In Comes I: Performance, Memory and Landscape

Pearson, Mike, In Comes I: Performance, Memory and Landscape (Exeter: University of Exeter Press, 2007) RAE2008

Diagnóstico Molecular na era da sequenciação de 3ª geração e da PCR digital

Projeto de Pós-Graduação/Dissertação apresentado à Universidade Fernando Pessoa como parte dos requisitos para obtenção do grau de Mestre em Ciências Farmacêuticas

Non-clinical outcomes of antiretroviral therapy for HIV/AIDS in developing countries: a systematic literature review

The impacts of antiretroviral therapy on quality of life, mental health, labor productivity, and economic wellbeing for people living with HIV/AIDS in developing countries are only beginning to be measured. We conducted a systematic literature review to analyze the effect of antiretroviral therapy (ART) on these non-clinical indicators in developing countries and assess the state of research on these topics. Both qualitative and quantitative studies were included, as were peer-reviewed articles, gray literature, and conference abstracts and presentations. Findings are reported from 12 full-length articles, 7 abstracts, and 1 presentation (representing 16 studies). Compared to HIV-positive patients not yet on treatment, patients on ART reported significant improvements in physical, emotional and mental health and daily function. Work performance improved and absenteeism decreased, with the most dramatic changes occurring in the first three months of treatment and then leveling off. Little research has been done on the impact of ART on household wellbeing, with modest changes in child and family wellbeing within households where adults are receiving ART reported so far. Studies from developing countries have not yet assessed non-clinical outcomes of therapy beyond the first year; therefore, longitudinal outcomes are still unknown. As ART roll out extends throughout high HIV prevalence, low-resource countries and is sustained over years and decades, both positive and adverse non-clinical outcomes need to be empirically measured and qualitatively explored in order to support patient adherence and maximize treatment benefits.

The Least of These: American Evangelical Parachurch Missions to the Poor, 1947-2005

This dissertation narrates the historical development of American evangelical missions to the poor from 1947-2005 and analyzes the discourse of its main parachurch proponents, especially World Vision, Compassion International, Food for the Hungry, Samaritan's urse, Sojourners, Evangelicals for Social Action, and the Christian Community Development Association. Although recent scholarship on evangelicalism has been prolific, much of the historical work has focused on earlier periods. Sociological and political scientific scholarship on the postwar period has been attracted mostly to controversies surrounding the Religious Right, leaving evangelicalism's resurgent concern for the poor relatively understudied. This dissertation addresses these lacunae. The study consists of three chronological parts, each marked by a distinctive model of mission to the poor. First, the 1950s were characterized by compassionate charity for individual emergencies, a model that cohered neatly with evangelicalism's individualism and emotionalism. This model should be regarded as the quintessential, bedrock evangelical theory of mission to the poor. It remained strong throughout the entire postwar period. Second, in the 1970s, a strong countercurrent emerged that advocated for penitent protest against structural injustice and underdevelopment. In contrast to the first model, it was distinguished by going against the grain of many aspects of evangelical culture, especially its reflexive patriotism and individualism. Third, in the 1990s, an important movement towards developing potential through hopeful holism gained prominence. Its advocates were confident that their integration of biblical principles with insights from contemporary economic development praxis would contribute to drastic, widespread reductions in poverty. This model signaled a new optimism in evangelicalism's engagement with the broader world. The increasing prominence of missions to the poor within American evangelicalism led to dramatic changes within the movement's worldview: by 2005, evangelicals were mostly unified in their expressed concern for the physical and social needs of the poor, a position that radically reversed their immediate postwar worldview of near-exclusive focus on the spiritual needs of individuals. Nevertheless, missions to the poor also paralleled, reinforced, and hastened the increasing fragmentation of evangelicalism's identity, as each missional model advocated for highly variant approaches to poverty amelioration that were undergirded by diverse sociological, political, and theological assumptions.

