A novel multiplex PCR-RFLP method for simultaneous detection of the MTHFR 677 C > T, eNOS +894 G > T and - eNOS -786 T > C variants among Malaysian Malays

Background Hyperhomocysteinemia as a consequence of the MTHFR 677 C > T variant is associated with cardiovascular disease and stroke. Another factor that can potentially contribute to these disorders is a depleted nitric oxide level, which can be due to the presence of eNOS +894 G > T and eNOS −786 T > C variants that make an individual more susceptible to endothelial dysfunction. A number of genotyping methods have been developed to investigate these variants. However, simultaneous detection methods using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis are still lacking. In this study, a novel multiplex PCR-RFLP method for the simultaneous detection of MTHFR 677 C > T and eNOS +894 G > T and eNOS −786 T > C variants was developed. A total of 114 healthy Malay subjects were recruited. The MTHFR 677 C > T and eNOS +894 G > T and eNOS −786 T > C variants were genotyped using the novel multiplex PCR-RFLP and confirmed by DNA sequencing as well as snpBLAST. Allele frequencies of MTHFR 677 C > T and eNOS +894 G > T and eNOS −786 T > C were calculated using the Hardy Weinberg equation. Methods The 114 healthy volunteers were recruited for this study, and their DNA was extracted. Primer pair was designed using Primer 3 Software version 0.4.0 and validated against the BLAST database. The primer specificity, functionality and annealing temperature were tested using uniplex PCR methods that were later combined into a single multiplex PCR. Restriction Fragment Length Polymorphism (RFLP) was performed in three separate tubes followed by agarose gel electrophoresis. PCR product residual was purified and sent for DNA sequencing. Results The allele frequencies for MTHFR 677 C > T were 0.89 (C allele) and 0.11 (T allele); for eNOS +894 G > T, the allele frequencies were 0.58 (G allele) and 0.43 (T allele); and for eNOS −786 T > C, the allele frequencies were 0.87 (T allele) and 0.13 (C allele). Conclusions Our PCR-RFLP method is a simple, cost-effective and time-saving method. It can be used to successfully genotype subjects for the MTHFR 677 C > T and eNOS +894 G > T and eNOS −786 T > C variants simultaneously with 100% concordance from DNA sequencing data. This method can be routinely used for rapid investigation of the MTHFR 677 C > T and eNOS +894 G > T and eNOS −786 T > C variants.

Creating a therapeutic environment : a non-randomised controlled trial of a quiet time intervention for patients in acute care

Background: Noise is a significant barrier to sleep for acute care hospital patients, and sleep has been shown to be therapeutic for health, healing and recovery. Scheduled quiet time interventions to promote inpatient rest and sleep have been successfully trialled in critical care but not in acute care settings. Objectives: The study aim was to evaluate as cheduled quiet time intervention in an acute care setting. The study measured the effect of a scheduled quiet time on noise levels, inpatients’ rest and sleep behaviour, and wellbeing. The study also examined the impact of the intervention on patients’, visitors’ and health professionals’ satisfaction, and organisational functioning. Design: The study was a multi-centred non-randomised parallel group trial. Settings: The research was conducted in the acute orthopaedic wards of two major urban public hospitals in Brisbane, Australia. Participants: All patientsadmitted to the two wards in the5-month period of the study were invited to participate, withafinalsample of 299 participants recruited. This sample produced an effect size of 0.89 for an increase in the number of patients asleep during the quiet time. Methods: Demographic data were collected to enable comparison between groups. Data for noise level, sleep status, sleepiness and well being were collected using previously validated instruments: a Castle Model 824 digital sound level indicator; a three point sleep status scale; the Epworth Sleepiness Scale; and the SF12 V2 questionnaire. The staff, patient and visitor surveys on the experimental ward were adapted from published instruments. Results: Significant differences were found between the two groups in mean decibel level and numbers of patients awake and asleep. The difference in mean measured noise levels between the two environments corresponded to a ‘perceived’ difference of 2 to 1. There were significant correlations between average decibel level and number of patients awake and asleep in the experimental group, and between average decibel level and number of patients awake in the control group. Overall, patients, visitors and health professionals were satisfied with the quiet time intervention. Conclusions: The findings show that a quiet time intervention on an acute care hospital ward can affect noise level and patient sleep/wake patterns during the intervention period. The overall strongly positive response from surveys suggests that scheduled quiet time would be a positively perceived intervention with therapeutic benefit.

