Managing memory and reducing I/O cost for correlation matrix calculation in bioinformatics

The generation of a correlation matrix from a large set of long gene sequences is a common requirement in many bioinformatics problems such as phylogenetic analysis. The generation is not only computationally intensive but also requires significant memory resources as, typically, few gene sequences can be simultaneously stored in primary memory. The standard practice in such computation is to use frequent input/output (I/O) operations. Therefore, minimizing the number of these operations will yield much faster run-times. This paper develops an approach for the faster and scalable computing of large-size correlation matrices through the full use of available memory and a reduced number of I/O operations. The approach is scalable in the sense that the same algorithms can be executed on different computing platforms with different amounts of memory and can be applied to different problems with different correlation matrix sizes. The significant performance improvement of the approach over the existing approaches is demonstrated through benchmark examples.

Reply - Malnutrition and its impact on cost of hospitalization, length of stay, readmission and 3-year mortality

Dear Editor We thank Dr Klek for his interest in our article and giving us the opportunity to clarify our study and share our thoughts. Our study looks at the prevalence of malnutrition in an acute tertiary hospital and tracked the outcomes prospectively.1 There are a number of reasons why we chose Subjective Global Assessment (SGA) to determine the nutritional status of patients. Firstly, we took the view that nutrition assessment tools should be used to determine nutrition status and diagnose presence and severity of malnutrition; whereas the purpose of nutrition screening tools are to identify individuals who are at risk of malnutrition. Nutritional assessment rather than screening should be used as the basis for planning and evaluating nutrition interventions for those diagnosed with malnutrition. Secondly, Subjective Global Assessment (SGA) has been well accepted and validated as an assessment tool to diagnose the presence and severity of malnutrition in clinical practice.2, 3 It has been used in many studies as a valid prognostic indicator of a range of nutritional and clinical outcomes.4, 5, 6 On the other hand, Malnutrition Universal Screening Tool (MUST)7 and Nutrition Risk Screening 2002 (NRS 2002)8 have been established as screening rather than assessment tools.

Hepatitis C and policy implementation : ethics as a dialogic process for resource allocation

Hepatitis C, which was first identified in 1988, has become an important issue for public health as epidemiological and clinical evidence has emerged. These disciplines have highlighted the extent of infection and its medical consequences. Now, governments at both the state and federal levels are sifting through this evidence and are attempting to create structures to deal with the problem of hepatitis C. These structures have generally taken the form of expert committees and working parties organised from established medical, scientific and public health bodies...

Conservatism, disclosure and the cost of equity capital

This study seeks insights into the economic consequences of accounting conservatism by examining the relation between conservatism and cost of equity capital. Appealing to the analytical and empirical literatures, we posit an inverse relation. Importantly, we also posit that the strength of the relation is conditional on the firm’s information environment, being the strongest for firms with high information asymmetry and the weakest (potentially negligible) for firms with low information asymmetry. Based on a sample of US-listed entities, we find, as predicted, an inverse relation between conservatism and the cost of equity capital, but further, that this relation is diminished for firms with low information asymmetry environments. This evidence indicates that there are economic benefits associated with the adoption of conservative reporting practices and leads us to conclude that conservatism has a positive role in accounting principles and practices, despite its increasing rejection by accounting standard setters.

Improved earthwork allocation planning for fuel consumption and emissions reduction in linear infrastructure construction – case study data

This document provides data for the case study presented in our recent earthwork planning papers. Some results are also provided in a graphical format using Excel.

