VictorJuiz/thesis huggingface dataset:
Invasive Species Distribution Models: An Analysis of Scale, Sample Selection Bias, Transferability and Prediction
Keywords: landscape ecology
biogeography
species distribution models
invasive species
climate change
land use change

Species distribution models must balance the need for model generality with that for precision and accuracy. This is critical when modelling range-expanding species such as invasive species. Given the increased use of species distribution models to study invasive species-landscape relationships, a better understanding of the effect of spatial scales, sampling biases, model transferability and discrepancies between different models’ future predictions is necessary. This dissertation addresses these knowledge gaps using mute swans (Cygnus olor) as a case study species. I specifically examine mute swan’s distributions in parts of their native range of Britain and their non-native range of Ontario, Canada. I first investigate which environmental variables at which spatial scales best explain mute swan’s distribution in its non-native range. Second, I perform a sample selection bias study to examine predictive accuracy when species distribution models are built using varying ranges of environmental variables and applied to broader spatial extents. Third, I examine the potential for, and limitations of model transferability between native and non-native regions. Finally, I use two different modelling approaches and three different climate change and land use change scenarios to predict future mute swan habitat suitability. The results indicate that (1) models with better predictive accuracy include environmental variables from multiple ecologically-meaningful scales and measured at spatial extents that include a broad range of environmental variable values; (2) models can exhibit asymmetrical transferability; (3) climate change will facilitate mute swan range expansion in the future more than land use change; and (4) mute swans are often found near urban waterbodies. When modelling invasive species distributions, I suggest that ecologists consider: (I) spatial scale of the underlying landscape processes and species’ use of the landscape; (II) variability and range of each environmental variable used for building models; and (III) stage of establishment of the invasive species.
Effects of Rotational Shepherding on Plant Dispersal and Gene Flow in Fragmented Calcareous Grasslands
Keywords: functional connectivity
spatial genetic structure
species conservation
plant communities and populations
zoochory
habitat colonization

Understanding dispersal and gene flow in human-modified landscapes is crucial for effective conservation. Seed dispersal governs colonization, recruitment, and distribution of plant species, whereas both pollen and seed dispersal determine gene flow among populations. This PhD thesis tests the effect of rotational shepherding on seed dispersal and gene flow in fragmented calcareous grasslands. Calcareous grasslands (Gentiano-Koelerietum pyramidatae vegetation) in Central Europe are semi-natural communities traditionally used for rotational grazing that experienced a decline of plant species during the 20th century due to abandonment of shepherding. This PhD profits from a management project started in 1989 in Bavaria, Germany to reconnect previously abandoned calcareous grasslands in three non-overlapping shepherding systems. Two vegetation surveys in 1989 and 2009 revealed colonizations in previously abandoned grasslands reconnected by shepherding. First, I propose a comprehensive approach to identify determinants of community-level patch colonization rates based on 48 habitat specialist plants by testing competing models of pre-dispersal and dispersal effects and accounting for post-dispersal effects. Mean source patch species occupancy in 1989, and structural elements in focal patches related to establishment explained community-level patch colonization rates. Secondly, by adapting the community analysis to all 31 individual species of the same community with sufficient data, I corroborate the role of shepherding to support dispersal for a range of species, even if they lack seed morphological traits related to zoochory. Thirdly, for the habitat specialist Dianthus carthusianorum, I genotyped 1,613 individuals from 64 populations at eleven microsatellites to test the effect of dispersal by sheep on spatial genetic structure at the landscape scale. Genetic distances between grazed patches of the same herding system were related to distance along herding routes, whereas ungrazed patches showed isolation by geographic distance. Lastly, within individual grassland patches, shepherding significantly decreases the degree of relatedness among neighboring individuals (kinship structure) and increases genetic diversity. My thesis contributes towards understanding the effects of zoochory on spatial dynamics in plant populations across scales.
Reconfiguring the Chorus: Adaptations of the Greek Tragic Chorus Since World War II
Keywords: Chorus
Greek Tragedy
Adaptation

