Implementation of an intelligent sensor for measurement and prediction of solar radiation and atmospheric temperature

Dissertação de mestrado, Engenharia Electrónica e Telecomunicações, Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2011

The specific shapes of gender imbalance in scientific authorships : a network approach

Gender differences in collaborative research have received little at- tention when compared with the growing importance that women hold in academia and research. Unsurprisingly, most of bibliomet- ric databases have a strong lack of directly available information by gender. Although empirical-based network approaches are often used in the study of research collaboration, the studies about the influence of gender dissimilarities on the resulting topological outcomes are still scarce. Here, networks of scientific subjects are used to characterize patterns that might be associated to five categories of authorships which were built based on gender. We find enough evidence that gen- der imbalance in scientific authorships brings a peculiar trait to the networks induced from papers published in Web of Science (WoS) in- dexed journals of Economics over the period 2010-2015 and having at least one author affiliated to a Portuguese institution. Our re- sults show the emergence of a specific pattern when the network of co-occurring subjects is induced from a set of papers exclusively au- thored by men. Such a male-exclusive authorship condition is found to be the solely responsible for the emergence that particular shape in the network structure. This peculiar trait might facilitate future network analyses of research collaboration and interdisciplinarity.

Use of acoustic telemetry techniques to understand the individual variability in movement ecology of juvenile lemon sharks, Negaprion brevirostris, in natural conditions, around Bimini Islands, Bahamas: a comparison study with preliminary personality traits observed in mesocosms

Dissertação de Mestrado, Biologia Marinha, Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2016

Acoustic manipulation and alignment of particles for applications in separation, micro-templating and device fabrication

This dissertation studies the manipulation of particles using acoustic stimulation for applications in microfluidics and templating of devices. The term particle is used here to denote any solid, liquid or gaseous material that has properties, which are distinct from the fluid in which it is suspended. Manipulation means to take over the movements of the particles and to position them in specified locations. ^ Using devices, microfabricated out of silicon, the behavior of particles under the acoustic stimulation was studied with the main purpose of aligning the particles at either low-pressure zones, known as the nodes or high-pressure zones, known as anti-nodes. By aligning particles at the nodes in a flow system, these particles can be focused at the center or walls of a microchannel in order to ultimately separate them. These separations are of high scientific importance, especially in the biomedical domain, since acoustopheresis provides a unique approach to separate based on density and compressibility, unparalleled by other techniques. The study of controlling and aligning the particles in various geometries and configurations was successfully achieved by controlling the acoustic waves. ^ Apart from their use in flow systems, a stationary suspended-particle device was developed to provide controllable light transmittance based on acoustic stimuli. Using a glass compartment and a carbon-particle suspension in an organic solvent, the device responded to acoustic stimulation by aligning the particles. The alignment of light-absorbing carbon particles afforded an increase in visible light transmittance as high as 84.5%, and it was controlled by adjusting the frequency and amplitude of the acoustic wave. The device also demonstrated alignment memory rendering it energy-efficient. A similar device for suspended-particles in a monomer enabled the development of electrically conductive films. These films were based on networks of conductive particles. Elastomers doped with conductive metal particles were rendered surface conductive at particle loadings as low as 1% by weight using acoustic focusing. The resulting films were flexible and had transparencies exceeding 80% in the visible spectrum (400-800 nm) These films had electrical bulk conductivities exceeding 50 S/cm. ^

Political Strategy, Leadership, and Policy Entrepreneurship in Japanese Defense Policy and Politics: A Comparison of Three Prime Ministerships

