Straminipilan protists : a study of their taxonomic position, morphology and abiotic stress-mediated gene expression

Thraustochytrids have become of considerable industrial and scientific interest in the past decade due to their health benefits. They have been proven to be the principle source in marine and estuarine fish diets with high percentage of long chain (LC) or polyunsaturated fatty acids (PUFA). Therefore, the oil extracted from fish for human document.forms[0].elements[13].select();consumption is rich in PUFA with high omega-3 fatty acid content. Docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA) of all of the omega-3 fatty acids, are considered beneficial essential oils for humans with a wide range of health benefits. These include brain and neural development in infants, general wellbeing of adults and drug delivery through precursor molecules. They have become one of the most extensively studied organisms for industrial oil preparations as PUFA extraction from fish becomes less profitable. Many forms of these Thraustochytrid oils are being trialled for human consumption all over the world. In Australia, there has been little research performed on these organisms in the past ten years. A few Australian studies have been conducted in the form of comparative studies related to PUFA production within the related genera, but not focussed on their identification or cellular and genomic characterisation. Therefore, the main aim of this study was to investigate the morphological and genetic characteristics of Australian Thraustochytrids in order to aid in their identification and characterisation, as well as to better understand the effect of environmental conditions in the regulation of PUFA production. It was also noted that there was a knowledge gap in the preservation and total genomic DNA extraction of these organisms for the purposes of scientific research. The cryopreservation of these organisms for studies around the world follows existing generic methods. However, it is well understood that many of these generic methods attract not only high costs for chemicals, but also uses considerable storage space and other resources, all of which can be improved with new or modified approaches. In this context, a simple and inexpensive bead preservation method is described, without compromising the storage shelf life. We also describe, for the first time, the effects of culture age on the successful cryopreservation of Thraustochytrids. It was evident in the literature that DNA and RNA extractions for molecular and genetic studies of Thraustochytrids follow the classical phenol-chloroform extraction methods. It was also observed that modern protocols failed to avoid the use of phenol-chloroform rather than improving preparation and cell disruption. In order to provide a high quantity and quality DNA extraction, a modified protocol has been introduced that employs the use of modern commercial extraction kits and standard laboratory equipment. Thraustochytrids have been shown to be highly conserved in their 18S rDNA gene sequences, which is used as the current standard for identification. It was demonstrated that the 18S rDNA gene sequence limits the recognition of closely related genera or within the genera from each member. Therefore, it was proposed that another profile, such as a randomly amplified polymorphic DNA (RAPD) based profiling system, be tested for use in the characterisation of Thraustochytrids. The RAPD profiles were shown to provide a unique DNA fingerprint for each isolate and small variations in their genome were able to be detected. This method involved the use of a minimum number of standard arbitrary primers and with an increase in the number of different primers used, a very high discrimination between organisms could be achieved. However, the method was not suitable for taxonomic purposes because the results did not correlate with other taxonomic features such as morphology. Another knowledge gap was found with respect to Australian Thraustochytrid growth characteristics, in that these had not been recorded and published. In order to rectify this, a record of colony and microscopic features of 12 selected isolates was performed. The results of preliminary studies indicated that further microbiological and biochemical studies are needed for full characterisation of these organisms. This information is of great importance to bio-prospecting of new Thraustochytrids from Australian ecosystems and would allow for their accurate identification, and so permit the prediction of their PUFA capability by comparison with related genera/species. It was well recognized that environmental stress plays a role in the PUFA production and is mainly due to the reactive oxygen species as abiotic stress (Chiou et al., 2001; Okuyama et al., 2008; Shabala et al., 2009; Shabala et al., 2001). In this aspect, this study makes the first attempt towards better understanding of this phenomenon by way of the use of real-time PCR for the detection of environmental effects on the regulation of PUFA production. Three main environmental conditions including temperature, pH and oxygen availability were monitored as stress inducers. In summary, this study provides novel approaches for the preservation and handling of Thraustochytrids, their molecular biological features, taxonomy, characterisation and responses to environmental factors with respect to their oil production enzymes. The information produced from this study will prove to be vital for both industrial and scientific investigations in the future.

