VictorJuiz/thesis huggingface dataset:
A Multi-Robot Coordination Methodology for Wilderness Search and Rescue

One of the applications where the use of robots can be beneficial is Wilderness Search and Rescue (WiSAR), which involves the search for a possibly mobile but non-trackable lost person (i.e., the target) in wilderness environments. A mobile target implies that the search area grows continuously and potentially without bound. This fact, combined with the presence of typically rugged, varying terrain and the possibility of inclement weather, poses a considerable challenge to human Search and Rescue (SAR) personnel with respect to the time and effort required to perform the search and the danger entailed to the searchers. Mobile robots can be advantageous in WiSAR due to their ability to provide consistent performance without getting tired and their lower susceptibility to harsh weather conditions compared to humans. Thus, a coordinated team of robots that can assist human SAR personnel by autonomously performing searches in WiSAR scenarios would be of great value. However, to date, a suitable multi-robot coordination methodology for autonomous search that can satisfactorily address the issues relevant to WiSAR is lacking. The objective of this Dissertation is, thus, to develop a methodology that can autonomously coordinate the search strategy of a multi-robot team in wilderness environments to locate a moving target that is neither continuously nor intermittently observed during the search process. Three issues in particular are addressed: (i) target-location prediction, (ii) robot deployment, and (iii) robot-path planning. The corresponding solution approaches devised to address these issues incorporate the influence of varying terrain that may contain a priori known and unknown obstacles, and deal with unique target physiology and psychology as well as found clues left behind by the target. The solution methods for these three tasks work seamlessly together resulting in a tractable MRC methodology for autonomous robotic WiSAR. Comprehensive simulations have been performed that validate the overall proposed methodology. Moreover, the tangible benefits provided by this methodology were further revealed through its comparison with an alternative search method.

Keywords: Multi-Robot Coordination
Search and Rescue
Advisor: Benhabib, Beno
Nejat, Goldie
The Social Citizenship Tradition in Anglo-American Thought

The right to belong and participate in some form of political community is the most fundamental social right there is. This dissertation argues that social rights have not been understood broadly enough, that there has not been enough attention paid to their historical roots, and that they must not be viewed as being simply passive welfare rights. Rather, they must be seen in their historical context, and they must be seen for what they are: a much larger and more substantive phenomenon than what liberal theory has projected: both theoretically and empirically. I am calling this body of discourse “the social citizenship tradition.” This dissertation hopes to show that there was more than one definition of social citizenship historically and that social rights are certainly not “new.” In surveying a vast literature in Britain, the United States, and Canada, it points to places where alternative social rights claims have entered politics and society. By looking at writings from these three countries over three centuries, the evidence points to some similarities as well as differences in how scholars approached questions of economic and social rights. In particular, similar arguments over labour and property figured prominently in all three countries. The contextual ground of right was different in each country but the voice of social action was similar. The objective here is to reunite this common tradition of social citizenship with its past. It is because of classical liberalism that social right has lost focus and power, and a whole tradition of political thinking has been lost.This tradition has been narrowed to the point that it might be unrecognizable to the more radical forces, those who also fought for it, in the American, Canadian and British pasts.

Keywords: social citizenship
social rights
labour and property
Anglo-American democracies
Advisor: Wolfe, David A.
Identification of PPP1CC2 Interacting Proteins in the Mouse Testis