Since the end of the Cold War, Japan’s defense policy and politics has gone through significant changes. Throughout the post cold war period, US-Japan alliance managers, politicians with differing visions and preferences, scholars, think tanks, and the actions of foreign governments have all played significant roles in influencing these changes. Along with these actors, the Japanese prime minister has played an important, if sometimes subtle, role in the realm of defense policy and politics. Japanese prime ministers, though significantly weaker than many heads of state, nevertheless play an important role in policy by empowering different actors (bureaucratic actors, independent commissions, or civil actors), through personal diplomacy, through agenda-setting, and through symbolic acts of state. The power of the prime minister to influence policy processes, however, has frequently varied by prime minister. My dissertation investigates how different political strategies and entrepreneurial insights by the prime minister have influenced defense policy and politics since the end of the Cold War. In addition, it seeks to explain how the quality of political strategy and entrepreneurial insight employed by different prime ministers was important in the success of different approaches to defense. My dissertation employs a comparative case study approach to examine how different prime ministerial strategies have mattered in the realm of Japanese defense policy and politics. Three prime ministers have been chosen: Prime Minister Hashimoto Ryutaro (1996-1998); Prime Minister Koizumi Junichiro (2001-2006); and Prime Minister Hatoyama Yukio (2009-2010). These prime ministers have been chosen to provide maximum contrast on issues of policy preference, cabinet management, choice of partners, and overall strategy. As my dissertation finds, the quality of political strategy has been an important aspect of Japan’s defense transformation. Successful strategies have frequently used the knowledge and accumulated personal networks of bureaucrats, supplemented bureaucratic initiatives with top-down personal diplomacy, and used a revitalized US-Japan strategic relationship as a political resource for a stronger prime ministership. Though alternative approaches, such as those that have looked to displace the influence of bureaucrats and the US in defense policy, have been less successful, this dissertation also finds theoretical evidence that alternatives may exist.

A Multi-Criteria GIS-Based Route Selection Tool for Hazardous Material Transport: Consideration of Environmental Consequence, Traffic Congestions and Costs

Hazardous materials are substances that, if not regulated, can pose a threat to human populations and their environmental health, safety or property when transported in commerce. About 1.5 million tons of hazardous material shipments are transported by truck in the US annually, with a steady increase of approximately 5% per year. The objective of this study was to develop a routing tool for hazardous material transport in order to facilitate reduced environmental impacts and less transportation difficulties, yet would also find paths that were still compelling for the shipping carriers as a matter of trucking cost. The study started with identification of inhalation hazard impact zones and explosion protective areas around the location of hypothetical hazardous material releases, considering different parameters (i.e., chemicals characteristics, release quantities, atmospheric condition, etc.). Results showed that depending on the quantity of release, chemical, and atmospheric stability (a function of wind speed, meteorology, sky cover, time and location of accidents, etc.) the consequence of these incidents can differ. The study was extended by selection of other evaluation criteria for further investigation because health risk as an evaluation criterion would not be the only concern in selection of routes. Transportation difficulties (i.e., road blockage and congestion) were incorporated as important factor due to their indirect impact/cost on the users of transportation networks. Trucking costs were also considered as one of the primary criteria in selection of hazardous material paths; otherwise the suggested routes would have not been convincing for the shipping companies. The last but not least criterion was proximity of public places to the routes. The approach evolved from a simple framework to a complicated and efficient GIS-based tool able to investigate transportation networks of any given study area, and capable of generating best routing options for cargos. The suggested tool uses a multi-criteria-decision-making method, which considers the priorities of the decision makers in choosing the cargo routes. Comparison of the routing options based on each criterion and also the overall suitableness of the path in regards to all the criteria (using a multi-criteria-decision-making method) showed that using similar tools as the one proposed by this study can provide decision makers insights in the area of hazardous material transport. This tool shows the probable consequences of considering each path in a very easily understandable way; in the formats of maps and tables, which makes the tradeoffs of costs and risks considerably simpler, as in some cases slightly compromising on trucking cost may drastically decrease the probable health risk and/or traffic difficulties. This will not only be rewarding to the community by making cities safer places to live, but also can be beneficial to shipping companies by allowing them to advertise as environmental friendly conveyors.

