Postmortem Demonstration of the Source of Pulmonary Thromboembolism: The Importance of the Autopsy

Periprostatic or paravaginal venous thromboses are rarely considered clinically as sites of clot origin in patients with pulmonary thromboembolism. The majority of emboli have been demonstrated to originate in the veins of the legs. This report raises awareness of pelvic vein thrombosis as a potential source of pulmonary embolism that is rarely considered or detected clinically, and which usually requires postmortem examination for recognition. It also reviews the possible routes emboli may take to reach the lungs.

Understanding the role of Dimethylsulfoniopropionate as a potential chemotactic cue for coral-associated bacteria

Most reef-building corals are known to engage in non-pathogenic symbiosis not only with unicellular dinoflagellates from the genus Symbiodinium, but also with other microscopic organisms such as bacteria, fungi, and viruses. The functional details of these highly complex associations remain largely unclear. The impetus of this study is to gain a better understanding of the symbiotic interaction between marine bacteria and their coral host. Studies have shown that certain bacterial orders associate with specific certain coral species, thus making the symbiotic synergy a non-random consortium. Consequently both corals and bacteria may be capable of emitting chemical cues that enable both parties to find one another and thus generate the symbiosis. The production of these cues by the symbionts may be the result of environmental stimuli such as elevated ocean temperatures, increased water acidity, and even predation. One potential chemical cue could be the compound DMSP (Dimethylsulfoniopropionate) and its sulphur derivatives. Reef-building corals are believed to be the major producers of the DMSP during times of stress. Marine bacteria utilize DMSP as a source of sulfur and carbon. As a result corals could potentially attract their bacterial consortium depending on their DMSP production. This would enable them to adapt to fluctuating environmental conditions by changing their bacterial communities to that which may aid in survival. To test the hypothesis that coral-produced DMSP plays a role in attracting symbiotic bacteria, this study utilized the advent of high-throughput sequencing paired with chemotactic assays to determine the response of coral-associated bacterial isolates towards the DMSP compound at differing concentrations. Chemotaxis assays revealed that some isolates responded positively towards the DMSP compound. This finding adds to existing evidence suggesting that coral-associated pathogens utilize chemotaxis as a host colonization and detection mechanism. Thus the symbiotic bacteria that make up the coral microbiome may also employ this process. Furthermore this study demonstrates that bacterial motility may be a strong contributing factor in the response to the chemotactic cue. Swarming motility may be better suited for bacteria that need to respond to a chemical gradient on the surface of the coral. Therefore the isolates that were able to swarm seemed to respond more strongly to the DMSP.

The song of humpback whale and the potential effects of whale-watching in the abrolhos bank, BA, Brazil

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

The song of humpback whale and the potential effects of whale-watching in the abrolhos bank, BA, Brazil

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Sea organisms as a source of collagen-derived polymers for skin tissue engineering applications

Advanced therapies combating acute and chronic skin wounds are likely to be brought about using our knowledge of regenerative medicine coupled with appropriately tissue engineered skin substitutes. At the present time, there are no models of an artificial skin that completely replicate normal uninjured skin and they are usually accompanied by fibrotic reactions that result in the production of a scar. Natural biopolymers such as collagen have been a lot investigated as potential source of biomaterial for skin replacement in Tissue Engineering. Collagens are the most abundant high molecular weight proteins in both invertebrate and vertebrate organisms, including mammals, and possess mainly a structural role in connective tissues. From this, they have been elected as one of the key biological materials in tissue regeneration approaches, as skin tissue engineering. In addition, industry is constantly searching for new natural sources of collagen and upgraded methodologies for their production. The most common sources are skin and bone from bovine and porcine origin. However, these last carry high risk of bovine spongiform encephalopathy or transmissible spongiform encephalopathy and immunogenic responses. On the other hand, the increase of jellyfish has led us to consider this marine organism as potential collagen source for tissue engineering applications. In the present study, novel form of acid and pepsin soluble collagen were extracted from dried Rhopilema hispidum jellyfish species in an effort to obtain an alternative and safer collagen. We studied different methods of collagen purification (tissues and experimental procedures). The best collagen yield was obtained using pepsin extraction method (34.16 mg collagen/g of tissue). The isolated collagen was characterized by SDS-polyacrylamide gel electrophoresis and circular dichroism spectroscopy.

Development of Swept Source Optical Coherence Tomography and Adaptive Optics Scanning Laser Ophthalmoscopy: Improved Imaging Speed and Handheld Applications

Optical coherence tomography (OCT) is a noninvasive three-dimensional interferometric imaging technique capable of achieving micrometer scale resolution. It is now a standard of care in ophthalmology, where it is used to improve the accuracy of early diagnosis, to better understand the source of pathophysiology, and to monitor disease progression and response to therapy. In particular, retinal imaging has been the most prevalent clinical application of OCT, but researchers and companies alike are developing OCT systems for cardiology, dermatology, dentistry, and many other medical and industrial applications.

