Exact solutions for cluster-growth kinetics with evolving size and shape profiles

In this paper we construct a model for the simultaneous compaction by which clusters are restructured, and growth of clusters by pairwise coagulation. The model has the form of a multicomponent aggregation problem in which the components are cluster mass and cluster diameter. Following suitable approximations, exact explicit solutions are derived which may be useful for the verification of simulations of such systems. Numerical simulations are presented to illustrate typical behaviour and to show the accuracy of approximations made in deriving the model. The solutions are then simplified using asymptotic techniques to show the relevant timescales of the kinetic processes and elucidate the shape of the cluster distribution functions at large times.

Otolith shape variation provides a marker of stock origin for north Atlantic bluefin tuna (Thunnus thynnus)

Two stocks of bluefin tuna (Thunnus thynnus) inhabit the north Atlantic; the western and eastern stocks spawn in the Gulf of Mexico and the Mediterranean Sea respectively. Trans-Atlantic movements occur outside spawning time whereas natal homing maintains stock structure. Commercial fisheries may exploit a mixed assemblage of both stocks. The incorporation of mixing rates into stock assessment is precluded by uncertainties surrounding stock discrimination. Otolith shape descriptors were used to characterise western and eastern stocks of Atlantic bluefin tuna in the present study and to estimate stock composition in catches of unknown origin. Otolith shape varied with length and between locations and years. Within a restricted size range (200-297-cm fork length (FL)) the two stocks were distinguished with an accuracy of 83%. Bayesian stock mixture analysis indicated that samples from the east Atlantic and Mediterranean were predominantly of eastern origin. The proportion assigned to the eastern stock showed slight spatial variation; however, overlapping 95% credible intervals indicated no significant difference (200-297 cm FL: central Atlantic, 73-100%; Straits of Gibraltar, 73-100%; Morocco, 50-99%; Portugal 64-100%). Otolith shape could be used in combination with other population markers to improve the accuracy of mixing rate estimates for Atlantic bluefin tuna.

Designing Hydrogels that Transform their Shape in Response to Molecular Cues

There has been considerable interest in developing shape-changing soft materials for potential applications in drug delivery, microfluidics and biosensing. These shape- changing materials are inspired by the morphological changes exhibited by plants in nature, such as the Venus flytrap. One specific class of shape-change is that from a flat sheet to a folded structure (e.g., a tube). Such “self-folding” materials are usually composed of polymer hydrogels, and these typically fold in response to external stimuli such as pH and temperature. In order to develop these hydrogels for the previously described applications, it is necessary to expand the range of triggers. The focus of this dissertation is the advancement of shape-changing polymer hydrogels that are sensitive to uncommon cues such as specific biomolecules (enzymes), the substrates for such enzymes, or specific multivalent cations. First, we describe a hybrid gel that responds to the presence of low concentrations of a class of enzymes known as matrix metalloproteinases (MMPs). The hybrid gel was created by utilizing photolithographic techniques to combine two or more gels with distinct chemical composition into the same material. Certain portions of the hybrid gel are composed of a biopolymer derivative with crosslinkable groups. The hybrid gel is flat in water; however, in the presence of MMPs, the regions containing the biopolymer are degraded and the flat sheet folds to form a 3D structure. We demonstrate that hydrogels with different patterns can transform into different 3D structures such as tubes, helices and pancakes. Furthermore, this shape change can be made to occur at physiological concentrations of enzymes. Next, we report a gel with two layers that undergoes a shape change in the presence of glucose. The enzyme glucose oxidase (GOx) is immobilized in one of the layers. GOx catalyzes the conversion of glucose to gluconic acid. The production of gluconic acid decreases the local pH. The decrease in local pH causes one of the layers to swell. As a result, the flat sheet folds to form a tube. The tube unfolds to form a flat sheet when it is transferred to a solution with no glucose present. Therefore, this biomolecule- triggered shape transformation is reversible, meaning the glucose sensing gel is reusable. Furthermore, this shape change only occurs in the presence of glucose and it does not occur in the presence of other small sugars such as fructose. In our final study, we report the shape change of a gel with two layers in the presence of multivalent ions such as Ca2+ and Sr2+. The gel consists of a passive layer and an active layer. The passive layer is composed of dimethylyacrylamide (DMAA), which does not interact with multivalent ions. The active layer consists of DMAA and the biopolymer alginate. In the presence of Ca2+ ions, the alginate chains crosslink and the active layer shrinks. As a result, the gel converts from a flat sheet to a folded tube. What is particularly unusual is the direction of folding. In most cases, when flat rectangular gels fold, they do so about their short-side. However, our gels typically fold about their long-side. We hypothesize that non-homogeneous swelling determines the folding axis.

