INNOVATIVE HUMAN-COMPUTER INTERACTIONS TO SUPPORT COGNITIVE COLLABORATIVE GEOSPATIAL ENVIRONMENTS

In the current world geospatial information is being demanded in almost real time, which requires the speed at which this data is processed and made available to the user to be at an all-time high. In order to keep up with this ever increasing speed, analysts must find ways to increase their productivity. At the same time the demand for new analysts is high, and current methods of training are long and can be costly. Through the use of human computer interactions and basic networking systems, this paper explores new ways to increase efficiency in data processing and analyst training.

Caractérisation des structures de septines hautement organisées chez la drosophile et leur interaction avec le cytosquelette d’actine

Les septines sont des GTPases conservées dérégulées dans le cancer et les maladies neurodégénératives. Elles servent de protéines d’échafaudage et forment une barrière de diffusion à la membrane plasmique et au corps central lors de la cytokinèse. Elles interagissent avec l’actine et s’organisent en complexes qui polymérisent et forment des structures hautement organisées (anneaux et filaments). Leur dynamique d’assemblage et leur rôle dans la cellule restent à être élucidés. La Drosophile est un modèle simple pour l’étude des septines puisqu’on n’y retrouve que 5 gènes (sep1, sep2, sep4, sep5, peanut) comparativement aux 13 gènes chez l’humain. À l’aide d’un anticorps contre Pnut, nous avons identifié des structures tubulaires dans 30% des cellules S2 de Drosophile. Mon projet a comme but de caractériser ces tubes en élucidant leurs constituants, leur comportement et leurs propriétés pour mieux clarifier le mécanisme par lequel les septines forment des structures hautement organisées et interagissent avec le cytosquelette d’actine. Par immunofluorescence, j’ai pu démontrer que ces tubes sont cytoplasmiques, en mitose ou interphase, ce qui suggère qu’ils ne sont pas régulés par le cycle cellulaire. Pour investiguer la composition et les propriétés dynamiques de ces tubes, j’ai généré une lignée cellulaire exprimant Sep2-GFP qui se localise aux tubes et des ARNi contre les cinq septines. Trois septines sont importantes pour la formation de ces tubes et anneaux notamment Sep1, Sep2 et Pnut. La déplétion de Sep1 cause la dispersion du signal GFP en flocons, tandis que la déplétion de Sep2 ou de Pnut mène à la dispersion du signal GFP uniformément dans la cellule. Des expériences de FRAP sur la lignée Sep2-GFP révèlent un signal de retour très lent, ce qui indique que ces structures sont très stables. J’ai aussi démontré une relation entre l’actine et les septines. Le traitement avec la Latrunculin A (un inhibiteur de la polymérisation de l’actine) ou la Jasplakinolide (un stabilisateur des filaments d’actine) mène à la dépolymérisation rapide (< 30 min) des tubes en anneaux flottants dans le cytoplasme, même si ces tubes ne sont pas reconnus suite à un marquage de la F-actine. L’Actin05C-mCherry se localise aux tubes, tandis que le mutant déficient de la polymérisation, Actin05C-R62D-mCherry perd cette localisation. On observe aussi que la déplétion de la Cofiline et de l’AIP1 (ce qui déstabilise l’actine) mène au même phénotype que le traitement avec la Latrunculine A ou la Jasplakinolide. Alors on peut conclure qu’un cytosquelette d’actine dynamique est nécessaire pour la formation et le maintien des tubes de septines. Les futures études auront comme but de mieux comprendre l’organisation des septines en structures hautement organisées et leur relation avec l’actine. Ceci sera utile pour l’élaboration du réseau d’interactions des septines qui pourra servir à expliquer leur dérégulation dans le cancer et les maladies neurodégénératives.

Sticking non-stick: surface and structure control of diamond-like carbon in plasma enhanced chemical vapour deposition

This short review article explores the practical use of diamond-like carbon (DLC) produced by plasma enhanced chemical vapour deposition (PECVD). Using as an example issues relating to the DLC coating of a hand-held surgical device, we draw on previous works using atomic force microscopy, X-ray photoelectron spectroscopy, Raman spectroscopy, scanning electron microscopy, tensiometry and electron paramagnetic resonance. Utilising data from these techniques, we examine the surface structure, substrate-film interface and thin film microstructure, such as sp2/sp3 ratio (graphitic/diamond-like bonding ratio) and sp2 clustering. We explore the variations in parameters describing these characteristics, and relate these to the final device properties such as friction, wear resistance, and diffusion barrier integrity. The material and device characteristics are linked to the initial plasma and substrate conditions.