PARAMETERS AFFECTING THE IMAGING AND DETECTION OF MICROBUBBLES IN BLOOD

Stabilized micron-sized bubbles, known as contrast agents, are often injected into the body to enhance ultrasound imaging of blood flow. The ability to detect such bubbles in blood depends on the relative magnitude of the acoustic power backscattered from the microbubbles (‘signal’) to the power backscattered from the red blood cells (‘noise’). Erythrocytes are acoustically small (Rayleigh regime), weak scatterers, and therefore the backscatter coefficient (BSC) of blood increases as the fourth power of frequency throughout the diagnostic frequency range. Microbubbles, on the other hand, are either resonant or super-resonant in the range 5-30 MHz. Above resonance, their total scattering cross-section remains constant with increasing frequency. In the present thesis, a theoretical model of the BSC of a suspension of red blood cells is presented and compared to the BSC of Optison® contrast agent microbubbles. It is predicted that, as the frequency increases, the BSC of red blood cell suspensions eventually exceeds the BSC of the strong scattering microbubbles, leading to a dramatic reduction in signal-to-noise ratio (SNR). This decrease in SNR with increasing frequency was also confirmed experimentally by use of an active cavitation detector for different concentrations of Optison® microbubbles in erythrocyte suspensions of different hematocrits. The magnitude of the observed decrease in SNR correlated well with theoretical predictions in most cases, except for very dense suspensions of red blood cells, where it is hypothesized that the close proximity of erythrocytes inhibits the acoustic response of the microbubbles.

EXPERIMENTAL INVESTIGATION OF LINEAR BUBBLE DYNAMICS IN A VISCOELASTIC XANTHAN GEL

Oceanic bubble plumes caused by ship wakes or breaking waves disrupt sonar communi- cation because of the dramatic change in sound speed and attenuation in the bubbly fluid. Experiments in bubbly fluids have suffered from the inability to quantitatively characterize the fluid because of continuous air bubble motion. Conversely, single bubble experiments, where the bubble is trapped by a pressure field or stabilizing object, are limited in usable frequency range, apparatus complexity, or the invasive nature of the stabilizing object (wire, plate, etc.). Suspension of a bubble in a viscoelastic Xanthan gel allows acoustically forced oscilla- tions with negligible translation over a broad frequency band. Assuming only linear, radial motion, laser scattering from a bubble oscillating below, through, and above its resonance is measured. As the bubble dissolves in the gel, different bubble sizes are measured in the range 240 – 470 μm radius, corresponding to the frequency range 6 – 14 kHz. Equalization of the cell response in the raw data isolates the frequency response of the bubble. Compari- son to theory for a bubble in water shows good agreement between the predicted resonance frequency and damping, such that the bubble behaves as if it were oscillating in water.

Large Decrease of Fluctuations for Supercooled Water in Hydrophobic Nanoconfinement

Using Monte Carlo simulations we study a coarse­grained model of a water layer confined in a fixed disordered matrix of hydrophobic nanoparticles at different particle concentrations c. For c = 0 we find a 1st order liquid­liquid phase transition (LLPT) ending in one critical point at low pressure P. For c > 0 our simulations are consistent with a LLPT line ending in two critical points at low and high pressure. For c = 25% at high P and low temperature T we find a dramatic decrease of compressibility, thermal expansion coefficient, and specific heat. Surprisingly, the effect is present also for c as low as 2.4%. We conclude that even a small presence of nanoscopic hydrophobes can drastically suppress thermodynamic fluctuations, making the detection of the LLPT more difficult.

On the Performance of Polynomial-time CLIQUE Approximation Algorithms on Very Large Graphs

The performance of a randomized version of the subgraph-exclusion algorithm (called Ramsey) for CLIQUE by Boppana and Halldorsson is studied on very large graphs. We compare the performance of this algorithm with the performance of two common heuristic algorithms, the greedy heuristic and a version of simulated annealing. These algorithms are tested on graphs with up to 10,000 vertices on a workstation and graphs as large as 70,000 vertices on a Connection Machine. Our implementations establish the ability to run clique approximation algorithms on very large graphs. We test our implementations on a variety of different graphs. Our conclusions indicate that on randomly generated graphs minor changes to the distribution can cause dramatic changes in the performance of the heuristic algorithms. The Ramsey algorithm, while not as good as the others for the most common distributions, seems more robust and provides a more even overall performance. In general, and especially on deterministically generated graphs, a combination of simulated annealing with either the Ramsey algorithm or the greedy heuristic seems to perform best. This combined algorithm works particularly well on large Keller and Hamming graphs and has a competitive overall performance on the DIMACS benchmark graphs.

