Search

Anfinsen's seminal work has shown that the information required for a protein to fold into its specific three-dimensional structure is encoded into its amino acid sequence. The protein structure was believed to determine its activity, meaning that a protein needs to fold in order to function. More recently, intrinsically disordered proteins (IDPs) have been shown to represent a significant portion of the proteome. Despite the lack of a predefined structure, they still play important roles in cellular function, challenging the structure-function paradigm. Proteins are largely studied in isolated conditions, but in a cellular environment they are part of a vastly more complex system. The work presented here aims to shed light on how context can influence folding and binding mechanisms. First, we used SasG - a bacterial protein that defies the disorder prediction with its unique sequence composition and unusual structure - as a template to investigate co-translational folding, and how the presence of the ribosome can affect its folding mechanism. SasG in vitro translation was investigated utilising force profile experiments. We showed that both the G52 and E-G52 constructs can fold very early, when still inside the vestibule of the ribosome. Moreover, our results suggest that non-native interactions can also provide sufficient force to release the stall sequence. Next we employed protein members of the BCL-2 family - involved in controlling the cell death mechanism - to understand what encodes a coupled folding and binding reaction. Although displaying a variety of conformations, some IDPs can fold upon binding to a partner protein. Promiscuous binding is a great advantage of disordered molecules, as multiple IDPs are able to bind and fold to the same partner protein. This raises the question of what orchestrates a coupled folding and binding reaction: the IDP or the partner protein? Using phi-value analysis we studied four IDP-partner protein complexes, composed of alternative pairs of BCL-2 family members. In the bimolecular context, the disordered protein dictates the transition state interactions. Therefore, analogous to Anfinsen's postulate, the folding pathway is encoded by the protein that folds, even when binding to another macromolecule is required. Finally, studies of the BCL-2 member BID on its full-length context showed that it cannot interact with its partner A1 unless it is cleaved (tBID). These results provide insights on the role of tBID as a player during programmed cell death and hence why the pathway of cleaving BID with caspase is energetically favourable.

Advances in technology and incentives from governments are enabling growing deployment of distributed energy resources (DER) and this raises challenges over how distribution network operators (DNOs) should host these resources other than through traditional grid reinforcement. The alternative is active network management (ANM) which can control non-firm connections of DERs to ensure the network is compliant with voltage and thermal operating limits while increasing the capacity of the network to host DER. Furthermore, with changes expected in the regulatory paradigm to create ancillary service markets to promote other benefits of DERs, new streams of revenue for DER owners are anticipated. ANM schemes should manage growing volume of DERs while minimising costs of ancillary services. In this context, it is proposed and evaluated a distributed form of ANM for radial networks that manages voltage and thermal constraints and does this cost-effectively by including the costs of ancillary services in its objective function. To distribute the ANM, a mathematical formulation for local calculation of voltage sensitivities is derived that enables each local controller (LC) to take decisions over power injections to solve constraints. These estimates are combined in a message passing process that results in a coordinated set of decisions that solve local and non-local network constraint. The proposed ANM, based on estimated sensitivities and local message passing, is compared with a centralised ANM based on optimal power flow (OPF). Case-studies examined through time-domain simulations showed that the proposed ANM successfully identified the most appropriate DER to act and produced near identical control actions to the OPF. The approach is evaluated across multiple randomly generated scenarios, providing good confidence that the method is widely applicable and accurate. Mismatches of the order of 10^{-2} p.u where observed when compared to centralised algorithm and considerable decrease in computational time and data transmission was achieved.