Innovation and Territorial Development: An Analysis of the Region of São José dos Campos - Brazil

This study aimed to identify and analyze the interrelations between companies, research centers, universities, government and other relevant players in the micro region of São José dos Campos, focusing on the creation and diffusion of innovations as a strategy for regional development. To this end, we made an interview with 12 regional players Involved in this process. It is hoped the results expand the knowledge of regional development in technologyoriented areas, as well as the dynamics of territorial development in the micro region studied. It is an academic contribution in developing strategies for expanding competitive regions through incentives for innovation and technology transfer.

Regional variation and change in the history of English strong verbs

This thesis investigates how the strong verb system inherited from Old English evolved in the regional dialects of Middle English (ca. 1100-1500). Old English texts preserve a relatively complex system of strong verbs, in which traditionally seven different ablaut classes are distinguished. This system becomes seriously disrupted from the Late Old English and Early Middle English periods onwards. As a result, many strong verbs die out, or have their ablaut patterns affected by sound change and morphological analogy, or transfer to the weak conjugation. In my thesis, I study the beginnings of two of these developments in two strong verb classes to find out what the evidence from Middle English regional dialects can tell us about their origins and diffusion. Chapter 2 concentrates on the strong-to-weak shift in Class III verbs, and investigates to what extent strong, mixed and weak past tense and participle forms vary in Middle English dialects, and whether the variation is more pronounced in the paradigms of specific verbs or sub-classes. Chapter 3 analyses the regional distribution of ablaut levelling in strong Class IV verbs throughout the Middle English period. The Class III and IV data for the Early Middle English period are drawn from A Linguistic Atlas of Early Middle English, and the data for the Late Middle English period from a sub-corpus of files from The Penn-Helsinki Parsed Corpus of Middle English and The Middle English Grammar Corpus. Furthermore, The English Dialect Dictionary and Grammar are consulted as an additional reference point to find out to what extent the Middle English developments are reflected in Late Modern English dialects. Finally, referring to modern insights into language variation and change and linguistic interference, Chapter 4 discusses to what extent intra- and extra-linguistc factors, such as token and type frequency, stem structure and language contact, might correlate with the strong-to-weak shift and ablaut levelling in Class III and IV verbs in the Middle English period. The thesis is accompanied by six appendices that contain further information about my distinction of Middle English dialect areas (Appendix A), historical Class III and IV verbs (B and C) and the text samples and linguistic data from the Middle English text corpora (D, E and F).

UT Austin | Portugal Workshop on Nonlinear Mechanics and Applications in Life Sciences

This is a CoLab Workshop organized as an initiative of the UT Austin | Portugal Program to reinforce the Portuguese competences in Nonlinear Mechanics and in complex problems arising from applications to the mathematical modeling and simulations in the Life Sciences. The Workshop provides a place to exchange recent developments, discoveries and progresses in this challenging research field. The main goal is to bring together doctoral candidates, postdoctoral scientists and graduates interested in the field, giving them the opportunity to make scientific interactions and new connections with established experts in the interdisciplinary topics covered by the event. Another important goal of the Workshop is to promote collaboration between members of the different areas of the UT Austin | Portugal community.

Liquid Mixtures Involving Hydrogenated and Fluorinated Alcohols: Thermodynamics, Spectroscopy, and Simulation

This article reports a combined thermodynamic, spectroscopic, and computational study on the interactions and structure of binary mixtures of hydrogenated and fluorinated substances that simultaneously interact through strong hydrogen bonding. Four binary mixtures of hydrogenated and fluorinated alcohols have been studied, namely, (ethanol + 2,2,2-trifluoroethanol (TFE)), (ethanol + 2,2,3,3,4,4,4-heptafluoro-1-butanol), (1-butanol (BuOH) + TFE), and (BuOH + 2,2,3,3,4,4,4-heptafluoro-1-butanol). Excess molar volumes and vibrational spectra of all four binary mixtures have been measured as a function of composition at 298 K, and molecular dynamics simulations have been performed. The systems display a complex behavior when compared with mixtures of hydrogenated alcohols and mixtures of alkanes and perfluoroalkanes. The combined analysis of the results from different approaches indicates that this results from a balance between preferential hydrogen bonding between the hydrogenated and fluorinated alcohols and the unfavorable dispersion forces between the hydrogenated and fluorinated chains. As the chain length increases, the contribution of dispersion increases and overcomes the contribution of H-bonds. In terms of the liquid structure, the simulations suggest the possibility of segregation between the hydrogenated and fluorinated segments, a hypothesis corroborated by the spectroscopic results. Furthermore, a quantitative analysis of the infrared spectra reveals that the presence of fluorinated groups induces conformational changes in the hydrogenated chains from the usually preferred all-trans to more globular arrangements involving gauche conformations. Conformational rearrangements at the CCOH dihedral angle upon mixing are also disclosed by the spectra.

