POEM, A 3-dimensional exon taxonomy and patterns in untranslated exons

Background: The existence of exons and introns has been known for thirty years. Despite this knowledge, there is a lack of formal research into the categorization of exons. Exon taxonomies used by researchers tend to be selected ad hoc or based on an information poor de-facto standard. Exons have been shown to have specific properties and functions based on among other things their location and order. These factors should play a role in the naming to increase specificity about which exon type(s) are in question.

Results: POEM (Protein Oriented Exon Monikers) is a new taxonomy focused on protein proximal exons. It integrates three dimensions of information (Global Position, Regional Position and Region), thus its exon categories are based on known statistical exon features. POEM is applied to two congruent untranslated exon datasets resulting in the following statistical properties. Using the POEM taxonomy previous wide ranging estimates of initial 5' untranslated region exons are resolved. According to our datasets, 29–36% of genes have wholly untranslated first exons. Untranslated exon containing sequences are shown to have consistently up to 6 times more 5' untranslated exons than 3' untranslated exons. Finally, three exon patterns are determined which account for 70% of untranslated exon genes.

Conclusion: We describe a thorough three-dimensional exon taxonomy called POEM, which is biologically and statistically relevant. No previous taxonomy provides such fine grained information and yet still includes all valid information dimensions. The use of POEM will improve the accuracy of genefinder comparisons and analysis by means of a common taxonomy. It will also facilitate unambiguous communication due to its fine granularity

3-dimensional characterization of membrane with nanoporous structure using TEM tomography and image analysis

The nanoporous structure of membrane varies in 3-dimensional (3-D) space and has remarkable influences on the filtration or desalination achieved, fouling potentials and therefore, the quality of yielded water. Knowledge of the 3-D nanoporous structure is thus vital to understanding and predicting its performance. A novel method by incorporating transmission electronic microtomography, image processing and 3-D reconstruction is introduced to characterize membranes with nano structures. The reconstruction algorithm allows for the visualization of 3-D nanoporous structure in a non-destructive way from any directions. This novel technique Ieads to in-depth understanding and accurate prediction of filtration performance.

3-dimensional characterization of membrane with nanoporous structure using TEM tomography and image analysis

The nanoporous structure of a membrane varies in a 3-dimensional (3-D) space and has remarkable influences on the filtration or desalination achieved, fouling potentials and therefore, the quality of yielded water. Knowledge of the 3-D nanoporous structure is thus vital to understanding and predicting its performance. A novel method by incorporating transmission electronic microtomography, image processing and 3-D reconstruction is introduced to characterize membranes with nano structures. The reconstruction algorithm allows for the visualization of 3-D nanoporous structure in a non-destructive way from any directions. This novel technique leads to in-depth understanding and accurate prediction of filtration performance.

Super-resolution of a 3-dimensional scene from novel viewpoints

Super-resolution is a method of post-processing image enhancement that increases the spatial resolution of video or images. Existing super-resolution techniques apply only to images captured of a planar scene. This paper aims to extend super-resolution concepts from the 2D domain to the 3D domain, drawing on ideas from both superresolution and multi-view geometry, two fields of research that until now have predominantly been studied in isolation. 2D super-resolution methods are not without their complexities and limitations. However, once multiple views of a scene are considered within a super-resolution framework, a new range of issues arise that must also be resolved. For example, when input images of a scene with variation in depth are considered, it is no longer clear how and where the images should be registered. This paper describes the use of sparse 3D reconstruction in order to ‘register’ the input images, which are then transferred to a novel image plane and combined to increase the perceived detail in the scene. Experimental results using real images captured from generally positioned input cameras are presented.

Super-resolution of 3-dimensional scenes

Super-resolution is an image enhancement method that increases the resolution of images and video. Previously this technique could only be applied to 2D scenes. The super-resolution algorithm developed in this thesis creates high-resolution views of 3-dimensional scenes, using low-resolution images captured from varying, unknown positions.

