Analyses of the genomic variation to study cork oak evolution and adaptation : from past to future climatic changes

Tese de doutoramento, Biologia e Ecologia das Alterações Globais (Biologia do Genoma e Evolução), Universidade de Lisboa, Faculdade de Ciências, 2018Current scientific literature indicates that climate change will cause an average world temperature increase between 1 and 4ºC, along with changes in precipitation patterns and extreme weather events in the next 50 years. These are likely to have a negative impact for biodiversity in general, and forest ecosystems should be particularly affected, especially those in Mediterranean areas, like the cork oak (Quercus suber L.) “montados”. In order to understand how species can respond to such alterations, it is important to know their evolutionary history and genetic architecture of adaptive traits. Advances in sequencing technologies have relatively recently brought down the cost of sequencing per base pair to a point where even small research facilities can obtain genomic information of non-model organisms. These advances made SNP markers become the most abundant type of genetic variation in eukaryotic genomes, especially with the advent of Reduced Representation libraries such as RAD-Seq and GBS. Yet, despite their widespread use, SNP data analyses still bore its own set of bioinformatics challenges. While most of these are related with the practical aspects of the process, such as being able to handle very large datasets, or discriminate between neutral and non-neutral markers, some fundamental problems, like reproducibility are also important issues affecting research in this area. In this thesis, genomic and transcriptomic data from Q. suber was used to assess the evolutionary history of the species, detect the effects of natural selection across the cork oak’s distribution range and find any associations between the obtained markers and environmental variables. The main methodological contributions of this thesis are in the form of three software suites: (1) 4Pipe4, a software for automatically mining SNP markers from NGS data when no reference genome nor strain information is present, (2) NCBI Mass Sequence Downloader, a program to automate the downloading of large datasets from the NCBI databases, and (3) Structure_threader, a software to automate and parallelize analyses using several popular clustering analyses programs. All of these programs were developed with the intent to improve the automation and reproducibility value of the analysis processes they are meant to be part of. The main findings of this thesis are that (1) the evolutionary history and population structure of Q. suber is not as neatly structured as chloroplastidial markers indicate, (2) local adaptation plays and important role in the distribution of the species’ genetic variability, and (3) the cork oak may be better equipped, from a genetic point of view, to adapt to climate change than what previous studies based solely on ecological modelling indicated

New insights into adaptation and population structure of cork oak using genotyping by sequencing

Species respond to global climatic changes in a local context. Understanding this process, including its speed and intensity, is paramount due to the pace at which such changes are currently occurring. Tree species are particularly interesting to study in this regard due to their long generation times, sedentarism, and ecological and economic importance. Quercus suber L. is an evergreen forest tree species of the Fagaceae family with an essentially Western Mediterranean distribution. Despite frequent assessments of the species' evolutionary history, large-scale genetic studies have mostly relied on plastidial markers, whereas nuclear markers have been used on studies with locally focused sampling strategies. In this work, "Genotyping by sequencing" is used to derive 1,996 single nucleotide polymorphism markers to assess the species' evolutionary history from a nuclear DNA perspective, gain insights into how local adaptation is shaping the species' genetic background, and to forecast how Q. suber may respond to global climatic changes from a genetic perspective. Results reveal (a) an essentially unstructured species, where (b) a balance between gene flow and local adaptation keeps the species' gene pool somewhat homogeneous across its distribution, but still allowing (c) variation clines for the individuals to cope with local conditions. "Risk of Non-Adaptedness" (RONA) analyses suggest that for the considered variables and most sampled locations, (d) the cork oak should not require large shifts in allele frequencies to survive the predicted climatic changes. Future directions include integrating these results with ecological niche modeling perspectives, improving the RONA methodology, and expanding its use to other species. With the implementation presented in this work, the RONA can now also be easily assessed for other organisms.info:eu-repo/semantics/publishedVersio

Factors Affecting Consistency in Supply of Pharmaceutical Products in Government Hospitals in Kenya: A Case Study of Maragua District Hospital

This research was made to establish the factors that affected consistency in supply of pharmaceutical products in government hospitals in Kenya. In most cases, the government run hospitals have had inconsistency in supply of pharmaceutical and previous researchers have not identified the reasons culminating to such situations regardless of the huge amounts of budget allocations. The study was carried out in Maragua district hospital with a sample size of 100 individuals comprising of management, procurement department, nursing department and the pharmacy department personnel. The researcher used stratified random sampling. Structured questionnaires were given out to the respondents to fill and the researcher conducted unstructured interviews. Data collected was analysed and it was clear that the procurement process and its management, legal requirements and internal tools used for enhancing procurement greatly determined the timely availability of supplies following. The researcher identified that the procurement department was understaffed and procurement process was at times not observed. Financing was a major problem. Legal requirements were bureaucratic and lengthened the procurement process leading to inconsistency in obtaining supplies.  The hospital had no core tool for enhancing procurement performance. The legal framework needed review to reduce bureaucracy and shorten the process and training on procurement issues to all hospital procurement players was required to boost their knowledge. The hospital faced several challenges, which included shortage of staff in the procurement department and financial constrains

