Using Terrestrial LiDAR to Monitor Erosion within the Gold Basin Landslide Complex, Verlot, WA

In 2014 the United States Forest Service closed the Gold Basin Campground of western Washington in an effort to protect the public from unstable hillslopes directly adjacent to the campground. The Gold Basin Landslide Complex (GBLC) is actively eroding via block fall, dry ravel, and debris flows, which contribute sediment into the South Fork of the Stillaguamish River. This sediment diminishes the salmonid population within the South Fork of the Stillaguamish River by reducing habitable spawning grounds, which is a big concern to the Stillaguamish Tribe of Indians. In this investigation, I quantified patterns of degradation and total volume of sediment erosion from the middle lobe of the GBLC over the period of July 2015 through January 2016 using terrestrial (ground-based) LiDAR (TLS). I characterized site specific stratigraphy and geomorphic processes, and laid the groundwork for future, long-term monitoring of this site. Results of this investigation determined that ~ 4,800m3 of sediment was eroded from the middle lobe of the GBLC during the 6 month study period (July 2015 – January 2016). This erosion likely occurred from debris flows, raveling of poorly sorted sand and gravel deposits and block failures of high plasticity silts and clays, and/or other mass wasting mechanisms. The generalized stratigraphic sequence in the GBLC consists of alternating massive beds of sand and gravel with silts and clays. The low permeability of these silts and clays provide a perfect venue for groundwater to percolate, as I observed during field investigations, which likely contributes to the active instability of the hillslopes. Continued monitoring and mapping of this complex will lead to viable information that could help both the United States Forest Service and the Stillaguamish Tribe.

Constraining storm-scale forecasts of deep convective initiation with surface weather observations

Thesis (Ph.D.)--University of Washington, 2016-06

Presynaptic Anchoring of PKA by AKAP7 is Required for Pattern Separation by Dentate Gyrus

Thesis (Ph.D.)--University of Washington, 2016-06

Specific modulation of airway epithelial tight junctions by apical application of an occludin peptide

Tight junctions are directly involved in regulating the passage of ions and macromolecules (gate functions) in epithelial and endothelial cells. The modulation of these gate functions to transiently regulate the paracellular permeability of large solutes and ions could increase the delivery of pharmacological agents or gene transfer vectors. To reduce the inflammatory responses caused by tight junction-regulating agents, alternative strategies directly targeting specific tight junction proteins could prove to be less toxic to airway epithelia. The apical delivery of peptides corresponding to the first extracellular loop of occludin to transiently modulate apical paracellular flux has been demonstrated in intestinal epithelia. We hypothesized that apical application of these occludin peptides could similarly modulate tight junction permeability in airway epithelia. Thus, we investigated the effects of apically applied occludin peptide on the paracellular permeability of molecular tracers and viral vectors in well differentiated human airway epithelial cells. The effects of occludin peptide on cellular toxicity, tight junction protein expression and localization, and membrane integrity were also assessed. Our data showed that apically applied occludin peptide significantly reduced transepithelial resistance in airway epithelia and altered tight junction permeability in a concentration-dependent manner. These alterations enhanced the paracellular flux of dextrans as well as gene transfer vectors. The occludin peptide redistributed occludin but did not alter the expression or distribution of ZO-1, claudin-1, or claudin-4. These data suggest that specific targeting of occludin could be a better-suited alternative strategy for tight junction modulation in airway epithelial cells compared with current agents that modulate tight junctions.

Experiments in outdoor operation of RatSLAM

This paper shows initial results in deploying the biologically inspired Simultaneous Localisation and Mapping system, RatSLAM, in an outdoor environment. RatSLAM has been widely tested in indoor environments on the task of producing topologically coherent maps based on a fusion of odometric and visual information. This paper details the changes required to deploy RatSLAM on a small tractor equipped with odometry and an omnidirectional camera. The principal changes relate to the vision system, with others required for RatSLAM to use omnidirectional visual data. The initial results from mapping around a 500 m loop are promising, with many improvements still to be made.