Validating the relationship between 3-dimensional body acceleration and oxygen consumption in trained Steller sea lions

We tested the ability of overall dynamic body acceleration (ODBA) to predict the rate of oxygen consumption ([Formula: see text]) in freely diving Steller sea lions (Eumetopias jubatus) while resting at the surface and diving. The trained sea lions executed three dive types-single dives, bouts of multiple long dives with 4-6 dives per bout, or bouts of multiple short dives with 10-12 dives per bout-to depths of 40 m, resulting in a range of activity and oxygen consumption levels. Average metabolic rate (AMR) over the dive cycle or dive bout calculated was calculated from [Formula: see text]. We found that ODBA could statistically predict AMR when data from all dive types were combined, but that dive type was a significant model factor. However, there were no significant linear relationships between AMR and ODBA when data for each dive type were analyzed separately. The potential relationships between AMR and ODBA were not improved by including dive duration, food consumed, proportion of dive cycle spent submerged, or number of dives per bout. It is not clear whether the lack of predictive power within dive type was due to low statistical power, or whether it reflected a true absence of a relationship between ODBA and AMR. The average percent error for predicting AMR from ODBA was 7-11 %, and standard error of the estimated AMR was 5-32 %. Overall, the extensive range of dive behaviors and physiological conditions we tested indicated that ODBA was not suitable for estimating AMR in the field due to considerable error and the inconclusive effects of dive type.

Multicellular spheroids in ovarian cancer metastases: Biology and pathology

Epithelial ovarian cancer (EOC) has a relatively high mortality rate (~55%). One of the presiding causes is that the current chemotherapeutic regimes are unable to achieve sustained remission, despite frequently producing a positive response at first treatment. One of the reasons that EOC is difficult to treat is that the mechanism of dissemination is unusual. EOC dissemination characteristically involves local invasion of pelvic and abdominal organs. Unlike many epithelial cancers, initial dissemination rarely requires the vasculature, although the vasculature is often implicated in the advanced stages of disease. Recently, it has become apparent that aggregates of malignant cells (spheroids) contained within malignant ascites represent a significant impediment to efficacious treatment of late stage EOC. In vivo, spheroids are present in the malignant ascites of EOC patients, while in vitro cultured spheroids are capable of tumorgenesis in vivo and display a reduced response to chemotherapeutic drugs when compared to monolayers. A major problem associated with the current generation of chemotherapy agents is that they do not address the anchorage and vascular-independent growth conditions associated with a 3-dimensional structure that has formed and/or grown in suspension. Thus, spheroid formation may represent a key component of platinum/taxanesensitive recurrence. If this is correct, a better understanding of spheroid biology may contribute to the identification of new treatment opportunities for the sustained treatment of metastatic EOC. This review article outlines the key biological features of spheroids, specifically discussing their role in EOC dissemination and chemo-response as well as providing insights into spheroid functionality.

Interobserver reliability of coronoid fracture classification : two-dimensional versus three-dimensional computed tomography

Purpose : This study tests the hypothesis that 3-dimensional computed tomography (CT) reconstructions improve interobserver agreement on classification and treatment of coronoid fractures compared with 2-dimensional CT.

Methods : A total of 29 orthopedic surgeons evaluated 10 coronoid fractures on 2 occasions (first with radiographs and 2-dimensional CT and then with radiographs and 3-dimensional CT), separated by a minimum of 2 weeks. Surgeons classified fractures according to the classifications of Regan and Morrey and of O'Driscoll et al., identified specific characteristics, recommended the most appropriate treatment approach, and made treatment recommendations. The kappa multirater measure (κ) was calculated to estimate agreement between observers.

Results : Regardless of the imaging modality used, there was fair to moderate agreement for most of the observations. Three-dimensional CT improved interobserver agreement in Regan and Morrey's classsication (κ3-dimensional = 0.51 vs κ2-dimensional = 0.40; p < .001) and O'Driscoll et al.'s classifications (κ3-dimensional = 0.48 vs κ2-dimensional = 0.42; p = .009). There were trends toward better reliability for 3-dimensional reconstruction in recognition of coronoid tip fractures (κ3-dimensional = 0.19, κ2-dimensional = 0.03; p = .268), comminution (κ3-dimensional = 0.41 vs κ2-dimensional = 0.29; p = .133), and impacted fragments (κ3-dimensional = 0.39 vs κ2-dimensional = 0.27; p = .094), and in surgeons' opinions on the need for something other than screws or plate for surgical fixation (κ3-dimensional = 0.31 vs κ2-dimensional = 0.15; p = .138). Interobserver agreement on treatment approach was better with 2-dimensional CT (κ3-dimensional = 0.27, κ2-dimensional = 0.32; p = .015).

