Predicting residue-wise contact orders in proteins by support vector regression

Background The residue-wise contact order (RWCO) describes the sequence separations between the residues of interest and its contacting residues in a protein sequence. It is a new kind of one-dimensional protein structure that represents the extent of long-range contacts and is considered as a generalization of contact order. Together with secondary structure, accessible surface area, the B factor, and contact number, RWCO provides comprehensive and indispensable important information to reconstructing the protein three-dimensional structure from a set of one-dimensional structural properties. Accurately predicting RWCO values could have many important applications in protein three-dimensional structure prediction and protein folding rate prediction, and give deep insights into protein sequence-structure relationships. Results We developed a novel approach to predict residue-wise contact order values in proteins based on support vector regression (SVR), starting from primary amino acid sequences. We explored seven different sequence encoding schemes to examine their effects on the prediction performance, including local sequence in the form of PSI-BLAST profiles, local sequence plus amino acid composition, local sequence plus molecular weight, local sequence plus secondary structure predicted by PSIPRED, local sequence plus molecular weight and amino acid composition, local sequence plus molecular weight and predicted secondary structure, and local sequence plus molecular weight, amino acid composition and predicted secondary structure. When using local sequences with multiple sequence alignments in the form of PSI-BLAST profiles, we could predict the RWCO distribution with a Pearson correlation coefficient (CC) between the predicted and observed RWCO values of 0.55, and root mean square error (RMSE) of 0.82, based on a well-defined dataset with 680 protein sequences. Moreover, by incorporating global features such as molecular weight and amino acid composition we could further improve the prediction performance with the CC to 0.57 and an RMSE of 0.79. In addition, combining the predicted secondary structure by PSIPRED was found to significantly improve the prediction performance and could yield the best prediction accuracy with a CC of 0.60 and RMSE of 0.78, which provided at least comparable performance compared with the other existing methods. Conclusion The SVR method shows a prediction performance competitive with or at least comparable to the previously developed linear regression-based methods for predicting RWCO values. In contrast to support vector classification (SVC), SVR is very good at estimating the raw value profiles of the samples. The successful application of the SVR approach in this study reinforces the fact that support vector regression is a powerful tool in extracting the protein sequence-structure relationship and in estimating the protein structural profiles from amino acid sequences.

Cultural support workers and long day care services

In Australia, eligible long day care services may apply for support at the state level to assist with the transition of children from culturally or linguistically diverse backgrounds into childcare settings. For staff in childcare services, this support comes in the form of a cultural support worker (CSW). The primary role of a CSW is to build capacity in childcare staff to support children and families as they enter the childcare program. This paper draws on interview data and documentation from multiple sources to report the perspectives of key stakeholders affiliated with a cultural support program in an Australian childcare setting. It concludes that a more flexible approach to policy that directs the work of CSWs is needed, as well as further research into ways to build capacity for cultural competence for both CSWs and childcare staff who work collaboratively to support young children as they transition to childcare.

Surrogacy : is it harder to relinquish genes?

Surrogacy has produced some positive outcomes creating an opportunity for otherwise childless couples to live their dream of parenthood. However it has also been problematic, particularly where the surrogate mother fails to relinquish a child born as a result of the surrogacy arrangement. This article examines whether a surrogate mother, who is genetically related to the child she delivers, is less likely to relinquish the child than one who has no genetic ties. An examination of empirical evidence provides support for this argument. Legislation and case law in three jurisdictions, Australia, the United States and the United Kingdom, is examined to determine which, if any, of these jurisdictions take into account the existence, or otherwise, of a genetic link between the surrogate mother and the child she bears. The article concludes that surrogacy legislation should, subject to exceptional circumstances, encourage surrogacy arrangements where the child and the surrogate are not genetically related.

Support teachers, learning difficulties and secondary school culture

This thesis will report on mixed method research which examined secondary Support Teachers Learning Difficulties (STLDs) and their modes of operation in New South Wales (NSW) government schools, Australia. Four modes of operation were identified in the literature as consultancy, team teaching, in-class support and withdrawal. An additional area of other duties was also included to examine the time when STLDs were not functioning in the four identified modes of operation. NSW government policy is in keeping with the literature as it recommends that STLDs should spend the majority of their time in consultancy and team teaching while in class with a minimum of withdrawal of students from their main classrooms for individual or small group instruction. STLDs, however, did not appear to be functioning in the recommended way. A number of factors identified in the literature, which may influence the modes of operation, can be grouped under the heading of school culture thus this research involved the examination of the effects of school culture on the modes of operation with the aim of expanding our understanding of the functioning of STLDs and providing suggestions for improvement. The theoretical base of social constructionism has informed this research which included survey and case study methods. Case studies of the STLDs in three secondary schools led to the conclusion that, in conjunction with factors such as flexibility and commitment, the involvement of the STLD in a sub-culture of learning support may lead to functioning in the recommended modes of operation.

