Phytoplankton versus macrophyte contribution to primary production and biogeochemical cycles of a coastal mesotidal system. A modelling approach

This study presents an assessment of the contributions of various primary producers to the global annual production and N/P cycles of a coastal system, namely the Arcachon Bay, by means of a numerical model. This 3D model fully couples hydrodynamic with ecological processes and simulates nitrogen, silicon and phosphorus cycles as well as phytoplankton, macroalgae and seagrasses. Total annual production rates for the different components were calculated for different years (2005, 2007 and 2009) during a time period of drastic reduction in seagrass beds since 2005. The total demand of nitrogen and phosphorus was also calculated and discussed with regards to the riverine inputs. Moreover, this study presents the first estimation of particulate organic carbon export to the adjacent open ocean. The calculated annual net production for the Arcachon Bay (except microphytobenthos, not included in the model) ranges between 22,850 and 35,300 tons of carbon. The main producers are seagrasses in all the years considered with a contribution ranging from 56% to 81% of global production. According to our model, the -30% reduction in seagrass bed surface between 2005 and 2007, led to an approximate 55% reduction in seagrass production, while during the same period of time, macroalgae and phytoplankton enhanced their productions by about +83% and +46% respectively. Nonetheless, the phytoplankton production remains about eightfold higher than the macroalgae production. Our results also highlight the importance of remineralisation inside the Bay, since riverine inputs only fulfill at maximum 73% nitrogen and 13% phosphorus demands during the years 2005, 2007 and 2009. Calculated advection allowed a rough estimate of the organic matter export: about 10% of the total production in the bay was exported, originating mainly from the seagrass compartment, since most of the labile organic matter was remineralised inside the bay.

Construção de modelos de interação in silico e in vitro do inibidor do tipo Kunitz de Adenanthera pavonina L. para as enzimas cisteínicas e serínicas

Serines proteinases inhibitors (PIs) are widely distributed in nature and are able to inhibit both in vitro and in vivo enzymatic activites. Seed PIs in than leguminous are classified in seven families, Bowman-Birk and Kunitz type families that most studied representing an important role in the first line of defense toward insects pests. Some Kunitz type inhibitors possess activities serine and cysteine for proteinases named bifunctional inhibitor, as ApTKI the inhibitor isolate from seed of Adenanthera pavonina. The A. pavonina inhibitor presenting the uncommon property and was used for interaction studies between proteinases serine (trypsin) and cysteine (papain). In order to determinate the in vitro interaction of ApTKI against enzymes inhibitor purification was carried cut by using chromatographic techniques and inhibition assays. The 3D model of the bifunctional inhibitor ApTKI was constructed SWISS-MODEL program by homology modeling using soybean trypsin inhibitor (STI, pdb:1ba7), as template which presented 40% of identity to A. pavonina inhibitor. Model quality was evaluated by PROCHECK program. Moreover in silico analyzes of formed complex between the enzymes and ApTKI was evaluated by HEX 4.5 program. In vitro results confirmed the inhibitory assays, where the inhibitor presented the ability to simultaneously inhibit trypsin and papain. The residues encountered in the inhibitor model of folder structural three-dimensional that make contact to enzymes target coud explain the specificity pattern against serine and cysteine proteinases

Coastal zone oil spill modeling

This work presents the development and application of a three-dimensional oil spill model for predicting the movement of an oil slick in the coastal waters of Singapore. In the model, the oil slick is divided into a number of small elements for simulating of the oil processes of spreading, advection, turbulent diffusion. This model is capable of predicting the horizontal movement of surface oil slick. Satellite images and field observations of oil slicks on the surface in the Singapore Straits are used to validate the newly developed model. Compared with the observations, the numerical results of the oil spill model show good conformity. In this study, the 3d model was generated using the geometrical data of Singapore Straits waters by GAMBIT which is a pre-processor of FLUENT programmed.

