A simple, rapid method for mapping bathymetry of small wetland basins

Many tools exist for determining and mapping the bathymetry and topography of aquatic systems, such as freshwater wetlands. However, these tools often require time-consuming survey work to produce accurate maps. In particular, the large quantity of data necessary may be prohibitive for projects where determining bathymetry is not a central focus, but instead a necessary step in achieving some other goal. We present a method to produce bathymetric surface maps with a minimum amount of effort using global positioning system receiver and laser transit survey data. We also demonstrate that this method is surprisingly accurate, given the small amount of data we use to generate the bathymetry maps.

Involvement of Islet-2 in the Slit signaling for axonal branching and defasciculation of the sensory neurons in embryonic zebrafish

In Drosophila melanogaster, Slit acts as a repulsive cue for the growth cones of the commissural axons which express a receptor for Slit, Roundabout (Robo), thus preventing the commissural axons from crossing the midline multiple times. Experiments using explant culture have shown that vertebrate Slit homologues also act repulsively for growth cone navigation and neural migration, and promote branching and elongation of sensory axons. Here, we demonstrate that overexpression of Slit2 in vivo in transgenic zebrafish embryos severely affected the behavior of the commissural reticulospinal neurons (Mauthner neurons), promoted branching of the peripheral axons of the trigeminal sensory ganglion neurons, and induced defasciculation of the medial longitudinal fascicles. In addition, Slit2 overexpression caused defasciculation and deflection of the central axons of the trigeminal sensory ganglion neurons from the hindbrain entry point. The central projection was restored by either functional repression or mutation of Robo2, supporting its role as a receptor mediating the Slit signaling in vertebrate neurons. Furthermore, we demonstrated that Islet-2, a LIM/homeodomain-type transcription factor, is essential for Slit2 to induce axonal branching of the trigeminal sensory ganglion neurons, suggesting that factors functioning downstream of Islet-2 are essential for mediating the Slit signaling for promotion of axonal branching. (C) 2004 Elsevier Ireland Ltd. All rights reserved.

A modified particle filter for simultaneous robot localization and landmark tracking in an indoor environment

This paper presents the implementation of a modified particle filter for vision-based simultaneous localization and mapping of an autonomous robot in a structured indoor environment. Through this method, artificial landmarks such as multi-coloured cylinders can be tracked with a camera mounted on the robot, and the position of the robot can be estimated at the same time. Experimental results in simulation and in real environments show that this approach has advantages over the extended Kalman filter with ambiguous data association and various levels of odometric noise.

UQ RoboRoos: Achieving power and agility in a small size robot

The UQ RoboRoos have been developed to participate in the RoboCup robot soccer small size league over several years. RoboCup 2001 saw a focus on the mechanical design of the RoboRoos, with the introduction of an omni-directional drive system and a high power kicker. The change in mechanical design had implications for the rest of the system particularly navigation and multi-robot planning. In addition, the overhead vision system was upgraded to improve reliability and robustness.

A new rapidly absorbed paracetamol tablet containing sodium bicarbonate. II. Dissolution studies and in vitro/in vivo correlation

The objective of this study was to compare the in vitro dissolution profile of a new rapidly absorbed paracetamol tablet containing sodium bicarbonate (PS) with that of a conventional paracetamol tablet (P), and to relate these by deconvolution and mapping to in vivo release. The dissolution methods used include the standard procedure described in the USP monograph for paracetamol tablets, employing buffer at pH5.8 or 0.05 M HCl at stirrer speeds between 10 and 50 rpm. The mapping process was developed and implemented in Microsoft Excel® worksheets that iteratively calculated the optimal values of scale and shape factors which linked in vivo time to in vitro time. The in vitro-in vivo correlation (IVIVC) was carried out simultaneously for both formulations to produce common mapping factors. The USP method, using buffer at pH5.8, demonstrated no difference between the two products. However, using an acidic medium the rate of dissolution of P but not of PS decreased with decreasing stirrer speed. A significant correlation (r=0.773; p<.00001) was established between in vivo release and in vitro dissolution using the profiles obtained with 0.05 M HCl and a stirrer speed of 30 rpm. The scale factor for optimal simultaneous IVIVC in the fasting state was 2.54 and the shape factor was 0.16; corresponding values for mapping in the fed state were 3.37 and 0.13 (implying a larger in vitro-in vivo time difference but reduced shape difference in the fed state). The current IVIVC explains, in part, the observed in vivo variability of the two products. The approach to mapping may also be extended to different batches of these products, to predict the impact of any changes of in vitro dissolution on in vivo release and plasma drug concentration-time profiles.