Insights into (S)-rivastigmine inhibition of butyrylcholinesterase (BuChE): Molecular docking and saturation transfer difference NMR (STD-NMR)

Rivastigmine is a very important drug prescribed for the treatment of Alzheimer's disease (AD) symptoms. It is a dual inhibitor, in that it inhibits both acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE). For our screening program on the discovery of new rivastigmine analogue hits for human butyrylcholinesterase (hBuChE) inhibition, we investigated the interaction of this inhibitor with BuChE using the complimentary approach of the biophysical method, saturation transfer difference (STD)-NMR and molecular docking. This allowed us to obtain essential information on the key binding interactions between the inhibitor and the enzyme to be used for screening of hit compounds. The main conclusions obtained from this integrated study was that the most dominant interactions were (a) H-bonding between the carbamate carbonyl of the inhibitor and the NH group of the imidazole unit of H434, (b) stacking of the aromatic unit of the inhibitor and the W82 aromatic unit in the choline binding pocket via pi-pi interactions and (c) possible CH/pi interactions between the benzylic methyl group and the N-methyl groups of the inhibitor and W82 of the enzyme.

Phenotypic and genotypic characterisation of antimicrobial resistance in Escherichia coli indicator of animal, food and human origin.

This thesis presents AMR phenotypic evaluation and whole genome sequencing analysis of 288 Escherichia coli strains isolated from different sources (livestock, companion animal, wildlife, food and human) in Italy. Our data reflects general resistance trends in Europe, reporting tetracycline, ampicillin, sulfisoxazole and aminoglycosides resistance as the most common phenotypic AMR profile among livestock, pets, wildlife and humans. Identification of human and animal (livestock and companion animal) AMR profiles in niches with a rare (fishery, mollusc) or absent (vegetable, wild animal, wild boar) direct exposure to antimicrobials, suggests widespread environmental pollution with ARGs conferring resistance to these antimicrobials. Phenotypic resistance to highest priority critically important antimicrobials was mainly observed in food-producing animals and related food such as rabbit, poultry, beef and swine. Discrepancies between AMR phenotypic pattern and genetic profile were observed. In particular, phenotypic aminoglycoside, cephalosporin, meropenem, colistin resistance and ESBL profile did not have a genetic explanation in different cases. This data could suggest the diffusion of new genetic variants of ARGs, associated to these antimicrobial classes. Generally, our collection shows a virulence profile typical of extraintestinal pathogenic Escherichia coli (ExPEC) pathotype. Different pandemic and emerging ExPEC lineages were identified, in particular in poultry meat (ST10; ST23; ST69, ST117; ST131). Rabbit was suggested as a source of ST20-ST40 potential hybrid pathogens. Wildlife carried a high average number (10) of VAGs (mostly associated to ExPEC pathotype) and different predominant ExPEC lineages (ST23, ST117, ST648), suggesting its possible involvement in maintenance and diffusion of virulence determinants. In conclusion, our study provides important knowledge related to the phenotypic/genetic AMR and virulence profiles circulating in E. coli in Italy. The role of different niches in AMR dynamics has been discussed. In particular, food-producing animals are worthy of continued investigation as a source of potential zoonotic pathogens, meanwhile wildlife might contribute to VAGs spread.

Water and sediments geochemistry and elemental fluxes on a Large Dam: case study of Ridracoli reservoir.