A Numerical study of fluid flow in peristaltic pumps and polymeric elastic pipes

This thesis work deals with a mathematical description of flow in polymeric pipe and in a specific peristaltic pump. This study involves fluid-structure interaction analysis in presence of complex-turbulent flows treated in an arbitrary Lagrangian-Eulerian (ALE) framework. The flow simulations are performed in COMSOL 4.4, as 2D axial symmetric model, and ABAQUS 6.14.1, as 3D model with symmetric boundary conditions. In COMSOL, the fluid and structure problems are coupled by monolithic algorithm, while ABAQUS code links ABAQUS CFD and ABAQUS Standard solvers with single block-iterative partitioned algorithm. For the turbulent features of the flow, the fluid model in both codes is described by RNG k-ϵ. The structural model is described, on the basis of the pipe material, by Elastic models or Hyperelastic Neo-Hookean models with Rayleigh damping properties. In order to describe the pulsatile fluid flow after the pumping process, the available data are often defective for the fluid problem. Engineering measurements are normally able to provide average pressure or velocity at a cross-section. This problem has been analyzed by McDonald's and Womersley's work for average pressure at fixed cross section by Fourier analysis since '50, while nowadays sophisticated techniques including Finite Elements and Finite Volumes exist to study the flow. Finally, we set up peristaltic pipe simulations in ABAQUS code, by using the same model previously tested for the fl uid and the structure.

Análise e Prevenção de avarias de um veio de manivelas de um motor Pielstick

Na engenharia mecânica há cada vez mais necessidade de utilizar e de prever o comportamento das máquinas térmicas, mais propriamente dos motores de combustão interna, em especial na área da manutenção e da prevenção de falha num dos componentes vitais de um motor a 4 tempos: o veio de manivelas. Esta situação já tem sido bastante observada na indústria mecânica naval, nomeadamente na Marinha Portuguesa e, devido ao seu elevado grau de importância no desempenho de qualquer motor, decidiu-se focar o trabalho desta tese no estudo dos motores a diesel S.E.M.T Pielstick das unidades navais da Marinha Portuguesa, mais especificamente das corvetas da classe “João Coutinho” e da classe “ Baptista de Andrade”, devido ao historial de ocorrência de falhas no veio de manivelas nesta classe de navios e em outras da Marinha Portuguesa. Para efetuar este estudo, utilizaram-se todos os dados relativos ao historial de ocorrências de falhas destes motores, bem como todos os dados disponíveis do fabricante destes motores, por forma a reproduzir da forma mais fiável possível um modelo tridimensional do veio de manivelas no programa de modelação informática CAD Solidworks®, e possibilitar a análise cinemática do veio de manivelas. Desta forma, foi possível simular as condições de funcionamento do motor, assim como analisar e determinar a causa de falha do veio de manivelas, visando prolongar a vida útil dos veios de manivelas, contribuindo não só para menores custos de manutenção mas também para o aumento da operacionalidade destes navios.

Radiobiological model comparison of 3D conformal radiotherapy and IMRT plans for the treatment of prostate cancer

The main aim of radiotherapy is to deliver a dose of radiation that is high enough to destroy the tumour cells while at the same time minimising the damage to normal healthy tissues. Clinically, this has been achieved by assigning a prescription dose to the tumour volume and a set of dose constraints on critical structures. Once an optimal treatment plan has been achieved the dosimetry is assessed using the physical parameters of dose and volume. There has been an interest in using radiobiological parameters to evaluate and predict the outcome of a treatment plan in terms of both a tumour control probability (TCP) and a normal tissue complication probability (NTCP). In this study, simple radiobiological models that are available in a commercial treatment planning system were used to compare three dimensional conformal radiotherapy treatments (3D-CRT) and intensity modulated radiotherapy (IMRT) treatments of the prostate. Initially both 3D-CRT and IMRT were planned for 2 Gy/fraction to a total dose of 60 Gy to the prostate. The sensitivity of the TCP and the NTCP to both conventional dose escalation and hypo-fractionation was investigated. The biological responses were calculated using the Källman S-model. The complication free tumour control probability (P+) is generated from the combined NTCP and TCP response values. It has been suggested that the alpha/beta ratio for prostate carcinoma cells may be lower than for most other tumour cell types. The effect of this on the modelled biological response for the different fractionation schedules was also investigated.

