Probiotic Bacillus amyloliquefaciens Strain H57 Improves the Performance of Pregnant and Lactating Ewes Fed a Diet Based on Palm Kernel Meal

Probiotic supplements are single or mixed strain cultures of live microorganisms that benefit the host by improving the properties of the indigenous microflora (Seo et al 2010). In a pilot study at the University of Queensland, Norton et al (2008) found that Bacillus amyloliquefaciens Strain H57 (H57), primarily investigated as an inoculum to make high-quality hay, improved feed intake and nitrogen utilisation over several weeks in pregnant ewes. The purpose of the following study was to further challenge the potential of H57 -to show it survives the steam-pelleting process, and that it improves the performance of ewes fed pellets based on an agro-industrial by-product with a reputation for poor palatability, palm kernel meal (PKM), (McNeill 2013). Thirty-two first-parity White Dorper ewes (day 37 of pregnancy, mean liveweight = 47.3 kg, mean age = 15 months) were inducted into individual pens in the animal house at the University of Queensland, Gatton. They were adjusted onto PKM-based pellets (g/kg drymatter (DM): PKM, 408; sorghum, 430; chick pea hulls, 103; minerals and vitamins; Crude protein, 128; ME: 11.1MJ/kg DM) until day 89 of pregnancy and thereafter fed a predominately pelleted diet incorporating with or without H57 spores (10 9 colony forming units (cfu)/kg pellet, as fed), plus 100g/ewe/day oaten chaff, until day 7 of lactation. From day 7 to 20 of lactation the pelleted component of the diet was steadily reduced to be replaced by a 50:50 mix of lucerne: oaten chaff, fed ad libitum, plus 100g/ewe/day of ground sorghum grain with or without H57 (10 9 cfu/ewe/day). The period of adjustment in pregnancy (day 37-89) extended beyond expectations due to some evidence of mild ruminal acidosis after some initially high intakes that were followed by low intakes. During that time the diet was modified, in an attempt to improve palatability, by the addition of oaten chaff and the removal of an acidifying agent (NH4Cl) that was added initially to reduce the risk of urinary calculi. Eight ewes were removed due to inappetence, leaving 24 ewes to start the trial at day 90 of pregnancy. From day 90 of pregnancy until day 63 of lactation, liveweights of the ewes and their lambs were determined weekly and at parturition. Feed intakes of the ewes were determined weekly. Once lambing began, 1 ewe was removed as it gave birth to twin lambs (whereas the rest gave birth to a single lamb), 4 due to the loss of their lambs (2 to dystocia), and 1 due to copper toxicity. The PKM pellets were suspected to be the cause of the copper toxicity and so were removed in early lactation. Hence, the final statistical analysis using STATISTICA 8 (Repeated measures ANOVA for feed intake, One-way ANOVA for liveweight change and birth weight) was completed on 23 ewes for the pregnancy period (n = 11 fed H57; n = 12 control), and 18 ewes or lambs for the lactation period (n = 8 fed H57; n = 10 control). From day 90 of pregnancy until parturition the H57 supplemented ewes ate 17 more DM (g/day: 1041 vs 889, sed = 42.4, P = 0.04) and gained more liveweight (g/day: 193 vs 24.0, sed = 25.4, P = 0.0002), but produced lambs with a similar birthweight (kg: 4.18 vs 3.99, sed = 0.19, P = 0.54). Over the 63 days of lactation the H57 ewes ate similar amounts of DM but grew slower than the control ewes (g/day: 1.5 vs 97.0, sed = 21.7, P = 0.012). The lambs of the H57 ewes grew faster than those of the control ewes for the first 21 days of lactation (g/day: 356 vs 265, sed = 16.5, P = 0.006). These data support the findings of Norton et al (2008) and Kritas et al (2006) that certain Bacillus spp. supplements can improve the performance of pregnant and lactating ewes. In the current study we particularly highlighted the capacity of H57 to stimulate immature ewes to continue to grow maternal tissue through pregnancy, possibly through an enhanced appetite, which appeared then to stimulate a greater capacity to partition nutrients to their lambs through milk, at least for the first few weeks of lactation, a critical time for optimising lamb survival. To conclude, H57 can survive the steam pelleting process to improve feed intake and maternal liveweight gain in late pregnancy, and performance in early lactation, of first-parity ewes fed a diet based on PKM.