Protein phosphorylation is a central regulatory mechanism in countless cellular processes. Deletion of the PP1 serine/threonine phosphatase gene Ppp1cc in mice results in male infertility due to a severe impairment in spermatogenesis. This disruption in spermatogenesis is hypothesized to arise due to a deficiency of the testis specific Ppp1cc isoform PPP1CC2. To learn more about the function of PPP1CC2 in spermatogenesis, we have employed several proteomic approaches aimed at identifying both regulatory proteins and substrates that interact with PPP1CC2 in the testis. First, we created transgenic mouse embryonic stem cell lines expressing a tandem affinity tagged version of PPP1CC2. Tandem affinity purification using these cell lines identified a number of known PP1 interacting proteins, and one novel interactor DDOST (dolichyl-di-phosphooligosaccharide-protein glycotransferase) which we hypothesize to have a role in spermatogenesis. In a second approach, we conducted GST pull down assays from mouse testis lysates to identify PPP1CC2 interacting proteins. TSSK1 (testis-specific serine kinase 1) was identified as a novel PPP1CC2 interacting protein. We then demonstrated that TSSK1 interacts with PPP1CC2 in an indirect manner via a common interacting protein TSKS (testis-specific serine kinase substrate). Binding of TSKS to PPP1CC2 is regulated via phosphorylation of a PP1 docking motif on the TSKS surface, and localization of TSSK1 and TSKS in the testis is disrupted in Ppp1cc mutants. Finally, to identify candidate substrates of PPP1CC2 in the testis, we conducted a comparative phosphoproteomic analysis and identified 33 different peptides that were hyperphosphorylated in the testis of 3 week old Ppp1cc knockout mice. Amongst these candidate substrates are several proteins essential for mouse spermatogenesis—HMGA1 (high mobility group AT-hook 1), HSPA4 (heat shock protein 4), YBX2 (Y box protein 2) and SYCP2 (synaptonemal complex protein 2). Taken together, our results suggest that PPP1CC2 interacts with a number of different proteins in the testis, and is likely to play a role at several different stages of spermatogenesis, in both meiotic and post-meiotic spermatogenic cells.

Keywords: Phosphatase
Spermatogenesis
Advisor: Varmuza, Susannah
The Suitability of Hybrid Waveforms for Advanced Gravitational Wave Detectors

The existence of Gravitational Waves from binary black holes is one of the most interesting predictions of General Relativity. These ripples in space-time should be visible to ground-based gravitational wave detectors worldwide in the next few years. One such detector, the Laser Interferometer Gravitational-wave Observatory (LIGO) is in the process of being upgraded to its Advanced sensitivity which should make gravitational wave detections routine. Even so, the signals that LIGO will detect will be faint compared to the detector noise, and so accurate waveform templates are crucial. In this thesis, we present a detailed analysis of the accuracy of hybrid gravitational waveforms. Hybrids are created by stitching a long post-Newtonian inspiral to the late inspiral, merger, and ringdown produced by numerical relativity simulations. We begin our investigation with a study of the systematic errors in the numerical waveform, and errors due to hybridization and choice of detector noise. For current NR waveforms, the largest source of error comes from the unknown high-order terms in the post-Newtonian waveform, which we first explore for equal-mass, non-spinning binaries, and also for unequal-mass, non-spinning binaries. We then consider the potential reduction in hybrid errors if these higher-order terms were known. Finally, we investigate the possibility of using hybrid waveforms as a detection template bank and integrating NR+PN hybrids into the LIGO detection pipeline.

Keywords: gravitational waves
black holes
Advance LIGO
hybrid waveform
post-newtonian
numerical relativity
Advisor: Pfeiffer, Harald
Centrosome and Mitotic Spindle Organization in Human Cells

Robust bipolar spindle formation and faithful transmission of genetic material are vital to the maintenance of genome integrity and cellular homeostasis. Chromosome segregation errors can result in aneuploidy, a hallmark of human solid tumors. The assembly of a microtubule-based mitotic spindle relies on the concerted action of centrosomes, spindle microtubules, molecular motors and nonmotor spindle proteins. Before mitosis, centrosomes need to duplicate and increase in size in order to gain sufficient microtubule nucleation activity during bipolar spindle formation. This process is called centrosome maturation and coincides with a dramatic change of centrosome structure. However, the architecture of centrosomes and the organization of centrosome components in both interphase and mitosis have long remained elusive. In this thesis, I describe the identification and characterization of novel regulators that are essential for centrosome and mitotic spindle organization in human cells. One such regulator is human Augmin, an evolutionarily conserved eight-subunit protein complex that has essential functions for centrosome and spindle integrity. I present evidence that human Augmin promotes microtubule-dependent nucleation of microtubules by targeting microtubule-nucleating complexes to the mitotic spindle. This function of Augmin is important for generation and/or stabilization of kinetochore microtubules within the mitotic spindle, and its loss results in destabilization of kinetochore microtubules and spindle assembly errors. These errors culminate in cells displaying multipolar spindles with fragmented centrosomes and mitotic arrest. A second regulator of centrosome and spindle organization described in this thesis is CEP192. I show that CEP192 is critical for recruitment of microtubule-nucleating complexes to centrosomes and, consequently, for centrosome maturation, mitotic spindle formation, and centriole duplication. Finally, I describe novel organizational features of the centrosome using a subdiffraction microscopy approach. Because of a lack of higher-order structural information, centrosomes have traditionally been described as amorphous clouds. My results now reveal that centrosome components instead occupy separable spatial domains throughout the cell cycle and highlight the role of higher-order protein organization in the regulation of centrosome assembly and function. Collectively, this work has significantly expanded our current knowledge of centrosome architecture and biogenesis and of the mechanisms that underlie robust bipolar spindle assembly.