Adaptive optics (AO) is a technique used to reduce monochromatic aberrations in optical instruments. It is used in astronomical telescopes, laser communications, high-power lasers, retinal imaging, optical fabrication and microscopy to improve system performance. Scanning laser ophthalmoscopy (SLO) is a noninvasive confocal imaging technique that produces high contrast two-dimensional retinal images. AO is combined with SLO (AOSLO) to compensate for the wavefront distortions caused by the optics of the eye, providing the ability to visualize the living retina with cellular resolution. AOSLO has shown great promise to advance the understanding of the etiology of retinal diseases on a cellular level.

Broadly, we endeavor to enhance the vision outcome of ophthalmic patients through improved diagnostics and personalized therapy. Toward this end, the objective of the work presented herein was the development of advanced techniques for increasing the imaging speed, reducing the form factor, and broadening the versatility of OCT and AOSLO. Despite our focus on applications in ophthalmology, the techniques developed could be applied to other medical and industrial applications. In this dissertation, a technique to quadruple the imaging speed of OCT was developed. This technique was demonstrated by imaging the retinas of healthy human subjects. A handheld, dual depth OCT system was developed. This system enabled sequential imaging of the anterior segment and retina of human eyes. Finally, handheld SLO/OCT systems were developed, culminating in the design of a handheld AOSLO system. This system has the potential to provide cellular level imaging of the human retina, resolving even the most densely packed foveal cones.

Bridging the Scale Gap from Leaf to Canopy in Biosphere-Atmosphere Gas and Particle Exchanges

Terrestrial ecosystems, occupying more than 25% of the Earth's surface, can serve as

`biological valves' in regulating the anthropogenic emissions of atmospheric aerosol

particles and greenhouse gases (GHGs) as responses to their surrounding environments.

While the signicance of quantifying the exchange rates of GHGs and atmospheric

aerosol particles between the terrestrial biosphere and the atmosphere is

hardly questioned in many scientic elds, the progress in improving model predictability,

data interpretation or the combination of the two remains impeded by

the lack of precise framework elucidating their dynamic transport processes over a

wide range of spatiotemporal scales. The diculty in developing prognostic modeling

tools to quantify the source or sink strength of these atmospheric substances

can be further magnied by the fact that the climate system is also sensitive to the

feedback from terrestrial ecosystems forming the so-called `feedback cycle'. Hence,

the emergent need is to reduce uncertainties when assessing this complex and dynamic

feedback cycle that is necessary to support the decisions of mitigation and

adaptation policies associated with human activities (e.g., anthropogenic emission

controls and land use managements) under current and future climate regimes.

With the goal to improve the predictions for the biosphere-atmosphere exchange

of biologically active gases and atmospheric aerosol particles, the main focus of this

dissertation is on revising and up-scaling the biotic and abiotic transport processes

from leaf to canopy scales. The validity of previous modeling studies in determining

iv

the exchange rate of gases and particles is evaluated with detailed descriptions of their

limitations. Mechanistic-based modeling approaches along with empirical studies

across dierent scales are employed to rene the mathematical descriptions of surface

conductance responsible for gas and particle exchanges as commonly adopted by all

operational models. Specically, how variation in horizontal leaf area density within

the vegetated medium, leaf size and leaf microroughness impact the aerodynamic attributes

and thereby the ultrane particle collection eciency at the leaf/branch scale

is explored using wind tunnel experiments with interpretations by a porous media

model and a scaling analysis. A multi-layered and size-resolved second-order closure

model combined with particle

uxes and concentration measurements within and

above a forest is used to explore the particle transport processes within the canopy

sub-layer and the partitioning of particle deposition onto canopy medium and forest

oor. For gases, a modeling framework accounting for the leaf-level boundary layer

eects on the stomatal pathway for gas exchange is proposed and combined with sap

ux measurements in a wind tunnel to assess how leaf-level transpiration varies with

increasing wind speed. How exogenous environmental conditions and endogenous

soil-root-stem-leaf hydraulic and eco-physiological properties impact the above- and

below-ground water dynamics in the soil-plant system and shape plant responses

to droughts is assessed by a porous media model that accommodates the transient

water

ow within the plant vascular system and is coupled with the aforementioned

leaf-level gas exchange model and soil-root interaction model. It should be noted

that tackling all aspects of potential issues causing uncertainties in forecasting the

feedback cycle between terrestrial ecosystem and the climate is unrealistic in a single

dissertation but further research questions and opportunities based on the foundation

derived from this dissertation are also brie

y discussed.