The protection and security of vulnerable populations in complex emergencies using the Dadaab refugee camps in the north eastern province of Kenya as a case study

The past two decades has seen a dramatic upheaval in the international world order: the end of the Cold War, the 9/11 attacks and the subsequent 'War on Terror', increased Jihadist activities, the accelerated pace of globalization, climate change and the 2008 global financial crisis have contributed to fear, uncertainty, poverty, conflict, massive displacements of populations of asylum seekers and refugees globally and a proliferation of Protracted Refugee Situations (PRS), defined as situations in which refugees have been in exile 'for 5 years or more after their initial displacement, without immediate prospects for implementation of durable solutions. In the past two decades there has been a huge proliferation of these with more than 7.2 million refugees now trapped in these PRS, with a further 16 million internally displaced persons (IDPs) trapped in camps within their own countries. The Dadaab refugee complex in Kenya, which of as March 2012, holds over 463,000 refugees, is the most significant and extreme example in recent times of a PRS. It was established in 1991 following the collapse of the Somali Government of Dictator Siad Barre, and the disintegration of Somalia into the chaos that still exists today. PRS such as Dadaab raise particular issues about humanitarianism in terms of aid, protection, security, human rights and the actions (or inaction) of the various stakeholders on an international, national and local level. This thesis investigates these issues by the use of a case study methodology on Dadaab as a PRS, framed in the context of humanitarianism and in particular the issues that arise in terms of how the international community, the UN system and individual states provide assistance and protection to vulnerable populations. Although the refugee camps have been in existence (as of 2012) for over 20 years, there has never been such a detailed study of Dadaab (or any other PRS) undertaken to date and would be of interest to academics in the areas of international relations, refugee/migration studies and global Governance as well as practitioners in both humanitarian response and development

The identification and characterisation of Rab4 interacting proteins

Rab4 is a member of the Rab superfamily of small GTPases. It is localized to the early sorting endosome and plays a role in regulating the transport from this compartment to the recycling and degradative pathways. In order to further our understanding of the role Rab4 plays in endocytosis, a yeast two-hybrid screen was performed to identify putative Rab4 effectors. A constitutively active mutant of Rab4, Rab4Q67L, when used as bait to screen a HeLa cDNA library, identified a novel 80kDa protein that interacted with Rab4-GTP. This protein was called Rab Coupling Protein (RCP). RCP interacts preferentially with the GTP-bound form of Rab4. Subsequent work demonstrated that RCP also interacts with Rab11, and that this interaction is not nucleotide-depenedent. RCP is predominantly membrane-bound and localised to the perinuclear recycling compartment. Expression of a truncation mutant of RCP, that contains the Rab binding domain, in HeLa cells, results in the formation of an extensive tubular network that can be labelled with transferrin. These tubules are derived from the recycling compartment since they are inaccessible to transferrin when the ligand is internalised at 18oC. The truncation mutant-induced morphology can be rescued by overexpression of active Rab11, but not active Rab4. This suggests that RCP functions between Rab4 and Rab11 in the receptor recycling pathway, and may act as a ‘molecular bridge’ between these two sequentially acting small GTPases. Quantitative assays demonstrated that overexpression of the truncation mutant results in a dramatic inhibition in the rate of receptor recycling. Database analysis revealed that RCP belongs to a family of Rab interacting proteins, each characterised by a carboxy-terminal coiled-coil domain and an amino-terminal phospholipid-binding domain. KIAA0941, an RCP homologue, interacts with Rab11, but not with Rab4. Overexpression of its Rab binding domain also results in a tubular network, however, this tubulation cannot be rescued by active Rab11.