This study is an investigation of adaptations of the Greek tragic chorus since World War II, including the historical, political, and aesthetic contexts that gave rise to these adaptations. Influenced by recent work in the field of Classical Performance Reception and Linda Hutcheon’s work on adaptation, this thesis is designed not around a set of case studies, but around a variety of research questions, including: the current definition of “the chorus” and how it might include the “one-person chorus”; the techniques of mediation used by modern choruses and how they might relate to techniques of the ancient chorus; the connection between political adaptations and the encouragement of audience “complicity”; and the complexities involved in the production and reception of intercultural choruses. I begin by arguing that although August Wilhelm Schlegel’s conception of the chorus as an “ideal spectator” remains the most persistently popular model of understanding the chorus, it should be replaced with a new model based on the concentric frames of performance described by Susan Bennett. Through the use of this model, the chorus is revealed as a liminal, oscillating figure that mediates the action for the audience, and I argue that these qualities have made the chorus an attractive element of tragedy to modern adapters. In the case studies that are offered throughout, I further develop this model in order to analyze the ways in which modern choruses create relationships with audiences, as well as what political or ideological functions these relationships are intended to serve. The model that I develop encourages an engagement with both the intentions of adapters and the realities of reception, and I therefore explore not only how communication strategies of the chorus are intended to operate, but also the issues these strategies raise and the challenges adapters - and their choruses - encounter.
Involvement and Targeted Intervention of Deregulated Hedgehog Pathway in Osteosarcoma
Keywords: Osteosarcoma
Hedgehog

Despite the combination of chemotherapy and surgery in osteosarcoma treatment, the survival of patients remains low. The lack of treatment improvement prompted me to investigate deregulated Hedgehog pathway as a potential target for intervention. During development, the Hedgehog pathway is tightly regulated to control organ and tissue development. Specifically, the Indian Hedgehog pathway (IHH) is important for bone development. Aberrantly activated Hedgehog pathway through ligand-dependent or ligand-independent mechanisms has been reported in numerous cancers. Several small molecule antagonists of the Hedgehog pathway are being explored clinically to improve patient outcome. I examined the expression of IHH pathway components, IHH, SMO, PTCH1 and GLI1, in 43 high-grade primary osteosarcoma tumors and 6 cell lines and found various transcript levels of IHH pathway components in osteosarcoma samples. The high levels of co-expressed IHH and targets, PTCH1 and GLI1, in a subset of osteosarcoma samples are indicative of ligand-dependent activation. Trends toward worse survival for patients with higher IHH (positive regulator) levels and toward better survival for patients with higher PTCH1 (negative regulator) levels were observed. Through genetic analyses, PTCH1 inactivating mutations and GLI1 amplification were found not to be responsible for ligand-independent activation in osteosarcoma. Characterization of Hedgehog signaling in osteosarcoma cell lines showed that cells with high IHH, PTCH1, and GLI1 levels were sensitive to small molecule modulators of both SMO and GLI, which supported the ligand-dependent activation observed in the clinical samples. The inverse correlation of endogenous GLI2 levels and Hedgehog pathway induction levels, and the sensitivity of high-GLI2 cells to GLI inhibition, but not SMO inhibition, in cell lines suggest that GLI2 overexpression may be a mechanism of ligand-independent activation in osteosarcoma. Furthermore, in patient-derived osteosarcoma xenograft models, I observed autocrine and possibly paracrine ligand-dependent Hedgehog signaling in the tumor and stromal compartments. I also showed that a clinically relevant SMO antagonist, IPI-926, was effective at specifically inhibiting all ligand-dependent Hedgehog signaling interactions. A trend toward decreased proliferation and increased apoptosis in treated tumors was observed warranting additional research and demonstrating the potential of Hedgehog pathway inhibitors as novel targeted therapeutics for osteosarcoma treatment.
Envisioning Agribusiness: Land, Labour and Value in a time of Oil Palm Expansion in Indonesia
Keywords: Agribusiness, oil palm, Indonesia, labour, land, value, planning, power, mobility, smallholder, plantation, state

