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.

People capabilities for promoting sustainability in facilities management practices

Sustainability needs to be embedded throughout the life-cycle of a construction project. From project conception, planning, design, construction stage, operation and maintenance to demolition, each phase of development should embrace principles of sustainability and the stakeholder involved should be empowered with the necessary skills. Past research explored the importance of ensuring sustainability measures during the occupancy phase based on considerations of Life-Cycle Cost Analysis and a project’s long-term detrimental impact on the environment. Facility managers are in a unique position to promote sustainability over longer periods of project engagement and can apply a high level of influence on the built assets through management and upgrades. There is growing interest among facility managers in incorporating sustainability measures into day-to-day practice. More, however, needs to be done. Previous studies have identified barriers such as the lack of sustainability knowledge and skills, poor access to information, and unwillingness to change among facility management (FM) practitioners and stakeholders. This inhibits proper implementation of sustainable practices in the FM sector. A number of key factors, such as knowledge discrepancy, time constraints, diversity of FM functions and a lack of incentives, require urgent remedy. The capability of FM professionals and stakeholders will be a key enabler in managing the sustainability agenda, as it is central to the improvement of competency and innovation in an organization. Compared to the attempts at developing sustainability guidelines and performance measurement, research efforts relating to people capabilities and skills are still lagging behind. This paper discusses the progress to date of a research project aimed at formulating a people capabilities framework for sustainable FM practices based on expert opinions and industry feedback. Through literature review, the paper explores the challenges of incorporating sustainability principles into general FM practices before focusing specifically on FM personnel capabilities that may impact on the implementation of a holistic sustainability agenda in real life practice. The results of an industry survey are used to propose an action framework to identify, promote and utilise people capabilities in order to promote sustainability integration in FM practices. The paper provides a useful information source for FM personnel and organizations to bridge the gap between extensive tools on sustainable design and construction assessment at the front end and the need to maintain focus throughout the project life-cycle.

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.

Grunt language versus accent : the perceived communication barriers between international medical graduates and patients in Central Wheatbelt catchments

Due to the chronic shortages of GPs in Australian rural and remote regions, considerable numbers of international medical graduates (IMG) have been recruited. IMG experience many difficulties when relocating to Australia with one of the most significant being effective GP-patient communication. Given that this is essential for effective consultation it can have a substantial impact on health care. A purposive sample of seven practising GPs (five IMG, two Australian-trained doctors (ATD)) was interviewed using a semistructured face-to-face interviewing technique. GPs from Nigeria, Egypt, United Kingdom, India, Singapore and Australia participated. Interviews were transcribed and then coded. The authors used qualitative thematic analysis of interview transcripts to identify common themes. IMG-patient communication barriers were considered significant in the Wheatbelt region as identified by both IMG and ATD. ATD indicated they were aware of IMG-patient communication issues resulting in subsequent consults with patients to explain results and diagnoses. Significantly, a lack of communication between ATD and IMG also emerged, creating a further barrier to effective communication. Analysis of the data generated several important findings that rural GP networks should consider when integrating new IMG into the community. Addressing the challenges related to cross-cultural differences should be a priority, in order to enable effective communication. More open communication between ATD and IMG about GP-patient communication barriers and education programs around GP-patient communication would help both GP and patient satisfaction.