Automated Defect Detection Tool For Sewer Pipelines

In sewer networks, the economic effects and costs that result from a pipeline break are rising sharply. In Qatar, majority of the sewer network pipelines were installed in the last 20 years and are currently in poor condition and constantly deteriorating. As a result, there is huge demand for inspection and rehabilitation of sewer pipelines. In addition to being inaccurate, current Practices of sewer pipelines inspection are time consuming and may not keep up with the deterioration rate of the pipelines. Consequently, this research aims to develop an automated tool to detect different defects such as cracks, deformation, settled deposits and joint displacement in sewer pipelines. The automated approach is dependent upon using image-processing techniques and several mathematical formulas to analyze output data from CCTV camera photos. Given that one inspection session can result in hundreds of CCTV Camera footage, introducing an automated tool would help yield faster results. Additionally, given the subjective nature of most defects, it will result in more systematic results since the current method rely heavily on the operator's experience. The automated tool was able to successfully detect cracks, displaced joints, ovality and settled deposits in pipelines using CCTV Camera inspection output footage. Using two different data sets, the constructed Matlab code could successfully differentiate between cracks and displaced joints with an overall crack detection success rate of 84% and an overall displaced joint detection rate of 94%. The code was also able to efficiently detect settled deposits in the pipelines with a detection rate of 90%. In addition, the automated ovality detection resulted in 100% compatibility with the manual circularity detection

Enhancing Teacher-Child Interactions: A Pilot Study Using Focal Child Data

Research suggests that teacher-child interactions in early childhood classrooms are an essential element to high quality programs and child outcomes. With the increase in state funded pre-kindergarten classrooms across the nation and the growing concentration on academic content for young children, careful attention is needed to children’s social-emotional development. Research suggests that it is a strong social emotional foundation that contributes to children’s successful transition into their elementary school years. Therefore, the purpose of this mixed method study was to pilot the use of focal child data as a professional development tool for pre-kindergarten teachers to examine teacher-child interactions. Studying eight teachers across two pre-kindergarten sites, the development of participant’s knowledge of teacher-child interactions was captured using focal-child classroom observations, face-to-face exchanges, teacher reflections, and researcher field notes. Data analysis involved descriptive statistics from quantitative sources, combined with emerging themes through iterative cycles of coding qualitative data. Situated in a conceptual framework that places individual development in context, this study exemplifies the value of using uniquely tailored focal child data as a professional development tool for pre-kindergarten teachers. Findings from this mixed method study reveal how focal child data provided participating teachers with a new lens for examining teacher-child interactions, which led to a heightened awareness of and intentionality in their interactions with children. Additionally, a collaborative community of practice model for professional development contributed to teacher understanding and transformation over the course of this study. Capturing the direct social ecology of a child’s pre-kindergarten experience aided in understanding the relationship between specific children’s experiences and the context in which those experiences take place. Findings from this study enhance participant understanding of the complex nature of teacher-child interactions

The role of decision making and management of construction projects in fostering sustainability for intensive urban development through public housing initiatives in South Africa.

Masters Degree. University of KwaZulu-Natal, Durban.The current discourse in sustainable development is centred on the 17 Sustainable Development Goals stipulated in the 2030 Agenda for Sustainable Development as well as the New Urban agenda. The resilience, inclusiveness and safeness of human settlements and the need to readdress the manner in which these are planned, financed, developed, governed and managed is at the forefront of the narrative. In the South African context this soughtafter target of integrated and sustainable human settlements delivery has seen a trajectory riddled with a myriad of policies and programmes. One of the predicaments at the heart of the new urban agenda globally, and South Africa specifically, is whether population growth should be accommodated by extensive or intensive urban development. Both approaches have gained support in the South African context in recent years. The research looked at the role of decision making and management of construction projects within the context of producing sustainable housing through intensive redevelopment in South Africa and particularly in Durban. The intensive redevelopment approach indeed seems to address the ideals of the New Urban Agenda, however a case study analysis and an overview of recent research related to intensive redevelopment through building conversion and renovation has revealed that efforts to date do not address sustainability issues comprehensively. The study paid special attention to the social aspect of sustainability, which reflects recent increasing awareness that the construction industry must support the sustainable development agenda by including social considerations throughout the construction project life cycle in hopes of achieving sustainable buildings and communities. An environmentally friendly building requires only the minimizing of its environmental impact, however a sustainable building asks for more. The sense of a community is fundamental for a sustainable building, since it should increase social equity, cultural and heritage issues, human health and social infrastructure, as well as safe and healthy environments. The research adopted a multi-dimensional approach involving an extensive literature review, individual and focus group interviews with stakeholders, a questionnaire-based survey conducted with the occupants of buildings involved in intensive urban redevelopment and case studies’ analysis. Findings demonstrated that the New Urban Agenda needs to recognise and respond to drivers such as the demand for central city living from low and middle income groups desperate for the access to amenities and economic opportunities it provides. Core urban areas, inner suburbs and old transport routes are full of derelict and under-utilised land, former buffer strips and run-down buildings in need of renewal and regeneration. There are unrivalled opportunities within South African municipalities to rehabilitate worn-out infrastructure, to install new energy and communication systems, and to refurbish and construct better buildings. Rerouting capital flows to retrofit existing urban assets makes sense from a resource efficiency perspective. Long-term considerations, global thinking and local action, responsibility and transparency from a management and decision making perspective, and the purposive application of the principles of sustainability throughout a project lifecycle and to all stakeholders promotes continual improvement and distinctive steps towards archiving sustainable buildings and communities through the process of conversions and rehabilitation of existing buildings in urban areas