Mutations of beta-arrestin 2 that limit self-association also interfere with interactions with the beta2-adrenoceptor and the ERK1/2 MAPKs:implications for beta2-adrenoceptor signalling via the ERK1/2 MAPKs

FRET (fluorescence resonance energy transfer) and co-immunoprecipitation studies confirmed the capacity of beta-arrestin 2 to self-associate. Amino acids potentially involved in direct protein-protein interaction were identified via combinations of spot-immobilized peptide arrays and mapping of surface exposure. Among potential key amino acids, Lys(285), Arg(286) and Lys(295) are part of a continuous surface epitope located in the polar core between the N- and C-terminal domains. Introduction of K285A/R286A mutations into beta-arrestin 2-eCFP (where eCFP is enhanced cyan fluorescent protein) and beta-arrestin 2-eYFP (where eYFP is enhanced yellow fluorescent protein) constructs substantially reduced FRET, whereas introduction of a K295A mutation had a more limited effect. Neither of these mutants was able to promote beta2-adrenoceptor-mediated phosphorylation of the ERK1/2 (extracellular-signal-regulated kinase 1/2) MAPKs (mitogen-activated protein kinases). Both beta-arrestin 2 mutants displayed limited capacity to co-immunoprecipitate ERK1/2 and further spot-immobilized peptide arrays indicated each of Lys(285), Arg(286) and particularly Lys(295) to be important for this interaction. Direct interactions between beta-arrestin 2 and the beta2-adrenoceptor were also compromised by both K285A/R286A and K295A mutations of beta-arrestin 2. These were not non-specific effects linked to improper folding of beta-arrestin 2 as limited proteolysis was unable to distinguish the K285A/R286A or K295A mutants from wild-type beta-arrestin 2, and the interaction of beta-arrestin 2 with JNK3 (c-Jun N-terminal kinase 3) was unaffected by the K285A/R286A or L295A mutations. These results suggest that amino acids important for self-association of beta-arrestin 2 also play an important role in the interaction with both the beta2-adrenoceptor and the ERK1/2 MAPKs. Regulation of beta-arrestin 2 self-association may therefore control beta-arrestin 2-mediated beta2-adrenoceptor-ERK1/2 MAPK signalling.

Protein oxidation:role in signalling and detection by mass spectrometry

Proteins can undergo a wide variety of oxidative post-translational modifications (oxPTM); while reversible modifications are thought to be relevant in physiological processes, non-reversible oxPTM may contribute to pathological situations and disease. The oxidant is also important in determining the type of oxPTM, such as oxidation, chlorination or nitration. The best characterized oxPTMs involved in signalling modulation are partial oxidations of cysteine to disulfide, glutathionylated or sulfenic acid forms that can be reversed by thiol reductants. Proline hydroxylation in HIF signalling is also quite well characterized, and there is increasing evidence that specific oxidations of methionine and tyrosine may have some biological roles. For some proteins regulated by cysteine oxidation, the residues and molecular mechanism involved have been extensively studied and are well understood, such as the protein tyrosine phosphatase PTP1B and MAP3 kinase ASK1, as well as transcription factor complex Keap1-Nrf2. The advances in understanding of the role oxPTMs in signalling have been facilitated by advances in analytical technology, in particular tandem mass spectrometry techniques. Combinations of peptide sequencing by collisionally induced dissociation and precursor ion scanning or neutral loss to select for specific oxPTMs have proved very useful for identifying oxidatively modified proteins and mapping the sites of oxidation. The development of specific labelling and enrichment procedures for S-nitrosylation or disulfide formation has proved invaluable, and there is ongoing work to establish analogous methods for detection of nitrotyrosine and other modifications.

The autonomous navigation of an electric vehicle

A navigation and positioning system for an electric automatic guided vehicle has been designed and implemented on an industrial pallet truck. The system includes an optical sensor mounted on the vehicle, capable of recognizing special markers at a distance of 0.3m. Software implemented in a z-80 microprocessor controls the sensor, performs all data processing and contains the decision making processes necessary for the vehicle to navigate its way to its task location. A second microprocessor is used to control the vehicle's drive motors under instruction from the navigation unit, to accurately position the vehicle at its destination. The sensor reliably recognises markers at vehicle speeds up to 1ms- 1, and the system has been integrated into a multiprocessor controlled wire-guidance system and applied to a prototype vehicle.