Keywords: Mitosis
Centrosome
Mitotic Spindle
Advisor: Pelletier, Laurence
Activation of Estrogen Receptor Alpha, Aryl Hydrocarbon Receptor, and Nuclear Factor Erythroid-2 Like 2 in Human Breast Cancer Cells

There is a strong association between estrogen exposure and breast cancer risk. Estrogen can activate estrogen receptor alpha (ERalpha) to increase cell proliferation. Estrogen can also be metabolized into genotoxic compounds to induce DNA damage and mutations. Activation of the aryl hydrocarbon receptor (AHR) and nuclear factor erythroid-2 like 2 (NFE2L2; NRF2) can alter the production of genotoxic estrogen. The present thesis investigated the signalling mechanisms of ERalpha, AHR, and NRF2 and how their interaction might modulate breast cancer risk. In Chapter 2, genome-wide, but promoter-focused analysis of ERalpha binding sites in T-47D breast cancer cells identified potential cell line specific differences in estrogen signalling between T-47D and the commonly used MCF-7 breast cancer cells. CYP2B6 was identified to be an ERalpha target gene in T-47D cells but not MCF-7 cells, supporting cell line dependent effect in estrogen signalling. In Chapter 3 and 4, genome-wide analyses of AHR binding sites were performed to investigate the molecular criteria governing genomic AHR transactivation in vivo in mouse and in vitro in MCF-7 breast cancer cells. Our analysis identified 1) the previously established aryl hydrocarbon response element to be an important, but not an absolute requirement in AHR transactivation and 2) key epigenetic modifications that modulate AHR-dependent gene regulation. Lastly, in Chapter 5, interaction among ERalpha, AHR, and NRF2 was presented at the regulatory region of two NRF2 target genes, NADPH Quinone Oxidoreductase 1 (NQO1) and Heme Oxygenase 1 (HMOX1). ERalpha repressed, whereas AHR enhanced NRF2-dependent NQO1 and HMOX1 mRNA expression through altered p300 recruitment and Histone H3 Lysine 9 acetylation. Collectively, this thesis examined novel molecular mechanisms that might alter breast cancer development/progression by modulating ER, AHR, and NRF2 activity.

Keywords: Estrogen Receptor
Aryl Hydrocarbon Receptor
Nuclear Factor Erythroid-2 Like 2
Advisor: Matthews, Jason
Wells, Peter G.
Investigating the Influence of Mechanical anisotropy on the Fracturing Behaviour of Brittle Clay Shales with Application to Deep Geological Repositories

