13,913 research outputs found

    Genomic prediction in plants: opportunities for ensemble machine learning based approaches [version 2; peer review: 1 approved, 2 approved with reservations]

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    Background: Many studies have demonstrated the utility of machine learning (ML) methods for genomic prediction (GP) of various plant traits, but a clear rationale for choosing ML over conventionally used, often simpler parametric methods, is still lacking. Predictive performance of GP models might depend on a plethora of factors including sample size, number of markers, population structure and genetic architecture. Methods: Here, we investigate which problem and dataset characteristics are related to good performance of ML methods for genomic prediction. We compare the predictive performance of two frequently used ensemble ML methods (Random Forest and Extreme Gradient Boosting) with parametric methods including genomic best linear unbiased prediction (GBLUP), reproducing kernel Hilbert space regression (RKHS), BayesA and BayesB. To explore problem characteristics, we use simulated and real plant traits under different genetic complexity levels determined by the number of Quantitative Trait Loci (QTLs), heritability (h2 and h2e), population structure and linkage disequilibrium between causal nucleotides and other SNPs. Results: Decision tree based ensemble ML methods are a better choice for nonlinear phenotypes and are comparable to Bayesian methods for linear phenotypes in the case of large effect Quantitative Trait Nucleotides (QTNs). Furthermore, we find that ML methods are susceptible to confounding due to population structure but less sensitive to low linkage disequilibrium than linear parametric methods. Conclusions: Overall, this provides insights into the role of ML in GP as well as guidelines for practitioners

    Exploring Potential Domains of Agroecological Transformation in the United States

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    There is now substantial evidence that agroecology constitutes a necessary pathway towards socially just and ecologically resilient agrifood systems. In the United States, however, agroecology remains relegated to the margins of research and policy spaces. This dissertation explores three potential domains of agroecological transformation in the US. Domains of transformation are sites of contestation in which agroecology interfaces with the industrial agrifood system; these material and conceptual spaces may point to important pathways for scaling agroecology. To explore this concept, I examine formal agroecology education (Chapter 1), extension services and statewide discourses around soil health (Chapter 2), and models of farmland access not based on private property (Chapter 3). While these constitute three distinct topics, I seek to demonstrate that they are linked by similar forces that enable and constrain the extent to which these domains can be sites of agroecological transformation. First, I use case study methodology to explore the evolution of an advanced undergraduate agroecology course at the University of Vermont. I examine how course content and pedagogy align with a transformative framing of agroecology as inherently transdisciplinary, participatory, action-oriented, and political. I find that student-centered pedagogies and experiential education on farms successfully promote transformative learning whereby students shift their understanding of agrifood systems and their role(s) within them. In my second chapter, I zoom out to consider soil health discourses amongst farmers and extension professionals in Vermont. Using co-created mental models and participatory analysis, I find that a singular notion of soil health based on biological, chemical, and physical properties fails to capture the diverse ways in which farmers and extension professionals understand soil health. I advocate for a principles-based approach to soil health that includes social factors and may provide a valuable heuristic for mobilizing knowledge towards agroecology transition pathways. My third chapter, conducted in collaboration with the national non-profit organization Agrarian Trust, considers equitable farmland access. Through semi-structured interviews with 13 farmers and growers across the US, I explore both farmer motivations for engaging with alternative land access models (ALAMs) and the potential role(s) these models may play within broader transformation processes. I argue that ALAMs constitute material and conceptual ‘third spaces’ within which the private property regime is challenged and new identities and language around land ownership can emerge; as such, ALAMs may facilitate a (re)imagining of land-based social-ecological relationships. I conclude the dissertation by identifying conceptual and practical linkages across the domains explored in Chapters 1-3. I pay particular attention to processes that challenge neoliberal logics, enact plural ways of knowing, and prefigure just futures. In considering these concepts, I apply an expansive notion of pedagogy to explore how processes of teaching and (un)learning can contribute to cultivating foundational capacities for transition processes

    Bridging technology and educational psychology: an exploration of individual differences in technology-assisted language learning within an Algerian EFL setting