Localization and navigation assisted by cooperating networked sensors and robots

In this paper we discuss how a network of sensors and robots can cooperate to solve important robotics problems such as localization and navigation. We use a robot to localize sensor nodes, and we then use these localized nodes to navigate robots and humans through the sensorized space. We explore these novel ideas with results from two large-scale sensor network and robot experiments involving 50 motes, two types of flying robot: an autonomous helicopter and a large indoor cable array robot, and a human-network interface. We present the distributed algorithms for localization, geographic routing, path definition and incremental navigation. We also describe how a human can be guided using a simple hand-held device that interfaces to this same environmental infrastructure.

Data and process requirements for product recall coordination

When an organisation becomes aware that one of its products may pose a safety risk to customers, it must take appropriate action as soon as possible or it can be held liable. The ability to automatically trace potentially dangerous goods through the supply chain would thus help organisations fulfill their legal obligations in a timely and effective manner. Furthermore, product recall legislation requires manufacturers to separately notify various government agencies, the health department and the public about recall incidents. This duplication of effort and paperwork can introduce errors and data inconsistencies. In this paper, we examine traceability and notification requirements in the product recall domain from two perspectives: the activities carried out during the manufacturing and recall processes and the data collected during the enactment of these processes. We then propose a workflow-based coordination framework to support these data and process requirements.

Towards participatory action design research : adapting action research and design science research methods for urban informatics

This paper proposes a new research method, Participatory Action Design Research (PADR), for studies in the Urban Informatics domain. PADR supports Urban Informatics research in developing new technological means (e.g. using mobile and ubiquitous computing) to resolve contemporary issues or support everyday life in urban environments. The paper discusses the nature, aims and inherent methodological needs of Urban Informatics research, and proposes PADR as a method to address these needs. Situated in a socio-technical context, Urban Informatics requires a close dialogue between social and design-oriented fields of research as well as their methods. PADR combines Action Research and Design Science Research, both of which are used in Information Systems, another field with a strong socio-technical emphasis, and further adapts them to the cross-disciplinary needs and research context of Urban Informatics.

Thermogravimetric analysis, PXRD, EDX and XPS study of chrysocolla (Cu,Al)2H2Si2O5(OH)4·nH2O : structural implications

Selected chrysocolla mineral samples from different origins have been studied by using PXRD, SEM, EDX and XPS. The XRD patterns show that the chrysocolla mineral samples are non-diffracting and no other phases are present in the minerals, thus showing the chrysocolla samples are pure. SEM analyses show the chrysocolla surfaces are featureless. EDX analyses enable the formulae of the chrysocolla samples to be calculated. The thermal decomposition of the mineral chrysocolla has been studied using a combination of thermogravimetric analysis and derivative thermogravimetric analysis. Five thermal decomposition mass loss steps are observed for the chrysocolla from Arizona (a) at 125 ◦C with the loss of water, (b) at 340 ◦C with the loss of hydroxyl units, (c) at 468.5 ◦C with a further loss of hydroxyls, (d) at 821 ◦C with oxygen loss and (e) at 895 ◦C with a further loss of oxygen. The thermal analysis of the chrysocolla from Congo shows mass losses at 125, 275.3, 805.6 and 877.4 ◦C and for the Nevada chrysocolla, mass loss steps at 268, 333, 463, 786.0 and 817.7 ◦C are observed. The thermal analysis of spertiniite is very different from that of chrysocolla and thermally decomposes at around 160 ◦C. XPS shows that there are two different copper species present, one which is bonded to oxygen and one to a hydroxyl unit. The O 1s is broad and very symmetrical suggesting two O species of equal number. The bond energy of 102.9 eV for the Si 2p suggests that it is in the form of a silicate. The bond energy is much higher for silicas around ∼103.5 eV. The reported value for silica gel has Si 2p at 103.4 eV. The combination of TG, PXRD, EDX and XPS adds to our fundamental knowledge of the structure of chrysocolla.

Peer review of teaching practice and resources : exploring new spaces to embrace cultural change

The implementation of systematic peer review as a professional development activity, and as a support for educational design activities is under-utilised in many Australian higher education institutions. This case study reports on the first stages of planning and implementation of an institution-wide project to enhance teaching and learning quality at a remote and regional university, where one of the major strategies for improvement is peer review. Through a systematic process of staff engagement in peer review, within and from outside the organisation, a substantial change in flexible learning is envisaged. A mix of new and different learning spaces are to be used in the project, including blended learning spaces for academic development. This paper describes the research framework that will guide the peer review process and examines the early findings of the design-based research. Leadership, awareness raising and development of a supportive community of inquiry are seen as key components for successful implementation of peer review. In addition, unique contextual elements add to the complexity of designing for transformative change within such a relatively new organization.