A loss of bioscience knowledge in nursing students

Background: Knowledge of the human biosciences is fundamental to the development of competent nurse practitioners (Smales, 2010) with the requisite knowledge and skills, necessary for high quality patient care and good patient outcomes (Logan and Angel, 2011). Many of these students study bioscience units which cover topics in anatomy, physiology, pathophysiology and microbiology. Studies of science recall in general and medical education, report up to 33% loss of knowledge in the first year which declines to 50% in the subsequent year (Custers, 2010). Objectives: The objectives were to test the recall of bioscience knowledge by nursing students and to ascertain their perceptions of the testing. Questions explored: What would the results be for multiple choice questions in fundamental microbiology and gastrointestinal anatomy and physiology (A&P) undertaken by nursing students 4, 9 and 16 months after their first bioscience exam on these topics? Would pre-warning the students of a microbiology quiz and not a gastrointestinal A&P quiz affect the findings? How would the students respond to the testing when surveyed? Recall results: The nursing students performed better in the final exam on gastrointestinal A&P than on fundamental microbiology. There was an approximate 20% loss in knowledge of gastrointestinal A&P after 4 months and this did not change significantly over the next 12 months. Although there was an improved performance in microbiology quizzes after 4 months, there was no significant difference in results over the next 12 months. Survey results: More than 50% of students thought the testing helped them focus for the lectures and made them aware they had some pre-knowledge of the lecture topics. Discussion: Although there was a loss of knowledge of gastrointestinal A&P, it appears that warning the students about the microbiology quiz may have helped their recall. The majority of students valued the testing as a useful learning exercise. References: Custers, E. J. F. M. (2010). Long-term retention of basic science knowledge: a review study. Advances in Health Science Education, 15, 109-128. Smales, K. (2010). Learning and applying biosciences to clinical practice in nursing. Nursing Standard, 24(33), 35-39. Logan, P.A., & Angel, L. (2011). Nursing as a scientific undertaking and the intersection with science in undergraduate studies: implications for nursing management. Journal of Nursing Management, 19(3), 407-417.

Experimental colonization of the canine urinary tract with the asymptomatic bacteriuria Escherichia coli strain 83972

Establishment of asymptomatic bacteriuria (ABU) with Escherichia coli 83972 is a viable prophylactic alternative to antibiotic therapy for the prevention of recurrent bacterial urinary tract infection in humans. Approximately 2 x 108 viable E. coli 83972 cells were introduced into the bladder of six healthy female dogs via a sterile urinary catheter. The presence of pyuria, depression, stranguria, pollakiuria and haematuria was documented for 6 weeks and urinalysis and aerobic bacterial cultures were performed every 24–72 h. Pyuria was present in all dogs on day 1 post-inoculation and 4/6 dogs (67%) had a positive urine culture on this day. Duration of colonization ranged from 0 to 10 days (median 4 days). Four dogs were re-inoculated on day 20. Duration of colonization following the second inoculation ranged from 1 to 3 days. No dog suffered pyrexia or appeared systemically unwell but all dogs initially exhibited mild pollakiuria and a small number displayed gross haematuria and/or stranguria. By day 3 of each trial all clinical signs had resolved. Persistent bacteriuria was not achieved in any dog but two dogs were colonized for 10 days following a single inoculation. Further research is required to determine whether establishment of ABU in dogs with recurrent urinary tract infection is a viable alternative to repeated doses of antimicrobial agents.

