11,748 research outputs found

    Implicit Loss of Surjectivity and Facial Reduction: Theory and Applications

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    Facial reduction, pioneered by Borwein and Wolkowicz, is a preprocessing method that is commonly used to obtain strict feasibility in the reformulated, reduced constraint system. The importance of strict feasibility is often addressed in the context of the convergence results for interior point methods. Beyond the theoretical properties that the facial reduction conveys, we show that facial reduction, not only limited to interior point methods, leads to strong numerical performances in different classes of algorithms. In this thesis we study various consequences and the broad applicability of facial reduction. The thesis is organized in two parts. In the first part, we show the instabilities accompanied by the absence of strict feasibility through the lens of facially reduced systems. In particular, we exploit the implicit redundancies, revealed by each nontrivial facial reduction step, resulting in the implicit loss of surjectivity. This leads to the two-step facial reduction and two novel related notions of singularity. For the area of semidefinite programming, we use these singularities to strengthen a known bound on the solution rank, the Barvinok-Pataki bound. For the area of linear programming, we reveal degeneracies caused by the implicit redundancies. Furthermore, we propose a preprocessing tool that uses the simplex method. In the second part of this thesis, we continue with the semidefinite programs that do not have strictly feasible points. We focus on the doubly-nonnegative relaxation of the binary quadratic program and a semidefinite program with a nonlinear objective function. We closely work with two classes of algorithms, the splitting method and the Gauss-Newton interior point method. We elaborate on the advantages in building models from facial reduction. Moreover, we develop algorithms for real-world problems including the quadratic assignment problem, the protein side-chain positioning problem, and the key rate computation for quantum key distribution. Facial reduction continues to play an important role for providing robust reformulated models in both the theoretical and the practical aspects, resulting in successful numerical performances

    Analysis of the ASR and LP3 homologous gene families reveal positive selection acting on LP3-3 gene

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    Drought has long been established as a major environmental stress for plants which have in turn developed several coping strategies, ranging from physiological to molecular mechanisms. LP3 that was first discovered in loblolly pine (Pinus taeda L.) is a homolog of the Abscisic Acid, Stress and Ripening (ASR) gene belonging to the ABA/WDS gene family that was first detected in tomato. LP3 has been shown to be present in four different paralogs in loblolly pine called LP3-0, LP3-1, LP3-2 and LP3-3. LP3 in loblolly pine has not been as extensively studied as the ASR in tomato. Similar to ASR, the different LP3 paralogs have been shown to be upregulated in response to water deficit stress and to act as transcription factors for genes likely involved in hexose transport. In the current study, we have investigated the evolutionary history of LP3 gene family, with the aim of relating it to that of ASR from a phylogenetic perspective and comparing the differences in selective pressure and codon usage. Phylogenetic trees revealed that LP3 is less divergent across species than ASR even when the trees were solely based on the different sub-sections of the gene. Phylogenetic, GC content, codon usage and selective pressure analyses suggest that LP3-3 is undergoing positive selection

    Constitutions of Value

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    Gathering an interdisciplinary range of cutting-edge scholars, this book addresses legal constitutions of value. Global value production and transnational value practices that rely on exploitation and extraction have left us with toxic commons and a damaged planet. Against this situation, the book examines law’s fundamental role in institutions of value production and valuation. Utilising pathbreaking theoretical approaches, it problematizes mainstream efforts to redeem institutions of value production by recoupling them with progressive values. Aiming beyond radical critique, the book opens up the possibility of imagining and enacting new and different value practices. This wide-ranging and accessible book will appeal to international lawyers, socio-legal scholars, those working at the intersections of law and economy and others, in politics, economics, environmental studies and elsewhere, who are concerned with rethinking our current ideas of what has value, what does not, and whether and how value may be revalued

    SODAPOP: Open-Ended Discovery of Social Biases in Social Commonsense Reasoning Models