Designing a Computer Vision System for Underwater Robotic Interventions

This thesis deals with the challenging problem of designing systems able to perceive objects in underwater environments. In the last few decades research activities in robotics have advanced the state of art regarding intervention capabilities of autonomous systems. State of art in fields such as localization and navigation, real time perception and cognition, safe action and manipulation capabilities, applied to ground environments (both indoor and outdoor) has now reached such a readiness level that it allows high level autonomous operations. On the opposite side, the underwater environment remains a very difficult one for autonomous robots. Water influences the mechanical and electrical design of systems, interferes with sensors by limiting their capabilities, heavily impacts on data transmissions, and generally requires systems with low power consumption in order to enable reasonable mission duration. Interest in underwater applications is driven by needs of exploring and intervening in environments in which human capabilities are very limited. Nowadays, most underwater field operations are carried out by manned or remotely operated vehicles, deployed for explorations and limited intervention missions. Manned vehicles, directly on-board controlled, expose human operators to risks related to the stay in field of the mission, within a hostile environment. Remotely Operated Vehicles (ROV) currently represent the most advanced technology for underwater intervention services available on the market. These vehicles can be remotely operated for long time but they need support from an oceanographic vessel with multiple teams of highly specialized pilots. Vehicles equipped with multiple state-of-art sensors and capable to autonomously plan missions have been deployed in the last ten years and exploited as observers for underwater fauna, seabed, ship wrecks, and so on. On the other hand, underwater operations like object recovery and equipment maintenance are still challenging tasks to be conducted without human supervision since they require object perception and localization with much higher accuracy and robustness, to a degree seldom available in Autonomous Underwater Vehicles (AUV). This thesis reports the study, from design to deployment and evaluation, of a general purpose and configurable platform dedicated to stereo-vision perception in underwater environments. Several aspects related to the peculiar environment characteristics have been taken into account during all stages of system design and evaluation: depth of operation and light conditions, together with water turbidity and external weather, heavily impact on perception capabilities. The vision platform proposed in this work is a modular system comprising off-the-shelf components for both the imaging sensors and the computational unit, linked by a high performance ethernet network bus. The adopted design philosophy aims at achieving high flexibility in terms of feasible perception applications, that should not be as limited as in case of a special-purpose and dedicated hardware. Flexibility is required by the variability of underwater environments, with water conditions ranging from clear to turbid, light backscattering varying with daylight and depth, strong color distortion, and other environmental factors. Furthermore, the proposed modular design ensures an easier maintenance and update of the system over time. Performance of the proposed system, in terms of perception capabilities, has been evaluated in several underwater contexts taking advantage of the opportunity offered by the MARIS national project. Design issues like energy power consumption, heat dissipation and network capabilities have been evaluated in different scenarios. Finally, real-world experiments, conducted in multiple and variable underwater contexts, including open sea waters, have led to the collection of several datasets that have been publicly released to the scientific community. The vision system has been integrated in a state of the art AUV equipped with a robotic arm and gripper, and has been exploited in the robot control loop to successfully perform underwater grasping operations.

Envisioning innovation : the communication of technological change through graphic representation

Graphic depiction is an established method for academics to present concepts about theories of innovation. These expressions have been adopted by policy-makers, the media and businesses. However, there has been little research on the extent of their usage or effectiveness ex-academia. In addition, innovation theorists have ignored this area of study, despite the communication of information about innovation being acknowledged as a major determinant of success for corporate enterprise. The thesis explores some major themes in the theories of innovation and compares how graphics are used to represent them. The thesis examines the contribution of visual sociology and graphic theory to an investigation of a sample of graphics. The methodological focus is a modified content analysis. The following expressions are explored: check lists, matrices, maps and mapping in the management of innovation; models, flow charts, organisational charts and networks in the innovation process; and curves and cycles in the representation of performance and progress. The main conclusion is that academia is leading the way in usage as well as novelty. The graphic message is switching from prescription to description. The computerisation of graphics has created a major role for the information designer. It is recommended that use of the graphic representation of innovation should be increased in all domains, though it is conceded that its content and execution need to improve, too. Education of graphic 'producers', 'intermediaries' and 'consumers' will play a part in this, as will greater exploration of diversity, novelty and convention. Work has begun to tackle this and suggestions for future research are made.