Clay shales are currently being assessed as possible host rock formations for the deep geological disposal of radioactive waste. However, one main concern is that the favourable long-term isolation properties of the intact rock mass could be negatively affected by the formation of an excavation damaged zone (EDZ) around the underground openings. This thesis investigated the deformation and failure process of a clay shale, namely Opalinus Clay, with particular focus on the inﬂuence of anisotropy on the short-term response of circular tunnels. To achieve this goal, a hybrid continuum-discontinuum numerical approach was used in combination with new ﬁeld measurements from the Mont Terri underground research laboratory. The response of Opalinus Clay during the excavation of a full-scale emplacement (FE) test tunnel was characterized by geodetic monitoring of wall displacements, radial extensometers and longitudinal inclinometers. The deformation measurements indicated strong directionality induced by the combined effect of in situ stress ﬁeld and presence of bedding planes striking parallel to the tunnel axis, with the most severe deformation occurring in the direction approximately perpendicular to the material layering. Computer simulations were conducted using a newly-extended combined ﬁnite-discrete element method (FEM/DEM), a numerical technique which allows the explicit simulation of brittle fracturing and associated seismicity. The numerical experimentation ﬁrstly focused on the laboratory-scale analysis of failure processes (e.g., acoustic activity) in brittle rocks, and on the role of strength and modulus anisotropy in the failure behaviour of Opalinus Clay in tension and compression. The fracturing behaviour of unsupported circular excavations in laminated rock masses was then analyzed under different in situ stress conditions. Lastly, the modelling methodology was applied to the aforementioned FE tunnel to obtain original insights into the possible EDZ formation process around emplacement tunnels for nuclear waste. The calibrated numerical model suggested delamination along bedding planes and subsequent extensional fracturing as key mechanisms of the damage process potentially leading to buckling and spalling phenomena. Overall, the research ﬁndings may have a potential impact on the constructability and support design of an underground repository as well as implications for its long-term safety assessment procedure.

Keywords: excavation damaged zone (EDZ)
numerical modelling
rock fracture
clay shales
Opalinus Clay
FEM/DEM
deep geological repositories
mechanical anisotropy
brittle failure
tunnelling
Advisor: Grasselli, Giovanni
Nanostructured Electrochemical Biosensors: Towards Point of Care Diagnostics

An important research area in medicine is molecular diagnostics of cancers and infectious diseases, which can be diagnosed, managed and treated more effectively with genetic information. We have developed an integrated sample to answer bacterial detection platform combining a simple, universal bacterial lysis approach and sensitive nanomaterial electrochemical biosensors. Lysis is rapid and effective at releasing intercellular nucleic acid targets. The platform was directly challenged with unpurified lysates and successful at determining the presence of clinically relevant concentrations within 30min from sample to answer. Another important aspect of biosensor development is the development of cheap and efficient methods for manufacturing nanostructured microelectrodes. Previously, we have used costly silicon wafers for fabrication. Here we explored alternate inexpensive materials for fabrication including printed circuit boards, plastics and glass. We show that plain borosilicate glass is effective for templated bottom-up fabrication, with comparable performance to expensive silicon based nanostructured microelectrodes. Current state-of-the-art readout of many biomarkers is hampered by serially addressing arrays of low cost biosensors, without the use of high cost active electronics. Here we have developed a new concept, solution-based electrochemical circuits, which makes highly multiplexed sensing feasible on the surface of low-cost, glass chips. This method utilizes the idea that physical separation of liquid on an insulator can result in electrochemical isolation. Using this we can reduce the number of outputs to 2&radic;n, where n would be the number of serially connected sensors. We use urinary tract infections as a model system and prove that we can accurately detect species and antimicrobial resistance in multiplexed formats at clinically relevant concentrations.

Keywords: Nanotechnology
Biosensor
Diagnostics
Sensor
Electrochemical
Electrochemistry
Advisor: Kelley, Shana O.
Lanthanide Luminescent Metal-Organic Frameworks with Linear Dicarboxylate Ligands: Synthesis, Structure and Sensing

The object of this thesis is to explore functionalized linear dicarboxylate ligands for constructing luminescent metal-organic framework (MOF) sensors. The first series of ligands developed is based on functionalized (E)-4,4'-(ethene-1,2-diyl)dibenzoic acids. Luminescent MOFs have been synthesized from these ligands and their porosity, thermal stability, luminescent properties have been discussed. The second series of ligands is based on functionalized [1,1':4',1''-terphenyl]-4,4''-dicarboxylic acid. Ligands bearing methyl, methoxyl, thioether, aldehyde, ketone, quaternary ammonium side chains have been synthesized and constructed into luminescent MOFs. Their structures, thermal stability, luminescent properties, solvent-dependent luminescence and the underlying mechanisms have been discussed. Vapor sensing experiments have been conducted with MOFs bearing ether and thioether side chains and strong luminescence turn-on is triggered by certain solvents. The MOF with ether side chains has been further tested as sensor slides to evaluate its response rate and recyclability.