Women-led Community Development Organizations (CDOs) in Miami-Dade County: A Model of Community Development Efforts Impacting the Economic Security of Women

Recent studies on the economic status of women in Miami-Dade County (MDC) reveal an alarming rate of economic insecurity and significant obstacles for women to achieve economic security. Consistent barriers to women’s economic security affect not only the health and wellbeing of women and their families, but also economic prospects for the community. A key study reveals in Miami-Dade County, “Thirty-nine percent of single female-headed families with at least one child are living at or below the federal poverty level” and “over half of working women do not earn adequate income to cover their basic necessities” (Brion 2009, 1). Moreover, conventional measures of poverty do not adequately capture women’s struggles to support themselves and their families, nor do they document the numbers of women seeking basic self-sufficiency. Even though there is lack of accurate data on women in the county, which is a critical problem, there is also a dearth of social science research on existing efforts to enhance women’s economic security in Miami-Dade County. My research contributes to closing the information gap by examining the characteristics and strategies of women-led community development organizations (CDOs) in MDC, working to address women’s economic insecurity. The research is informed by a framework developed by Marilyn Gittell, who pioneered an approach to study women-led CDOs in the United States. On the basis of research in nine U.S. cities, she concluded that women-led groups increased community participation and “by creating community networks and civic action, they represent a model for community development efforts” (Gittell, et al. 2000, 123). My study documents the strategies and networks of women-led CDOs in MDC that prioritize women’s economic security. Their strategies are especially important during these times of economic recession and government reductions in funding towards social services. The focus of the research is women-led CDOs that work to improve social services access, economic opportunity, civic participation and capacity, and women’s rights. Although many women-led CDOs prioritize building social infrastructures that promote change, inequalities in economic and political status for women without economic security remain a challenge (Young 2004). My research supports previous studies by Gittell, et al., finding that women-led CDOs in Miami-Dade County have key characteristics of a model of community development efforts that use networking and collaboration to strengthen their broad, integrated approach. The resulting community partnerships, coupled with participation by constituents in the development process, build a foundation to influence policy decisions for social change. In addition, my findings show that women-led CDOs in Miami-Dade County have a major focus on alleviating poverty and economic insecurity, particularly that of women. Finally, it was found that a majority of the five organizations network transnationally, using lessons learned to inform their work of expanding the agency of their constituents and placing the economic empowerment of women as central in the process of family and community development.

A Mutational Hotspot and Strong Selection Contribute to the Order of Mutations Selected for during Escherichia coli Adaptation to the Gut

The relative role of drift versus selection underlying the evolution of bacterial species within the gut microbiota remains poorly understood. The large sizes of bacterial populations in this environment suggest that even adaptive mutations with weak effects, thought to be the most frequently occurring, could substantially contribute to a rapid pace of evolutionary change in the gut. We followed the emergence of intra-species diversity in a commensal Escherichia coli strain that previously acquired an adaptive mutation with strong effect during one week of colonization of the mouse gut. Following this first step, which consisted of inactivating a metabolic operon, one third of the subsequent adaptive mutations were found to have a selective effect as high as the first. Nevertheless, the order of the adaptive steps was strongly affected by a mutational hotspot with an exceptionally high mutation rate of 10-5. The pattern of polymorphism emerging in the populations evolving within different hosts was characterized by periodic selection, which reduced diversity, but also frequency-dependent selection, actively maintaining genetic diversity. Furthermore, the continuous emergence of similar phenotypes due to distinct mutations, known as clonal interference, was pervasive. Evolutionary change within the gut is therefore highly repeatable within and across hosts, with adaptive mutations of selection coefficients as strong as 12% accumulating without strong constraints on genetic background. In vivo competitive assays showed that one of the second steps (focA) exhibited positive epistasis with the first, while another (dcuB) exhibited negative epistasis. The data shows that strong effect adaptive mutations continuously recur in gut commensal bacterial species.

A Transcriptome Atlas of Physcomitrella patens Provides Insights into the Evolution and Development of Land Plants

Post-print version of the article.

