Computational science for undergraduate biologists via QUT.Bio.Excel

Molecular biology is a scientific discipline which has changed fundamentally in character over the past decade to rely on large scale datasets – public and locally generated - and their computational analysis and annotation. Undergraduate education of biologists must increasingly couple this domain context with a data-driven computational scientific method. Yet modern programming and scripting languages and rich computational environments such as R and MATLAB present significant barriers to those with limited exposure to computer science, and may require substantial tutorial assistance over an extended period if progress is to be made. In this paper we report our experience of undergraduate bioinformatics education using the familiar, ubiquitous spreadsheet environment of Microsoft Excel. We describe a configurable extension called QUT.Bio.Excel, a custom ribbon, supporting a rich set of data sources, external tools and interactive processing within the spreadsheet, and a range of problems to demonstrate its utility and success in addressing the needs of students over their studies.

Common secure index for conjunctive keyword-based retrieval over encrypted data

We consider the following problem: users in a dynamic group store their encrypted documents on an untrusted server, and wish to retrieve documents containing some keywords without any loss of data confidentiality. In this paper, we investigate common secure indices which can make multi-users in a dynamic group to obtain securely the encrypted documents shared among the group members without re-encrypting them. We give a formal definition of common secure index for conjunctive keyword-based retrieval over encrypted data (CSI-CKR), define the security requirement for CSI-CKR, and construct a CSI-CKR based on dynamic accumulators, Paillier’s cryptosystem and blind signatures. The security of proposed scheme is proved under strong RSA and co-DDH assumptions.

Multi-scale bio-inspired place recognition

This paper presents a novel place recognition algorithm inspired by the recent discovery of overlapping and multi-scale spatial maps in the rodent brain. We mimic this hierarchical framework by training arrays of Support Vector Machines to recognize places at multiple spatial scales. Place match hypotheses are then cross-validated across all spatial scales, a process which combines the spatial specificity of the finest spatial map with the consensus provided by broader mapping scales. Experiments on three real-world datasets including a large robotics benchmark demonstrate that mapping over multiple scales uniformly improves place recognition performance over a single scale approach without sacrificing localization accuracy. We present analysis that illustrates how matching over multiple scales leads to better place recognition performance and discuss several promising areas for future investigation.

Vertical graphene gas- and bio-sensors via catalyst-free, reactive plasma reforming of natural honey

A rapid reforming of natural honey exposed to reactive low-temperature Ar + H2 plasmas produced high-quality, ultra-thin vertical graphenes, without any metal catalyst or external heating. This transformation is only possible in the plasma and fails in similar thermal processes. The process is energy-efficient, environmentally benign, and is much cheaper than common synthesis methods based on purified hydrocarbon precursors. The graphenes retain the essential minerals of natural honey, feature reactive open edges and reliable gas- and bio-sensing performance.

Reactive plasma-aided RF sputtering deposition of hydroxyapatite bio-implant coatings

The plasma-assisted RF sputtering deposition of a biocompatible, functionally graded calcium phosphate bioceramic on a Ti6A14 V orthopedic alloy is reported. The chemical composition and presence of hydroxyapatite (HA), CaTiO3, and CaO mineral phases can be effectively controlled by the process parameters. At higher DC biases, the ratio [Ca]/[P] and the amount of CaO increase, whereas the HA content decreases. Optical emission spectroscopy suggests that CaO+ is the dominant species that responds to negative DC bias and controls calcium content. Biocompatibility tests in simulated body fluid confirm a positive biomimetic response evidenced by in-growth of an apatite layer after 24 h of immersion.

Stoichiometry, crystallinity, and nano-scale surface morphology of the graded calcium phosphate-based bio-ceramic interlayer on Ti-Al-V

A plasma-assisted concurrent Rf sputtering technique for fabrication of biocompatible, functionally graded CaP-based interlayer on Ti-6Al-4V orthopedic alloy is reported. Each layer in the coating is designed to meet a specific functionality. The adherent to the metal layer features elevated content of Ti and supports excellent ceramic-metal interfacial stability. The middle layer features nanocrystalline structure and mimics natural bone apatites. The technique allows one to reproduce Ca/P ratios intrinsic to major natural calcium phosphates. Surface morphology of the outer, a few to few tens of nanometers thick, layer, has been tailored to fit the requirements for the bio-molecule/protein attachment factors. Various material and surface characterization techniques confirm that the optimal surface morphology of the outer layer is achieved for the process conditions yielding nanocrystalline structure of the middle layer. Preliminary cell culturing tests confirm the link between the tailored nano-scale surface morphology, parameters of the middle nanostructured layer, and overall biocompatibility of the coating.

Reactive species in RF plasma sputtering deposition of nanocrystalline calcium phosphate bio-active films

Optical emission of reactive plasma species during the synthesis of functionally graded calcium phosphate-based bioactive films has been investigated. The coatings have been deposited on Ti-6Al-4V orthopedic alloy by co-sputtering of hydroxyapatite (HA) and titanium targets in reactive plasmas of Ar + H2O gas mixtures. The species, responsible for the Ca-P-Ti film growth have been non-intrusively monitored in situ by a high-resolution optical emission spectroscopy (OES). It is revealed that the optical emission originating from CaO species dominates throughout the deposition process. The intensities of CaO, PO and CaPO species are strongly affected by variations of the operating pressure, applied RF power, and DC substrate bias. The optical emission intensity (OEI) of reaction species can efficiently be controlled by addition of H2O reactant.