REGULATION OF SHAPE DYNAMICS AND ACTIN POLYMERIZATION DURING COLLECTIVE CELL MIGRATION

This thesis aims to understand how cells coordinate their motion during collective migration. As previously shown, the motion of individually migrating cells is governed by wave-like cell shape dynamics. The mechanisms that regulate these dynamic behaviors in response to extracellular environment remain largely unclear. I applied shape dynamics analysis to Dictyostelium cells migrating in pairs and in multicellular streams and found that wave-like membrane protrusions are highly coupled between touching cells. I further characterized cell motion by using principle component analysis (PCA) to decompose complex cell shape changes into a serial shape change modes, from which I found that streaming cells exhibit localized anterior protrusion, termed front narrowing, to facilitate cell-cell coupling. I next explored cytoskeleton-based mechanisms of cell-cell coupling by measuring the dynamics of actin polymerization. Actin polymerization waves observed in individual cells were significantly suppressed in multicellular streams. Streaming cells exclusively produced F-actin at cell-cell contact regions, especially at cell fronts. I demonstrated that such restricted actin polymerization is associated with cell-cell coupling, as reducing actin polymerization with Latrunculin A leads to the assembly of F-actin at the side of streams, the decrease of front narrowing, and the decoupling of protrusion waves. My studies also suggest that collective migration is guided by cell-surface interactions. I examined the aggregation of Dictyostelim cells under distinct conditions and found that both chemical compositions of surfaces and surface-adhesion defects in cells result in altered collective migration patterns. I also investigated the shape dynamics of cells suspended on PEG-coated surfaces, which showed that coupling of protrusion waves disappears on touching suspended cells. These observations indicate that collective migration requires a balance between cell-cell and cell-surface adhesions. I hypothesized such a balance is reached via the regulation of cytoskeleton. Indeed, I found cells actively regulate cytoskeleton to retain optimal cell-surface adhesions on varying surfaces, and cells lacking the link between actin and surfaces (talin A) could not retain the optimal adhesions. On the other hand, suspended cells exhibited enhanced actin filament assembly on the periphery of cell groups instead of in cell-cell contact regions, which facilitates their aggregation in a clumping fashion.

Elemental Anisotropic Growth and Atomic-Scale Structure of Shape-Controlled Octahedral Pt–Ni–Co Alloy Nanocatalysts

Multimetallic shape-controlled nanoparticles offer great opportunities to tune the activity, selectivity, and stability of electrocatalytic surface reactions. However, in many cases, our synthetic control over particle size, composition, and shape is limited requiring trial and error. Deeper atomic-scale insight in the particle formation process would enable more rational syntheses. Here we exemplify this using a family of trimetallic PtNiCo nanooctahedra obtained via a low-temperature, surfactant-free solvothermal synthesis. We analyze the competition between Ni and Co precursors under coreduction “one-step” conditions when the Ni reduction rates prevailed. To tune the Co reduction rate and final content, we develop a “two-step” route and track the evolution of the composition and morphology of the particles at the atomic scale. To achieve this, scanning transmission electron microscopy and energy dispersive X-ray elemental mapping techniques are used. We provide evidence of a heterogeneous element distribution caused by element-specific anisotropic growth and create octahedral nanoparticles with tailored atomic composition like Pt1.5M, PtM, and PtM1.5 (M = Ni + Co). These trimetallic electrocatalysts have been tested toward the oxygen reduction reaction (ORR), showing a greatly enhanced mass activity related to commercial Pt/C and less activity loss than binary PtNi and PtCo after 4000 potential cycles.

How monuments shape urban identity

Monuments in our society commemorate historical events, acts or heroes, and educate people about them. Monuments are landmarks that stand out from other buildings to give the city identity and order. This thesis asks how a monument can be designed to project a clear image at a distance and articulate a spatial experience at close range. Two important monuments that form part of the life of America serve as examples: (1) The Statue of Liberty, in the New York Harbor, that has become the visual icon of New York if not the nation and (2) The Holocaust Memorial in Miami Beach, Florida, that leads the visitor through a poignant experience at close range. The second part of the thesis is the design of a monument and museum for The Port of Miami, as part of the Port Boulevard Enhancement Project, sponsored by the Florida Foreign Trade Association, to celebrate the trade pioneers who helped Miami-Dade County achieve its prominence. The site for the monument is located at Biscayne Boulevard and Fifth Street, between Bayside Market Place and The American Airlines Arena in downtown Miami, at the Biscayne Bay.