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    A common limitation of diagnostic tests for detecting social biases in NLP models is that they may only detect stereotypic associations that are pre-specified by the designer of the test. Since enumerating all possible problematic associations is infeasible, it is likely these tests fail to detect biases that are present in a model but not pre-specified by the designer. To address this limitation, we propose SODAPOP (SOcial bias Discovery from Answers about PeOPle) in social commonsense question-answering. Our pipeline generates modified instances from the Social IQa dataset (Sap et al., 2019) by (1) substituting names associated with different demographic groups, and (2) generating many distractor answers from a masked language model. By using a social commonsense model to score the generated distractors, we are able to uncover the model's stereotypic associations between demographic groups and an open set of words. We also test SODAPOP on debiased models and show the limitations of multiple state-of-the-art debiasing algorithms.Comment: EACL 202

    Characterising Shape Variation in the Human Right Ventricle Using Statistical Shape Analysis: Preliminary Outcomes and Potential for Predicting Hypertension in a Clinical Setting

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    Variations in the shape of the human right ventricle (RV) have previously been shown to be predictive of heart function and long term prognosis in Pulmonary Hypertension (PH), a deadly disease characterised by high blood pressure in the pulmonary arteries. The extent to which ventricular shape is also affected by non-pathological features such as sex, body mass index (BMI) and age is explored in this thesis. If fundamental differences in the shape of a structurally normal RV exist, these might also impact the success of a predictive model. This thesis evaluates the extent to which non-pathological features affect the shape of the RV and determines the best ways, in terms of procedure and analysis, to adapt the model to consistently predict PH. It also identifies areas where the statistical shape analysis procedure is robust, and considers the extent to which specific, non-pathological, characteristics impact the diagnostic potential of the statistical shape model. Finally, recommendations are made on next steps in the development of a classification procedure for PH. The dataset was composed of clinically-obtained, cardiovascular magnetic resonance images (CMR) from two independent sources; The University of Pittsburgh Medical Center and Newcastle University. Shape change is assessed using a 3D statistical shape analysis technique, which topologically maps heart meshes through an harmonic mapping approach to create a unique shape function for each shape. Proper Orthogonal Decomposition (POD) was applied to the complete set of shape functions in order to determine and rank a set of shape features (i.e. modes and corresponding coefficients from the decomposition). MRI scanning protocol produced the most significant difference in shape; a shape mode associated with detail at the RV apex and ventricular length from apex to base strongly correlated with the MRI sequence used to record each subject. Qualitatively, a protocol which skipped slices produced a shorter RV with less detail at the apex. Decomposition of sex, age and BMI also derives unique RV shape descriptors which correspond to anatomically meaningful features. The shape features are shown to be able to predict presence of PH. The predictive model can be improved by including BMI as a factor, but these improvements are mainly concentrated in identification of healthy subjects