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    The implementation of technology in language learning and teaching has a great influence onthe teaching and learning process as a whole and its impact on the learners’ psychological state seems of paramount significance, since it could be either an aid or a barrier to students’ academic performance. This thesis therefore explores individual learner differences in technology-assisted language learning (TALL) and when using educational technologies in higher education within an Algerian English as a Foreign Language (EFL) setting. Although I initially intended to investigate the relationship between TALL and certain affective variables mainly motivation, anxiety, self-confidence, and learning styles inside the classroom, the collection and analysis of data shifted my focus to a holistic view of individual learner differences in TALL environments and when using educational technologies within and beyond the classroom. In an attempt to bridge technology and educational psychology, this ethnographic case study considers the nature of the impact of technology integration in language teaching and learning on the psychology of individual language learners inside and outside the classroom. The study considers the reality constructed by participants and reveals multiple and distinctive views about the relationship between the use of educational technologies in higher education and individual learner differences. It took place in a university in the north-west of Algeria and involved 27 main and secondary student and teacher participants. It consisted of focus-group discussions, follow-up discussions, teachers’ interviews, learners’ diaries, observation, and field notes. It was initially conducted within the classroom but gradually expanded to other settings outside the classroom depending on the availability of participants, their actions, and activities. The study indicates that the impact of technology integration in EFL learning on individual learner differences is both complex and dynamic. It is complex in the sense that it is shown in multiple aspects and reflected on the students and their differences. In addition to various positive and different negative influences of different technology uses and the different psychological reactions among students to the same technology scenario, the study reveals the unrecognised different manifestations of similar psychological traits in the same ELT technology scenario. It is also dynamic since it is characterised by constant change according to contextual approaches to and practical realities of technology integration in language teaching and learning in the setting, including discrepancies between students’ attitudes and teacher’ actions, mismatches between technological experiences inside and outside the classroom, local concerns and generalised beliefs about TALL in the context, and the rapid and unplanned shift to online educational delivery during the Covid-19 pandemic situation. The study may therefore be of interest, not only to Algerian teachers and students, but also to academics and institutions in other contexts through considering the complex and dynamic impact of TALL and technology integration at higher education on individual differences, and to academics in similar low-resource contexts by undertaking a context approach to technology integration

    A Decision Support System for Economic Viability and Environmental Impact Assessment of Vertical Farms

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    Vertical farming (VF) is the practice of growing crops or animals using the vertical dimension via multi-tier racks or vertically inclined surfaces. In this thesis, I focus on the emerging industry of plant-specific VF. Vertical plant farming (VPF) is a promising and relatively novel practice that can be conducted in buildings with environmental control and artificial lighting. However, the nascent sector has experienced challenges in economic viability, standardisation, and environmental sustainability. Practitioners and academics call for a comprehensive financial analysis of VPF, but efforts are stifled by a lack of valid and available data. A review of economic estimation and horticultural software identifies a need for a decision support system (DSS) that facilitates risk-empowered business planning for vertical farmers. This thesis proposes an open-source DSS framework to evaluate business sustainability through financial risk and environmental impact assessments. Data from the literature, alongside lessons learned from industry practitioners, would be centralised in the proposed DSS using imprecise data techniques. These techniques have been applied in engineering but are seldom used in financial forecasting. This could benefit complex sectors which only have scarce data to predict business viability. To begin the execution of the DSS framework, VPF practitioners were interviewed using a mixed-methods approach. Learnings from over 19 shuttered and operational VPF projects provide insights into the barriers inhibiting scalability and identifying risks to form a risk taxonomy. Labour was the most commonly reported top challenge. Therefore, research was conducted to explore lean principles to improve productivity. A probabilistic model representing a spectrum of variables and their associated uncertainty was built according to the DSS framework to evaluate the financial risk for VF projects. This enabled flexible computation without precise production or financial data to improve economic estimation accuracy. The model assessed two VPF cases (one in the UK and another in Japan), demonstrating the first risk and uncertainty quantification of VPF business models in the literature. The results highlighted measures to improve economic viability and the viability of the UK and Japan case. The environmental impact assessment model was developed, allowing VPF operators to evaluate their carbon footprint compared to traditional agriculture using life-cycle assessment. I explore strategies for net-zero carbon production through sensitivity analysis. Renewable energies, especially solar, geothermal, and tidal power, show promise for reducing the carbon emissions of indoor VPF. Results show that renewably-powered VPF can reduce carbon emissions compared to field-based agriculture when considering the land-use change. The drivers for DSS adoption have been researched, showing a pathway of compliance and design thinking to overcome the ‘problem of implementation’ and enable commercialisation. Further work is suggested to standardise VF equipment, collect benchmarking data, and characterise risks. This work will reduce risk and uncertainty and accelerate the sector’s emergence