The scaffold protein KSR1, a novel therapeutic target for the treatment of Merlin-deficient tumors

Merlin has broad tumor-suppressor functions as its mutations have been identified in multiple benign tumors and malignant cancers. In all schwannomas, the majority of meningiomas and 1/3 of ependymomas Merlin loss is causative. In neurofibromatosis type 2, a dominantly inherited tumor disease because of the loss of Merlin, patients suffer from multiple nervous system tumors and die on average around age 40. Chemotherapy is not effective and tumor localization and multiplicity make surgery and radiosurgery challenging and morbidity is often considerable. Thus, a new therapeutic approach is needed for these tumors. Using a primary human in vitro model for Merlin-deficient tumors, we report that the Ras/Raf/mitogen-activated protein, extracellular signal-regulated kinase kinase (MEK)/extracellular signal-regulated kinase (ERK) scaffold, kinase suppressor of Ras 1 (KSR1), has a vital role in promoting schwannomas development. We show that KSR1 overexpression is involved in many pathological phenotypes caused by Merlin loss, namely multipolar morphology, enhanced cell-matrix adhesion, focal adhesion and, most importantly, increased proliferation and survival. Our data demonstrate that KSR1 has a wider role than MEK1/2 in the development of schwannomas because adhesion is more dependent on KSR1 than MEK1/2. Immunoprecipitation analysis reveals that KSR1 is a novel binding partner of Merlin, which suppresses KSR1's function by inhibiting the binding between KSR1 and c-Raf. Our proteomic analysis also demonstrates that KSR1 interacts with several Merlin downstream effectors, including E3 ubiquitin ligase CRL4DCAF1. Further functional studies suggests that KSR1 and DCAF1 may co-operate to regulate schwannomas formation. Taken together, these findings suggest that KSR1 serves as a potential therapeutic target for Merlin-deficient tumors.

Matrix-free mass spectrometric imaging using laser desorption ionisation Fourier transform ion cyclotron resonance mass spectrometry

Mass spectrometry imaging (MSI) is a powerful tool in metabolomics and proteomics for the spatial localization and identification of pharmaceuticals, metabolites, lipids, peptides and proteins in biological tissues. However, sample preparation remains a crucial variable in obtaining the most accurate distributions. Common washing steps used to remove salts, and solvent-based matrix application, allow analyte spreading to occur. Solvent-free matrix applications can reduce this risk, but increase the possibility of ionisation bias due to matrix adhesion to tissue sections. We report here the use of matrix-free MSI using laser desorption ionisation performed on a 12 T Fourier transform ion cyclotron resonance (FTICR) mass spectrometer. We used unprocessed tissue with no post-processing following thaw-mounting on matrix-assisted laser desorption ionisation (MALDI) indium-tin oxide (ITO) target plates. The identification and distribution of a range of phospholipids in mouse brain and kidney sections are presented and compared with previously published MALDI time-of-flight (TOF) MSI distributions.

AP-2 complex-mediated endocytosis of Drosophila Crumbs regulates polarity via antagonizing Stardust

Maintenance of epithelial polarity depends on the correct localization and levels of polarity determinants. The evolutionarily conserved transmembrane protein Crumbs is crucial for the size and identity of the apical membrane, yet little is known about the molecular mechanisms controlling the amount of Crumbs at the surface. Here, we show that Crumbs levels on the apical membrane depend on a well-balanced state of endocytosis and stabilization. The adaptor protein 2 (AP-2) complex binds to a motif in the cytoplasmic tail of Crumbs that overlaps with the binding site of Stardust, a protein known to stabilize Crumbs on the surface. Preventing endocytosis by mutations in AP-2 causes expansion of the Crumbs-positive plasma membrane and polarity defects, which can be partially rescued by removing one copy of crumbs. Strikingly, knocking-down both AP-2 and Stardust retains Crumbs on the membrane. This study provides evidence for a molecular mechanism, based on stabilization and endocytosis, to adjust surface levels of Crumbs, which are essential for maintaining epithelial polarity.