    PLACING THE EVOLUTIONARY HISTORY OF \u3ci\u3eDESMOGNATHUS\u3c/i\u3e SALAMANDERS IN CONTEXT: A PHYLOGEOGRAPHIC APPROACH

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    Patterns of genetic variation do not arise in a vacuum but are instead shaped by the interplay between evolutionary forces and ecological constraints. Here, I use a phylogeographic approach to examine the role that ecology played in lineage divergence in the Desmognathus quadramaculatus species complex (Family: Plethodontidae), which consists of three nominal species: D. quadramaculatus, D. marmoratus, and D. folkertsi. Previous phylogenetic studies have shown that individuals from these species do not form clades based on phenotype. My approach to reconciling phylogenetic discordance was two-fold, using (1) genome-wide markers to provide insight into the relationships among lineages and (2) geographic and climate data to provide context for patterns of genetic diversity. First, I obtained genome-wide nuclear markers using double-digest restriction-site associated DNA sequencing (ddRAD) to examine whether two morphologically divergent species, D. marmoratus and D. quadramaculatus, represent independently evolving lineages. Phylogenetic, population structure, and model testing analyses all confirmed that D. marmoratus and D. quadramaculatus do not group based on phenotype. Instead, I found that there were two cryptic genetic lineages (Nantahala and Pisgah) that each contained both phenotypes. Additionally, ecological niche modeling showed that the two genetic lineages primarily occupy geographic areas with significantly different climates, suggesting that climate may have played a role in divergence. Next, I assembled loci from publicly available sequencing data using a draft transcriptome of Desmognathus fuscus as a reference to assess the three nominal species in the quadramaculatus species complex across their entire range. I used phylogenetic and population structure analyses, alongside haplowebs and conspecificity matrices, to determine if the loci supported the hypothesis that the phenotypes represent multiple independently evolving lineages within the broader genetic clades found in the previous chapter. I found that the loci were not informative enough to determine whether the phenotypes had a genetic basis in Pisgah, but did support genetic divergence between phenotypes in Nantahala. Finally, I used ecological niche models (ENMs) and resistance modeling to place the genetic results and phenotypic diversity within the context of time and space. I found that though the quadramaculatus and marmoratus phenotypes were nearly indistinguishable in niche space in the present day, they were projected to occupy different geographic areas in the past and future. The southern portion of the study area had areas of high habitat suitability from the Last Glacial Maximum (~22 kya) to the present, which aligns with the higher genetic divergence between groups in Nantahala. Anthropogenic land use changes reduced habitat availability but likely did not drive genetic divergence in the past, and may be of more consequence to genetic diversity than climate change over the next 50 years. Like many taxa that underwent adaptive radiations, the evolutionary history of Desmognathus has been obfuscated by high rates of within-species phenotypic diversity and shared morphology between distantly related lineages. My findings emphasize the importance of interrogating complex patterns of genetic variation within the context of the dynamic, heterogeneous landscapes in which they arise

    An integrative ecological and evolutionary genomic study of lake Daphnia across time

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    An undisputable fact of the modern age is that human activities are now a major force shaping the biosphere. Some have called for a new geological epoch called the “Anthropocene” or the age of humans— the search is underway for a reliable and unambiguous mark in the geological record for the designation of this new epoch. As a biologist, however, I am reminded daily of the “marks” this age has left on the world around us. The American philosopher and ecologist Aldo Leopold perhaps said it best when he described an “ecological education” as “living alone in a world of wounds.” What follows in this dissertation is maybe best described as searching for wounds, for marks, in biological archives that allow us to better understand the ecosystems of the Anthropocene. My dissertation is focused primarily on studying the widespread crustacean zooplankter, Daphnia pulicaria. A common refrain in the following chapters will be to point out the function of this and related species in lake ecosystems and their value to the humans that enjoy and benefit from lakes. Daphnia in lakes are important for two reasons; first, they are keystone species of the pelagic food webs, connecting primary production from algae to higher trophic levels namely fish. Daphnia thus support the recreational and commercial fisheries of freshwater lakes. A knock-on benefit of Daphnia trophic position is they control the standing crop of algae in freshwater ecosystems and maintain water clarity, so lakes are not choked with noxious algal blooms. My dissertation is separated into three chapters. In the first chapter, I sequence, assemble, and annotate a genome for D. pulicaria using the latest long-read DNA sequencing technology. We use the genomic resources developed for this species to better understand its evolutionary history, especially its split from the closely related “sister” species D. pulex. This reference genome is important for enabling other work, a thread we pick up in the third and final chapter. In my second chapter, I chronicled the 175-years history of D. pulicaria and other Daphnia species in a small lake that will be the primary focus of the last two chapters. Tanners Lake is an ecosystem replete with wounds from the numerous human activities that dominate the landscape surrounding it. Due to their landscape position, lakes integrate vast amounts of information about their watersheds in their sediments. Tanners Lake records in its sediments the history of a landscape dominated by humans with the development of a major city surrounding it. Located just outside of Saint Paul, MN, Tanners Lake is impacted by two major human impacts inflicted on Northern Temperate Lakes. It is not only eutrophic, from the export of unprecedented amounts of nutrients but also it is severely salinized. Freshwater salinization is a consequence of the widespread use of de-icing salts on impervious surfaces such as roads and parking lots- a ubiquitous feature of human-dominated landscapes. I collected sediment cores from Tanners Lake to reconstruct the ecological dynamics of the Daphnia community across time in this lake by examining the abundance and diversity of resting eggs (encased in durable sclerotized structures called ephippia) across time in the core. I found that only modest changes in diversity and abundance occurred in the lake during salinization. This result suggests that Daphnia may be resilient to the threat of salinization- perhaps maintaining the ecosystems they support despite salinization. The results of my second chapter set up an important question to tackle in my third chapter. Since D. pulicaria remains in Tanners Lake despite salinization, is this population evolving higher tolerance to these conditions? We tackle this question using an approach that is somewhat unique to Daphnia, by hatching the eggs contained in the ephippia from across time. This method known as Resurrection Ecology, allows us to sample individuals from across time and study their phenotypes and genotypes. I hatched Daphnia from across approximately 25 years (~1994-2019) and resequenced their genomes. In addition, we also evaluated these D. pulicaria clones for their tolerance to salinity using phenotypic (i.e., survivorship) assays. I compiled this data set together to understand the evolution of this population through time. The genomic data supports the idea that salinity is a driving force for evolution in this population. In particular, genes related to osmoregulation and salinity tolerance are enriched within the statistical outliers. The phenotypic data supported this finding, as we observed that the salinity tolerance of modern Daphnia was higher than that of the ancestors hatched from the sediment. Interestingly, while I initially described this work as a search for ecological and or evolutionary wounds, I was surprised to find that while they exist in very real ways in the biological archives studied, they are not mortal. My research, taken together, suggests that Daphnia populations should have the potential to respond to human threats and evolve to maintain the ecosystems they support. However, this resiliency will be highly dependent on the speed and intensity of the threats that these systems will face, as well as the strength of the evolutionary forces (i.e., selection, drift, migration, mutation) that will shape the underlying genetic structure of these populations