Our bodies are the medium through which we experience the world around us, so human-computer interaction can highly benefit from the richness of body movements and postures as an input modality. In recent years, the widespread availability of inertial measurement units and depth sensors led to the development of a plethora of applications for the body in human-computer interaction. However, the main focus of these works has been on using the upper body for explicit input. This thesis investigates the research space of full-body human-computer interaction through three propositions. The first proposition is that there is more to be inferred by natural users’ movements and postures, such as the quality of activities and psychological states. We develop this proposition in two domains. First, we explore how to support users in performing weight lifting activities. We propose a system that classifies different ways of performing the same activity; an object-oriented model-based framework for formally specifying activities; and a system that automatically extracts an activity model by demonstration. Second, we explore how to automatically capture nonverbal cues for affective computing. We developed a system that annotates motion and gaze data according to the Body Action and Posture coding system. We show that quality analysis can add another layer of information to activity recognition, and that systems that support the communication of quality information should strive to support how we implicitly communicate movement through nonverbal communication. Further, we argue that working at a higher level of abstraction, affect recognition systems can more directly translate findings from other areas into their algorithms, but also contribute new knowledge to these fields. The second proposition is that the lower limbs can provide an effective means of interacting with computers beyond assistive technology To address the problem of the dispersed literature on the topic, we conducted a comprehensive survey on the lower body in HCI, under the lenses of users, systems and interactions. To address the lack of a fundamental understanding of foot-based interactions, we conducted a series of studies that quantitatively characterises several aspects of foot-based interaction, including Fitts’s Law performance models, the effects of movement direction, foot dominance and visual feedback, and the overhead incurred by using the feet together with the hand. To enable all these studies, we developed a foot tracker based on a Kinect mounted under the desk. We show that the lower body can be used as a valuable complementary modality for computing input. Our third proposition is that by treating body movements as multiple modalities, rather than a single one, we can enable novel user experiences. We develop this proposition in the domain of 3D user interfaces, as it requires input with multiple degrees of freedom and offers a rich set of complex tasks. We propose an approach for tracking the whole body up close, by splitting the sensing of different body parts across multiple sensors. Our setup allows tracking gaze, head, mid-air gestures, multi-touch gestures, and foot movements. We investigate specific applications for multimodal combinations in the domain of 3DUI, specifically how gaze and mid-air gestures can be combined to improve selection and manipulation tasks; how the feet can support the canonical 3DUI tasks; and how a multimodal sensing platform can inspire new 3D game mechanics. We show that the combination of multiple modalities can lead to enhanced task performance, that offloading certain tasks to alternative modalities not only frees the hands, but also allows simultaneous control of multiple degrees of freedom, and that by sensing different modalities separately, we achieve a more detailed and precise full body tracking.

Research suggests that people may hold positive explicit attitudes whilst holding negative implicit attitudes towards Lesbian and Gay (LG) people. While this seems evident amongst the general population, a previous systematic review (e.g. Boysen, 2009) only identified one study investigating explicit and implicit attitudes towards LG identities amongst counsellors. There are no similar systematic reviews using samples of psychologists, so this review aims to bridge that gap by conducting an analysis on studies completed between January 1990 and May 2013. In this review were included studies that: a) investigated attitudes of psychologists or psychologists-in-training towards LG people; b) included original data and findings; c) included comparison groups; and d) had been carried out in countries where homosexuality is not criminalised and where there is anti-homophobia legislation currently in place. Of the initial 933 studies identified, 18 met the main inclusion criteria. Designs were diverse and used a range of attitude measures. Only one study investigated implicit attitudes. Despite the diverse range of designs and measures it appears that positive attitudes to LG people may be conditional upon several factors, including gender, religiosity, socialisation, training, and level of education of psychologists. Training courses can potentially address such needs, but these need to be designed specifically to address LG topics, since general training on diversity topics may not promote positive implicit attitudes to LG people.

Transition zones are problematic in biogeographical classification because they represent artificial areas. A review of transition zones into existing biogeographical classifications shows conflicting area taxonomies. While many authors consider transition zones as overlap zones or areas of biotic mixing, only a few have considered excluding them from biogeographical classification all together. One way of incorporating transition zones into a natural classification is by treating them as artefacts of geographically overlapping temporally disjunct areas. In doing so, geographically overlapping areas may occupy the same space but have different boundaries and histories. Temporally disjunct areas do form natural hierarchical classifications, as seen in the paleobiogeographical literature. A revision of each transition zone will determine whether they are artificial areas, areas within their own right or potentially geographically overlapping temporally disjunct regions. The Neotropics is an ideal place to investigate transition zones as it is “tectonically” dynamic and a highly biodiverse region that is bound by two other such areas, namely the Nearctic and Andean regions. Two comparative biogeographic methods will be used in this thesis: Paralogy-free Subtree Analysis (Nelson and Ladiges 1996) and the Transparent Method (Ebach et al. 2005). Both of these methods are used to construct general areagrams in which all uninformative data has been removed. Paralogy-free subtree analysis converts areagrams into smaller unique area relationships called subtrees. The South American Transition Zone (SATZ) is the first area within the Neotropics to be examined. The SATZ extends from the Caribbean to the south of the South American continent where it is mostly constrained to the Andean orogeny. In this thesis, an analysis is undertaken to determine whether: 1. the SATZ is monophyletic; 2. to understand if the topography of the area contributed to the bioregionalisation; and 3. to attempt to identify a barrier between the Andean region and other parts of the Neotropical. The analysis shows that the SATZ is non-monophyletic, and that the Páramo, Desert, Puna, Atacama, Monte and Comechingones provinces are more closely related to the Neotropical region than to any of the Andean provinces, including the Cuyan High Andean province. The non-monophyly of the SATZ shows that transition zones are biogeographical artefacts and represent areas of overlap. Moreover, it also shows that tectonics, in the form of uplift due to slab subduction resulting in crustal shortening and thrusting, may be responsible for creating the SATZ provinces over the last 30Ma. The barrier between the Andean and Neotropical regions is, however, older and may be due to the formation of the North Patagonian High Plateau during the Paleogene (60Ma), an area located in the Monte province. The second area of investigation is the Caribbean Plate, also known as the Antillean subregion. There are currently two models proposed for the geological formation of the Antillean subregion, namely an in situ model and a Pacific model. Here a comparative biogeographic analysis was performed for three reasons: 1. To determine the monophyly of the Antillean subregion; 2. to see which geological model is supported by the results; and 3, to determine if the Antillean subregion is potentially a transition zone. The analysis shows that the Antillean subregion is non-monophyletic. It shows that the Greater Antilles are more closely related to south Florida/Bahamas than they are to other parts of the Antillean sub-region, and that the Lesser Antilles province is more closely related to South America than it is with other parts of the Antillean sub-region. The result shows that the Antillean subregion has the same characteristics as the SATZ, Mexican and Indo-Malayan Transition zones; indicating that it is potentially a transition zone. The result is not surprising given the close proximity of the Antillean subregion to the Nearctic. The result is also in line with previous predictions that the Antillean subregion and SATZ are examples of Marginal-Plate Biotectonics.