Approach to developing a 3D conceptual hydrogeology model, in a system with multiple bore logs, Howard East, Darwin, using in-house software (GVS)

The Howard East rural area has experienced a rapid growth of small block subdivisions and horticulture over the last 40 years, which has been based on groundwater supply. Early bores in the area provide part of the water supply for Darwin City and are maintained and monitored by NT Power & Water Corporation. The Territory government (NRETAS) has established a monitoring network, and now 48 bores are monitored. However, in the area there are over 2700 private bores that are unregulated.Although NRETAS has both FDM and FEM simulations for the region, community support for potential regulation is sought. To improve stakeholder understanding of the resource QUT was retained by the TRaCKconsortium to develop a 3D visualisation of the groundwater system.

Creation of a validated 3D finite element model of an ovine tibia

Introduction Ovine models are widely used in orthopaedic research. To better understand the impact of orthopaedic procedures computer simulations are necessary. 3D finite element (FE) models of bones allow implant designs to be investigated mechanically, thereby reducing mechanical testing. Hypothesis We present the development and validation of an ovine tibia FE model for use in the analysis of tibia fracture fixation plates. Material & Methods Mechanical testing of the tibia consisted of an offset 3-pt bend test with three repetitions of loading to 350N and return to 50N. Tri-axial stacked strain gauges were applied to the anterior and posterior surfaces of the bone and two rigid bodies – consisting of eight infrared active markers, were attached to the ends of the tibia. Positional measurements were taken with a FARO arm 3D digitiser. The FE model was constructed with both geometry and material properties derived from CT images of the bone. The elasticity-density relationship used for material property determination was validated separately using mechanical testing. This model was then transformed to the same coordinate system as the in vitro mechanical test and loads applied. Results Comparison between the mechanical testing and the FE model showed good correlation in surface strains (difference: anterior 2.3%, posterior 3.2%). Discussion & Conclusion This method of model creation provides a simple method for generating subject specific FE models from CT scans. The use of the CT data set for both the geometry and the material properties ensures a more accurate representation of the specific bone. This is reflected in the similarity of the surface strain results.

Interactions between human osteoblasts and prostate cancer cells in a novel 3D in vitro model

Cell-cell and cell-matrix interactions play a major role in tumor morphogenesis and cancer metastasis. Therefore, it is crucial to create a model with a biomimetic microenvironment that allows such interactions to fully represent the pathophysiology of a disease for an in vitro study. This is achievable by using three-dimensional (3D) models instead of conventional two-dimensional (2D) cultures with the aid of tissue engineering technology. We are now able to better address the complex intercellular interactions underlying prostate cancer (CaP) bone metastasis through such models. In this study, we assessed the interaction of CaP cells and human osteoblasts (hOBs) within a tissue engineered bone (TEB) construct. Consistent with other in vivo studies, our findings show that intercellular and CaP cell-bone matrix interactions lead to elevated levels of matrix metalloproteinases, steroidogenic enzymes and the CaP biomarker, prostate specific antigen (PSA); all associated with CaP metastasis. Hence, it highlights the physiological relevance of this model. We believe that this model will provide new insights for understanding of the previously poorly understood molecular mechanisms of bone metastasis, which will foster further translational studies, and ultimately offer a potential tool for drug screening. © 2010 Landes Bioscience.

A 3D visualisation model applied to a thick, multi-layered alluvial groundwater system under stress : Condamine Valley, QLD

The upper Condamine River in southern Queensland has formed extensive alluvial deposits which have been used for irrigation of cotton crops for over 40 years. Due to excessive use and long term drought conditions these groundwater resources are under substantial threat. This condition is now recognised by all stakeholders, and Qld Department of Environment and Resource Management (DERM) are currently undertaking a water planning process for the Central Condamine Alluvium with water users and other stakeholders. DERM aims to effectively demonstrate the character of the groundwater system and its current status, and notably the continued long-term drawdown of the watertable. It was agreed that 3D visualisation was an ideal tool to achieve this. The Groundwater Visualisation System (GVS) developed at QUT was utilised and the visualisation model developed in conjunction with DERM to achieve a planning-management tool for this particular application