Expansion of support for first year law students : an overview from a first year coordinator

In the context of government funding and targets for increased participation in higher education and equity groups, as well as attrition rates, the literature on first year higher education highlights the importance of appropriate levels of support for students transitioning to higher education. In the law school context, support of first year students is also important in the response to the high levels of stress among law students. It is therefore necessary for universities to provide a variety of support to first year students from both a student perspective and a curriculum perspective. This paper explores the process of investigating the expansion of student support, including peer support programs, staff led programs, appointing a first year coordinator and developing a curriculum plan. These programs promote engagement and ensure a cohesive and integrated first year experience from both curriculum design and student experience perspectives. This paper will explain the process undertaken at QUT of expanding support for first year law students, overview the program details and will reflect on the feedback from students, peer facilitators and staff of expanding support for first year law students at QUT. The paper will conclude with recommendations for improvement to the program.

Me and my body : the relevance of the difference for the distinction between withdrawing life support and euthanasia

In this paper I discuss David Shaw’s claim that the body of a terminally ill person can be conceived as a kind of life-support, akin to an artificial ventilator. I claim that this position rests upon an untenable dualism between the mind and the body. Given that dualism continues to be attractive to some thinkers, I attempt to diagnose the reasons why it continues to be attractive, as well as to demonstrate its incoherence, drawing on some recent work in the philosophy of psychology. I conclude that, if my criticisms are sound, Shaw’s attempt to deny the distinction between withdrawal and euthanasia fails.

Support for energy-oriented design in the Australian context

There is a need for decision support tools that integrate energy simulation into early design in the context of Australian practice. Despite the proliferation of simulation programs in the last decade, there are no ready-to-use applications that cater specifically for the Australian climate and regulations. Furthermore, the majority of existing tools focus on achieving interaction with the design domain through model-based interoperability, and largely overlook the issue of process integration. This paper proposes an energy-oriented design environment that both accommodates the Australian context and provides interactive and iterative information exchanges that facilitate feedback between domains. It then presents the structure for DEEPA, an openly customisable system that couples parametric modelling and energy simulation software as a means of developing a decision support tool to allow designers to rapidly and flexibly assess the performance of early design alternatives. Finally, it discusses the benefits of developing a dynamic and concurrent performance evaluation process that parallels the characteristics and relationships of the design process.

Closing the loop of design and analysis : Parametric modelling tools for early decision support

There is a growing need for parametric design software that communicates building performance feedback in early architectural exploration to support decision-making. This paper examines how the circuit of design and analysis process can be closed to provide active and concurrent feedback between architecture and services engineering domains. It presents the structure for an openly customisable design system that couples parametric modelling and energy analysis software to allow designers to assess the performance of early design iterations quickly. Finally, it discusses how user interactions with the system foster information exchanges that facilitate the sharing of design intelligence across disciplines.

The Use of Social Technology to Support Organisational Knowledge

In the current economy, knowledge has been recognized to be a valuable organisational asset, a crucial factor that aids organisations to succeed in highly competitive environments. Many organisations have begun projects and special initiatives aimed at fostering better knowledge sharing amongst their employees. Not surprisingly, information technology (IT) has been a central element of many of these projects and initiatives, as the potential of emerging information technologies such as Web 2.0 for enabling the process of managing organisational knowledge is recognised. This technology could be used as a collaborative system for knowledge management (KM) within enterprises. Enterprise 2.0 is the application of Web 2.0 in an organisational context. Enterprise 2.0 technologies are web-based social software that facilitate collaboration, communication and information flow in a bidirectional manner: an essential aspect of organisational knowledge management. This chapter explains how Enterprise 2.0 technologies (Web 2.0 technologies within organisations) can support knowledge management. The chapter also explores how such technologies support the codifying (technology-centred) and social network (people-centred) approaches of KM, towards bridging the current gap between these two approaches.

Making it creatively : building sustainable careers in the arts and creative industries

Many people aspire to careers in the arts and creative industries. However, it has long been known that it can be challenging to navigate a creative career: that competition for work can be intense, particularly for entry-level positions, and that success requires advanced skill sets in addition to a high degree of artistic talent and proficiency. In this article, Dr Ruth Bridgstock draws upon her doctoral and post-doctoral research to explore the challenges involved in building a creative career in Australia and suggest ways to support emerging creatives to build satisfying and sustainable careers.

Understanding evaluation of learning support in mathematics and statistics

With rapid and continuing growth of learning support initiatives in mathematics and statistics found in many parts of the world, and with the likelihood that this trend will continue, there is a need to ensure that robust and coherent measures are in place to evaluate the effectiveness of these initiatives. The nature of learning support brings challenges for measurement and analysis of its effects. After briefly reviewing the purpose, rationale for, and extent of current provision, this article provides a framework for those working in learning support to think about how their efforts can be evaluated. It provides references and specific examples of how workers in this field are collecting, analysing and reporting their findings. The framework is used to structure evaluation in terms of usage of facilities, resources and services provided, and also in terms of improvements in performance of the students and staff who engage with them. Very recent developments have started to address the effects of learning support on the development of deeper approaches to learning, the affective domain and the development of communities of practice of both learners and teachers. This article intends to be a stimulus to those who work in mathematics and statistics support to gather even richer, more valuable, forms of data. It provides a 'toolkit' for those interested in evaluation of learning support and closes by referring to an on-line resource being developed to archive the growing body of evidence. © 2011 Taylor & Francis.