Effect of pharmacological pupil dilation on measurements and iol power calculation made using the new swept-source optical coherence tomography-based optical biometer

Purpose: to determine whether pupil dilation affects biometric measurements and intraocular lens (IOL) power calculation made using the new swept-source optical coherence tomography-based optical biometer (IOLMaster 700©; Carl Zeiss Meditec, Jena, Germany). Procedures: eighty-one eyes of 81 patients evaluated for cataract surgery were prospectively examined using the IOLMaster 700© before and after pupil dilation with tropicamide 1%. The measurements made were: axial length (AL), central corneal thickness (CCT), aqueous chamber depth (ACD), lens thickness (LT), mean keratometry (MK), white-to-white distance (WTW) and pupil diameter (PD). Holladay II and SRK/T formulas were used to calculate IOL power. Agreement between measurement modes (with and without dilation) was assessed through intraclass correlation coefficients (ICC) and Bland-Altman plots. Results: mean patient age was 75.17 ± 7.54 years (range: 57–92). Of the variables determined, CCT, ACD, LT and WTW varied significantly according to pupil dilation. Excellent intraobserver correlation was observed between measurements made before and after pupil dilation. Mean IOL power calculation using the Holladay 2 and SRK/T formulas were unmodified by pupil dilation. Conclusions: the use of pupil dilation produces statistical yet not clinically significant differences in some IOLMaster 700© measurements. However, it does not affect mean IOL power calculation.

Theoretical and experimental study on electron interactions with chlorobenzene: Shape resonances and differential cross sections

In this work, we report theoretical and experimental cross sections for elastic scattering of electrons by chlorobenzene (ClB). The theoretical integral and differential cross sections (DCSs) were obtained with the Schwinger multichannel method implemented with pseudopotentials (SMCPP) and the independent atom method with screening corrected additivity rule (IAM-SCAR). The calculations with the SMCPP method were done in the static-exchange (SE) approximation, for energies above 12 eV, and in the static-exchange plus polarization approximation, for energies up to 12 eV. The calculations with the IAM-SCAR method covered energies up to 500 eV. The experimental differential cross sections were obtained in the high resolution electron energy loss spectrometer VG-SEELS 400, in Lisbon, for electron energies from 8.0 eV to 50 eV and angular range from 7 degrees to 110 degrees. From the present theoretical integral cross section (ICS) we discuss the low-energy shape-resonances present in chlorobenzene and compare our computed resonance spectra with available electron transmission spectroscopy data present in the literature. Since there is no other work in the literature reporting differential cross sections for this molecule, we compare our theoretical and experimental DCSs with experimental data available for the parent molecule benzene. Published by AIP Publishing.

An allometric modelling approach to identify the optimal body shape sssociated with, and differences between brazilian and peruvian youth motor performance

Children fromdevelopedanddevelopingcountriesdifferintheirbodysizeandshapedueto markeddifferencesacrosstheirlifehistorycausedbysocial,economicandculturaldifferenceswhicharealsolinkedtotheirmotorperformance(MP).Weusedallometricmodelsto identifysize/shapecharacteristicsassociatedwithMPtestsbetweenBrazilianandPeruvianschoolchildren.Atotalof4,560subjects,2,385girlsand2,175boysaged9–15years werestudied.Heightandweightweremeasured;biological maturation wasestimated with thematurityoffsettechnique;MPmeasuresincludedthe12minuterun(12MR),handgrip strength(HG),standinglongjump(SLJ)andtheshuttlerunspeed(SR)tests;physicalactivity(PA)wasassessedusingtheBaeckequestionnaire.Amultiplicativeallometricmodel wasadoptedtoadjustforbodysizedifferencesacrosscountries.Reciprocalponderalindex (RPI)wasfoundtobethemostsuitablebodyshapeindicatorassociatedwiththe12MR, SLJ,HGandSRperformance.Apositivematurationoffset parameterwasalsoassociated withabetterperformanceinSLJ,HGandSRtests.Sexdifferenceswerefoundinallmotor tests.BrazilianyouthshowedbetterscoresinMPthantheirPeruvianpeers,evenwhen controlling fortheirbodysizedifferencesThecurrentstudyidentifiedthekeybodysize associatedwithfourbodymass-dependentMPtests.Biological maturationandPAwere associatedwithstrengthandmotorperformance.Sexdifferenceswerefoundinallmotor tests,aswellasacrosscountriesfavoringBrazilianchildrenevenwhenaccountingfortheir bodysize/shapedifferences.