Incremental Lifecycle Validation Of Knowledge-based Systems Through Commonkads

This dissertation introduces a novel validation method for knowledge-based systems (KBS). Validation is an essential phase in the development lifecycle of knowledge-based systems. Validation ensures that the system is valid, reliable and that it reflects the knowledge of the expert and meets the specifications. Although many validation methods have been introduced for knowledge-based systems, there is still a need for an incremental validation method based on a lifecycle model. Lifecycle models provide a general framework for the developer and a mapping technique from the system into the validation process. They support reusability, modularity and offer guidelines for knowledge engineers to achieve high quality systems. CommonKADS is a set of models that helps to represent and analyze knowledge-based systems. It offers a de facto standard for building knowledge-based systems. Additionally, CommonKADS is a knowledge representation-independent model. It has powerful models that can represent many domains. Defining an incremental validation method based on a conceptual lifecycle model (such as CommonKADS) has a number of advantages such as reducing time and effort, ease of implementation when having a template to follow, well-structured design, and better tracking of errors when they occur. Moreover, the validation method introduced in this dissertation is based on case testing and selecting an appropriate set of test cases to validate the system. The validation method defined makes use of results of prior test cases in an incremental validation procedure. This facilitates defining a minimal set of test cases that provides complete and effective system coverage. CommonKADS doesn’t define validation, verification or testing in any of its models. This research seeks to establish a direct relation between validation and lifecycle models, and introduces a validation method for KBS embedded into CommonKAD

Young Adults with Visual Impairments and Driver\u27s Education: Journeys of Self-Efficacy, Identity, and Transition to Adulthood

A person’s ability to travel independently can determine whether he or she transitions successfully from one life stage to another. One critically important aspect of independent travel is coming to understand how vehicles move in the built environment. For youth without visual disabilities, this information is addressed in depth in driver’s education courses. In the case of adolescents with visual impairments, the acquisition of this information is more complex and raises a number of complicated questions. In this qualitative study, seven adults with visual impairments ages 18-27 and six of their family members are interviewed to determine the impact of driver’s education on future independent travel for individuals with low vision/blindness. Social theories from other disciplines are used to analyze data (HeavyRunner & Marshall, 2003; Kim, 2015; Tuck, 2009). Findings indicate the emergence of three key themes: people with visual impairments are perceived as incapable by people without disabilities, driving serves as a metaphor for ableism, and schools may be actively pushing students with visual impairments out of their home schools to attend residential schools for students with visual impairments to preserve resources for able-bodied students

Sustainability Strategies in Supply Chain Management

Managers no longer view sustainability of organizations only in terms of profitability and economic growth of shareholders. Various competitive pressures are forcing managers to broaden the scope of sustainability to include explicit environmental and societal objectives too. These pressures are emanating from various sources such as depleting natural resources, regulatory policies from governments, erratic weather cycles, demanding customers and brand damage due to exposure about poor working conditions in supplier factories located in other countries. This dissertation consists of three essays that contribute to the practice and literature of strategic sustainable supply chain management by examining its four aspects: measure, manage, mitigate, and market. The purpose of this dissertation is to utilize a multi-method approach and multiple secondary data sources to examine sustainable supply chain management from a strategy point of view. Three separate but connected studies form the core of this dissertation. Chapter Two of this dissertation proposes a framework of seven market-oriented sustainability strategies by objectively analyzing sustainability reports of leading organizations of four industry sectors using structured content analysis and linear programming techniques. Chapter Three utilizes linear aggregation methodology and data envelopment analysis to form a sustainability index comprising of various sustainability indicators in logistics and shipping services industry. This index may be used as a decision making tool by managers to evaluate sustainability efforts of their organizations and also to benchmark their sustainability performance over the competition. Chapter Four examines the sources of differential environmental performance of manufacturing facilities using risk screening environmental indicators database and Markov chain Monte Carlo estimation procedure. The results provide support that resource-based view explains the maximum differential environmental performance of firms as opposed to industry-based view or institutional theory