Modeling naturalistic argumentation in research literatures:representation and interaction design issues

This article characterizes key weaknesses in the ability of current digital libraries to support scholarly inquiry, and as a way to address these, proposes computational services grounded in semiformal models of the naturalistic argumentation commonly found in research literatures. It is argued that a design priority is to balance formal expressiveness with usability, making it critical to coevolve the modeling scheme with appropriate user interfaces for argument construction and analysis. We specify the requirements for an argument modeling scheme for use by untrained researchers and describe the resulting ontology, contrasting it with other domain modeling and semantic web approaches, before discussing passive and intelligent user interfaces designed to support analysts in the construction, navigation, and analysis of scholarly argument structures in a Web-based environment. © 2007 Wiley Periodicals, Inc. Int J Int Syst 22: 17–47, 2007.

Importance of storm events in controlling ecosystem structure and function in a Florida gulf coast estuary

From 8/95 to 2/01, we investigated the ecological effects of intra- and inter-annual variability in freshwater flow through Taylor Creek in southeastern Everglades National Park. Continuous monitoring and intensive sampling studies overlapped with an array of pulsed weather events that impacted physical, chemical, and biological attributes of this region. We quantified the effects of three events representing a range of characteristics (duration, amount of precipitation, storm intensity, wind direction) on the hydraulic connectivity, nutrient and sediment dynamics, and vegetation structure of the SE Everglades estuarine ecotone. These events included a strong winter storm in November 1996, Tropical Storm Harvey in September 1999, and Hurricane Irene in October 1999. Continuous hydrologic and daily water sample data were used to examine the effects of these events on the physical forcing and quality of water in Taylor Creek. A high resolution, flow-through sampling and mapping approach was used to characterize water quality in the adjacent bay. To understand the effects of these events on vegetation communities, we measured mangrove litter production and estimated seagrass cover in the bay at monthly intervals. We also quantified sediment deposition associated with Hurricane Irene's flood surge along the Buttonwood Ridge. These three events resulted in dramatic changes in surface water movement and chemistry in Taylor Creek and adjacent regions of Florida Bay as well as increased mangrove litterfall and flood surge scouring of seagrass beds. Up to 5 cm of bay-derived mud was deposited along the ridge adjacent to the creek in this single pulsed event. These short-term events can account for a substantial proportion of the annual flux of freshwater and materials between the mangrove zone and Florida Bay. Our findings shed light on the capacity of these storm events, especially when in succession, to have far reaching and long lasting effects on coastal ecosystems such as the estuarine ecotone of the SE Everglades.

Crossing boundaries to education: Haitian transnational families and the quest to raise the family up

Nearly 175, 000 Haitian immigrants have settled in South Florida since the 1970s. Their lives are often lived transnationally with persistent connections and obligations to family members in Haiti. Yet, traditional theories of immigrant assimilation focus on the integration of immigrants into host countries, giving little consideration to relationships and activities that extend into migrants' countries of origin. Conversely, studies of transnational families do not explicitly address incorporation into the receiving country. This dissertation, through the experiences of Haitian immigrants in South Florida, reveals a transnational quest "to raise the family up" through migration, remittances, and the pursuit of higher levels of education. I argue that familial duties and obligations, which have cultural foundations in the Haitian lakou, structure the activities of Haitian transnational families as they pursue socioeconomic advancement through migration and education. With the support of transnational families, many students cross boundaries to academic achievement and improve their opportunities for socioeconomic mobility in the US. With higher levels of education, these individuals contributed to a more favorable incorporation into the United States for their extended families, as well. The data were collected through participant observation and 78 in-depth interviews documenting the migration histories of 27 Haitian immigrant families in South Florida. This dissertation contributes to the existing literature on Haitian immigrants in the United States and to an understanding of the transnational dimensions of immigrant incorporation more broadly.

3D navigation with six degrees-of-freedom using a multi-touch display

With the introduction of new input devices, such as multi-touch surface displays, the Nintendo WiiMote, the Microsoft Kinect, and the Leap Motion sensor, among others, the field of Human-Computer Interaction (HCI) finds itself at an important crossroads that requires solving new challenges. Given the amount of three-dimensional (3D) data available today, 3D navigation plays an important role in 3D User Interfaces (3DUI). This dissertation deals with multi-touch, 3D navigation, and how users can explore 3D virtual worlds using a multi-touch, non-stereo, desktop display. ^ The contributions of this dissertation include a feature-extraction algorithm for multi-touch displays (FETOUCH), a multi-touch and gyroscope interaction technique (GyroTouch), a theoretical model for multi-touch interaction using high-level Petri Nets (PeNTa), an algorithm to resolve ambiguities in the multi-touch gesture classification process (Yield), a proposed technique for navigational experiments (FaNS), a proposed gesture (Hold-and-Roll), and an experiment prototype for 3D navigation (3DNav). The verification experiment for 3DNav was conducted with 30 human-subjects of both genders. The experiment used the 3DNav prototype to present a pseudo-universe, where each user was required to find five objects using the multi-touch display and five objects using a game controller (GamePad). For the multi-touch display, 3DNav used a commercial library called GestureWorks in conjunction with Yield to resolve the ambiguity posed by the multiplicity of gestures reported by the initial classification. The experiment compared both devices. The task completion time with multi-touch was slightly shorter, but the difference was not statistically significant. The design of experiment also included an equation that determined the level of video game console expertise of the subjects, which was used to break down users into two groups: casual users and experienced users. The study found that experienced gamers performed significantly faster with the GamePad than casual users. When looking at the groups separately, casual gamers performed significantly better using the multi-touch display, compared to the GamePad. Additional results are found in this dissertation.^