Barriers to sustainable economic development : the Dallas–Fort Worth experience

This article examines the scope of existing economic development activity and the motivations and perceptions of practitioners to shed light on the barriers to sustainable practice. In contrast to related fields like urban planning, the economic development literature has minimally examined how practitioners think about sustainable development and the extent to which sustainable development principles are adopted in practice. This omission is significant because economic development policies can have a notable impact on the sustainable development goals of environmental protection and social equity alongside economic growth. To capture the extent to which economic developers engage in sustainable development and the barriers that practitioners face, we study fifteen cities in the Dallas–Fort Worth region. We find that six key barriers – a conventional economic development mindset, incentive-based practice, a lack of resources, ad hoc planning, inter-regional competition, and a lack of coordinated regional planning – impede sustainable economic development in the region.

Art spaces in community and economic development : connections to neighborhoods, artists, and the cultural economy

There is growing interest in the arts in community and economic development, yet little research examines the dynamics of community-based arts institutions to inform urban planning and policy. Drawing on interviews with participants and organizers of small and midsized art spaces, the study explores the factors that influence their involvement in neighborhood revitalization and outreach, support for artistic communities, and efforts to build bridges to commercial cultural sectors. Art spaces function as a conduit for building social networks that contribute to both community revitalization and artistic development. But issues pertaining to the location, organization, and management of art spaces may limit their community and economic development potential. The article concludes with proposals to craft stronger arts-based community and economic development programs.

Application of a hybrid Entropy–McKinsey Matrix method in evaluating sustainable urbanization : a China case study

Although urbanization can promote social and economic development, it can also cause various problems. As the key decision makers of urbanization, local governments should be able to evaluate urbanization performance, summarize experiences, and find problems caused by urbanization. This paper introduces a hybrid Entropy–McKinsey Matrix method for evaluating sustainable urbanization. The McKinsey Matrix is commonly referred to as the GE Matrix. The values of a development index (DI) and coordination index (CI) are calculated by employing the Entropy method and are used as a basis for constructing a GE Matrix. The matrix can assist in assessing sustainable urbanization performance by locating the urbanization state point. A case study of the city of Jinan in China demonstrates the process of using the evaluation method. The case study reveals that the method is an effective tool in helping policy makers understand the performance of urban sustainability and therefore formulate suitable strategies for guiding urbanization toward better sustainability.

Towards prosperous sustainable cities : a multiscalar urban sustainability assessment approach

Prosperity and environmental sustainability of cities are inextricably linked. Cities can only maintain their prosperity when environmental and social objectives are fully integrated with economic goals for the purpose of a sustainable urban development. Sustainability assessment helps policy-makers decide what actions they should and should not take in an attempt to make our cities more sustainable. There are numerous models available for measuring and evaluating urban sustainability, and they focus their analysis on a specific scale—i.e., micro, mezzo, or macro. In most cases these results are inadequate for the other scales, though generating reliable results for that particular scale. The paper introduces a multiscalar urban sustainability approach by linking two sustainability assessment models evaluate sustainability performances in micro- and mezzo-levels and generate multiscalar results for the macro-level. The paper puts this approach into test in Gold Coast, Australia, and sheds light on the development of a more accurate sustainability analysis that may be interconnected with UN-Habitat’s City Prosperity Index.

Economic development and construction productivity in Malaysia

The productivity of the construction industry has a significant effect on national economic growth. Gains from higher construction productivity flow through the economy, as all industries rely on construction to some extent as part of their business investment. Contractions and expansions of economic activity are common phenomena in an economy. Three construction cycles occurred between the years 1970 and 2011 in Malaysia. The relationships between construction productivity and economic development are examined by the partial correlation method to establish the underlying factors driving the change in construction productivity. Construction productivity is statistically significantly correlated with gross domestic product (GDP) per capita in a positive direction for the 1985–98 and 1998–2009 cycles, but not the 1970–85 cycle. Fluctuations in construction activities and the influx of foreign workers underlie the changes of construction productivity in the 1985–98 cycle. There was less fluctuation in construction activities in the 1998–2009 cycle, with changes being mainly due to the fiscal stimulation policies of the government in attempting to stabilize the economy. The intensive construction of mega-projects resulted in resource constraints and cost pressures during the 1980s and 1990s. A better management of the ‘boom-bust’ nature of the construction business cycle is required to maintain the capability and capacity of the industry.

Desalination with a solar-assisted heat pump : an economic optimization

The solar-assisted heat pump (SAHP) desalination, based on the Rankin cycle, operates in low temperature and utilizes both solar and ambient energy. An experimental SAHP desalination system has been constructed at the National University of Singapore, Singapore. The system consisted of two main sections: an SAHP and a water distillation section. Experiments were carried out under the different meteorological condition of Singapore and results showed that the system had a performance ratio close to 1.3. The heat pump has a coefficient of performance of about 8, with solar collector efficiencies of 80% and 60% for evaporator and liquid collectors, respectively. Economic analysis showed that at a production rate of 900 L/day and an evaporator collector area of around 70m2 will have a payback period of about 3.5 years.

Parent's socio-economic status and social support as risks for child mortality : consideration of health equity in The Gambia

A matched case-control study of mortality to children under age five was conducted to consider associations with parents' socio-economic status and social support in the Farafenni Demographic Surveillance Site (DSS). Cases and controls were selected from Farafenni DSS, matched on date of birth, and parents were interviewed about personal resources and social networks. Parents with the lowest personal socio-economic status and social support were identified. Multivariate multinomial regression was used to consider whether the children of these parents were at increased risk of either infant or 1-4 mortality, in separate models using either parents' characteristics. There was no benefit found for higher SES or better social support with respect to child mortality. Children of fathers who had the poorest social support had lower 1-4 mortality risk (OR=0.52, p=0.037). Given that socio-economic status was not associated with child mortality, it seems unlikely that the explanation for the link between father's social support and mortality is linked to resource availability. Explanations for the risk effect of father's social ties may lie in decision-making around health maintenance and health care for children.