Evolution of classifiers for pitch estimation of piano music using cartesian genetic programming

Pitch Estimation, also known as Fundamental Frequency (F0) estimation, has been a popular research topic for many years, and is still investigated nowadays. The goal of Pitch Estimation is to find the pitch or fundamental frequency of a digital recording of a speech or musical notes. It plays an important role, because it is the key to identify which notes are being played and at what time. Pitch Estimation of real instruments is a very hard task to address. Each instrument has its own physical characteristics, which reflects in different spectral characteristics. Furthermore, the recording conditions can vary from studio to studio and background noises must be considered. This dissertation presents a novel approach to the problem of Pitch Estimation, using Cartesian Genetic Programming (CGP).We take advantage of evolutionary algorithms, in particular CGP, to explore and evolve complex mathematical functions that act as classifiers. These classifiers are used to identify piano notes pitches in an audio signal. To help us with the codification of the problem, we built a highly flexible CGP Toolbox, generic enough to encode different kind of programs. The encoded evolutionary algorithm is the one known as 1 + , and we can choose the value for . The toolbox is very simple to use. Settings such as the mutation probability, number of runs and generations are configurable. The cartesian representation of CGP can take multiple forms and it is able to encode function parameters. It is prepared to handle with different type of fitness functions: minimization of f(x) and maximization of f(x) and has a useful system of callbacks. We trained 61 classifiers corresponding to 61 piano notes. A training set of audio signals was used for each of the classifiers: half were signals with the same pitch as the classifier (true positive signals) and the other half were signals with different pitches (true negative signals). F-measure was used for the fitness function. Signals with the same pitch of the classifier that were correctly identified by the classifier, count as a true positives. Signals with the same pitch of the classifier that were not correctly identified by the classifier, count as a false negatives. Signals with different pitch of the classifier that were not identified by the classifier, count as a true negatives. Signals with different pitch of the classifier that were identified by the classifier, count as a false positives. Our first approach was to evolve classifiers for identifying artifical signals, created by mathematical functions: sine, sawtooth and square waves. Our function set is basically composed by filtering operations on vectors and by arithmetic operations with constants and vectors. All the classifiers correctly identified true positive signals and did not identify true negative signals. We then moved to real audio recordings. For testing the classifiers, we picked different audio signals from the ones used during the training phase. For a first approach, the obtained results were very promising, but could be improved. We have made slight changes to our approach and the number of false positives reduced 33%, compared to the first approach. We then applied the evolved classifiers to polyphonic audio signals, and the results indicate that our approach is a good starting point for addressing the problem of Pitch Estimation.

Vortex evolution in the wake of accelerating low-aspect-ratio plates and three-dimensional bodies of revolution

To find examples of effecient locomotion and manoeuvrability, one need only turn to the elegant solutions natural flyers and swimmers have converged upon. This dissertation is specifically motivated by processes of evolutionary convergence, which have led to the propulsors and body shapes in nature that exhibit strong geometric collapse over diverse scales. These body features are abstracted in the studies presented herein using low-aspect-ratio at plates and a three-dimensional body of revolution (a sphere). The highly-separated vortical wakes that develop during accelerations are systematically characterized as a function of planform shape, aspect ratio, Reynolds number, and initial boundary conditions. To this end, force measurements and time-resolved (planar) particle image velocimetry have been used throughout to quantify the instantaneous forces and vortex evolution in the wake of the bluff bodies. During rectilinear motions, the wake development for the flat plates is primarily dependent on plate aspect ratio, with edge discontinuities and curvature playing only a secondary role. Furthermore, the axisymmetric case, i.e. the circular plate, shows strong sensitivity to Reynolds number, while this sensitivity quickly diminishes with increasing aspect ratio. For rotational motions, global insensitivity to plate aspect ratio has been observed. For the sphere, it has been shown that accelerations play an important role in the mitigation of flow separation. These results - expounded upon in this dissertation - have begun to shed light on the specific vortex dynamics that may be coopted by flying and swimming species of all shapes and sizes towards efficient locomotion.