An allometric modelling approach to identify the optimal body shape associated with, and differences between brazilian and peruvian youth motor performance

Children fromdevelopedanddevelopingcountriesdifferintheirbodysizeandshapedueto markeddifferencesacrosstheirlifehistorycausedbysocial,economicandculturaldifferenceswhicharealsolinkedtotheirmotorperformance(MP).Weusedallometricmodelsto identifysize/shapecharacteristicsassociatedwithMPtestsbetweenBrazilianandPeruvianschoolchildren.Atotalof4,560subjects,2,385girlsand2,175boysaged9–15years werestudied.Heightandweightweremeasured;biological maturation wasestimated with thematurityoffsettechnique;MPmeasuresincludedthe12minuterun(12MR),handgrip strength(HG),standinglongjump(SLJ)andtheshuttlerunspeed(SR)tests;physicalactivity(PA)wasassessedusingtheBaeckequestionnaire.Amultiplicativeallometricmodel wasadoptedtoadjustforbodysizedifferencesacrosscountries.Reciprocalponderalindex (RPI)wasfoundtobethemostsuitablebodyshapeindicatorassociatedwiththe12MR, SLJ,HGandSRperformance.Apositivematurationoffset parameterwasalsoassociated withabetterperformanceinSLJ,HGandSRtests.Sexdifferenceswerefoundinallmotor tests.BrazilianyouthshowedbetterscoresinMPthantheirPeruvianpeers,evenwhen controlling fortheirbodysizedifferencesThecurrentstudyidentifiedthekeybodysize associatedwithfourbodymass-dependentMPtests.Biological maturationandPAwere associatedwithstrengthandmotorperformance.Sexdifferenceswerefoundinallmotor tests,aswellasacrosscountriesfavoringBrazilianchildrenevenwhenaccountingfortheir bodysize/shapedifferences.

How do medium naturalness and personality traits shape academic achievement and perceived learning? An experimental study of face-to-face and synchronous e-learning

This controlled experiment examined how academic achievement and cognitive, emotional and social aspects of perceived learning are affected by the level of medium naturalness (face-to-face, one-way and two-way videoconferencing) and by learners’ personality traits (extroversion–introversion and emotional stability–neuroticism). The Media Naturalness Theory explains the degree of medium naturalness by comparing its characteristics to face-to-face communication, considered to be the most natural form of communication. A total of 76 participants were randomly assigned to three experimental conditions: face-to-face, one-way and two-way videoconferencing. E-learning conditions were conducted through Zoom videoconferencing, which enables natural and spontaneous communication. Findings shed light on the trade-off involved in media naturalness: one-way videoconferencing, the less natural learning condition, enhanced the cognitive aspect of perceived learning but compromised the emotional and social aspects. Regarding the impact of personality, neurotic students tended to enjoy and succeed more in face-to-face learning, whereas emotionally stable students enjoyed and succeeded in all of the learning conditions. Extroverts tended to enjoy more natural learning environments but had lower achievements in these conditions. In accordance with the ‘poor get richer’ principle, introverts enjoyed environments with a low level of medium naturalness. However, they remained focused and had higher achievements in the face-to-face learning.

Nuclear shape instability caused by lamin A deregulation promotes invasiveness in pediatric bone sarcomas: from nucleo-cytoskeleton dynamics to novel therapeutic opportunities