Differences between first episode schizophrenia and schizoaffective disorder

Background: The diagnostic and clinical overlap between schizophrenia and schizoaffective disorder is an important nosological issue in psychiatry that is yet to be resolved. The aim of this study was to compare the clinical and functional characteristics of an epidemiological treated cohort of first episode patients with an 18-month discharge diagnosis of schizophrenia (FES) or schizoaffective disorder (FESA). Methods: This study was part of the larger First Episode Psychosis Outcome Study (FEPOS) which involved a medical file audit study of all 786 patients treated at the Early Psychosis Prevention and Intervention Centre between 1998 and 2000. Of this cohort, 283 patients had a 18-month discharge diagnosis of FES and 64 had a diagnosis of FESA. DSM-IV diagnoses, clinical and functional ratings were derived and validated by two consultant psychiatrists. Results: Compared to FES patients, those with FESA were significantly more likely to have a later age of onset (p=.004), longer prodrome (p=.020), and a longer duration of untreated psychosis (p<.001). At service entry, FESA patients presented with a higher illness severity (p=.020), largely due to the presence of more severe manic symptoms (p<.001). FESA patients also had a greater number of subsequent inpatient admissions (p=.017), had more severe depressive symptoms (p=.011), and higher levels of functioning at discharge. Discussion: The findings support the notion that these might be considered two discernable disorders; however, further research is required to ascertain the ways and extent to which these disorders are discriminable at presentation and over time.

Acoustic Masking of a Stealthy Outdoor Robot Tracking a Dynamic Target

This work is motivated by the desire to covertly track mobile targets, either animal or human, in previously unmapped outdoor natural environments using off-road robotic platforms with a non-negligible acoustic signature. The use of robots for stealthy surveillance is not new. Many studies exist but only consider the navigation problem to maintain visual covertness. However, robotic systems also have a significant acoustic footprint from the onboard sensors, motors, computers and cooling systems, and also from the wheels interacting with the terrain during motion. All these can jepordise any visual covertness. In this work, we experimentally explore the concepts of opportunistically utilizing naturally occurring sounds within outdoor environments to mask the motion of a robot, and being visually covert whilst maintaining constant observation of the target. Our experiments in a constrained outdoor built environment demonstrate the effectiveness of the concept by showing a reduced acoustic signature as perceived by a mobile target allowing the robot to covertly navigate to opportunistic vantage points for observation.

A novel route in bone tissue engineering : magnetic biomimetic scaffolds

In recent years, interest in tissue engineering and its solutions has increased considerably. In particular, scaffolds have become fundamental tools in bone graft substitution and are used in combination with a variety of bio-agents. However, a long-standing problem in the use of these conventional scaffolds lies in the impossibility of re-loading the scaffold with the bio-agents after implantation. This work introduces the magnetic scaffold as a conceptually new solution. The magnetic scaffold is able, via magnetic driving, to attract and take up in vivo growth factors, stem cells or other bio-agents bound to magnetic particles. The authors succeeded in developing a simple and inexpensive technique able to transform standard commercial scaffolds made of hydroxyapatite and collagen in magnetic scaffolds. This innovative process involves dip-coating of the scaffolds in aqueous ferrofluids containing iron oxide nanoparticles coated with various biopolymers. After dip-coating, the nanoparticles are integrated into the structure of the scaffolds, providing the latter with magnetization values as high as 15 emu g�1 at 10 kOe. These values are suitable for generating magnetic gradients, enabling magnetic guiding in the vicinity and inside the scaffold. The magnetic scaffolds do not suffer from any structural damage during the process, maintaining their specific porosity and shape. Moreover, they do not release magnetic particles under a constant flow of simulated body fluids over a period of 8 days. Finally, preliminary studies indicate the ability of the magnetic scaffolds to support adhesion and proliferation of human bone marrow stem cells in vitro. Hence, this new type of scaffold is a valuable candidate for tissue engineering applications, featuring a novel magnetic guiding option.

Design of a least-cost battery-supercapacitor energy storage system for realizing dispatchable wind power

A statistical approach is used in the design of a battery-supercapacitor energy storage system for a wind farm. The design exploits the technical merits of the two energy storage mediums, in terms of the differences in their specific power and energy densities, and their ability to accommodate different rates of change in the charging/discharging powers. By treating the input wind power as random and using a proposed coordinated power flows control strategy for the battery and the supercapacitor, the approach evaluates the energy storage capacities, the corresponding expected life cycle cost/year of the storage mediums, and the expected cost/year of unmet power dispatch. A computational procedure is then developed for the design of a least-cost/year hybrid energy storage system to realize wind power dispatch at a specified confidence level.