Exploring the usefulness of structural–functional approaches to analyse governance of planning systems

Existing planning theories tend to be limited in their analytical scope and often fail to account for the impact of many interactions between the multitudes of stakeholders involved in strategic planning processes. Although many theorists rejected structural–functional approaches from the 1970s, this article argues that many of structural–functional concepts remain relevant and useful to planning practitioners. In fact, structural–functional approaches are highly useful and practical when used as a foundation for systemic analysis of real-world, multi-layered, complex planning systems to support evidence-based governance reform. Such approaches provide a logical and systematic approach to the analysis of the wider governance of strategic planning systems that is grounded in systems theory and complementary to existing theories of complexity and planning. While we do not propose its use as a grand theory of planning, this article discusses how structural–functional concepts and approaches might be applied to underpin a practical analysis of the complex decision-making arrangements that drive planning practice, and to provide the evidence needed to target reform of poorly performing arrangements.

Theorizing the use of multiple conceptual models in combination

Conceptual modelling continues to be an important means for graphically capturing the requirements of an information system. Observations of modelling practice suggest that modellers often use multiple conceptual models in combination, because they articulate different aspects of real-world domains. Yet, the available empirical as well as theoretical research in this area has largely studied the use of single models, or single modelling grammars. We develop a Theory of Combined Ontological Coverage by extending an existing theory of ontological expressiveness of conceptual modelling grammars. Our new theory posits that multiple conceptual models are used to increase the maximum coverage of the real-world domain being modelled, whilst trying to minimize the ontological overlap between the models. We illustrate how the theory can be applied to analyse sets of conceptual models. We develop three propositions of the theory about evaluations of model combinations in terms of users’ selection, understandability and usefulness of conceptual models.

The impact of incidents on macroscopic fundamental diagrams

The macroscopic fundamental diagram (MFD) traffic modelling method has been proved for large urban roads and freeway networks, but hysteresis and scatter have been found in both such networks. This paper investigates how incident variables affect the shape and scatter of the MFD using both simulated data and real data collected from the M3 Pacific motorway in Brisbane, Australia. Three key components of incidents are investigated based on the simulated data (i.e. incident location, incident duration and traffic demand). The results based on simulated data indicate that the diagram shape is a property not only of the network itself but also of the incident variables. Diagrams for three types of real incidents (crash, hazard and vehicle breakdown) are explored separately. The results based on the empirical data are consistent with the simulated results. The hysteresis phenomenon occurs both upstream and downstream of the incident location, but for opposite hysteresis loops. The gradient of the upstream diagram is greater than that downstream on the incident site, when traffic demand is for an off-peak period.

Age-related changes in perception of movement in driving scenes

Purpose Age-related changes in motion sensitivity have been found to relate to reductions in various indices of driving performance and safety. The aim of this study was to investigate the basis of this relationship in terms of determining which aspects of motion perception are most relevant to driving. Methods Participants included 61 regular drivers (age range 22–87 years). Visual performance was measured binocularly. Measures included visual acuity, contrast sensitivity and motion sensitivity assessed using four different approaches: (1) threshold minimum drift rate for a drifting Gabor patch, (2) Dmin from a random dot display, (3) threshold coherence from a random dot display, and (4) threshold drift rate for a second-order (contrast modulated) sinusoidal grating. Participants then completed the Hazard Perception Test (HPT) in which they were required to identify moving hazards in videos of real driving scenes, and also a Direction of Heading task (DOH) in which they identified deviations from normal lane keeping in brief videos of driving filmed from the interior of a vehicle. Results In bivariate correlation analyses, all motion sensitivity measures significantly declined with age. Motion coherence thresholds, and minimum drift rate threshold for the first-order stimulus (Gabor patch) both significantly predicted HPT performance even after controlling for age, visual acuity and contrast sensitivity. Bootstrap mediation analysis showed that individual differences in DOH accuracy partly explained these relationships, where those individuals with poorer motion sensitivity on the coherence and Gabor tests showed decreased ability to perceive deviations in motion in the driving videos, which related in turn to their ability to detect the moving hazards. Conclusions The ability to detect subtle movements in the driving environment (as determined by the DOH task) may be an important contributor to effective hazard perception, and is associated with age, and an individuals' performance on tests of motion sensitivity. The locus of the processing deficits appears to lie in first-order, rather than second-order motion pathways.