Probabilistic topographic information visualisation

The focus of this thesis is the extension of topographic visualisation mappings to allow for the incorporation of uncertainty. Few visualisation algorithms in the literature are capable of mapping uncertain data with fewer able to represent observation uncertainties in visualisations. As such, modifications are made to NeuroScale, Locally Linear Embedding, Isomap and Laplacian Eigenmaps to incorporate uncertainty in the observation and visualisation spaces. The proposed mappings are then called Normally-distributed NeuroScale (N-NS), T-distributed NeuroScale (T-NS), Probabilistic LLE (PLLE), Probabilistic Isomap (PIso) and Probabilistic Weighted Neighbourhood Mapping (PWNM). These algorithms generate a probabilistic visualisation space with each latent visualised point transformed to a multivariate Gaussian or T-distribution, using a feed-forward RBF network. Two types of uncertainty are then characterised dependent on the data and mapping procedure. Data dependent uncertainty is the inherent observation uncertainty. Whereas, mapping uncertainty is defined by the Fisher Information of a visualised distribution. This indicates how well the data has been interpolated, offering a level of ‘surprise’ for each observation. These new probabilistic mappings are tested on three datasets of vectorial observations and three datasets of real world time series observations for anomaly detection. In order to visualise the time series data, a method for analysing observed signals and noise distributions, Residual Modelling, is introduced. The performance of the new algorithms on the tested datasets is compared qualitatively with the latent space generated by the Gaussian Process Latent Variable Model (GPLVM). A quantitative comparison using existing evaluation measures from the literature allows performance of each mapping function to be compared. Finally, the mapping uncertainty measure is combined with NeuroScale to build a deep learning classifier, the Cascading RBF. This new structure is tested on the MNist dataset achieving world record performance whilst avoiding the flaws seen in other Deep Learning Machines.

Structural determinants of oligomerization of the aquaporin-4 channel

The aquaporins (AQP) family of integral membrane protein channels mediate cellular water and solute flow. Although qualitative and quantitative differences in channel permeability, selectivity, subcellular localization and trafficking responses have been observed for different members of the AQP family, the signature homotetrameric quaternary structure is conserved. Using a variety of biophysical techniques, we show that mutations to an intracellular loop (loop D) of human AQP4 reduce oligomerization. Non-tetrameric AQP4 mutants are unable to relocalize to the plasma membrane in response to changes in extracellular tonicity, despite equivalent constitutive surface expression levels and water permeability to wild-type AQP4. A network of AQP4 loop D hydrogen bonding interactions, identified using molecular dynamics simulations and based on a comparative mutagenic analysis of AQPs 1, 3 and 4, suggest that loop D interactions may provide a general structural framework for tetrameric assembly within the AQP family.

Situações geográficas em movimento nas praias da área de proteção ambiental de Jenipabu: das ideologias ambientais ao território usado pelo circuito inferior do turismo

The Área de Proteção Ambiental de Jenipabu was created by Decreto 12,620/95, covering the beaches of Redinha Nova, Santa Rita and Jenipabu and Campina communities in the municipality of Extremoz, and Africa community fragment, in Natal. This protected area was created in the context of expansion of tourism in Rio Grande do Norte, in the 1990s, in which PRODETUR investments made possible the installation of infrastructure equipment, mainly in the Via Costeira and Ponta Negra beach in Natal by inserting it in the sun and sea tourism route to Northeast Brazil. In this context the beach Jenipabu in Extremoz, became one of the main attractions for those visiting Natal, due to the natural elements of its landscape, its dune field, which is offered to tourists the buggy ride. In December 1994 the excess buggy rides held in these dunes led to IBAMA ban their access to buggy for carrying out environmental study. This measure resulted in the creation of APAJ in 1995 with the goal of ordering the use and occupation to protect its ecosystems, especially the dunes, the disordered tourism. Given this context, this work aims to analyze the process of creating the APAJ and changes in the geographic space of its beaches, Redinha Nova, Santa Rita and Jenipabu, from the materialization of tourism process, as well as their implications for its residents. To this end, this paper presents a discussion of environmental currents that developed in the western portion of the globe, focusing on the need to regulate small areas of the national territory in protected areas, and an analysis of public policies that enabled the implementation tourism in APAJ as well as the laws and decrees governing the process of creation and management. Using the theory of circuits of urban economy of the Santos (2008) to analyze the territory used by tourism on the beaches of Redinha Nova, Santa Rita and Jenipabu, showing their dependent relationship with the territory used by the upper circuit on the Via Costeira and in the Ponta Negra beach and its influence on the APAJ urbanization process. Ending with the analysis of the influence of the materialization of tourism in the transformation of stocks ways of being-in-space and space-be of the Santa Rita and Jenipabu beaches in each geographical situation of APAJ among the first decades of the twentieth century to the 2014. Fieldwork was conducted between 2012 and 2014, performing actions of qualitative interviews with older residents of Santa Rita and Jenipabu beaches, interviews with structured questionnaire with merchants of APAJ and collecting GPS points trades, identifying and mapping the territory used by the lower circuit in APAJ beaches.