Conclusions : Three-dimensional CT reconstructions improve interobserver agreement with respect to fracture classification compared with 2-dimensional CT.

Evaluation of selective growth in a Fe-2.8% Si single crystal using Rodrigues-Frank space

A Fe-2.8%Si single crystal was scratched in order to randomise the texture in the neighbourhood of the notch. Annealing resulted in recrystallization and grain growth starting from the deformed zone. Misorientations between the single crystal matrix and the grown grains were gathered and were studied in order to investigate the possibility for selective growth based on a specific misorientation. However, instead of studying the misorientation angle or axis profiles separately in a 1D or 2D projection a full misorientation analysis was carried out in the 3-dimensional Rodrigues-Frank misorientation space, which offers an unambiguous interpretation of the data because no features are hidden or masked by a projection. It is concluded that the selective growth phenomenon following the <110>26.5deg misorientation relationship is strongly supported by the gathered orientation data, after appropriately normalizing these data with respect to a random misorientation distribution.

Interacting amino acid preferences of 3D pattern pairs at the binding sites of transient and obligate protein complexes

To assess the physico-chemical characteristics of protein-protein interactions, protein sequences and overall structural folds have been analyzed previously. To highlight this, discovery and examination of amino acid patterns at the binding sites defined by structural proximity in 3-dimensional (3D) space are essential. In this paper, we investigate the interacting preferences of 3D pattern pairs discovered separately in transient and obligate protein complexes. These 3D pattern pairs are not necessarily sequence-consecutive, but each residue in two groups of amino acids from two proteins in a complex is within certain °A threshold to most residues in the other group. We develop an algorithm called AA-pairs by which every pair of interacting proteins is represented as a bipartite graph, and it discovers all maximal quasi-bicliques from every bipartite graph to form our 3D pattern pairs. From 112 and 2533 highly conserved 3D pattern pairs discovered in the transient and obligate complexes respectively, we observe that Ala and Leu is the highest occuring amino acid in interacting 3D patterns of transient (20.91%) and obligate (33.82%) complexes respectively. From the study on the dipeptide composition on each side of interacting 3D pattern pairs, dipeptides Ala-Ala and Ala-Leu are popular in 3D patterns of both transient and obligate complexes. The interactions between amino acids with large hydrophobicity difference are present more in the transient than in the obligate complexes. On contrary, in obligate complexes, interactions between hydrophobic residues account for the top 5 most occuring amino acid pairings.

Convection suppression in an attic shaped enclosure

In recent times there has been growing interest in the integration of solar collectors, for water heating, into the façade of buildings. However, the design methodology of these devices remains largely the same as typical “stand-alone” collectors. As such it is still common for materials with a high thermal resistance to be used for insulating the rear surface of these collectors.

Unlike a “stand-alone” solar collector that is exposed to the atmosphere at all faces; a building integrated system allows the opportunity for air to act as an insulator at the rear surface of the solar collector. The use of convection suppression devices has been widely discussed in the literature as a means of reducing natural convection heat loss from the front surface of glazed solar collectors. However in this study the use of baffles in an attic was examined as a means of suppressing heat loss by natural convection from the rear surface of a roof-integrated solar collector. The aim of the study was to examine whether the use of baffles would allow the cost of building integrated collectors to be reduced by removing the cost of insulating material.