Construction of a global map of human gene expression : the process, tools and analysis

This thesis studies human gene expression space using high throughput gene expression data from DNA microarrays. In molecular biology, high throughput techniques allow numerical measurements of expression of tens of thousands of genes simultaneously. In a single study, this data is traditionally obtained from a limited number of sample types with a small number of replicates. For organism-wide analysis, this data has been largely unavailable and the global structure of human transcriptome has remained unknown. This thesis introduces a human transcriptome map of different biological entities and analysis of its general structure. The map is constructed from gene expression data from the two largest public microarray data repositories, GEO and ArrayExpress. The creation of this map contributed to the development of ArrayExpress by identifying and retrofitting the previously unusable and missing data and by improving the access to its data. It also contributed to creation of several new tools for microarray data manipulation and establishment of data exchange between GEO and ArrayExpress. The data integration for the global map required creation of a new large ontology of human cell types, disease states, organism parts and cell lines. The ontology was used in a new text mining and decision tree based method for automatic conversion of human readable free text microarray data annotations into categorised format. The data comparability and minimisation of the systematic measurement errors that are characteristic to each lab- oratory in this large cross-laboratories integrated dataset, was ensured by computation of a range of microarray data quality metrics and exclusion of incomparable data. The structure of a global map of human gene expression was then explored by principal component analysis and hierarchical clustering using heuristics and help from another purpose built sample ontology. A preface and motivation to the construction and analysis of a global map of human gene expression is given by analysis of two microarray datasets of human malignant melanoma. The analysis of these sets incorporate indirect comparison of statistical methods for finding differentially expressed genes and point to the need to study gene expression on a global level.

Optimal maintenance policy for equipment subject to random deterioration and random failure A modern control theory approach.

The stochastic version of Pontryagin's maximum principle is applied to determine an optimal maintenance policy of equipment subject to random deterioration. The deterioration of the equipment with age is modelled as a random process. Next the model is generalized to include random catastrophic failure of the equipment. The optimal maintenance policy is derived for two special probability distributions of time to failure of the equipment, namely, exponential and Weibull distributions Both the salvage value and deterioration rate of the equipment are treated as state variables and the maintenance as a control variable. The result is illustrated by an example

Nonlinear Control Design for an Air-breathing Engine with State Estimation

A nonlinear control design approach is presented in this paper for a challenging application problem of ensuring robust performance of an air-breathing engine operating at supersonic speed. The primary objective of control design is to ensure that the engine produces the required thrust that tracks the commanded thrust as closely as possible by appropriate regulation of the fuel flow rate. However, since the engine operates in the supersonic range, an important secondary objective is to ensure an optimal location of the shock in the intake for maximum pressure recovery with a sufficient margin. This is manipulated by varying the throat area of the nozzle. The nonlinear dynamic inversion technique has been successfully used to achieve both of the above objectives. In this problem, since the process is faster than the actuators, independent control designs have also been carried out for the actuators as well to assure the satisfactory performance of the system. Moreover, an extended Kalman Filter based state estimation design has been carried out both to filter out the process and sensor noises as well as to make the control design operate based on output feedback. Promising simulation results indicate that the proposed control design approach is quite successful in obtaining robust performance of the air-breathing system.

An absolute digital positioning numerical control system

A module containing all the functional components required for a digital absolute positioning process of one axis of a machine tool has been designed and constructed. Circuit realization makes use of integrated circuit elements.

Second-order statistical structure of geomagnetic field reversals

From the autocorrelation function of geomagnetic polarity intervals, it is shown that the field reversal intervals are not independent but form a process akin to the Markov process, where the random input to the model is itself a moving average process. The input to the moving average model is, however, an independent Gaussian random sequence. All the parameters in this model of the geomagnetic field reversal have been estimated. In physical terms this model implies that the mechanism of reversal possesses a memory.

Cluster randomised-control trial for an Australian child protection education program: Study protocol for the Learn to be safe with Emmy and friends™