The thesis examines the social and economic implications of large-scale agribusiness expansion in Indonesia by analyzing how this economic system, as it is envisioned and materialised, reshapes livelihood possibilities. Based on original interviews with oil palm plantation workers, plantation company officials, smallholders, and on secondary research, this thesis scrutinises the forms of knowledge and practices that constitute large-scale oil palm agribusiness. While oil palm agribusiness produces economic opportunities for groups of individuals from certain social categories, it constrains the prospects of others in systematic ways. Oil palm agribusiness, as a project and as a set of practices, is deployed by a broad range of economic actors at different scales in an attempt to govern access to resources. However, the power of oil palm companies and investors over land, labour, and value is contested and negotiated by workers and smallholders who engage creatively with this economy. The thesis shows that oil palm agribusiness forms a field of power that produces specific subjectivities which transform the meanings and constraints related to this mode of production. The first part of the thesis (chapters 2 and 3) identifies the objectives pursued by those who plan and envision oil palm agribusiness. I emphasise that oil palm agribusiness serves a number of often competing and shifting aims that range from capital accumulation to welfare provision. The second part of the thesis (chapters 4 and 5) demonstrates how the modes of visioning examined in the first part of the thesis produce a broad set of material conditions for populations. I analyse the ways in which these conditions are constantly reshaped by everyday power relations and articulated around the value of labour and land. Based on ethnographic fieldwork that I conducted in West Kalimantan, Lombok, and Nias, these chapters shed light on the lived geographies of labour and the livelihood strategies used by individuals and social groups in the space of oil palm agribusiness.
Bringing Labor Back In: Varieties of Unionism and the Evolution of Employment Protection and Unemployment Benefits in the Rich Democracies
Keywords: Labour market policy
Unions
Employment Protection
Unemployment Benefits

This thesis looks at the politics of labor market policy in the postwar period in the advanced industrialized democracies. Specifically, the dissertation seeks to explain stark cross-national differences in unemployment benefit systems and employment protection legislation. The theory advanced in this thesis emphasizes significant differences in union organization across the rich democracies. This view, “Varieties of Unionism”, shows how the varying political capacities and policy preferences of labor movements explain most of the cross-national policy differences. In particular, the research points to union movements’ ideological traditions and varying rates of union density, union centralization, and involvement in unemployment benefit administration as crucial explanatory forces. Each feature of union movements captures an important part of why they might choose to advocate on behalf of the unemployed and to their differential ability to have those policy preferences realized, as well as indicating the kinds of preferences they will have for employment protection legislation. In the case of policies directed at the unemployed (or so-called labor market ‘Outsiders’), these insights lead to the construction of an index of “Outsider-oriented Unionism”, which correlates very closely to cross-national variations in unemployment benefit generosity as well as to active labor market policy spending. The thesis also introduces a new fourfold typology of unionism that helps to explain the different combinations of employment protection legislation and ‘Outsider policy’ generosity that exist among the rich democracies, or labor market policy ‘regimes’. The thesis makes this argument with multiple regression analysis of fifteen rich democracies and with detailed historical case studies of Britain, The Netherlands, and Sweden. In making this case, the thesis strongly challenges the explanations of labor market policy put forward by the Varieties of Capitalism literature and Insider-Outsider theory. In addition, the thesis reformulates the traditional Power Resource view by introducing a more rigorous theory of labor movements’ policy preferences and thereby qualifies recent statements that have emphasized partisanship almost alone. Most broadly, the theory challenges the “individualist turn” in recent comparative political economy scholarship and suggests that the field needs to return its gaze far more toward organized interests.
Group Processes Supporting the Development of Progressive Discourse in Online Graduate Courses
Keywords: online education
computer-supported collaborative learning
progressive discourse
knowledge building
elearning
online discussion
teacher professional develpment
discourse processes

This design-based research study investigates the development of progressive discourse among participants (n=15, n=17, n=20) in three online graduate course contexts. Progressive discourse is a kind of discourse for inquiry in which participants share, question, and revise their ideas to deepen understanding and build knowledge. Although progressive discourse is central to knowledge building pedagogy, it is not known whether it is possible to detect its emergence in the patterns of participation in asynchronous conferencing environments or what kinds of instructional scaffolding are most effective to support its development. This study offers a unique perspective by characterizing episodes of discourse where participants honor the commitments for progressive discourse and by refining designs of peer and software-based scaffolding for progressive discourse. Results showed that measures such as note count, replies, and thread sizes can determine some qualities of online discourse but do not shed light on the development of progressive discourse. Thus an in-depth analysis of discourse for groups was developed to trace the interdependent individual contributions to the group discourse. Peer scaffolding that made norms for progressive discourse explicit was introduced to encourage participants to engage in sustained student-centered discourse for inquiry. Findings show that this intervention was most effective at the beginning of a course for newer online learners and newer graduate students, and least effective for students who were practicing K-12 teachers. A significant barrier to fostering progressive discourse is the tendency for teachers to reject these norms and revert to belief-mode thinking and devotional discourse typical of traditional schooling. Additionally, findings suggest that software-based scaffolding (as found in Knowledge Forum’s scaffold support feature) is a promising avenue for future design innovations to encourage progressive discourse. Although the results of this study are only suggestive, the findings do illustrate ways in which graduate students can uphold the commitments to move beyond expressions of socio- affective connection and opinion to discuss ideas in ways that lead to more useful explanations. The implications for these results for analyzing the quality of online discourse and the designs of instructional scaffolding in online learning environments are discussed.
The Autotransporter Protease EspP: Crystal Structure of the Passenger Domain and Relation to Clot Formation and Stability in Human Blood
Keywords: EspP
autotransporter
coagulation
crystallography
fibrinolysis
EHEC