Synthesis and evaluation of novel ellipticines as potential anti-cancer agents

Ellipticine is a natural product which possesses multimodal anti-cancer activity. This thesis encompasses the synthesis and biological evaluation of novel ellipticine and isoellipticine derivatives as anti-cancer agents. Expanding on previous work within the group utilising vinylmagnesium bromide, derivatisation of the C5 position of ellipticine was accomplished by reaction of a key ketolactam intermediate with Grignard reagents. Corresponding attempts to introduce diverse substitution at the C11 position were unsuccessful, although one novel C11 derivative was produced using an alkyllithium reagent. A panel of novel ellipticinium salts encompassing a range of substitutions at the N2, C9 and N6 positions were prepared. Extensive derivatisation of the N10 position of isoellipticine was undertaken for the first time. Novel substitution in the form of acid and methyl ester functionalities were introduced at the C7 position of isoellipticine while novel C7 aldehyde and alcohol derivatives were synthesised. A large panel of isoellipticinium salts were prepared with conditions adjusted for the reactivity of the alkyl halide. Novel coupling reactions to increase the yield of isoellipticine were attempted but proved unsuccessful. A panel of 54 novel derivatives was prepared and a multimodal analysis of their anti-cancer activity was conducted. The NCI 60-human tumour cell lines screen was a primary source of information on the in vitro activity of compounds with derivatives found to exert potent anticancer effects, with mean GI50 values as low as 1.01 μM across the full range of cancer types and as low as 16 nM in individual cell lines. A second in vitro screen in collaboration with researchers in the University of Nantes identified derivatives which could potently inhibit growth in a p53 mutant NSCLC cell line. The cell cycle effects of a selected panel of isoellipticines were studied in leukaemia cell lines by researchers in the Department of Biochemistry and Cell Biology, UCC. Emerging from this, the therapeutic potential of one of the derivatives in AML was then assessed in vivo in an AML xenograft mouse model, with tumour weight reduced by a factor of 7 in treated mice relative to control.

A stereo-image analysis JAVA software with links to executable and source code

Scientists planning to use underwater stereoscopic image technologies are often faced with numerous problems during the methodological implementations: commercial equipment is too expensive; the setup or calibration is too complex; or the imaging processing (i.e. measuring objects in the stereo-images) is too complicated to be performed without a time-consuming phase of training and evaluation. The present paper addresses some of these problems and describes a workflow for stereoscopic measurements for marine biologists. It also provides instructions on how to assemble an underwater stereo-photographic system with two digital consumer cameras and gives step-by-step guidelines for setting up the hardware. The second part details a software procedure to correct stereo-image pairs for lens distortions, which is especially important when using cameras with non-calibrated optical units. The final part presents a guide to the process of measuring the lengths (or distances) of objects in stereoscopic image pairs. To reveal the applicability and the restrictions of the described systems and to test the effects of different types of camera (a compact camera and an SLR type), experiments were performed to determine the precision and accuracy of two generic stereo-imaging units: a diver-operated system based on two Olympus Mju 1030SW compact cameras and a cable-connected observatory system based on two Canon 1100D SLR cameras. In the simplest setup without any correction for lens distortion, the low-budget Olympus Mju 1030SW system achieved mean accuracy errors (percentage deviation of a measurement from the object's real size) between 10.2 and -7.6% (overall mean value: -0.6%), depending on the size, orientation and distance of the measured object from the camera. With the single lens reflex (SLR) system, very similar values between 10.1% and -3.4% (overall mean value: -1.2%) were observed. Correction of the lens distortion significantly improved the mean accuracy errors of either system. Even more, system precision (spread of the accuracy) improved significantly in both systems. Neither the use of a wide-angle converter nor multiple reassembly of the system had a significant negative effect on the results. The study shows that underwater stereophotography, independent of the system, has a high potential for robust and non-destructive in situ sampling and can be used without prior specialist training.