Since the study of Large Dam Reservoirs is of worldwide interest, in this PhD project we investigated the Ridracoli reservoir, one of the main water supply in Emilia-Romagna (north-eastern Italy). This work aims to characterize waters and sediments to better understand their composition, interactions and any process that occurs, for a better geochemical and environmental knowledge of the area. Physical and chemical analyses on the water column have shown an alternation of stratification and mixing of water in the reservoir’s water body due to seasonal variations in temperature and density. In particular, it was observed the establishment, in late summer, of anoxic conditions at the bottom, which in turn affects the concentration and mobility of some elements of concern (e.g. Fe and Mn) for the water quality. Sediments within the reservoir and from surrounding areas were analysed for organic matter, total inorganic composition and grain size, assessing the inter-element relationship, grain size, geological background and damming influences on their chemistry, through descriptive statistics, Principal Component Analysis and Cluster Analysis. The reservoir’s area was also investigated by pseudo total composition (Aqua Regia digestion), degree of elements extractability, and enrichment factors, then analysed and compared to limits by law and literature. Sediment cores, interstitial waters, and benthic chamber data from the bottom were of great interest due to organic matter degradation, early diagenesis, mineral formation at water-sediment interface and observed flows. Finally, leaching test and extraction procedures, of environmental interest, showed peculiar partitioning, both regarding spatial and in-depth distribution, and the absence of pollution. Collectively, our results are useful for the comprehension of processes that occur in water and sediments of Ridracoli reservoir, providing important knowledges on the site that could be relevant for the management of the resource and the planning of future interventions.

Temporary teams learning and performance: the case of 3D printing technology in orthopaedic surgery

This dissertation contributes to the scholarly debate on temporary teams by exploring team interactions and boundaries.The fundamental challenge in temporary teams originates from temporary participation in the teams. First, as participants join the team for a short period of time, there is not enough time to build trust, share understanding, and have effective interactions. Consequently, team outputs and practices built on team interactions become vulnerable. Secondly, as team participants move on and off the teams, teams’ boundaries become blurred over time. It leads to uncertainty among team participants and leaders about who is/is not identified as a team member causing collective disagreement within the team. Focusing on the above mentioned challenges, we conducted this research in healthcare organisations since the use of temporary teams in healthcare and hospital setting is prevalent. In particular, we focused on orthopaedic teams that provide personalised treatments for patients using 3D printing technology. Qualitative and quantitative data were collected using interviews, observations, questionnaires and archival data at Rizzoli Orthopaedic Institute, Bologna, Italy. This study provides the following research outputs. The first is a conceptual study that explores temporary teams’ literature using bibliometric analysis and systematic literature review to highlight research gaps. The second paper qualitatively studies temporary relationships within the teams by collecting data using group interviews and observations. The results highlighted the role of short-term dyadic relationships as a ground to share and transfer knowledge at the team level. Moreover, hierarchical structure of the teams facilitates knowledge sharing by supporting dyadic relationships within and beyond the team meetings. The third paper investigates impact of blurred boundaries on temporary teams’ performance. Using quantitative data collected through questionnaires and archival data, we concluded that boundary blurring in terms of fluidity, overlap and dispersion differently impacts team performance at high and low levels of task complexity.

Effective field theories and their phenomenological applications

Effective field theories (EFTs) are ubiquitous in theoretical physics and in particular in field theory descriptions of quantum systems probed at energies much lower than one or few characterizing scales. More recently, EFTs have gained a prominent role in the study of fundamental interactions and in particular in the parametriasation of new physics beyond the Standard Model, which would occur at scales Λ, much larger than the electroweak scale. In this thesis, EFTs are employed to study three different physics cases. First, we consider light-by-light scattering as a possible probe of new physics. At low energies it can be described by dimension-8 operators, leading to the well-known Euler-Heisenberg Lagrangian. We consider the explicit dependence of matching coefficients on type of particle running in the loop, confirming the sensitiveness to the spin, mass, and interactions of possibly new particles. Second, we consider EFTs to describe Dark Matter (DM) interactions with SM particles. We consider a phenomenologically motivated case, i.e., a new fermion state that couples to the Hypercharge through a form factor and has no interactions with photons and the Z boson. Results from direct, indirect and collider searches for DM are used to constrain the parameter space of the model. Third, we consider EFTs that describe axion-like particles (ALPs), whose phenomenology is inspired by the Peccei-Quinn solution to strong CP problem. ALPs generically couple to ordinary matter through dimension-5 operators. In our case study, we investigate the rather unique phenomenological implications of ALPs with enhanced couplings to the top quark.