A transcriptome resource for the koala (Phascolarctos cinereus) : insights into koala retrovirus transcription and sequence diversity

Background The koala, Phascolarctos cinereus, is a biologically unique and evolutionarily distinct Australian arboreal marsupial. The goal of this study was to sequence the transcriptome from several tissues of two geographically separate koalas, and to create the first comprehensive catalog of annotated transcripts for this species, enabling detailed analysis of the unique attributes of this threatened native marsupial, including infection by the koala retrovirus. Results RNA-Seq data was generated from a range of tissues from one male and one female koala and assembled de novo into transcripts using Velvet-Oases. Transcript abundance in each tissue was estimated. Transcripts were searched for likely protein-coding regions and a non-redundant set of 117,563 putative protein sequences was produced. In similarity searches there were 84,907 (72%) sequences that aligned to at least one sequence in the NCBI nr protein database. The best alignments were to sequences from other marsupials. After applying a reciprocal best hit requirement of koala sequences to those from tammar wallaby, Tasmanian devil and the gray short-tailed opossum, we estimate that our transcriptome dataset represents approximately 15,000 koala genes. The marsupial alignment information was used to look for potential gene duplications and we report evidence for copy number expansion of the alpha amylase gene, and of an aldehyde reductase gene. Koala retrovirus (KoRV) transcripts were detected in the transcriptomes. These were analysed in detail and the structure of the spliced envelope gene transcript was determined. There was appreciable sequence diversity within KoRV, with 233 sites in the KoRV genome showing small insertions/deletions or single nucleotide polymorphisms. Both koalas had sequences from the KoRV-A subtype, but the male koala transcriptome has, in addition, sequences more closely related to the KoRV-B subtype. This is the first report of a KoRV-B-like sequence in a wild population. Conclusions This transcriptomic dataset is a useful resource for molecular genetic studies of the koala, for evolutionary genetic studies of marsupials, for validation and annotation of the koala genome sequence, and for investigation of koala retrovirus. Annotated transcripts can be browsed and queried at http://koalagenome.org

An upstream open reading frame is essential for feedback regulation of ascorbate biosynthesis in arabidopsis

Ascorbate (vitamin C) is an essential antioxidant and enzyme cofactor in both plants and animals. Ascorbate concentration is tightly regulated in plants, partly to respond to stress. Here, we demonstrate that ascorbate concentrations are determined via the posttranscriptional repression of GDP-l-galactose phosphorylase (GGP), a major control enzyme in the ascorbate biosynthesis pathway. This regulation requires a cis-acting upstream open reading frame (uORF) that represses the translation of the downstream GGP open reading frame under high ascorbate concentration. Disruption of this uORF stops the ascorbate feedback regulation of translation and results in increased ascorbate concentrations in leaves. The uORF is predicted to initiate at a noncanonical codon (ACG rather than AUG) and encode a 60- to 65-residue peptide. Analysis of ribosome protection data from Arabidopsis thaliana showed colocation of high levels of ribosomes with both the uORF and the main coding sequence of GGP. Together, our data indicate that the noncanonical uORF is translated and encodes a peptide that functions in the ascorbate inhibition of translation. This posttranslational regulation of ascorbate is likely an ancient mechanism of control as the uORF is conserved in GGP genes from mosses to angiosperms.

Cardiovascular disease is increased prior to onset of rheumatoid arthritis but not osteoarthritis: The population-based Nord-Trøndelag health study (HUNT)

Introduction: Patients with rheumatoid arthritis (RA) have increased risk of cardiovascular (CV) events. We sought to test the hypothesis that due to increased inflammation, CV disease and risk factors are associated with increased risk of future RA development. Methods: The population-based Nord-Trøndelag health surveys (HUNT) were conducted among the entire adult population of Nord-Trøndelag, Norway. All inhabitants 20 years or older were invited, and information was collected through comprehensive questionnaires, a clinical examination, and blood samples. In a cohort design, data from HUNT2 (1995-1997, baseline) and HUNT3 (2006-2008, follow-up) were obtained to study participants with RA (n = 786) or osteoarthritis (n = 3,586) at HUNT3 alone, in comparison with individuals without RA or osteoarthritis at both times (n = 33,567). Results: Female gender, age, smoking, body mass index, and history of previous CV disease were associated with self-reported incident RA (previous CV disease: odds ratio 1.52 (95% confidence interval 1.11-2.07). The findings regarding previous CV disease were confirmed in sensitivity analyses excluding participants with psoriasis (odds ratio (OR) 1.70 (1.23-2.36)) or restricting the analysis to cases with a hospital diagnosis of RA (OR 1.90 (1.10-3.27)) or carriers of the shared epitope (OR 1.76 (1.13-2.74)). History of previous CV disease was not associated with increased risk of osteoarthritis (OR 1.04 (0.86-1.27)). Conclusion: A history of previous CV disease was associated with increased risk of incident RA but not osteoarthritis.