Background Child maltreatment has severe short-and long-term consequences for children’s health, development, and wellbeing. Despite the provision of child protection education programs in many countries, few have been rigorously evaluated to determine their effectiveness. We describe the design of a multi-site gold standard evaluation of an Australian school-based child protection education program. The intervention has been developed by a not-for-profit agency and comprises 5 1-h sessions delivered to first grade students (aged 5–6 years) in their regular classrooms. It incorporates common attributes of effective programs identified in the literature, and aligns with the Australian education curriculum. Methods/Design A three-site cluster randomised controlled trial (RCT) of Learn to be safe with Emmy and friends™ will be conducted with children in approximately 72 first grade classrooms in 24 Queensland primary (elementary) schools from three state regions, over a period of 2 years. Entire schools will be randomised, using a computer generated list of random numbers, to intervention and wait-list control conditions, to prevent contamination effects across students and classes. Data will be collected at baseline (pre-assessment), immediately after the intervention (post-assessment), and at 6-, 12-, and 18-months (follow-up assessments). Outcome assessors will be blinded to group membership. Primary outcomes assessed are children’s knowledge of program concepts; intentions to use program knowledge, skills, and help-seeking strategies; actual use of program material in a simulated situation; and anxiety arising from program participation. Secondary outcomes include a parent discussion monitor, parent observations of their children’s use of program materials, satisfaction with the program, and parental stress. A process evaluation will be conducted concurrently to assess program performance. Discussion This RCT addresses shortcomings in previous studies and methodologically extends research in this area by randomising at school-level to prevent cross-learning between conditions; providing longer-term outcome assessment than any previous study; examining the degree to which parents/guardians discuss intervention content with children at home; assessing potential moderating/mediating effects of family and child demographic variables; testing an in-vivo measure to assess children’s ability to discriminate safe/unsafe situations and disclose to trusted adults; and testing enhancements to existing measures to establish greater internal consistency.

Conceptual and statistical modelling of environmental effects in population dynamics

Population dynamics are generally viewed as the result of intrinsic (purely density dependent) and extrinsic (environmental) processes. Both components, and potential interactions between those two, have to be modelled in order to understand and predict dynamics of natural populations; a topic that is of great importance in population management and conservation. This thesis focuses on modelling environmental effects in population dynamics and how effects of potentially relevant environmental variables can be statistically identified and quantified from time series data. Chapter I presents some useful models of multiplicative environmental effects for unstructured density dependent populations. The presented models can be written as standard multiple regression models that are easy to fit to data. Chapters II IV constitute empirical studies that statistically model environmental effects on population dynamics of several migratory bird species with different life history characteristics and migration strategies. In Chapter II, spruce cone crops are found to have a strong positive effect on the population growth of the great spotted woodpecker (Dendrocopos major), while cone crops of pine another important food resource for the species do not effectively explain population growth. The study compares rate- and ratio-dependent effects of cone availability, using state-space models that distinguish between process and observation error in the time series data. Chapter III shows how drought, in combination with settling behaviour during migration, produces asymmetric spatially synchronous patterns of population dynamics in North American ducks (genus Anas). Chapter IV investigates the dynamics of a Finnish population of skylark (Alauda arvensis), and point out effects of rainfall and habitat quality on population growth. Because the skylark time series and some of the environmental variables included show strong positive autocorrelation, the statistical significances are calculated using a Monte Carlo method, where random autocorrelated time series are generated. Chapter V is a simulation-based study, showing that ignoring observation error in analyses of population time series data can bias the estimated effects and measures of uncertainty, if the environmental variables are autocorrelated. It is concluded that the use of state-space models is an effective way to reach more accurate results. In summary, there are several biological assumptions and methodological issues that can affect the inferential outcome when estimating environmental effects from time series data, and that therefore need special attention. The functional form of the environmental effects and potential interactions between environment and population density are important to deal with. Other issues that should be considered are assumptions about density dependent regulation, modelling potential observation error, and when needed, accounting for spatial and/or temporal autocorrelation.

Scattering theory and the discrete linear optimal control problem

This paper deals with the interpretation of the discrete-time optimal control problem as a scattering process in a discrete medium. We treat the discrete optimal linear regulator, constrained end-point and servo and tracking problems, providing a unified approach to these problems. This approach results in an easy derivation of the desired results as well as several new ones.

Microbial diversity in the municipal composting process and development of detection methods