Spectroscopic investigation on photoreactivity, structure and polymorphism of organic molecular crystals

The study of the spectroscopic phenomena in organic solids, in combination with other techniques, is an effective tool for the understanding of the structural properties of materials based on these compounds. This Ph.D. work was dedicated to the spectroscopic investigation of some relevant processes occurring in organic molecular crystals, with the goal of expanding the knowledge on the relationship between structure, dynamics and photoreactivity of these systems. Vibrational spectroscopy has been the technique of choice, always in combination with X-ray diffraction structural studies and often the support of computational methods. The vibrational study of the molecular solid state reaches its full potential when it includes the low-wavenumber region of the lattice-phonon modes, which probe the weak intermolecular interactions and are the fingerprints of the lattice itself. Microscopy is an invaluable addition in the investigation of processes that take place in the micro-meter scale of the crystal micro-domains. In chemical and phase transitions, as well as in polymorph screening and identification, the combination of Raman microscopy and lattice-phonon detection has provided useful information. Research on the fascinating class of single-crystal-to-single-crystal photoreactions, has shown how the homogeneous mechanism of these transformations can be identified by lattice-phonon microscopy, in agreement with the continuous evolution of their XRD patterns. On describing the behavior of the photodimerization mechanism of vitamin K3, the focus was instead on the influence of its polymorphism in governing the product isomerism. Polymorphism is the additional degree of freedom of molecular functional materials, and by advancing in its control and properties, functionalities can be promoted for useful applications. Its investigation focused on thin-film phases, widely employed in organic electronics. The ambiguities in phase identification often emerging by other experimental methods were successfully solved by vibrational measurements.

Modelling the influence of diradical character and aggregation on conjugated molecular materials

Molecular materials are made by the assembly of specifically designed molecules to obtain bulk structures with desired solid-state properties, enabling the development of materials with tunable chemical and physical properties. These properties result from the interplay of intra-molecular constituents and weak intermolecular interactions. Thus, small changes in individual molecular and electronic structure can substantially change the properties of the material in bulk. The purpose of this dissertation is, thus, to discuss and to contribute to the structure-property relationships governing the electronic, optical and charge transport properties of organic molecular materials through theoretical and computational studies. In particular, the main focus is on the interplay of intra-molecular properties and inter-molecular interactions in organic molecular materials. In my three-years of research activity, I have focused on three major areas: 1) the investigation of isolated-molecule properties for the class of conjugated chromophores displaying diradical character which are building blocks for promising functional materials; 2) the determination of intra- and intermolecular parameters governing charge transport in molecular materials and, 3) the development and application of diabatization procedures for the analysis of exciton states in molecular aggregates. The properties of diradicaloids are extensively studied both regarding their ground state (diradical character, aromatic vs quinoidal structures, spin dynamics, etc.) and the low-lying singlet excited states including the elusive double-exciton state. The efficiency of charge transport, for specific classes of organic semiconductors (including diradicaloids), is investigated by combining the effects of intra-molecular reorganization energy, inter-molecular electronic coupling and crystal packing. Finally, protocols aimed at unravelling the nature of exciton states are introduced and applied to different molecular aggregates. The role of intermolecular interactions and charge transfer contributions in determining the exciton state character and in modulating the H- to J- aggregation is also highlighted.

Changes In Liver Cell Dna Methylation Status In Diabetic Mice Affect Its Ft-ir Characteristics.

Lower levels of cytosine methylation have been found in the liver cell DNA from non-obese diabetic (NOD) mice under hyperglycemic conditions. Because the Fourier transform-infrared (FT-IR) profiles of dry DNA samples are differently affected by DNA base composition, single-stranded form and histone binding, it is expected that the methylation status in the DNA could also affect its FT-IR profile. The DNA FT-IR signatures obtained from the liver cell nuclei of hyperglycemic and normoglycemic NOD mice of the same age were compared. Dried DNA samples were examined in an IR microspectroscope equipped with an all-reflecting objective (ARO) and adequate software. Changes in DNA cytosine methylation levels induced by hyperglycemia in mouse liver cells produced changes in the respective DNA FT-IR profiles, revealing modifications to the vibrational intensities and frequencies of several chemical markers, including νas -CH3 stretching vibrations in the 5-methylcytosine methyl group. A smaller band area reflecting lower energy absorbed in the DNA was found in the hyperglycemic mice and assumed to be related to the lower levels of -CH3 groups. Other spectral differences were found at 1700-1500 cm(-1) and in the fingerprint region, and a slight change in the DNA conformation at the lower DNA methylation levels was suggested for the hyperglycemic mice. The changes that affect cytosine methylation levels certainly affect the DNA-protein interactions and, consequently, gene expression in liver cells from the hyperglycemic NOD mice.