across the process to test the previous hypothesis. The preliminary trial demonstrated that both androgen inhibition and non-aromatisable testosterone could stimulate inversion in female L. bergylta. From this, the second trial then determined that although there was a dose dependant effect in that high androgen dosages appeared to compress the inversion process, relative size was not a factor. Gonad histology was used to create a unified scale of protogynous transition which could be expressed as a gradient to structure the biliverdin analysis. Although the biliverdin data demonstrated cryptic trends at the higher resolution gender scales, when the endpoint was condensed back to the binary gender scale employed previously (Chapter 3), the prior assertion of depletion during transition, and therefore the association with sex change associated tissue remodelling was supported. Ultimately this thesis revealed links between the biliverdin macromolecule and the highly unusual metabolic and physiological demands of gender transition in sequentially protogynous hermaphroditic temperate wrasse species

A study of change in human trabecular bone structure with age and during osteoporosis

The objective of this work was to develop new techniques to view trabecular bone three-dimensionally, and to study its structure and the changes that occur with age and in osteoporosis; the methods used included 3D methods in the SEM, laser confocal microscopy, pseudo-holograms and a "continuous motion parallax method". A detailed analysis of trabecular bone from fourth lumbar vertebral bodies used macro-stereophotographs produced by tilting a sample 10°. Models are proposed for both normal and osteoporotic architecture. A quantitative analysis of the lengths of horizontally oriented trabeculae was carried out. A significant decrease in the number of both vertically and horizontally oriented trabeculae was found. The importance of the influence of different developmental patterns on the formation of the normal structure and of the changing vascularisation on osteoporotic structure are emphasised. Two-dimensional fast Fourier transform methods were employed to study changes in the spatial frequency of trabeculae as a function of orientation. A decrease in spatial frequency was observed in both sexes, but in males this was evident only after the mid-sixth decade in the limited sample studied. Contoured power spectra discriminated different trabecular patterns and the intensity mapping of optical density provided volume density information. Templated reverse transformation was used to study individual orientations of trabeculae. Changes in the quality of trabecular bone with age were also investigated using techniques that analyse bone before and after removal of unmineralised matrix. All specimens were less stiff after removal of osteoid; this was more marked in older specimens. Locally defective mineralisation would explain the changed behaviour observed in some old and osteoporotic specimens. Trabecular fracture patterns had a strong relationship to architecture and microstructure. Scanning electron microscopy was used to study trabecular surfaces. An uncoupling between resorption and formation was evident in older specimens. Two resorption patterns responsible for thinning and perforation and removal trabecular elements were identified. Trabecular microfractures were also investigated

Multi-scale imaging and modelling of bone

The multi-level organization of bone facilitates the exploitation of in-vivo micro-scale information which is currently lacking for clinical applications. The three sub-projects presented in this thesis investigate the human skeletal system at multiple scales using magnetic resonance imaging (MRI) with the aim of providing new techniques for extracting finer scale information in-vivo. At the whole organ level, human knee joint kinematics was studied using a combined MRI strategy. This new strategy enables the in-vivo investigation of tibiofemoral locomotion under body weight-bearing conditions by modelling the knee flexion angle as a function of the femur and tibia cartilage surfaces in contact. The resultant "contact" trajectory may potentially be used to understand the mechanical cause of cartilage degeneration and as a biomarker to detect abnormalities in the lower limb. At the molecular level, in-vivo MR diffusion tensor imaging (DTI) has been performed for the first time in the human tibia epiphysis. By tracking the water molecules inside the red marrow, the organization of trabecular bone network may be understood as the streamlines formed by anisotropic diffusion trajectories. This sub-project aims to understand the organization of trabecular bone networks non-invasively, which is usually performed ex-vivo through biopsies. The feasibility and reproducibility of DTI is studied. Finally, a new MR imaging protocol named multi-directional sub-pixel enhancement (mSPENT) is proposed and developed to quantify the trabecular bone structural arrangement at the meso-scale. By modulating a dephasing gradient to manipulate the underlying spin system inside each voxel, the resulting mSPENT image contrast varies with gradient at different directions based on the magnetization at the corresponding voxel. A tensor-based method is further developed to model this contrast change, leading to a localized quantification of tissue structural orientation beyond the conventional MR imaging resolution