Measuring Competence in Supervisees and Supervisors : Satisfaction and Related Reactions in Supervision

Supervision is a highly valued component of practitioner training. This chapter discusses the following: factors influencing perceived satisfaction and alliance; and how satisfaction, alliance, and supervision relationships are currently measured; and reviews issues with the concept and its assessment. Given the importance of the supervisory relationship and of the supervisory alliance for the effectiveness of supervision and for the welfare of supervisees, the routine, repeated measurement of both these concepts, together with supervisee satisfaction, also assumes considerable utility. The chapter describes a selection of some commonly used measures: Supervisee Satisfaction Questionnaire (SSQ), Supervisory Relationship Questionnaire (SRQ), Supervisory Relationship Measure (SRM), Supervision Attitude Scale (SAS), Supervisory Working Alliance Inventory (SWAI), Supervisory Styles Inventory (SSI), Role Conflict and Ambiguity Inventory (RCAIC), and Evaluation Process within Supervision Inventory (EPSI).

A new look at the restrictions on the speed and magnitude of train loads for bridge management

In current bridge management systems (BMSs), load and speed restrictions are applied on unhealthy bridges to keep the structure safe and serviceable for as long as possible. But the question is, whether applying these restrictions will always decrease the internal forces in critical components of the bridge and enhance the safety of the unhealthy bridges. To find the answer, this paper for the first time in literature, looks into the design aspects through studying the changes in demand by capacity ratios of the critical components of a bridge under the train loads. For this purpose, a structural model of a simply supported bridge, whose dynamic behaviour is similar to a group of real railway bridges, is developed. Demand by capacity ratios of the critical components of the bridge are calculated, to identify their sensitivity to increase of speed and magnitude of live load. The outcomes of this study are very significant as they show that, on the contrary to what is expected, by applying restriction on speed, the demand by capacity ratio of components may increase and make the bridge unsafe for carrying live load. Suggestions are made to solve the problem.

Approximation of Bayesian predictive p-values with regression ABC

In the Bayesian framework a standard approach to model criticism is to compare some function of the observed data to a reference predictive distribution. The result of the comparison can be summarized in the form of a p-value, and it's well known that computation of some kinds of Bayesian predictive p-values can be challenging. The use of regression adjustment approximate Bayesian computation (ABC) methods is explored for this task. Two problems are considered. The first is the calibration of posterior predictive p-values so that they are uniformly distributed under some reference distribution for the data. Computation is difficult because the calibration process requires repeated approximation of the posterior for different data sets under the reference distribution. The second problem considered is approximation of distributions of prior predictive p-values for the purpose of choosing weakly informative priors in the case where the model checking statistic is expensive to compute. Here the computation is difficult because of the need to repeatedly sample from a prior predictive distribution for different values of a prior hyperparameter. In both these problems we argue that high accuracy in the computations is not required, which makes fast approximations such as regression adjustment ABC very useful. We illustrate our methods with several samples.

Fruit-feeding behaviour and use of olfactory cues by the fruit bat Rousettus leschenaulti: an experimental study

This paper describes the feeding behaviour ofRousettus leschenaulti Desmarest, 1820 on lychees, the preferred cultivated food of this bat in captive conditions. We found that feeding comprised 25–30% of the total activity of these animals in a flight cage and that feeding durations were not significantly different between two sexes. To evaluate the role of odor and vision in foraging behaviour, we provided animals with artificial lychees, real lychees and artificial lychees soaked in the juice of real lychees and we recorded the number of feeding approaches to the different “fruit” types. The results indicated that bats approached real fruit significantly more than artificial fruit, and that the number of approaches to the soaked artificial fruit was also significantly higher than to the unsoaked artificial fruit. There were no significant differences between sexes in approach rates to any “fruit” type. We discuss the role of different sensory cues in the foraging behaviour of these bats and emphasize that the olfactory cue is important in detecting food resources and discriminating between different kinds of food items.

