Predictive modelling for health and health-care utilisation : an observational study for Australians aged 45 and up

The burden of chronic disease is growing at a fast pace, leading to poor quality of life and high healthcare expenditures in a large portion of the Australian population. Much of the burden is borne by hospitals, and therefore there is an ever-increasing interest in preventative interventions that can keep people out of hospitals and healthier for longer periods. There is a wide range of potential interventions that may be able to achieve this goal, and policy makers need to decide which one should be funded and implemented. This task is difficult for two reasons: first it is often not clear what is the short-term effectiveness of an intervention, and how it varies in specific sub-populations, and second it is also not clear what the long-term intended and unintended consequences might be. In this thesis I make contributions to address both these difficulties. On the short-term side I focus on the use of physical activity to prevent the development of chronic disease and to reduce hospital costs. Increasing physical activity has been long heralded as a way to achieve these goals but evidence of its effectiveness has been elusive. In this thesis I provide data driven evidence to justify policies that encourage higher levels of physical activity (PA) in middle age and older Australian population. I use data from the “45 and up” and the Social, Economic and Environmental Factors (SEEF) study, linked with the Admitted Patient Data Collection (APDC), to identify and study the cost and health trajectories of individuals with different levels of physical activity. The results show a clear statistically significant association between PA and lower hospitalisation cost, as well as between PA and reduced risk of heart disease, diabetes and stroke. On the long-term side of the analysis, I placed this thesis in the context of a larger program of work performed at Western Sydney University that aims to build a microsimulation model for the analysis of health policy interventions. In this framework I studied predictive models that use survey and/or administrative data to predict hospital costs and resource utilisation. I placed particular emphasis on the application of methods borrowed from Natural Language Processing to understand how to use the thousands of diagnosis and procedure codes found in administrative data as input to predictive models. The methods developed in this thesis go beyond the application to hospital data and can be used in any predictive model that relies on complex coding of healthcare information

The Architectural Formation of Stadiums in Different Periods of Time

Stadiums are places that can bring thousands of people together and create a very sensational architectural atmosphere. Unfortunately, they are seen as monumental objects in big cities and it is as if they were used as sculptures but it has to mention that they are durable volumes but have remained unknown in architectural studies. Looking at stadiums shows that their interior and exterior spaces should be interlocked and makes harmony as the exterior walls can create a city façade and the interior can make balance in people’s emotion, providing that the same regulations and codes should be applied to stadiums in order to increase the coherence with the city

Impact of residue accessible surface area on the prediction of protein secondary structures

<p>Abstract</p> <p>Background</p> <p>The problem of accurate prediction of protein secondary structure continues to be one of the challenging problems in Bioinformatics. It has been previously suggested that amino acid relative solvent accessibility (RSA) might be an effective factor for increasing the accuracy of protein secondary structure prediction. Previous studies have either used a single constant threshold to classify residues into discrete classes (buries vs. exposed), or used the real-value predicted RSAs in their prediction method.</p> <p>Results</p> <p>We studied the effect of applying different RSA threshold types (namely, fixed thresholds vs. residue-dependent thresholds) on a variety of secondary structure prediction methods. With the consideration of DSSP-assigned RSA values we realized that improvement in the accuracy of prediction strictly depends on the selected threshold(s). Furthermore, we showed that choosing a single threshold for all amino acids is not the best possible parameter. We therefore used residue-dependent thresholds and most of residues showed improvement in prediction. Next, we tried to consider predicted RSA values, since in the real-world problem, protein sequence is the only available information. We first predicted the RSA classes by RVP-net program and then used these data in our method. Using this approach, improvement in prediction was also obtained.</p> <p>Conclusion</p> <p>The success of applying the RSA information on different secondary structure prediction methods suggest that prediction accuracy can be improved independent of prediction approaches. Thus, solvent accessibility can be considered as a rich source of information to help the improvement of these methods.</p

The Architectural Formation of Stadiums in Different Periods of Time

Stadiums are places that can bring thousands of people together and create a very sensational architectural atmosphere. Unfortunately, they are seen as monumental objects in big cities and it is as if they were used as sculptures but it has to mention that they are durable volumes but have remained unknown in architectural studies. Looking at stadiums shows that their interior and exterior spaces should be interlocked and makes harmony as the exterior walls can create a city façade and the interior can make balance in people’s emotion, providing that the same regulations and codes should be applied to stadiums in order to increase the coherence with the city

Impact of RNA structure on the prediction of donor and acceptor splice sites

BACKGROUND: gene identification in genomic DNA sequences by computational methods has become an important task in bioinformatics and computational gene prediction tools are now essential components of every genome sequencing project. Prediction of splice sites is a key step of all gene structural prediction algorithms. RESULTS: we sought the role of mRNA secondary structures and their information contents for five vertebrate and plant splice site datasets. We selected 900-nucleotide sequences centered at each (real or decoy) donor and acceptor sites, and predicted their corresponding RNA structures by Vienna software. Then, based on whether the nucleotide is in a stem or not, the conventional four-letter nucleotide alphabet was translated into an eight-letter alphabet. Zero-, first- and second-order Markov models were selected as the signal detection methods. It is shown that applying the eight-letter alphabet compared to the four-letter alphabet considerably increases the accuracy of both donor and acceptor site predictions in case of higher order Markov models. CONCLUSION: Our results imply that RNA structure contains important data and future gene prediction programs can take advantage of such information