Engineered silk fibroin protein 3D matrices for in vitro tumor model

3D in vitro model systems that are able to mimic the in vivo microenvironment are now highly sought after in cancer research. Antheraea mylitta silk fibroin protein matrices were investigated as potential biomaterial for in vitro tumor modeling. We compared the characteristics of MDA-MB-231 cells on A. mylitta, Bombyx mori silk matrices, Matrigel, and tissue culture plates. The attachment and morphology of the MDA-MB-231 cell line on A. mylitta silk matrices was found to be better than on B. mori matrices and comparable to Matrigel and tissue culture plates. The cells grown in all 3D cultures showed more MMP-9 activity, indicating a more invasive potential. In comparison to B. mori fibroin, A. mylitta fibroin not only provided better cell adhesion, but also improved cell viability and proliferation. Yield coefficient of glucose consumed to lactate produced by cells on 3D A. mylitta fibroin was found to be similar to that of cancer cells in vivo. LNCaP prostate cancer cells were also cultured on 3D A. mylitta fibroin and they grew as clumps in long term culture. The results indicate that A. mylitta fibroin scaffold can provide an easily manipulated microenvironment system to investigate individual factors such as growth factors and signaling peptides, as well as evaluation of anticancer drugs.

A bioengineered 3D ovarian cancer model for the assessment of peptidase-mediated enhancement of spheroid growth and intraperitoneal spread

Cancer-associated proteases promote peritoneal dissemination and chemoresistance in malignant progression. In this study, kallikrein-related peptidases 4, 5, 6, and 7 (KLK4-7)-cotransfected OV-MZ-6 ovarian cancer cells were embedded in a bioengineered three-dimensional (3D) microenvironment that contains RGD motifs for integrin engagement to analyze their spheroid growth and survival after chemotreatment. KLK4-7-cotransfected cells formed larger spheroids and proliferated more than controls in 3D, particularly within RGD-functionalized matrices, which was reduced upon integrin inhibition. In contrast, KLK4-7-expressing cell monolayers proliferated less than controls, emphasizing the relevance of the 3D microenvironment and integrin engagement. In a spheroid-based animal model, KLK4-7-overexpression induced tumor growth after 4 weeks and intraperitoneal spread after 8 weeks. Upon paclitaxel administration, KLK4-7-expressing tumors declined in size by 91% (controls: 87%) and showed 90% less metastatic outgrowth (controls: 33%, P<0.001). KLK4-7-expressing spheroids showed 53% survival upon paclitaxel treatment (controls: 51%), accompanied by enhanced chemoresistance-related factors, and their survival was further reduced by combination treatment of paclitaxel with KLK4/5/7 (22%, P=0.007) or MAPK (6%, P=0.006) inhibition. The concomitant presence of KLK4-7 in ovarian cancer cells together with integrin activation drives spheroid formation and proliferation. Combinatorial approaches of paclitaxel and KLK/MAPK inhibition may be more efficient for late-stage disease than chemotherapeutics alone as these inhibitory regimens reduced cancer spheroid growth to a greater extent than paclitaxel alone.

Augmenting and assisting model elicitation tasks with 3D virtual world context metadata

Accurate process model elicitation continues to be a time consuming task, requiring skill on the part of the interviewer to extract explicit and tacit process information from the interviewee. Many errors occur in this elicitation stage that would be avoided by better activity recall, more consistent specification methods and greater engagement in the elicitation process by interviewees. Theories of situated cognition indicate that interactive 3D representations of real work environments engage and prime the cognitive state of the viewer. In this paper, our major contribution is to augment a previous process elicitation methodology with virtual world context metadata, drawn from a 3D simulation of the workplace. We present a conceptual and formal approach for representing this contextual metadata, integrated into a process similarity measure that provides hints for the business analyst to use in later modelling steps. Finally, we conclude with examples from two use cases to illustrate the potential abilities of this approach.

Model as you do : engaging an S-BPM vendor on process modelling in 3D virtual worlds

Accurate process model elicitation continues to be a time consuming task, requiring skill on the part of the interviewer to extract explicit and tacit process information from the interviewee. Many errors occur in this elicitation stage that would be avoided by better activity recall, more consistent specification methods and greater engagement in the elicitation process by interviewees. Metasonic GmbH has developed a process elicitation tool for their process suite. As part of a research engagement with Metasonic, staff from QUT, Australia have developed a 3D virtual world approach to the same problem, viz. eliciting process models from stakeholders in an intuitive manner. This book chapter tells the story of how QUT staff developed a 3D Virtual World tool for process elicitation, took the outcomes of their research project to Metasonic for evaluation, and finally, Metasonic’s response to the initial proof of concept.