Synonymous co-variation across the E1/E2 gene junction of hepatitis C virus defines virion fitness

Hepatitis C virus is a positive-sense single-stranded RNA virus. The gene junction partitioning the viral glycoproteins E1 and E2 displays concurrent sequence evolution with the 3′-end of E1 highly conserved and the 5′-end of E2 highly heterogeneous. This gene junction is also believed to contain structured RNA elements, with a growing body of evidence suggesting that such structures can act as an additional level of viral replication and transcriptional control. We have previously used ultradeep pyrosequencing to analyze an amplicon library spanning the E1/E2 gene junction from a treatment naïve patient where samples were collected over 10 years of chronic HCV infection. During this timeframe maintenance of an in-frame insertion, recombination and humoral immune targeting of discrete virus sub-populations was reported. In the current study, we present evidence of epistatic evolution across the E1/E2 gene junction and observe the development of co-varying networks of codons set against a background of a complex virome with periodic shifts in population dominance. Overtime, the number of codons actively mutating decreases for all virus groupings. We identify strong synonymous co-variation between codon sites in a group of sequences harbouring a 3 bp in-frame insertion and propose that synonymous mutation acts to stabilize the RNA structural backbone.

Turning conflict into coexistence: cross-cutting ties and institutions in the agro-pastoral borderlands of Lake Naivasha basin, Kenya

The Maasai/Kikuyu agro-pastoral borderlands of Maiella and Enoosupukia, located in the hinterlands of Lake Naivasha’s agro-industrial hub, are particularly notorious in the history of ethnicised violence in the Kenya’s Rift Valley. In October 1993, an organised assault perpetrated by hundreds of Maasai vigilantes, with the assistance of game wardens and administration police, killed more than 20 farmers of Kikuyu descent. Consequently, thousands of migrant farmers were violently evicted from Enoosupukia at the instigation of leading local politicians. Nowadays, however, intercommunity relations are surprisingly peaceful and the cooperative use of natural resources is the rule rather than the exception. There seems to be a form of reorganization. Violence seems to be contained and the local economy has since recovered. This does not mean that there is no conflict, but people seem to have the facility to solve them peacefully. How did formerly violent conflicts develop into peaceful relations? How did competition turn into cooperation, facilitating changing land use? This dissertation explores the value of cross-cutting ties and local institutions in peaceful relationships and the non-violent resolution of conflicts across previously violently contested community boundaries. It mainly relies on ethnographic data collected between 2014 and 2015. The discussion therefore builds on several theoretical approaches in anthropology and the social sciences – that is, violent conflicts, cross-cutting ties and conflicting loyalties, joking relationships, peace and nonviolence, and institutions, in order to understand shared spaces that are experiencing fairly rapid social and economic changes, and characterised by conflict and coexistence. In the researched communities, cross-cutting ties and the split allegiances associated with them result from intermarriages, land transactions, trade, and friendship. By institutions, I refer to local peace committees, an attempt to standardise an aspect of customary law, and Nyumba Kumi, a strategy of anchoring community policing at the household level. In 2010, the state “implanted” these grassroots-level institutions and conferred on them the rights to handle specific conflicts and to prevent crime. I argue that the studied groups utilise diverse networks of relationships as adaptive responses to landlessness, poverty, and socio-political dynamics at the local level. Material and non-material exchanges and transfers accompany these social and economic ties and networks. In addition to being instrumental in nurturing a cohesive social fabric, I argue that such alliances could be thought of as strategies of appropriation of resources in the frontiers – areas that are considered to have immense agricultural potential and to be conducive to economic enterprise. Consequently, these areas are continuously changed and shaped through immigration, population growth, and agricultural intensification. However, cross-cutting ties and intergroup alliances may not necessarily prevent the occurrence or escalation of conflicts. Nevertheless, disputes and conflicts, which form part of the social order in the studied area, create the opportunities for locally contextualised systems of peace and non-violence that inculcate the values of cooperation, coexistence, and restraint from violence. Although the neo-traditional institutions (local peace committees and Nyumba Kumi) face massive complexities and lack the capacity to handle serious conflicts, their application of informal constraints in dispute resolution provides room for some optimism. Notably, the formation of ties and alliances between the studied groups, and the use of local norms and values to resolve disputes, are not new phenomena – they are reminiscent of historical patterns. Their persistence, particularly in the context of Kenya, indicates a form of historical continuity, which remains rather “undisturbed” despite the prevalence of ethnicised political economies. Indeed, the formation of alliances, which are driven by mutual pursuit of commodities (livestock, rental land, and agricultural produce), markets, and diversification, tends to override other identities. While the major thrust of social science literature in East Africa has focused on the search for root causes of violence, very little has been said about the conditions and practices of cooperation and non-violent conflict resolution. In addition, situations where prior violence turned into peaceful interaction have attracted little attention, though the analysis of such transitional phases holds the promise of contributing to applicable knowledge on conflict resolution. This study is part of a larger multidisciplinary project, “Resilience in East African Landscapes” (REAL), which is a Marie Curie Actions Innovative Training Networks (ITN) project. The principal focus of this multidisciplinary project is to study past, present, and future thresholds and sustainable trajectories in human-landscape interactions in East Africa over the last millennia. While other individual projects focus on long-term ecosystem dynamics and societal interactions, my project examines human-landscape interactions in the present and the very recent past (i.e. the period in which events and processes were witnessed or can still be recalled by today’s population). The transition from conflict to coexistence and from competition to cooperative use of previously violently contested land resources is understood here as enhancing adaptation in the face of social-political, economic, environmental, and climatic changes. This dissertation is therefore a contribution to new modes of resilience in human-landscape interactions after a collapse situation.