Communication and the casualisation of nursing : a critical ethnography

The contemporary working environment is being rapidly reshaped by technological, industrial and political forces. Increased global competitiveness and an emphasis on productivity have led to the appearance of alternative methods of employment, such as part-time, casual and itinerant work, allowing greater flexibility. This allows for the development of a core permanent staff and the simultaneous utilisation of casual staff according to business needs. Flexible workers across industries are generally referred to as the non-standard workforce and full-time permanent workers as the standard workforce. Even though labour flexibility favours the employer, increased opportunity for flexible work has been embraced by women for many reasons, including the gender struggle for greater economic independence and social equality. Consequently, the largely female nursing industry, both nationally and internationally, has been caught up in this wave of change. This ageing workforce has been at the forefront of the push for flexibility with recent figures showing almost half the nursing workforce is employed in non-standard capacity. In part, this has allowed women to fulfil caring roles outside their work, to ease off nearing retirement and to supplement the family income. More significantly, however, flexibility has developed as an economic management initiative, as a strategy for cost constraint. The result has been the development of a dual workforce and as suggested by Pocock, Buchanan and Campbell (2004), associated deep-seated resentment and the marginalisation of part-time and casual workers by their full-time colleagues and managers. Additionally, as nursing currently faces serious recruitment and retention problems there is urgent need to understand the factors which are underlying present discontent in the nursing profession. There is an identified gap in nursing knowledge surrounding the issues relating to recruitment and retention. Communication involves speaking, listening, reading and writing and is an interactive process which is central to the lives of humans. Workplace communication refers to human interaction, information technology, and multimedia and print. It is the means to relationship building between workers, management, and their external environment and is critical to organisational effectiveness. Communication and language are integral to nursing performance (Hall, 2005), in twenty-four hour service however increasing fragmentation due to part-time and casual work in the nursing industry means that effective communication management has become increasingly difficult. More broadly it is known that disruption to communication systems impacts negatively on consumer outcomes. Because of this gap in understanding how nurses view their contemporary nursing world, an interpretative ethnographic study which progressed to a critical ethnographic study, based on the conceptual framework of constructionism and interpretativism was used. The study site was a division within an acute health care facility, and the relationship between increasing casualisation of the nursing workforce and the experiences of communication of standard and non-standard nurses was explored. For this study, full-time standard nurses were those employed to work in a specific unit for forty hours per week. Non-standard nurses were those employed part-time in specific units or those nurses employed to work as relief pool nurses for shift short falls where needed. Nurses employed by external agencies, but required to fill in for shifts at the facility were excluded from this research. This study involved an analysis of observational, interview and focus group data of standard and non-standard nurses within this facility. Three analytical findings - the organisation of nursing work; constructing the casual nurse as other; and the function of space, situate communication within a broader discussion about non-standard work and organisational culture. The study results suggest that a significant culture of marginalisation exists for nurses who work in a non-standard capacity and that this affects communication for nurses and has implications for the quality of patient care. The discussion draws on the seven elements of marginalisation described by Hall, Stephen and Melius (1994). The arguments propose that these elements underpin a culture which supports remnants of the historically gendered stereotype "the good nurse" and these cultural values contribute to practices and behaviour which marginalise all nurses, particularly those who work less than full-time. Gender inequality is argued to be at the heart of marginalising practices because of long standing subordination of nurses by the powerful medical profession, paralleling historical subordination of women in society. This has denied nurses adequate representation and voice in decision making. The new knowledge emanating from this study extends current knowledge of factors surrounding recruitment and retention and as such contributes to an understanding of the current and complex nursing environment.

Natural disaster risk-informed for a better public infrastructure asset planning in Indonesian Central Government

The natural disasters incident that frequently hit Indonesia are floods, severe droughts, tsunamis, earth-quakes, volcano, eruptions, landslides, windstorm and forest fires. The impact of those natural disasters are significantly severe and affecting the quality of life of the community due to the breakdown of the public as-sets as one source to deliver public services. This paper is aimed to emphasis the importance of natural disaster risk-informed in relation to public asset management in Indonesian Central Government, particularly in asset planning stage where asset decision is made as the gate into the whole public asset management processes. A Case study in the Ministry of Finance Indonesia as the central government public asset manager and in 5 (five) line ministries/governmental agencies as public asset users was used as the approach to achieved the research objective. The case study devoured three data collection techniques i.e. interviews, observations and document archival which will be analysed by a content analysis approach. The result of the study indicates that Indonesian geographical position exposing many of public infra-structure assets as a high vulnerability to natural disasters. Information on natural-disaster trends and predictions to identify and measure the risks are available, however, such information are not utilise and integrated to the process of public infrastructure asset planning as the gate to the whole public asset management processes. Therefore, in order to accommodate and incorporate this natural disaster risk-information into public asset management processes, particularly in public asset planning, a public asset performance measurements framework should be adopted and applied in the process as one sources in making decision for infrastructure asset planning. Findings from this study provide useful input for the Ministry of Finance as public asset manager, scholars and private asset management practitioners in Indonesia to establish natural disaster risks awareness in public infrastructure asset management processes.

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.

Surgical treatment approaches and reimbursement costs of surgical site infections post hip arthroplasty in Australia : a retrospective analysis

BACKGROUND: The treatment for deep surgical site infection (SSI) following primary total hip arthroplasty (THA) varies internationally and it is at present unclear which treatment approaches are used in Australia. The aim of this study is to identify current treatment approaches in Queensland, Australia, show success rates and quantify the costs of different treatments. METHODS: Data for patients undergoing primary THA and treatment for infection between January 2006 and December 2009 in Queensland hospitals were extracted from routinely used hospital databases. Records were linked with pathology information to confirm positive organisms. Diagnosis and treatment of infection was determined using ICD-10-AM and ACHI codes, respectively. Treatment costs were estimated based on AR-DRG cost accounting codes assigned to each patient hospital episode. RESULTS: A total of n=114 patients with deep surgical site infection were identified. The majority of patients (74%) were first treated with debridement, antibiotics and implant retention (DAIR), which was successful in eradicating the infection in 60.3% of patients with an average cost of $13,187. The remaining first treatments were 1-stage revision, successful in 89.7% with average costs of $27,006, and 2-stage revisions, successful in 92.9% of cases with average costs of $42,772. Multiple treatments following 'failed DAIR' cost on average $29,560, for failed 1-stage revision were $24,357, for failed 2-stage revision were $70,381 and were $23,805 for excision arthroplasty. CONCLUSIONS: As treatment costs in Australia are high primary prevention is important and the economics of competing treatment choices should be carefully considered. These currently vary greatly across international settings.