Mortality and cost outcomes of elderly trauma patients admitted to intensive care and the general wards of an Australian tertiary referral hospital

Mortality and cost outcomes of elderly intensive care unit (ICU) trauma patients were characterised in a retrospective cohort study from an Australian tertiary ICU. Trauma patients admitted between January 2000 and December 2005 were grouped into three major age categories: aged ≥65 years admitted into ICU (n=272); aged ≥65 years admitted into general ward (n=610) and aged <65 years admitted into ICU (n=1617). Hospital mortality predictors were characterised as odds ratios (OR) using logistic regression. The impact of predictor variables on (log) total hospital-stay costs was determined using least squares regression. An alternate treatment-effects regression model estimated the mortality cost-effect as an endogenous variable. Mortality predictors (P ≤0.0001, comparator: ICU ≥65 years, ventilated) were: ICU <65 not-ventilated (OR 0.014); ICU <65 ventilated (OR 0.090); ICU age ≥65 not-ventilated (OR 0.061) and ward ≥65 (OR 0.086); increasing injury severity score and increased Charlson comorbidity index of 1 and 2, compared with zero (OR 2.21 [1.40 to 3.48] and OR 2.57 [1.45 to 4.55]). The raw mean daily ICU and hospital costs in A$ 2005 (US$) for age <65 and ≥65 to ICU, and ≥65 to the ward were; for year 2000: ICU, $2717 (1462) and $2777 (1494); hospital, $1837 (988) and $1590 (855); ward $933 (502); for year 2005: ICU, $3202 (2393) and $3086 (2307); hospital, $1938 (1449) and $1914 (1431); ward $1180 (882). Cost increments were predicted by age ≥65 and ICU admission, increasing injury severity score, mechanical ventilation, Charlson comorbidity index increments and hospital survival. Mortalitycost-effect was estimated at -63% by least squares regression and -82% by treatment-effects regression model. Patient demographic factors, injury severity and its consequences predict both cost and survival in trauma. The cost mortality effect was biased upwards by conventional least squares regression estimation.

Cost-informed operational process support

The ability to steer business operations in alignment with the true origins of costs, and to be informed about this on a real-time basis, allows businesses to increase profitability. In most organisations however, high-level cost-based managerial decisions are still being made separately from process-related operational decisions. In this paper, we describe how process-related decisions at the operational level can be guided by cost considerations and how these cost-informed decision rules can be supported by a workflow management system. The paper presents the conceptual framework together with data requirements and technical challenges that need to be addressed to realise cost-informed workflow execution. The feasibility of our approach is demonstrated using a prototype implementation in the YAWL workflow environment.

Sustainable and affordable housing : a myth or reality

The Australian government has released a draft National Building Framework that will likely tighten the building standard for new houses to meet higher sustainability requirements. There are uncertainties about the impact this could have on the cost of housing and the supply of affordable housing. This paper aims to provide evidence-based conclusions on the possibility of delivering sustainable and affordable housing for low income people. The case studies are gathered from Brisbane and Gold Coast. Case studies are analysed by unpacking the features that were included to meet sustainability and affordability goals for housing. This paper outlines the key factors for their success and also challenges for replication of the projects. The study shows that the key success drivers for delivering sustainable and affordable housing are providing planning incentives, subsidies for increased energy efficiency, supportive regulatory frameworks and appropriate allocation of infrastructure charges. It shows that government can prioritise their resources to support affordable and sustainable housing for low income people.

Double tax agreements and the international allocation of business income in Australia

Increasingly, the effectiveness of the present system of taxation of international businesses is being questioned. The problem associated with the taxation of such businesses is twofold. A system of international taxation must be a fair and equitable system, distributing profits between the relevant jurisdictions and, in doing so, avoiding double taxation. At the same time, the prevention of fiscal evasion must be secured. In an attempt to achieve a fair and equitable system Australia adopts unilateral, bilateral and multilateral measures to avoid double taxation and restrict the avoidance of tax. The first step in ascertaining the international allocation of business income is to consider the taxation of business income according to domestic law, that is, the unilateral measures. The treatment of international business income under the Australian domestic law, that is, the Income Tax Assessment Act 1936 (Cth) and Income Tax Assessment Act 1997 (Cth), will depend on two concepts, first, whether the taxpayer is a resident of Australia and secondly, whether the income is sourced in Australia. After the taxation of business profits has been determined according to domestic law it is necessary to consider the applicability of the bilateral measures, that is, the Double Tax Agreements (DTAs) to which Australia is a party, as the DTAs will override the domestic law where there is any conflict. Australia is a party to 40 DTAs with another seven presently being negotiated. The preamble to Australia's DTAs provides that the purpose of such agreements is 'to conclude an Agreement for the avoidance of double taxation and the prevention of fiscal evasion with respect to taxes on income'. Both purposes, for different reasons, are equally important. It has been said that: The taxpayer hopes the treaty will prevent the double taxation of his income; the tax gatherer hopes the treaty will prevent fiscal evasion; and the politician just hopes. The first purpose, the avoidance of double taxation, is achieved through the provision of rules whereby the Contracting States agree to the classification of income and the allocation of that income to a particular State. In this sense DTAs do not allocate jurisdiction to tax but rather provide an arrangement whereby the States agree to restrict their substantive law. The restriction is either through the non-taxing of the income or via the provision of a tax credit.