Dynamic Compartmentalization of Persistent UPEC in the Superficial Bladder Epithelium

Urinary tract infections (UTIs) are typically caused by bacteria that colonize different regions of the urinary tract, mainly the bladder and the kidney. Approximately 25% of women that suffer from UTIs experience a recurrent infection within 6 months of the initial bout, making UTIs a serious economic burden resulting in more than 10 million hospital visits and $3.5 billion in healthcare costs in the United States alone. Type-1 fimbriated Uropathogenic E. coli (UPEC) is the major causative agent of UTIs, accounting for almost 90 % of bacterial UTIs. The unique ability of UPEC to bind and invade the superficial bladder epithelium allows the bacteria to persist inside epithelial niches and survive antibiotic treatment. Persistent, intracellular UPEC are retained in the bladder epithelium for long periods, making them a source of recurrent UTIs. Hence, the ability of UPEC to persist in the bladder is a matter of major health and economic concern, making studies exploring the underlying mechanism of UPEC persistence highly relevant.

In my thesis, I will describe how intracellular Uropathogenic E.coli (UPEC) evade host defense mechanisms in the superficial bladder epithelium. I will also describe some of the unique traits of persistent UPEC and explore strategies to induce their clearance from the bladder. I have discovered that the UPEC virulence factor Alpha-hemolysin (HlyA) plays a key role in the survival and persistence of UPEC in the superficial bladder epithelium. In-vitro and in-vivo studies comparing intracellular survival of wild type (WT) and hemolysin deficient UPEC suggested that HlyA is vital for UPEC persistence in the superficial bladder epithelium. Further in-vitro studies revealed that hemolysin helped UPEC persist intracellularly by evading the bacterial expulsion actions of the bladder cells and remarkably, this virulence factor also helped bacteria avoid t degradation in lysosomes.

To elucidate the mechanistic basis for how hemolysin promotes UPEC persistence in the urothelium, we initially focused on how hemolysin facilitates the evasion of UPEC expulsion from bladder cells. We found that upon entry, UPEC were encased in “exocytic vesicles” but as a result of HlyA expression these bacteria escaped these vesicles and entered the cytosol. Consequently, these bacteria were able to avoid expulsion by the cellular export machinery.

Since bacteria found in the cytosol of host cells are typically recognized by the cellular autophagy pathway and transported to the lysosomes where they are degraded, we explored why this was not the case here. We observed that although cytosolic HlyA expressing UPEC were recognized and encased by the autophagy system and transported to lysosomes, the bacteria appeared to avoid degradation in these normally degradative compartments. A closer examination of the bacteria containing lysosomes revealed that they lacked V-ATPase. V-ATPase is a well-known proton pump essential for the acidification of mammalian intracellular degradative compartments, allowing for the proper functioning of degradative proteases. The absence of V-ATPase appeared to be due to hemolysin mediated alteration of the bladder cell F-actin network. From these studies, it is clear that UPEC hemolysin facilitates UPEC persistence in the superficial bladder epithelium by helping bacteria avoid expulsion by the exocytic machinery of the cell and at the same time enabling the bacteria avoid degradation when the bacteria are shuttled into the lysosomes.

Interestingly even though UPEC appear to avoid elimination from the bladder cell their ability to multiple in bladder cells seem limited.. Indeed, our in-vitro and in-vivo experiments reveal that UPEC survive in superficial bladder epithelium for extended periods of time without a significantly change in CFU numbers. Indeed, we observed these bacteria appeared quiescent in nature. This observation was supported by the observation that UPEC genetically unable to enter a quiescence phase exhibited limited ability to persist in bladder cells in vitro and in vivo, in the mouse bladder.

The studies elucidated in this thesis reveal how UPEC toxin, Alpha-hemolysin plays a significant role in promoting UPEC persistence via the modulation of the vesicular compartmentalization of UPEC at two different stages of the infection in the superficial bladder epithelium. These results highlight the importance of UPEC Alpha-hemolysin as an essential determinant of UPEC persistence in the urinary bladder.