What patient information allows us to make accurate predictions of outcome?

Only some of the information contained in a medical record will be useful to the prediction of patient outcome. We describe a novel method for selecting those outcome predictors which allow us to reliably discriminate between adverse and benign end results. Using the area under the receiver operating characteristic as a nonparametric measure of discrimination, we show how to calculate the maximum discrimination attainable with a given set of discrete valued features. This upper limit forms the basis of our feature selection algorithm. We use the algorithm to select features (from maternity records) relevant to the prediction of failure to progress in labour. The results of this analysis motivate investigation of those predictors of failure to progress relevant to parous and nulliparous sub-populations.

Balancing information disclosure and “Red Tape” : Queensland’s proposal of seller disclosure

The Queensland Property Law Review is currently reviewing seller disclosure laws in Queensland. The review will consider if the desire to provide consumers of real estate with valuable timely information about a property offered for sale can be effectively delivered with a minimum of red tape. This article examines the principles proposed by the first discussion paper on seller disclosure and their likely effect in practice.

Security Analysis of Randomize-Hash-then-Sign Digital Signatures

At CRYPTO 2006, Halevi and Krawczyk proposed two randomized hash function modes and analyzed the security of digital signature algorithms based on these constructions. They showed that the security of signature schemes based on the two randomized hash function modes relies on properties similar to the second preimage resistance rather than on the collision resistance property of the hash functions. One of the randomized hash function modes was named the RMX hash function mode and was recommended for practical purposes. The National Institute of Standards and Technology (NIST), USA standardized a variant of the RMX hash function mode and published this standard in the Special Publication (SP) 800-106. In this article, we first discuss a generic online birthday existential forgery attack of Dang and Perlner on the RMX-hash-then-sign schemes. We show that a variant of this attack can be applied to forge the other randomize-hash-then-sign schemes. We point out practical limitations of the generic forgery attack on the RMX-hash-then-sign schemes. We then show that these limitations can be overcome for the RMX-hash-then-sign schemes if it is easy to find fixed points for the underlying compression functions, such as for the Davies-Meyer construction used in the popular hash functions such as MD5 designed by Rivest and the SHA family of hash functions designed by the National Security Agency (NSA), USA and published by NIST in the Federal Information Processing Standards (FIPS). We show an online birthday forgery attack on this class of signatures by using a variant of Dean’s method of finding fixed point expandable messages for hash functions based on the Davies-Meyer construction. This forgery attack is also applicable to signature schemes based on the variant of RMX standardized by NIST in SP 800-106. We discuss some important applications of our attacks and discuss their applicability on signature schemes based on hash functions with ‘built-in’ randomization. Finally, we compare our attacks on randomize-hash-then-sign schemes with the generic forgery attacks on the standard hash-based message authentication code (HMAC).

On hash functions using checksums

We analyse the security of iterated hash functions that compute an input dependent checksum which is processed as part of the hash computation. We show that a large class of such schemes, including those using non-linear or even one-way checksum functions, is not secure against the second preimage attack of Kelsey and Schneier, the herding attack of Kelsey and Kohno and the multicollision attack of Joux. Our attacks also apply to a large class of cascaded hash functions. Our second preimage attacks on the cascaded hash functions improve the results of Joux presented at Crypto’04. We also apply our attacks to the MD2 and GOST hash functions. Our second preimage attacks on the MD2 and GOST hash functions improve the previous best known short-cut second preimage attacks on these hash functions by factors of at least 226 and 254, respectively. Our herding and multicollision attacks on the hash functions based on generic checksum functions (e.g., one-way) are a special case of the attacks on the cascaded iterated hash functions previously analysed by Dunkelman and Preneel and are not better than their attacks. On hash functions with easily invertible checksums, our multicollision and herding attacks (if the hash value is short as in MD2) are more efficient than those of Dunkelman and Preneel.