    Microbial symbiosis and host disease resistance in marine macroalgae

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    Marine macroalgae (seaweeds) are ecologically and economically important organisms. However, with increasing environmental stress, disease in seaweeds is likely to become more frequent and/or severe, leading to a reduction of both wild and farmed populations. Eukaryotic hosts (e.g., from humans, terrestrial plants to seaweeds) are associated with microbial communities (microbiota) that play critical roles in host health and fitness. However, to what extent microbiota can be harnessed for seaweed disease management and the influence of host immunity on the native microbiota remains underexplored. Here I identified over 30 bacterial isolates that can antagonise opportunistic pathogens responsible for a bleaching disease observed in the red seaweed Delisea pulchra. Subsequent in vivo testing found inoculation with either a Pseudoalteromonas sp. strain PB2-1 or Phaeobacter sp. strain BS52 (later BS52) significantly reduced bleaching occurrence in D. pulchra, even in the presence of a known pathogen. Analysis of the D. pulchra associated bacterial community post-infection suggested that disease protection afforded by BS52 was likely due to its mitigation of dysbiosis rather than direct inhibition of the pathogen. Using comparative genomic analysis of BS52 with closely related commensal strains I identified putative functions such as prophage induction and antibiotic production that may contribute to the protective ability of BS52. Interestingly I found that inoculation with the disease protective bacteria from D. pulchra reduced the risk of tip bleaching disease in the geographically and phylogenetically distinct seaweed Agarophyton vermiculophyllum, suggesting these bacteria could act as general probiotics for seaweeds. Moreover, through the application of different bacterial community assessment tools (amplicon-sequencing, epifluorescence microscopy, and qPCR) I found that elicitation of seaweed immunity reduced epibacterial loads while causing minor changes in the community composition and structure, suggesting the seaweed immunity may also function to control the microbiota. Overall, my thesis demonstrated the feasibility of manipulating microbiota to reduce disease in seaweeds and advanced our understanding of the roles played by both symbiotic bacteria and the host immunity in maintaining holobiont homeostasis. It is hoped that these findings will benefit disease management in seaweeds with future applications for conservation and aquaculture
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