FFCA: a feasibility-based method for flux coupling analysis of metabolic networks

<p>Abstract</p> <p>Background</p> <p>Flux coupling analysis (FCA) is a useful method for finding dependencies between fluxes of a metabolic network at steady-state. FCA classifies reactions into subsets (called coupled reaction sets) in which activity of one reaction implies activity of another reaction. Several approaches for FCA have been proposed in the literature.</p> <p>Results</p> <p>We introduce a new FCA algorithm, FFCA (Feasibility-based Flux Coupling Analysis), which is based on checking the feasibility of a system of linear inequalities. We show on a set of benchmarks that for genome-scale networks FFCA is faster than other existing FCA methods.</p> <p>Conclusions</p> <p>We present FFCA as a new method for flux coupling analysis and prove it to be faster than existing approaches. A corresponding software tool is freely available for non-commercial use at <url>http://www.bioinformatics.org/ffca/</url>.</p

A Systems-Based Approach for Cyanide Overproduction by Bacillus megaterium for Gold Bioleaching Enhancement

With the constant accumulation of electronic waste, extracting precious metals contained therein is becoming a major challenge for sustainable development. Bacillus megaterium is currently one of the microbes used for the production of cyanide, which is the main leaching agent for gold recovery. The present study aimed to propose a strategy for metabolic engineering of B. megaterium to overproduce cyanide, and thus ameliorate the bioleaching process. For this, we employed constraint-based modeling, running in silico simulations on iJA1121, the genome-scale metabolic model of B. megaterium DSM319. Flux balance analysis (FBA) was initially used to identify amino acids to be added to the culture medium. Considering cyanide as the desired product, we used growth-coupled methods, constrained minimal cut sets (cMCSs) and OptKnock to identify gene inactivation targets. To identify gene overexpression targets, flux scanning based on enforced objective flux (FSEOF) was performed. Further analysis was carried out on the identified targets to determine compounds with beneficial regulatory effects. We have proposed a chemical-defined medium for accelerating cyanide production on the basis of microplate assays to evaluate the components with the greatest improving effects. Accordingly, the cultivation of B. megaterium DSM319 in a chemically-defined medium with 5.56 mM glucose as the carbon source, and supplemented with 413 μM cysteine, led to the production of considerably increased amounts of cyanide. Bioleaching experiments were successfully performed in this medium to recover gold and copper from telecommunication printed circuit boards. The results of inductively coupled plasma (ICP) analysis confirmed that gold recovery peaked out at around 55% after 4 days, whereas copper recovery continued to increase for several more days, peaking out at around 85%. To further validate the bioleaching results, FESEM, XRD, FTIR, and EDAX mapping analyses were performed. We concluded that the proposed strategy represents a viable route for improving the performance of the bioleaching processes

A tale of two symmetrical tails: Structural and functional characteristics of palindromes in proteins

<p>Abstract</p> <p>Background</p> <p>It has been previously shown that palindromic sequences are frequently observed in proteins. However, our knowledge about their evolutionary origin and their possible importance is incomplete.</p> <p>Results</p> <p>In this work, we tried to revisit this relatively neglected phenomenon. Several questions are addressed in this work. (1) It is known that there is a large chance of finding a palindrome in low complexity sequences (i.e. sequences with extreme amino acid usage bias). What is the role of sequence complexity in the evolution of palindromic sequences in proteins? (2) Do palindromes coincide with conserved protein sequences? If yes, what are the functions of these conserved segments? (3) In case of conserved palindromes, is it always the case that the whole conserved pattern is also symmetrical? (4) Do palindromic protein sequences form regular secondary structures? (5) Does sequence similarity of the two "sides" of a palindrome imply structural similarity? For the first question, we showed that the complexity of palindromic peptides is significantly lower than randomly generated palindromes. Therefore, one can say that palindromes occur frequently in low complexity protein segments, without necessarily having a defined function or forming a special structure. Nevertheless, this does not rule out the possibility of finding palindromes which play some roles in protein structure and function. In fact, we found several palindromes that overlap with conserved protein Blocks of different functions. However, in many cases we failed to find any symmetry in the conserved regions of corresponding Blocks. Furthermore, to answer the last two questions, the structural characteristics of palindromes were studied. It is shown that palindromes may have a great propensity to form α-helical structures. Finally, we demonstrated that the two sides of a palindrome generally do not show significant structural similarities.</p> <p>Conclusion</p> <p>We suggest that the puzzling abundance of palindromic sequences in proteins is mainly due to their frequent concurrence with low-complexity protein regions, rather than a global role in the protein function. In addition, palindromic sequences show a relatively high tendency to form helices, which might play an important role in the evolution of proteins that contain palindromes. Moreover, reverse similarity in peptides does not necessarily imply significant structural similarity. This observation rules out the importance of palindromes for forming symmetrical structures. Although palindromes frequently overlap with conserved Blocks, we suggest that palindromes overlap with Blocks only by coincidence, rather than being involved with a certain structural fold or protein domain.</p