Autotransporters represent a large superfamily of known and putative virulence factors produced by Gram-negative bacteria. They consist of an N-terminal “passenger domain” responsible for the specific effector functions of the molecule and a C-terminal “β domain” responsible for translocation of the passenger across the bacterial outer membrane. The serine protease autotransporters of Enterobacteriaceae (SPATEs) represent those autotransporters produced by Enterobacteriaceae where, as the name suggests, the passenger domain functions as a serine protease. Members of this family of autotransporters include among others the extracellular serine protease EspP produced by enterohemorrhagic Escherichia coli (EHEC) O157:H7. EHEC, especially those of serotype O157:H7, have been implicated as causative agents of hemorrhagic colitis and hemolytic-uremic syndrome, both of which include disruption of the normal processes in human blood responsible for maintaining good health. EspP has previously been shown to cleave human coagulation factors V and VIII and has been hypothesized to possibly contribute to the mucosal hemorrhage in patients infected with EHEC. This thesis aims to better understand the functional significance of EspP in EHEC pathogenesis by analyzing the crystallographic structure of the mature passenger domain of EspP and by investigating, in vitro, its effects on the coagulation and fibrinolytic processes in human blood. Like the previously determined autotransporter passenger domains, the EspP passenger domain is found to contain an extended right-handed parallel β-helix preceded by an N-terminal globular domain housing the catalytic function of the protease. Of note, however, is the absence of a second globular domain protruding from this β-helix. Furthermore, EspP is found to alter hemostasis in vitro by drastically decreasing the activities of human blood coagulation factors V, VII, VIII and XII, by enhancing platelet-fibrin clot formation, and by accelerating fibrinolysis. These results provide compelling evidence for a pathogenic role played by EspP during EHEC infection.
Screening for Prenatal Alcohol Exposure using Fatty Acid Ethyl Esters as Biomarkers
Keywords: Fetal Alcohol Spectrum Disorders
Neonatal Screening
Biomarkers
Prenatal alcohol exposure
Meconium
Fatty Acid Ethyl Esters

Diagnosis of fetal alcohol spectrum disorders (FASD) is challenging and typically requires confirmation of in utero alcohol exposure. Due to the poor reliability of maternal self-reports, biomarkers have emerged to address the problem of obtaining exposure history. A relatively novel method for detecting prenatal alcohol exposure is analysis of meconium for fatty acid ethyl esters (FAEEs), which are non-oxidative ethanol metabolites. Screening newborns using meconium FAEEs may facilitate early diagnosis and intervention in alcohol-affected individuals. The overall objective of this thesis is to further investigate, validate, and assess the clinical utility of meconium FAEE analysis as a screening tool for the identification of neonates at-risk for FASD. This objective was addressed in four separate studies. The first study assessed whether meconium FAEE concentrations can be predictive of ethanol-induced organ injury in fetal sheep, and determined that the levels of these esters could be used to identify fetuses at-risk for organ dysfunction that do not display overt physical signs of ethanol teratogenicity. The second study investigated the effect of delayed meconium collection and contamination with postnatal stool on FAEE analysis, and determined it to be a risk factor for false positive test results. In the third study, maternal willingness to partake in an open meconium screening program was assessed and found to be low enough to diminish the utility of meconium FAEE testing for population-based open screening. Lastly, a systematic review examining the capacity for FAEE synthesis and the enzymology of this non-oxidative metabolic pathway in mammalian organs and tissues revealed that FAEE synthesis is mediated by numerous enzymes and isoenzymes, many of which have other primary physiological functions, and that their contribution to overall FAEE-synthesis may be tissue-specific. Overall, the results of this research provide new information on the benefits, limitations, and utility of meconium FAEE testing as a screening tool for identifying prenatal alcohol exposure − a test that may be of great clinical value in the diagnosis and management of FASD.