Drama Grammatik: Dramapädagogische Ansätze für den Grammatikunterricht Deutsch als Fremdsprache

This dissertation introduces and evaluates dramagrammar, a new concept for the teaching and learning of foreign language grammar. Grammar, traditionally taught in a predominantly cognitive, abstract mode, often fails to capture the minds of foreign language learners, who are then unable to integrate this grammatical knowledge into their use of the foreign language in a meaningful way. The consequences of this approach are manifested at university level in German departments in England and Ireland, where the outcomes are unconvincing at best, abysmal at worst. Language teaching research suggests that interaction plays an important role in foreign language acquisition. Recent studies also stress the significance of grammatical knowledge in the learning process. Dramagrammar combines both interactive negotiation of meaning and explicit grammar instruction in a holistic approach, taking up the concept of drama in foreign language education and applying it to the teaching and learning of grammar. Techniques from dramatic art forms allow grammar to be experienced not only cognitively but also in social, emotional, and bodily-kinaesthetic ways. Dramagrammar lessons confront the learner with fictitious situations in which grammar is experienced 'hands-on'. Learners have to use grammatical structures in a variety of contexts, reflect upon their use, and then enlarge and enrich the dramatic situations with their newly acquired or more finely nuanced knowledge. The initial hypothesis of this dissertation is that the drammagrammar approach is beneficial to the acquisition of foreign language grammar. This hypothesis is corroborated by research findings from language teaching pedagogy and drama in education. It is further confirmed by empirical data gained from specifically designed dramagrammar modules that have been put into practice in German departments at the University of Leicester (England), the University Colleges Cork and Dublin (Ireland), the University of Bologna (Italy), as well as the Goethe-Institute Bratislava (Slovenia). The data suggests that drammagrammar has positive effects on both understanding of and attitudes towards grammar.

Molecular characterisation of the mechanisms of compatible solute accumulation in Listeria monocytogenes

The ability of the Gram-positive foodborne pathogen Listeria monocytogenes to survive and grow in environments of elevated osmolarity can be attributed, at least in part, to the accumulation of a restricted range of low molecular mass solutes compatible with cellular function. Accumulated to high internal concentrations in hyper-saline environments, compatible solutes, either transported into the cell or synthesized de novo, play a dual role: helping to stabilize protein structure and function while also counterbalancing external osmotic strength, thus preventing water loss from the cell and plasmolysis. While previous physiological investigations identified glycine betaine, carnitine, and proline as the principal compatible solutes in the listerial osmostress response, genetic alanysis of the uptake/synthesis systems governing the accumulation of these compounds has, until now, remained largely unexplored. Representing the first genetic analysis of compatible solute accumulation in L. monocytogenes, this thesis describes the molecular characterization of BetL; a highly specific secondary glycine betaine transport system, OpuC; a multicomponent carnitine/glycine betaine transporter, and finally proBA; a two-gene operon encoding the first two enzymes of the listerial proline piosynthesis pathway. In addition to their role in osmotolerance, the potential of each system in contributing to listerial pathogenesis was investigated. While mutations in each gene cluster exhibited dramatic reductions in listerial osmotolerance, OpuC- mutants were additionally shown to exhibit reduced virulence when admisistered via the oral route. This represents the first direct link between the salt stress response and virulence in L. monocytogenes.

Rallying to a cause: the plays of Zakes Mda 1979-1989

Zakes Mda, dubbed one of South Africa's most prolific playwrights, produced his richest and most powerful theatre work during the 70s and 80s. Ironically, it is only in the 90s that he has been acknowledged in his own country as one of its foremost dramatists - ironic since he has recently moved away from drama into the realms of fiction. Fortunately Mda has accumulated a worthy canon of dramatic works, spanning radio and film, as well as theatre, and there is no reason to believe that he will not return to play writing. Mda has worked extensively in theatre in various capacities but most notably in the area of theatre-for-development. For example, he worked as director with Maratholi Travelling Theatre in Lesotho, an experience which contributed, in part, towards his book "When People Play People: Development Communication Through Theatre". Mda's plays have been produced in the United States, Britain, Spain, France and Russia as well as in southern Africa. "The Nun's Romantic Story" has been translated into Castilian and Catalan and "We Shall Sing for the Fatherland" and "Dark Voices Ring" have both been translated into Russian and French. In South Africa he won the Merit Award of the Amstel Playwright of the Year Society for "We Shall Sing for the Fatherland" in 1978 and in 1979 he was Amstel Playright of the Year for "The Hill". For his novel "She Plays with the Darkness", he won the Sanlam Literary Award in 1995.