Padrões temporais e grau de diversificação cariotípica em espécies atlânticas da família Acanthuridae (Perciformes)

The Acanthuridae family is a representative group from the marine fish that plays a key role in ecological dynamics of coral reefs. Three species are common along coastal reefs of Western Atlantic: Acanthurus coeruleus, Acanthurus bahianus and Acanthurus chirurgus. In the present study, cytogenetic data are presented for these three species Acanthurus based on classical cytogenetic methods and mapping of repetitive sequences such as ribosomal 18S and 5S rDNA and telomeric repeats to improve their karyotype evolutionary analyses. The cytogenetic pattern of these species indicated sequential steps of chromosomal rearrangements dating back 19 to 5 millions of years ago (M.a.) that accounted for their interspecific differences. A. coeruleus (2n=48; 2sm+4st+42a), A. bahianus (2n=36; 12m+2sm+4st+18a) and A. chirurgus (2n=34; 12m+2sm+4st+16a) share an older set of three chromosomal pairs that were originated through pericentric inversions. A set of six large metacentric pairs formed by Robertsonian (Rb) translocations found in A. bahianus and A. chirurgus and a putative in tandem fusion found in A. chirurgus are more recent events. The lack of interstitial telomeric sequences (ITS) in spite of several centric fusions in A. bahianus and A. chirurgus might be related to the long period of time after their occurrence (estimated in 5 M.a.). Furthermore, the homeologies among the chromosome pairs bearing ribosomal genes, in addition to other structural features, highlight large conserved chromosomal regions in the three species. Our findings indicate that macrostructural changes occurred during the cladogenesis of these species were not followed by conspicuous microstructural rearrangements in the karyotypes.

Representações discursivas de Lula nas capas das revistas Época e Veja

This doctoral dissertation proposes to analyze the discursive representations of Lula, as they appear on the covers of the magazines, Época and Veja, targeting the verbo visual elements that comprise the genre, magazine covers. In this way, we seek to describe and interpret the discursive representations (Drs), using a theoretical framework based on the Textual Discourse Analysis –TDA, developed by Jean Michel Adam (2011a), focusing on the semantic level of the text, that is, on the dimension that allows for the comprehension of Drs present in a text. For a discussion about the Drs and their categories of analysis referencing, predication, modification, relation and spatial localization and time we use as a starting point, the study by Brize about the logical discursive operations (1990, 1996), and continue through the studies that discuss linguistic, textual, and discursive operations in concrete utterances, such as Castilho (2010), Rodrigues; Passeggi; Silva Neto (2010), Neves (2011), Rodrigues et al. (2012), Passeggi (2001; 2012), Queiroz (2013), among others. In addition, we rely on Multimodal Discourse for the verbo visual aspects present on magazine covers (KRESS; van LEEUWEN, 2006; DIONISIO, 2011; DIONISIO; VASCONCELOS, 2013). Using aresearch approach that is qualitative with quantitative support, and which is documental, and based on deductive inductive methods, we describe and interpret a corpus (SEVERINO, 2007; CHIZZOTTI, 2010; OLIVEIRA, M., 2013), aiming to reconstruct Lula’s Drs. The cor pusis comprised of forty one magazine covers sixteen from Época and twenty four from Veja. The covers date from the election period in which the candidate, Lula, was elected President of Brazil in 2002, the last mandate after his reelection in 2006, and in the year 2010 a period of 9 years. Based on the analysis carried out, we can affirm that the magazines, Época and Veja, construct diverse Drs by Lula, such as: candidate; elected candidate; governing member and member of a political party; reelected president; politics; workers party acronym PT; international governments as allies; accomplices and participants in scandals of corruption; friend, brother, cousin, nephew, father, parent and man; among others that unfold throughout these by the mediation of the modifiers of the referents and processes, and by the very processes and connections, and analogies made on the object of discourse, Lula. Nonetheless, the reconstruction of these is derived from the description and interpretation of the textual linguistic and discursive choices that the magazines make to produce the proposition utterances, as well as by the choices of images and other visual resources, all operating as co(n)textually articulated to produce the magazine’s desired effect. In conclusion, the Drs verified demand the reflection, description and interpretation of the referencing, prediction, the relationship and spatial temporal localization, which was only possible through the textual discursive analysis of the verbo visual arrangements that comprise texts in the genre magazine cover.