Ultra-high performance concrete (UHPC) is a new class of concrete that has superior workability, as well as mechanical and durability properties that far exceed those of conventional concrete. To achieve these properties, a very dense internal structure and the very low water-to-binder ratio (w/b) generally are necessary. While particle packing models are typically used to design UHPC, due to the complexity of the composition interaction and characteristics of UHPC, these models might not necessarily provide the best design, which leads to the need of experimental study to justify UHPC performance. The evaluation of the impact of various design parameters on the properties of UHPC is also needed. A study and evaluation were performed with multiple series of UHPC mixtures prepared with different design parameters and considerations. The impacts of different aggregate, types of fibers, High Range Water Reducing (HRWR), w/b, types of cement, types and quantities of supplemental cementitious materials (SCMs), and different total binder content on UHPC performance were presented. Furthermore, the extensive amount of fine materials, the absence of coarse aggregate, and the very low w/b often make the process of UHPC production challenging. This study included evaluations of the impacts of mixers on the properties of fresh and hardened UHPC. The comparison of these mixers was used to determine whether mixtures developed in the laboratory were comparable to those used in the field. Advisor: Jiong Hu

Brazilian composer Leopoldo Américo Miguéz (1850–1902) lived in the cosmopolitan city of Rio de Janeiro at a time when the prevailing cultural background of the aristocracy was still prominently European. His entire production consisted of thirty-eight works with opus numbers and few other works that have not yet been published, all of which were influenced by European romantic music traditions while demonstrating no strong connection with Brazilian local and popular culture. He wrote a small quantity of twelve piano works represented in ten opus numbers, one collection of pieces without opus number, and one unpublished piece. These are mostly in short forms such as mazurkas, nocturnes, and character pieces with suggestive titles in the manner of short piano works by Brahms, Chopin, Fauré, Grieg, Mendelssohn, Liszt, and Schumann. With few exceptions, no great significance has been attributed to his piano works throughout the written history of Brazilian music. This is partly due to the lingering effect of two lines of negative criticism published during and after his lifetime that hurt his reputation and turned him into an obscure and forgotten composer. One was regarding his symphonic works, which were heavily influenced by Wagner, Berlioz, and Liszt. The other was in the context of an enduring process of nationalization of Brazilian arts and a rupture from European influences in the beginning of the 20th century. The music of Miguéz fell greatly out of favor during this campaign, resulting in lasting damage to his name that has yet to be reversed. The purpose of this dissertation is to draw attention to his pianistic output, asserting its integrity, quality, and valuable contribution to the development of music in Brazil. Biographical information as well as in-depth musical analysis of each piano work are supplied in the course of the narrative. My hope is that by providing and disseminating this information, Leopoldo Miguéz will be better understood, accepted, and more often performed.