Sugar matrices in stabilization of bioactives by dehydration

Development of functional foods with bioactive components requires component stability in foods and ingredients. Stabilization of sensitive bioactive components can be achieved by entrapment or encapsulation of these components in solid food matrices. Lactose or trehalose was used as the structure-forming material for the entrapment of hydrophilic ascorbic acid and thiamine hydrochloride or the encapsulation of oil particles containing hydrophobic α-tocopherol. In the delivery of hydrophobic components, milk protein isolate, soy protein isolate, or whey protein isolate were used as emulsifiers and, in some cases, applied in excess amount to form matrices together with sugars. Dehydrated amorphous structures with bioactives were produced by freezing and freeze-drying. Experimental results indicated that: (i) lactose and trehalose showed similar water sorption and glass transition but very different crystallization behavior as pure sugars; (ii) the glass transition of sugar-based systems was slightly affected by the presence of other components in anhydrous systems but followed closely that of sugar after water plasticization; (iii) sugar crystallization in mixture systems was composition-dependent; (iv) the stability of bioactives was better retained in the amorphous matrices, although small losses of stability were observed for hydrophilic components above glass transition and for hydrophobic components as a function of water activity; (v) sugar crystallization caused significant loss of hydrophilic bioactives as a result of the exclusion from the continuous crystalline phase; (vi) loss of hydrophobic bioactives upon sugar crystallization was a result of dramatic change of emulsion properties and the exclusion of oil particles from the protecting structure; (vii) the double layers at the hydrophilic-hydrophobic interfaces improved the stability of hydrophobic bioactives in dehydrated systems. The present study provides information on the physical and chemical stability of sugar-based dehydrated delivery systems, which could be helpful in designing foods and ingredients containing bioactive components with improved storage stability.

Finding optimal alternatives based on efficient comparative preference inference

Choosing the right or the best option is often a demanding and challenging task for the user (e.g., a customer in an online retailer) when there are many available alternatives. In fact, the user rarely knows which offering will provide the highest value. To reduce the complexity of the choice process, automated recommender systems generate personalized recommendations. These recommendations take into account the preferences collected from the user in an explicit (e.g., letting users express their opinion about items) or implicit (e.g., studying some behavioral features) way. Such systems are widespread; research indicates that they increase the customers' satisfaction and lead to higher sales. Preference handling is one of the core issues in the design of every recommender system. This kind of system often aims at guiding users in a personalized way to interesting or useful options in a large space of possible options. Therefore, it is important for them to catch and model the user's preferences as accurately as possible. In this thesis, we develop a comparative preference-based user model to represent the user's preferences in conversational recommender systems. This type of user model allows the recommender system to capture several preference nuances from the user's feedback. We show that, when applied to conversational recommender systems, the comparative preference-based model is able to guide the user towards the best option while the system is interacting with her. We empirically test and validate the suitability and the practical computational aspects of the comparative preference-based user model and the related preference relations by comparing them to a sum of weights-based user model and the related preference relations. Product configuration, scheduling a meeting and the construction of autonomous agents are among several artificial intelligence tasks that involve a process of constrained optimization, that is, optimization of behavior or options subject to given constraints with regards to a set of preferences. When solving a constrained optimization problem, pruning techniques, such as the branch and bound technique, point at directing the search towards the best assignments, thus allowing the bounding functions to prune more branches in the search tree. Several constrained optimization problems may exhibit dominance relations. These dominance relations can be particularly useful in constrained optimization problems as they can instigate new ways (rules) of pruning non optimal solutions. Such pruning methods can achieve dramatic reductions in the search space while looking for optimal solutions. A number of constrained optimization problems can model the user's preferences using the comparative preferences. In this thesis, we develop a set of pruning rules used in the branch and bound technique to efficiently solve this kind of optimization problem. More specifically, we show how to generate newly defined pruning rules from a dominance algorithm that refers to a set of comparative preferences. These rules include pruning approaches (and combinations of them) which can drastically prune the search space. They mainly reduce the number of (expensive) pairwise comparisons performed during the search while guiding constrained optimization algorithms to find optimal solutions. Our experimental results show that the pruning rules that we have developed and their different combinations have varying impact on the performance of the branch and bound technique.