Cost effectiveness of patient education for the prevention of falls in hospital : economic evaluation from a randomized controlled trial

Background Falls are one of the most frequently occurring adverse events that impact upon the recovery of older hospital inpatients. Falls can threaten both immediate and longer-term health and independence. There is need to identify cost-effective means for preventing falls in hospitals. Hospital-based falls prevention interventions tested in randomized trials have not yet been subjected to economic evaluation. Methods Incremental cost-effectiveness analysis was undertaken from the health service provider perspective, over the period of hospitalization (time horizon) using the Australian Dollar (A$) at 2008 values. Analyses were based on data from a randomized trial among n = 1,206 acute and rehabilitation inpatients. Decision tree modeling with three-way sensitivity analyses were conducted using burden of disease estimates developed from trial data and previous research. The intervention was a multimedia patient education program provided with trained health professional follow-up shown to reduce falls among cognitively intact hospital patients. Results The short-term cost to a health service of one cognitively intact patient being a faller could be as high as A$14,591 (2008). The education program cost A$526 (2008) to prevent one cognitively intact patient becoming a faller and A$294 (2008) to prevent one fall based on primary trial data. These estimates were unstable due to high variability in the hospital costs accrued by individual patients involved in the trial. There was a 52% probability the complete program was both more effective and less costly (from the health service perspective) than providing usual care alone. Decision tree modeling sensitivity analyses identified that when provided in real life contexts, the program would be both more effective in preventing falls among cognitively intact inpatients and cost saving where the proportion of these patients who would otherwise fall under usual care conditions is at least 4.0%. Conclusions This economic evaluation was designed to assist health care providers decide in what circumstances this intervention should be provided. If the proportion of cognitively intact patients falling on a ward under usual care conditions is 4% or greater, then provision of the complete program in addition to usual care will likely both prevent falls and reduce costs for a health service.

Monocular vision based autonomous navigation for a cost-effective MAV in GPS-denied environments

In this paper, we present a monocular vision based autonomous navigation system for Micro Aerial Vehicles (MAVs) in GPS-denied environments. The major drawback of monocular systems is that the depth scale of the scene can not be determined without prior knowledge or other sensors. To address this problem, we minimize a cost function consisting of a drift-free altitude measurement and up-to-scale position estimate obtained using the visual sensor. We evaluate the scale estimator, state estimator and controller performance by comparing with ground truth data acquired using a motion capture system. All resources including source code, tutorial documentation and system models are available online.

Modelling risk at low exposure railway level crossings : supporting an argument for low-cost level crossing warning devices with lower levels of safety integrity

This paper describes a risk model for estimating the likelihood of collisions at low-exposure railway level crossings, demonstrating the effect that differences in safety integrity can have on the likelihood of a collision. The model facilitates the comparison of safety benefits between level crossings with passive controls (stop or give-way signs) and level crossings that have been hypothetically upgraded with conventional or low-cost warning devices. The scenario presented illustrates how treatment of a cross-section of level crossings with low cost devices can provide a greater safety benefit compared to treatment with conventional warning devices for the same budget.