Osteosarcoma (OS) and Ewing sarcoma (EWS) are the two most frequent primary bone tumors, in which metastases remain the most relevant adverse prognostic factor. Lamin A is the main constituent of the nuclear lamina, with a fundamental role in maintaining the connection between nucleus and cytoskeleton (through LINC complex proteins interactions), and its alterations can be implicated in tumor progression. We investigated how nucleo-cytoskeleton dynamics is influenced by lamin A modulation in OS and EWS, demonstrating that both these cancer models had low levels of lamin A, which are linked to a significantly more marked nuclear misshaping. In our in vitro studies, reduced levels of lamin A promoted migratory abilities in these tumors. Moreover, these findings were corroborated by gene expression analyses on EWS patient samples, showing that LMNA levels were significantly lower in metastatic lesions compared to primary tumors and that patients with low LMNA had a significant worse overall survival. We also found that LMNA expression significantly impaired EWS metastases formation in vivo. We demonstrated that low lamin A expression was linked to a severe mislocalization of LINC complex proteins, thus disrupting nucleo-cytoskeleton interactions, with a corresponding gain in malignant properties, which resulted in increased invasiveness. Lamin A overexpression or its accumulation by a statin-based pharmacological treatment allowed us to reconstitute a functional nucleo-cytoskeleton interplay, which resulted in significant downmodulation of ROCK2 and YAP, two crucial drivers of EWS aggressiveness. Our study demonstrated that lamin A is a favorable mediator of nuclear shape stability in bone sarcomas, and its modulation rescues LINC complex protein localization and regulates mechano-signaling pathways, thus promoting a less aggressive cancer phenotype. We also identified statins, already employed in clinical practice, as a tool capable to increase lamin A levels, and to reconstitute functional nucleo-cytoskeletal dynamics, resulting in reduced cellular migration.

Different dietary fibres included in the gestation and lactation diet shape sow's microbiota, modify colostrum and milk composition and affect piglet growth and health

This thesis reports three experimental studies that may contribute to understand how the sources or types of dietary fibres (DFs) included in sow diet with similar level of total DFs influence the composition of colostrum and milk and their related effects on offspring performance and gut microbiota. The first study showed that decreasing the level of hemicelluloses (HCs) in sow’s lactation diet increased the proportion of butyrate and the concentration of volatile fatty acids (VFAs), copper and threonine in milk. Simultaneously, the post-weaning growth of low birthweight piglets was improved, and the diarrhoea occurrence was reduced during the second week post-weaning. The second study showed that the level of HCs in the diet of lactating sows affected their faecal microbiota, modified the VFA profile in sow’s faeces during lactation and barely impacted the faecal microbiota of slow and fast growing piglets. The third study showed that replacing a source soluble DFs by one of insoluble DFs in sow’s diet during late gestation and lactation reduced farrowing duration, increased total VFAs and lactoferrin concentrations in colostrum, improved growth performance from birth to 1 day of lactation, during the post-weaning period and throughout the study, and reduced diarrhoea occurrence during the first week post-weaning. Finally, a fourth study proposed a workflow to analyse low biomass samples from the umbilical cord blood aiming at investigating the existence of a pre-birth microbiota with no substantial findings to confirm this hypothesis. Overall, the results of these studies confirmed that, besides the level of DFs, the sources, and the types of DFs included in the sow's diet shape the sow's microbiota, influence the composition of colostrum and milk, and improve offspring performance, but with limited impacts on the microbiota of piglets.

A Trans-dimensional inversion algorithm to model deformation sources with unconstrained shape in finite element domains

Ground deformation provides valuable insights on subsurface processes with pattens reflecting the characteristics of the source at depth. In active volcanic sites displacements can be observed in unrest phases; therefore, a correct interpretation is essential to assess the hazard potential. Inverse modeling is employed to obtain quantitative estimates of parameters describing the source. However, despite the robustness of the available approaches, a realistic imaging of these reservoirs is still challenging. While analytical models return quick but simplistic results, assuming an isotropic and elastic crust, more sophisticated numerical models, accounting for the effects of topographic loads, crust inelasticity and structural discontinuities, require much higher computational effort and information about the crust rheology may be challenging to infer. All these approaches are based on a-priori source shape constraints, influencing the solution reliability. In this thesis, we present a new approach aimed at overcoming the aforementioned limitations, modeling sources free of a-priori shape constraints with the advantages of FEM simulations, but with a cost-efficient procedure. The source is represented as an assembly of elementary units, consisting in cubic elements of a regular FE mesh loaded with a unitary stress tensors. The surface response due to each of the six stress tensor components is computed and linearly combined to obtain the total displacement field. In this way, the source can assume potentially any shape. Our tests prove the equivalence of the deformation fields due to our assembly and that of corresponding cavities with uniform boundary pressure. Our ability to simulate pressurized cavities in a continuum domain permits to pre-compute surface responses, avoiding remeshing. A Bayesian trans-dimensional inversion algorithm implementing this strategy is developed. 3D Voronoi cells are used to sample the model domain, selecting the elementary units contributing to the source solution and those remaining inactive as part of the crust.