Practical decision support system evaluation for consultant selection

The widespread development of Decision Support System (DSS) in construction indicate that the evaluation of software become more important than before. However, it is identified that most research in construction discipline did not attempt to assess its usability. Therefore, little is known about the approach on how to properly evaluate a DSS for specific problem. In this paper, we present a practical framework that can be guidance for DSS evaluation. It focuses on how to evaluate software that is dedicatedly designed for consultant selection problem. The framework features two main components i.e. Sub-system Validation and Face Validation. Two case studies of consultant selection at Malaysian Department of Irrigation and Drainage were integrated in this framework. Some inter-disciplinary area such as Software Engineering, Human Computer Interaction (HCI) and Construction Project Management underpinned the discussion of the paper. It is anticipated that this work can foster better DSS development and quality decision making that accurately meet the client’s expectation and needs

A capabilities-based approach to obtaining a deeper understanding of information technology governance effectiveness : evidence from IT steering committees

Given the substantial investment in information technology (IT), and the significant impact IT has on organizational success, organizations consume considerable resources to manage acquisition and use of their IT resources. While various arguments proposed suggest which IT governance arrangements may work best, our understanding of the effectiveness of such initiatives is limited. We examine the relationship between the effectiveness of IT steering committee driven IT governance initiatives and firm's IT management and IT infrastructure related capabilities. We further propose that firm's ITrelated capabilities generated through IT governance initiatives should improve its business processes and firm-level performance. We test these relationships empirically by a field survey. Results suggest that firms' effectiveness of IT steering committee driven IT governance initiatives positively relates to the level of their IT-related capabilities. We also found positive relationships between IT-related capabilities and internal process-level performance. Our results also support that improvement in internal process-level performance positively relates to improvement in customer service and firm-level performance.

Philanthropic capacity to support Indigenous causes : the journey to improvement

The role of philanthropy in addressing Indigenous causes is still conceptually emerging in Australia despite many years of practice. This paper reports on a qualitative study with grantmakers and grantseekers to better understand the issues affecting the philanthropic grantmaking system for Indigenous causes in Australia. An attitudinal emphasis on human rights for politically, economically and socially disadvantaged groups and an impetus for structural change emerged that has yet to deliver real funding equity. The way forward is still largely focussed on ‘improving’ Indigenous community capacity in organisational governance systems. In contrast, this study points to strategic leverage points within philanthropic organisations which could be used to first assess and then develop policies, processes and their underlying attitudes which impact on cross-cultural work i.e. the ‘cultural competence ’ of philanthropic organisations. It is argued such an approach would support improved social justice practice in the sector and subsequently Indigenous outcomes.

The effect of lumbar support on the trunk muscle activity and pelvic tilt in a passenger vehicle car seat

In order to gain a competitive edge in the market, automotive manufacturers and automotive seat suppliers have identified seat ergonomics for further development to improve overall vehicle comfort. Adjustable lumbar support devices have been offered since long as comfort systems in either a 2-way or 4-way adjustable configuration, although their effect on lumbar strain is not well documented. The effect of a lumbar support on posture and muscular strain, and therefore the relationship between discomfort and comfort device parameter settings, requires clarification. The aim of this paper is to study the effect of a 4-way lumbar support on lower trunk and pelvis muscle activity, pelvic tilt and spine curvature during a car seating activity. 10 healthy subjects (5 m/f; age 19-39) performed a seating activity in a passenger vehicle with seven different static lumbar support positions. The lumbar support was tested in 3 different height positions in relation to the seatback surface centreline (high, centre, low), each having 2 depths positions (lumbar prominence). An extra depth position was added for the centre position. Posture data were collected using a VICON MX motion capture system and NORAXON DTS goniometers and inclinometer. A rigid-body model of an adjustable car seat with four-way adjustable lumbar support was constructed in UGS Siemens NX and connected to a musculoskeletal model of a seated-human, modelled in AnyBody. Wireless electromyography (EMG) was used to calibrate the musculoskeletal model and assess the relationship between (a) muscular strain and lumbar prominence (normal to seatback surface) respective to the lumbar height (alongside seatback surface), (b) hip joint moment and lumbar prominence (normal to seatback surface) respective to lumbar height (alongside seatback surface) and (c) pelvic tilt and lumbar prominence (normal to seatback surface) respective to the lumbar height (alongside seatback surface). This study was based on the assumption that the musculoskeletal human model was seated at the correct R-Point (SgRP), determined via the occupant packaging toolkit in the JACK digital human model. The effect of the interaction between the driver/car-seat has been investigated for factors resulting from the presence and adjustment of a 4-way lumbar support. The results obtained show that various seat adjustments, and driver’s lumbar supports can have complex influence on the muscle activation, joint forces and moments, all of which can affect the comfort perception of the driver. This study enables the automotive industry to optimise passenger vehicle seat development and design. It further more supports the evaluation of static postural and dynamic seat comfort in normal everyday driving tasks and can be applied for future car design to reduce investment and improve comfort.