Keywords: MOF
sensor
luminescence
Advisor: Song, Datong
Boron-Diol Interactions as the Basis for Novel Catalytic Transformations

The central theme of the research described in this thesis involves taking advantage of the reversible covalent interactions of organoboron species with diols, and exploiting them as catalyst-substrate interactions. Using this philosophy, novel catalytic transformations have been developed to form carbon-carbon and carbon-oxygen bonds. Chapter 1 describes a method that uses organoboron species to activate pyruvic acids in the direct aldol reaction with aldehydes. Formation of an anionic tetracoordinate boron adduct was the key step in the proposed mechanism. A wide range of aldehydes may be employed, delivering useful isotetronic acid products in high yields. The efficient synthesis of oligosaccharides requires methods for regioselective manipulation of hydroxyl groups in monosaccharides. Catalysis represents a potentially general solution to this problem, and recently, the development of catalyst-controlled methods towards this goal has intensified. Chapter 2 highlights the range of catalysts that may be exploited to alter the reactivity of hydroxyl groups in carbohydrates. Chapter 3 describes a novel diphenylborinic acid-catalyzed protocol, which enables the site-selective functionalization of carbohydrate derivatives and non-carbohydrate-derived 1,2- and 1,3-diols with a wide diversity of electrophiles. Mechanistic details of the organoboron-catalyzed processes are explored using competition experiments, kinetics and catalyst structure-activity relationships. These studies are consistent with reaction of a tetracoordinate borinate complex with the electrophilic species in the turnover-limiting step of the catalytic cycle. Chapter 4 further explores the utility of borinic acid activation in the first small-molecule-catalyzed glycosylation reaction of unprotected or minimally protected glycosyl acceptors. High levels of selectivity for the equatorial hydroxyl group of cis-1,2-diol motifs are demonstrated in reactions of several glycosyl acceptors using a variety of glycosyl halide donors. Chapter 5 describes a novel mode of catalysis using a boronic acid/Lewis base co-catalyst system. The proposed mode of activation involves the formation of a tetracoordinate adduct that displays enhanced nucleophilicity at the boron-bound alkoxide groups. This concept was applied to the regioselective silylation of carbohydrate derivatives as well as the desymmetrization of diols. Finally, Chapter 6 summarizes the work described in this thesis, discusses the challenges encountered in the development of the methodologies, and speculates on future directions that can be taken.

Keywords: Organic synthesis
Carbohydrate chemistry
Advisor: Taylor, Mark S.
Bimba's Rhythm is One, Two, Three: From Resistance to Transformation Through Brazilian Capoeira

Capoeira is a Brazilian fighting art with roots in slavery that blends live music, dance, play and ritual. It is also an embodied form of knowledge that is holistic and sometimes profoundly transformative - a way of seeing and being that embraces an Afro-Brazilian vision of the world. Using personal lived experience and collected oral testimony related in a story-telling form, the study explores the knowledge embedded within capoeira through the lives of practitioners and through practitioners' explanations of their teachings. The question of whether capoeira has a common essence, or more specifically, whether the capoeira of twentieth century Bahia from which all modern schools ultimately trace their origins has an essence, is explored. In the thesis, capoeira is discovered to be an expression of resistance and transformation. Capoeira, the author discovers, is a form of resistance in that its traditional teachings reflect a communal, non-materialistic and sensuous stance, in opposition to the dominant individualistic, capitalistic, techno-scientific approach that has dominated the industrialized West. Capoeira is also a source of transformation in that it allows individuals to develop to their fullest expression - a self that encompasses the physical, spiritual, emotional and intellectual dimensions - and helps people integrate within a web of relations, human, animal, or other. Using a Transformative Learning approach informed by an Indigenous framework, this dissertation attempts to bring the reader on a journey of the mind, body and spirit. In three books, each one describing a separate fieldwork trip to Brazil, the author weaves a tale that is both personal and profound in its planetary implications.

Keywords: Education
Capoeira
Embodied Learning
Transformative Learning
Indigenous Knowledge
Holistic Education
Brazil
Afro-Brazilian
Resistance
storytelling
Advisor: Restoule, Jean-Paul