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.

Urban transit quality of service : user perception and behaviour

Despite its potential multiple contributions to sustainable policy objectives, urban transit is generally not widely used by the public in terms of its market share compared to that of automobiles, particularly in affluent societies with low-density urban forms like Australia. Transit service providers need to attract more people to transit by improving transit quality of service. The key to cost-effective transit service improvements lies in accurate evaluation of policy proposals by taking into account their impacts on transit users. If transit providers knew what is more or less important to their customers, they could focus their efforts on optimising customer-oriented service. Policy interventions could also be specified to influence transit users’ travel decisions, with targets of customer satisfaction and broader community welfare. This significance motivates the research into the relationship between urban transit quality of service and its user perception as well as behaviour. This research focused on two dimensions of transit user’s travel behaviour: route choice and access arrival time choice. The study area chosen was a busy urban transit corridor linking Brisbane central business district (CBD) and the St. Lucia campus of The University of Queensland (UQ). This multi-system corridor provided a ‘natural experiment’ for transit users between the CBD and UQ, as they can choose between busway 109 (with grade-separate exclusive right-of-way), ordinary on-street bus 412, and linear fast ferry CityCat on the Brisbane River. The population of interest was set as the attendees to UQ, who travelled from the CBD or from a suburb via the CBD. Two waves of internet-based self-completion questionnaire surveys were conducted to collect data on sampled passengers’ perception of transit service quality and behaviour of using public transit in the study area. The first wave survey is to collect behaviour and attitude data on respondents’ daily transit usage and their direct rating of importance on factors of route-level transit quality of service. A series of statistical analyses is conducted to examine the relationships between transit users’ travel and personal characteristics and their transit usage characteristics. A factor-cluster segmentation procedure is applied to respodents’ importance ratings on service quality variables regarding transit route preference to explore users’ various perspectives to transit quality of service. Based on the perceptions of service quality collected from the second wave survey, a series of quality criteria of the transit routes under study was quantitatively measured, particularly, the travel time reliability in terms of schedule adherence. It was proved that mixed traffic conditions and peak-period effects can affect transit service reliability. Multinomial logit models of transit user’s route choice were estimated using route-level service quality perceptions collected in the second wave survey. Relative importance of service quality factors were derived from choice model’s significant parameter estimates, such as access and egress times, seat availability, and busway system. Interpretations of the parameter estimates were conducted, particularly the equivalent in-vehicle time of access and egress times, and busway in-vehicle time. Market segmentation by trip origin was applied to investigate the difference in magnitude between the parameter estimates of access and egress times. The significant costs of transfer in transit trips were highlighted. These importance ratios were applied back to quality perceptions collected as RP data to compare the satisfaction levels between the service attributes and to generate an action relevance matrix to prioritise attributes for quality improvement. An empirical study on the relationship between average passenger waiting time and transit service characteristics was performed using the service quality perceived. Passenger arrivals for services with long headways (over 15 minutes) were found to be obviously coordinated with scheduled departure times of transit vehicles in order to reduce waiting time. This drove further investigations and modelling innovations in passenger’ access arrival time choice and its relationships with transit service characteristics and average passenger waiting time. Specifically, original contributions were made in formulation of expected waiting time, analysis of the risk-aversion attitude to missing desired service run in the passengers’ access time arrivals’ choice, and extensions of the utility function specification for modelling passenger access arrival distribution, by using complicated expected utility forms and non-linear probability weighting to explicitly accommodate the risk of missing an intended service and passenger’s risk-aversion attitude. Discussions on this research’s contributions to knowledge, its limitations, and recommendations for future research are provided at the concluding section of this thesis.

How to improve pupils' literacy? A cost-effectiveness analysis of a French educational project

The Action Lecture program is an innovative teaching method run in some nursery and primary schools in Paris and designed to improve pupils’ literacy. We report the results of an evaluation of this program. We describe the experimental protocol that was built to estimate the program’s impact on several types of indicators. Data were processed following a Differences-in-Differences (DID) method. Then we use the estimation of the impact on academic achievement to conduct a cost-effectiveness analysis and take a reduction of the class size program as a benchmark. The results are positive for the Action Lecture program.

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.