Evaluating Spirulina as a protein source in Nile Tilapia (Oreochromis niloticus) grow-out diets

Aquaculture growth has intensified the need for a diversification of nutritionally appropriate aquafeed ingredients. The purpose of this study was to evaluate Spirulina, a blue-green microalgae, and soybean meal as the sole protein sources in grow-out Tilapia diets. We constructed 3 experimental diets with soybean meal and 0,15, 30, and 45% Spirulina (SBM, SP15, SP30, and SP45 respectively) as their main protein sources. We compared these diets to a commercial Tilapia diet (CC). Additionally, to evaluate the benefit of fishmeal inclusion, fishmeal was added (2 and 10%) to the most successful Spirulina containing diet (FM2, FM10). We evaluated these experimental diets based on their physical properties, palatability, growth potential, waste production, and overall cost. No significant differences in growth performance were found between any of the diets. Total ammonia nitrogen (TAN) and total phosphorus (TP) levels in each tank were significantly affected by diet (p<0.05). CC had significantly higher TP than the experimental diets and SP15 had significantly higher TAN than the other diets. Only CC was found to be significantly more palatable than the experimental diets, and Spirulina inclusion was inversely correlated to pellet stability. Lastly, SP15 was the most profitable experimental diet. We recommend eliminating fishmeal from grow-out Tilapia diets in favour of soybean meal and Spirulina. Spirulina should, however, be limited to 15% to avoid the negative effects it has on stability and profitability, and its possible effect on feed intake.

Potential Shifts in Canadian High Arctic Sedimentary Organic Matter Composition With Permafrost Active Layer Detachments

Increased temperature and precipitation in Arctic regions have led to deeper thawing and structural instability in permafrost soil. The resulting localized disturbances, referred to as active layer detachments (ALDs), may transport organic matter (OM) to more biogeochemically active zones. To examine this further, solid state cross polarization magic angle spinning 13C nuclear magnetic resonance (CPMAS NMR) and biomarker analysis were used to evaluate potential shifts in riverine sediment OM composition due to nearby ALDs within the Cape Bounty Arctic Watershed Observatory, Nunavut, Canada. In sedimentary OM near ALDs, NMR analysis revealed signals indicative of unaltered plant-derived material, likely derived from permafrost. Long chain acyclic aliphatic lipids, steroids, cutin, suberin and lignin occurred in the sediments, consistent with a dominance of plant-derived compounds, some of which may have originated from permafrost-derived OM released by ALDs. OM degradation proxies for sediments near ALDs revealed less alteration in acyclic aliphatic lipids, while constituents such as steroids, cutin, suberin and lignin were found at a relatively advanced stage of degradation. Phospholipid fatty acid analysis indicated that microbial activity was higher near ALDs than downstream but microbial substrate limitation was prevalent within disturbed regions. Our study suggests that, as these systems recover from disturbance, ALDs likely provide permafrost-derived OM to sedimentary environments. This source of OM, which is enriched in labile OM, may alter biogeochemical patterns and enhance microbial respiration within these ecosystems.

Endothelial cell-derived Pentraxin 3 limits the vasoreparative therapeutic potential of Circulating Angiogenic Cells

AIMS: Circulating Angiogenic Cells (CACs) promote revascularization of ischemic tissues although their underlying mechanism of action and the consequences of delivering varying numbers of these cells for therapy remain unknown. This study investigates molecular mechanisms underpinning CAC modulation of blood vessel formation.

METHODS & RESULTS: CACs at low (2x10(5)cells/ml) and mid (2x10(6)cells/ml) cellular densities significantly enhanced endothelial cell (EC) tube formation in vitro, while high density CACs (2x10(7)cells/ml) significantly inhibited this angiogenic process. In vivo, Matrigel-based angiogenesis assays confirmed mid-density CACs as pro-angiogenic and high density CACs as anti-angiogenic. Secretome characterization of CAC-EC conditioned media identified pentraxin 3 (PTX3) as only present in the high density CAC-EC co-culture. Recombinant PTX3 inhibited endothelial tube formation in vitro and in vivo Importantly, our data revealed that the anti-angiogenic effect observed in high density CAC-EC co-cultures was significantly abrogated when PTX3 bioactivity was blocked using neutralizing antibodies or PTX3 siRNA in endothelial cells. We show evidence for an endothelial source of PTX3, triggered by exposure to high density CACs. In addition, we confirmed that PTX3 inhibits FGF2-mediated angiogenesis, and that the PTX3 N-terminus, containing the FGF-binding site, is responsible for such anti-angiogenic effects.

CONCLUSIONS: Endothelium, when exposed to high density CACs, releases PTX3 which markedly impairs the vascular regenerative response in an autocrine manner. Therefore, CAC density and accompanying release of angiocrine PTX3 are critical considerations when using these cells as a cell therapy for ischemic disease.