Women's writing networks in Spanish magazines around 1900

As an output of the HERA Travelling Texts project, created with the aim of uncovering the realities of women’s literary culture on the fringes of Europe during the long nineteenth century, this study was conceptualised to find out more about the networks of women writers in Spain around 1900, using the digitised corpuses of contemporaneous periodicals as the primary source material. Each chapter of the study centres on a particular periodical, which is used as the starting point for the community of writers and readers, both real and imagined. This thesis looks at the realities of the literary culture for creative women in the late nineteenth century-early twentieth century, exploring the strategies used by women (and men) to support each other in their literary endeavours, how they took inspiration and courage from each other, how they promoted their own names, and how they were received by wider society. The study will also focus on the transnational nature of this literary culture, looking at how women of different nations influenced each other’s work, with a view to understanding more about how cultural change takes place. Finally, this thesis hopes to persuade the reader that the periodical is a rich and under-utilised resource for discovering more about the lives of women writers and their network of relationships.

El efecto de la definición regulatoria de banda ancha sobre la difusión y la competencia del mercado de servicios de Internet fijo en Colombia

A partir de la dinámica evolutiva de la economía de las Tecnologías de la Información y las Comunicaciones y el establecimiento de estándares mínimos de velocidad en distintos contextos regulatorios a nivel mundial, en particular en Colombia, en el presente artículo se presentan diversas aproximaciones empíricas para evaluar los efectos reales que conlleva el establecimiento de definiciones de servicios de banda ancha en el mercado de Internet fijo. Con base en los datos disponibles para Colombia sobre los planes de servicios de Internet fijo ofrecidos durante el periodo 2006-2012, se estima para los segmentos residencial y corporativo el proceso de difusión logístico modificado y el modelo de interacción estratégica para identificar los impactos generados sobre la masificación del servicio a nivel municipal y sobre las decisiones estratégicas que adoptan los operadores, respectivamente. Respecto a los resultados, se encuentra, por una parte, que las dos medidas regulatorias establecidas en Colombia en 2008 y 2010 presentan efectos significativos y positivos sobre el desplazamiento y el crecimiento de los procesos de difusión a nivel municipal. Por otra parte, se observa sustituibilidad estratégica en las decisiones de oferta de velocidad de descarga por parte de los operadores corporativos mientras que, a partir del análisis de distanciamiento de la velocidad ofrecida respecto al estándar mínimo de banda ancha, se demuestra que los proveedores de servicios residenciales tienden a agrupar sus decisiones de velocidad alrededor de los niveles establecidos por regulación.