To determine the effect of baffles in the attic space at the rear surface of the collector, a 3-dimensional triangular cross sectioned enclosure with a vertical aspect ratio of 0.5 and a horizontal aspect ratio of 3.3 was modelled. The flow patterns and heat transfer in the enclosure were determined for Grashof Numbers in the range of 106 to 107 using a commercially available finite volume CFD solver.
It was found that the use of a single adiabatic baffle mounted vertically downwards from the apex, and extending the length of the enclosure, would alter the flow such that the heat transfer due to natural convection was reduced with respect to the length of the baffle.

Furthermore, it was observed that a series of convection cells, not previously reported in the literature, appeared to exist along the length of the enclosure. As such, it may be possible to derive additional benefit in reducing the heat transfer by adding lateral baffles in addition to the single longitudinal baffle modelled in this study.

Development and application of a microelectrode based scanning voltammetric detector

A large part of the work presented in this thesis describes the development and use of a novel electrochemical detector designed to allow the electrochemical characterisation of compounds in flowing solution by means of cyclic voltammetry. The detector was microprocessor controlled, which provides digital generation of the potential waveform and collection of data for subsequent analysis. Microdisk working electrodes are employed to permit both thermodynamic and kinetically controlled processes to be studied under steady-state conditions in flowing solutions without the distortion or hysteresis normally encountered with larger sized electrodes. The effect of electrode size, potential scan rate, and solution flow rate are studied extensively with the oxidation of ferrocene used as an example of a thermodynamically controlled process and a series of catecholamines as examples of a kinetically controlled process. The performance of the detector was best demonstrated when used as a HPLC post-column detector. The 3-dimensional chromatovoltammograms obtained allow on-line characterisation of each fraction as it elutes from the column. The rest of the work presented in this thesis involves the study of the oxidative degradation pathway of dithranol. The oxidative pathway was shown to involve a complex free radical mechanism, dependent on the presence of both oxygen and, in particular light. The pathway is further complicated by the fact that dithranol may exist in either a keto or enol form, the enol being most susceptible to oxidation. A likely mechanism is proposed from studies performed with cyclic voltammetry and controlled potential electrolysis, then defined by subsequent kinetic studies.

Virtual worlds to enhance student engagement

Both the School of Education and the discipline of Criminology at Deakin University have been using the 3-dimensional environment Second Life to deliver curriculum content and to engage students with each other and with teaching staff. The nature of this platform is facilitating more proactive student engagement with technology, including increased student competence in sharing artwork, problem solving and general discussion of complex criminological issues. In this paper, we provide some examples of how we are using Second Life in our curriculum offerings in Education and Criminology as a tool to promote greater engagement, particularly for students undertaking their courses by distance. We outine how the immersive nature of this platform can enhance the level of student interaction to produce a deeper form of engagement with our Unit material than is possible through conventional text and web-based document repositories.

Obstacles in the optimization of bone health outcomes in the female athlete triad

Maintaining low body weight for the sake of performance and aesthetic purposes is a common feature among young girls and women who exercise on a regular basis, including elite, college and high-school athletes, members of fitness centres, and recreational exercisers. High energy expenditure without adequate compensation in energy intake leads to an energy deficiency, which may ultimately affect reproductive function and bone health. The combination of low energy availability, menstrual disturbances and low bone mineral density is referred to as the ‘female athlete triad’. Not all athletes seek medical assistance in response to the absence of menstruation for 3 or more months as some believe that long-term amenorrhoea is not harmful. Indeed, many women may not seek medical attention until they sustain a stress fracture.
This review investigates current issues, controversies and strategies in the clinical management of bone health concerns related to the female athlete triad. Current recommendations focus on either increasing energy intake or decreasing energy expenditure, as this approach remains the most efficient strategy to prevent further bone health complications. However, convincing the athlete to increase energy availability can be extremely challenging.
Oral contraceptive therapy seems to be a common strategy chosen by many physicians to address bone health issues in young women with amenorrhoea, although there is little evidence that this strategy improves bone mineral density in this population. Assessment of bone health itself is difficult due to the limitations of dual-energy X-ray absorptiometry (DXA) to estimate bone strength. Understanding how bone strength is affected by low energy availability, weight gain and resumption of menses requires further investigations using 3-dimensional bone imaging techniques in order to improve the clinical management of the female athlete triad.