Exploring the potential of cassava in promoting agricultural growth in Nigeria

Cassava is one of the major food crops in Nigeria, with multiple uses from human consumption to industrial applications. This study explores the potential of cassava in Nigerian agriculture based on a review of cassava development policies; performs a trend analysis of the cultivation area, production, productivity, and real price of cassava and other competing crops for the period 1961–2013; identifies the sources of growth in production; and examines the production constraints at the local level based on a survey of 315 farmers/processors and 105 marketers from Delta State. The results revealed that several policies and programmes were implemented to develop the cassava sector with mixed outcomes. Although cassava productivity grew at 1.5% per annum (p.a.) during the post-structural adjustment programme period (1993–2013), its real price declined at a rate of 3.5% p.a. The effect of yield is the main source of growth in production, contributing 76.4% of the total growth followed by the area effect (28.2%). The cassava sector is constrained by inadequate market infrastructure, processing facilities, and lack of information and unstable prices at the local level. The widespread diffusion of improved tropical manioc selection technologies and investments in market and marketing infrastructure, processing technologies, irrigation/water provision and information dissemination are recommended to enhance the potential of the cassava sector to support agricultural growth in Nigeria.

Assessing Potential Laser Strike Protection Engineering Control for United States Coast Guard Aircraft

Thesis (Master's)--University of Washington, 2016-06

Sediment Budget for Cane Land on the Lower Herbert River Floodplain, North Queensland, Australia

Land use in the river catchments of tropical North Queensland appears to have increased the export of sediment and nutrients to the coast. Although evidence of harmful effect of sediment on coastal and riverine ecosystems is limited, there is a growing concern about its possible negative impacts. Sugarcane cultivation on the floodplains of the tropical North Queensland river catchments is thought to be an important source of excess sediment in the river drainage systems. Minimum-tillage, trash blanket harvesting has been shown to reduce erosion from sloping sugarcane fields, but in the strongly modified floodplain landscape other elements (e.g. drains, water furrows and headlands) could still be important sediment sources. The main objectives of this thesis are to quantify the amount of sediment coming from low-lying cane land and identify the important sediment sources in the landscape. The results of this thesis enable sugarcane farmers to take targeted measures for further reduction of the export of sediment and nutrients. Sediment budgets provide a useful approach to identify and quantify potential sediment sources. For this study a sediment budget is calculated for a part of the Ripple Creek catchment, which is a sub-catchment of the Lower Herbert River. The input of sediment from all potential sources in cane land and the storage of sediment within the catchment have been quantified and compared with the output of sediment from the catchment. Input from, and storage on headlands, main drains, minor drains and water furrows, was estimated from erosion pin and surface profile measurements. Input from forested upland, input from fields and the output at the outlet of the catchment was estimated with discharge data from gauged streams and flumes. Data for the sediment budget were collected during two ‘wet’-seasons: 1999-2000 and 2000-2001. The results of the sediment budget indicate that this tropical floodplain area is a net source of sediment. Plant cane fields, which do not have a protective trash cover, were the largest net source of sediment during the 1999-2000 season. Sediment input from water furrows was higher, but there was also considerable storage of sediment in this landscape element. Headlands tend to act as sinks. The source or sink function of drains is less clear, but seems to depend on their shape and vegetation cover. An important problem in this study is the high uncertainty in the estimates of the sediment budget components and is, for example, likely to be the cause of the imbalance in the sediment budget. High uncertainties have particularly affected the results from the 20002001 season. The main source of uncertainty is spatial variation in the erosion and deposition processes. Uncertainty has to be taken into consideration when interpreting the budget results. The observation of a floodplain as sediment source contradicts the general understanding that floodplains are areas of sediment storage within river catchments. A second objective of this thesis was therefore to provide an answer to the question: how can floodplains in the tropical North Queensland catchments can be a source of sediment? In geomorphic literature various factors have been pointed out, that could control floodplain erosion processes. However, their importance is not 'uniquely identified'. Among the most apparent factors are the stream power of the floodwater and the resistance of the floodplain surface both through its sedimentary composition and the vegetation cover. If the cultivated floodplains of the North Queensland catchments are considered in the light of these factors, there is a justified reason to expect them to be a sediment source. Cultivation has lowered the resistance of their surface; increased drainage has increased the drainage velocity and flood control structures have altered flooding patterns. For the Ripple Creek floodplain four qualitative scenarios have been developed that describe erosion and deposition under different flow conditions. Two of these scenarios were experienced during the budget study, involving runoff from local hillslopes and heavy rainfall, which caused floodplain erosion. In the longer term larger flood events, involving floodwater from the Herbert River, may lead to different erosion and deposition processes. The present study has shown that the tropical floodplain of the Herbert River catchment can be a source of sediment under particular flow conditions. It has also shown which elements in the sugarcane landscape are the most important sediment sources under these conditions. This understanding will enable sugarcane farmers to further reduce sediment export from cane land and prevent the negative impact this may have on the North Queensland coastal ecosystems.