Active remote sensing techniques, such as Light Detection and Ranging (LiDAR), have transformed the field of forestry and natural resource management in the last decade. Intensive assessments of forest resources and detailed structural assessments can now be accomplished faster and at multiple landscape scales. The ecological applications of having this valuable information at-hand are still only being developed. This work explores the use of two active remote sensing techniques, airborne and portable LiDAR for forestry applications in a rapidly changing landscape, Southeastern Coastal Pine woodlands. Understanding the strengths and weaknesses of airborne and portable LiDAR, the tools used to extract structural information, and how to apply these to managing fire regimes are key to conserving unique upland pine ecosystems. Measuring habitat structure remotely and predicting habitat suitability through modeling will allow for the management of specific species of interest, such as threatened and endangered species. Chapter one focuses on the estimation of canopy cover and height measures across a variety of conditions of secondary upland pine and hardwood forests at Tall Timbers Research Station, FL. This study is unique since it uses two independent high resolution small-footprint LiDAR datasets (years 2002 and 2008) and extensive field plot and transect sampling for validation. Chapter One explores different tools available for metric derivation and tree extraction from discrete return airborne LiDAR data, highlighting strengths and weaknesses of each. Field and LiDAR datasets yielded better correlations for stand level comparisons, especially in canopy cover and mean height data extracted. Individual tree crown extraction from airborne LiDAR data significantly under-reported the total number of trees reported in the field datasets using either Fusion/LVD and LiDAR Analyst (Overwatch). Chapter two evaluates stand structure at the site of one of the longest running fire ecology studies in the US, located at Tall Timbers Research Station (TTRS) in the southeastern U.S. Small footprint high resolution discrete return LiDAR was used to provide an understanding of the impact of multiple disturbance regimes on forest structure, especially on the 3-dimensional spatial arrangement of multiple structural elements and structural diversity indices. LiDAR data provided sensitive detection of structural metrics, diversity, and fine-scale vertical changes in the understory and mid-canopy structure. Canopy cover and diversity indices were shown to be statistically higher in fire suppressed and less frequently burned plots than in 1- and 2-year fire interval treated plots, which is in general agreement with the increase from 2- to 3-year fire return interval being considered an "ecological threshold" for these systems (Masters et al. 2005). The results from this study highlight the value of the use of LiDAR in evaluating disturbance impacts on the three-dimensional structure of pine forest systems, particularly over large landscapes. Chapter three uses an affordable portable LiDAR system, first presented by Parker et al. (2004) and further modified for extra portability, to provide an understanding of structural differences between old-growth and secondary-growth forests in the Red Hills area of southwestern Georgia and North Florida. It also provides insight into the strengths and weaknesses in structural determination of ground-based portable systems in contrast to airborne LiDAR systems. Structural plot metrics obtained from airborne and portable LiDAR systems presented some similarities (i.e. canopy cover), but distinct differences appeared when measuring canopy heights (maximum and mean heights) using these different methods. Both the airborne and portable systems were able to provide gap detection and canopy cover estimation at the plot level. The portable system, when compared to the airborne LiDAR sensor, provides an underestimation of canopy cover in open forest systems ([less than]50% canopy cover), but is more sensitive in detection of cover in hardwood woodland plots ([greater than]60% canopy cover). The strength of the portable LiDAR system lies in the detection of 3-dimensional fine structural changes (i.e. recruitment, encroachment) and with higher sensitivity in detecting lower canopy levels, often missed by airborne systems. Chapter four addresses a very promising application for fine-scale airborne LiDAR data, the creation of habitat suitability models for species of management and conservation concerns. This Chapter uses fine scale LiDAR metrics, such as canopy cover at various height strata, canopy height information, and a measure of horizontal vegetation distribution (clumped versus dispersed) to model the preferences of 10 songbirds of interest in southeast US woodlands. The results from this study highlight the rapidly changing nature of habitat conditions and how these impact songbird occurrence. Furthermore, Chapter four provides insight into the use of airborne LiDAR to provide specific management guidance to enhance the suitable habitat for 10 songbird species. The collection of studies presented here provides applied tools for the use of airborne and portable LiDAR for rapid assessment and responsive management in southeastern pine woodlands. The advantages of detecting small changes in three-dimensional vegetation structure and how these can impact habitat functionality and suitability for species of interest are explored throughout the next four chapters. The research presented here provides an original and important contribution in the application of airborne and portable LiDAR datasets in forest management and ecological studies.

This exploratory study aims to profile the field of Competitive Intelligence (CI) academic research in Brazil. A characterization of research groups in CI is performed using data from Brazil’s National Council for Scientific and Technological Development (Conselho Nacional de Desenvolvimento Científico e Tecnológico - CNPq). Research groups are defined by institutional affiliation, department affiliation, composition, size, location, and research lines. In the context of the current research groups, a citation analysis is performed based on journal publications authored by primary research group leaders and secondary leaders taking into consideration the types of works cited, language and origin of works cited, their relative age, most cited journals and most cited authors.