    In vitro investigation of the effect of disulfiram on hypoxia induced NFκB, epithelial to mesenchymal transition and cancer stem cells in glioblastoma cell lines

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    A thesis submitted in partial fulfilment of the requirements of the University of Wolverhampton for the degree of Doctor of Philosophy.Glioblastoma multiforme (GBM) is one of the most aggressive and lethal cancers with a poor prognosis. Advances in the treatment of GBM are limited due to several resistance mechanisms and limited drug delivery into the central nervous system (CNS) compartment by the blood-brain barrier (BBB) and by actions of the normal brain to counteract tumour-targeting medications. Hypoxia is common in malignant brain tumours such as GBM and plays a significant role in tumour pathobiology. It is widely accepted that hypoxia is a major driver of GBM malignancy. Although it has been confirmed that hypoxia induces GBM stem-like-cells (GSCs), which are highly invasive and resistant to all chemotherapeutic agents, the detailed molecular pathways linking hypoxia, GSC traits and chemoresistance remain obscure. Evidence shows that hypoxia induces cancer stem cell phenotypes via epithelial-to-mesenchymal transition (EMT), promoting therapeutic resistance in most cancers, including GBM. This study demonstrated that spheroid cultured GBM cells consist of a large population of hypoxic cells with CSC and EMT characteristics. GSCs are chemo-resistant and displayed increased levels of HIFs and NFκB activity. Similarly, the hypoxia cultured GBM cells manifested GSC traits, chemoresistance and invasiveness. These results suggest that hypoxia is responsible for GBM stemness, chemoresistance and invasiveness. GBM cells transfected with nuclear factor kappa B-p65 (NFκB-p65) subunit exhibited CSC and EMT markers indicating the essential role of NFκB in maintaining GSC phenotypes. The study also highlighted the significance of NFκB in driving chemoresistance, invasiveness, and the potential role of NFκB as the central regulator of hypoxia-induced stemness in GBM cells. GSC population has the ability of self-renewal, cancer initiation and development of secondary heterogeneous cancer. The very poor prognosis of GBM could largely be attributed to the existence of GSCs, which promote tumour propagation, maintenance, radio- and chemoresistance and local infiltration. In this study, we used Disulfiram (DS), a drug used for more than 65 years in alcoholism clinics, in combination with copper (Cu) to target the NFκB pathway, reverse chemoresistance and block invasion in GSCs. The obtained results showed that DS/Cu is highly cytotoxic to GBM cells and completely eradicated the resistant CSC population at low dose levels in vitro. DS/Cu inhibited the migration and invasion of hypoxia-induced CSC and EMT like GBM cells at low nanomolar concentrations. DS is an FDA approved drug with low toxicity to normal tissues and can pass through the BBB. Further research may lead to the quick translation of DS into cancer clinics and provide new therapeutic options to improve treatment outcomes in GBM patients

    On the Mechanism of Building Core Competencies: a Study of Chinese Multinational Port Enterprises

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    This study aims to explore how Chinese multinational port enterprises (MNPEs) build their core competencies. Core competencies are firms’special capabilities and sources to gain sustainable competitive advantage (SCA) in marketplace, and the concept led to extensive research and debates. However, few studies include inquiries about the mechanisms of building core competencies in the context of Chinese MNPEs. Accordingly, answers were sought to three research questions: 1. What are the core competencies of the Chinese MNPEs? 2. What are the mechanisms that the Chinese MNPEs use to build their core competencies? 3. What are the paths that the Chinese MNPEs pursue to build their resources bases? The study adopted a multiple-case study design, focusing on building mechanism of core competencies with RBV. It selected purposively five Chinese leading MNPEs and three industry associations as Case Companies. The study revealed three main findings. First, it identified three generic core competencies possessed by Case Companies, i.e., innovation in business models and operations, utilisation of technologies, and acquisition of strategic resources. Second, it developed the conceptual framework of the Mechanism of Building Core Competencies (MBCC), which is a process of change of collective learning in effective and efficient utilization of resources of a firm in response to critical events. Third, it proposed three paths to build core competencies, i.e., enhancing collective learning, selecting sustainable processes, and building resource base. The study contributes to the knowledge of core competencies and RBV in three ways: (1) presenting three generic core competencies of the Chinese MNPEs, (2) proposing a new conceptual framework to explain how Chinese MNPEs build their core competencies, (3) suggesting a solid anchor point (MBCC) to explain the links among resources, core competencies, and SCA. The findings set benchmarks for Chinese logistics industry and provide guidelines to build core competencies
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