Composting refers to aerobic degradation of organic material and is one of the main waste treatment methods used in Finland for treating separated organic waste. The composting process allows converting organic waste to a humus-like end product which can be used to increase the organic matter in agricultural soils, in gardening, or in landscaping. Microbes play a key role as degraders during the composting-process, and the microbiology of composting has been studied for decades, but there are still open questions regarding the microbiota in industrial composting processes. It is known that with the traditional, culturing-based methods only a small fraction, below 1%, of the species in a sample is normally detected. In recent years an immense diversity of bacteria, fungi and archaea has been found to occupy many different environments. Therefore the methods of characterising microbes constantly need to be developed further. In this thesis the presence of fungi and bacteria in full-scale and pilot-scale composting processes was characterised with cloning and sequencing. Several clone libraries were constructed and altogether nearly 6000 clones were sequenced. The microbial communities detected in this study were found to differ from the compost microbes observed in previous research with cultivation based methods or with molecular methods from processes of smaller scale, although there were similarities as well. The bacterial diversity was high. Based on the non-parametric coverage estimations, the number of bacterial operational taxonomic units (OTU) in certain stages of composting was over 500. Sequences similar to Lactobacillus and Acetobacteria were frequently detected in the early stages of drum composting. In tunnel stages of composting the bacterial community comprised of Bacillus, Thermoactinomyces, Actinobacteria and Lactobacillus. The fungal diversity was found to be high and phylotypes similar to yeasts were abundantly found in the full-scale drum and tunnel processes. In addition to phylotypes similar to Candida, Pichia and Geotrichum moulds from genus Thermomyces and Penicillium were observed in tunnel stages of composting. Zygomycetes were detected in the pilot-scale composting processes and in the compost piles. In some of the samples there were a few abundant phylotypes present in the clone libraries that masked the rare ones. The rare phylotypes were of interest and a method for collecting them from clone libraries for sequencing was developed. With negative selection of the abundant phylotyps the rare ones were picked from the clone libraries. Thus 41% of the clones in the studied clone libraries were sequenced. Since microbes play a central role in composting and in many other biotechnological processes, rapid methods for characterization of microbial diversity would be of value, both scientifically and commercially. Current methods, however, lack sensitivity and specificity and are therefore under development. Microarrays have been used in microbial ecology for a decade to study the presence or absence of certain microbes of interest in a multiplex manner. The sequence database collected in this thesis was used as basis for probe design and microarray development. The enzyme assisted detection method, ligation-detection-reaction (LDR) based microarray, was adapted for species-level detection of microbes characteristic of each stage of the composting process. With the use of a specially designed control probe it was established that a species specific probe can detect target DNA representing as little as 0.04% of total DNA in a sample. The developed microarray can be used to monitor composting processes or the hygienisation of the compost end product. A large compost microbe sequence dataset was collected and analysed in this thesis. The results provide valuable information on microbial community composition during industrial scale composting processes. The microarray method was developed based on the sequence database collected in this study. The method can be utilised in following the fate of interesting microbes during composting process in an extremely sensitive and specific manner. The platform for the microarray is universal and the method can easily be adapted for studying microbes from environments other than compost.

Systematic review of interventions to improve the provision of information for adults with primary brain tumours and their caregivers

Background: Adults with primary brain tumors and their caregivers have significant information needs. This review assessed the effect of interventions to improve information provision for adult primary brain tumor patients and/or their caregivers. Methods: We included randomized or nonrandomized trials testing educational interventions that had outcomes of information provision, knowledge, understanding, recall, or satisfaction with the intervention, for adults diagnosed with primary brain tumors and/or their family or caregivers. PubMed, MEDLINE, EMBASE and Cochrane Reviews databases were searched for studies published between 1980 and June 2014. Results: Two randomized controlled, one non-randomized controlled, and 10 single group pre-post trials enrolled more than 411 participants. Five group, four practice/process change and four individual interventions assessed satisfaction (12 studies), knowledge (four studies) or information provision (2 studies). Nine studies reported high rates of satisfaction. Three studies showed statistically significant improvements over time in knowledge and two showed greater information was provided to intervention than control group participants, although statistical testing was not performed. Discussion: The trials assessed intermediate outcomes such as satisfaction, and only 4/13 reported on knowledge improvements. Few trials had a randomized controlled design and risk of bias was either evident or could not be assessed in most domains.

Credentialing of Australian and New Zealand infection control professionals: An exploratory study

Background Despite evidence from overseas that certification and credentialing of infection control professionals (ICPs) is important to patient outcomes, there are no standardized requirements for the education and preparation of ICPs in Australia. A credentialing process (now managed by the Australasian College of Infection Prevention and Control) has been in existence since 2000; however, no evaluation has occurred. Methods A cross-sectional study design was used to identify the perceived barriers to credentialing and the characteristics of credentialed ICPs. Results There were 300 responses received; 45 (15%) of participants were credentialed. Noncredentialed ICPs identified barriers to credentialing as no employer requirement and no associated remuneration. Generally credentialed ICPs were more likely to hold higher degrees and have more infection control experience than their noncredentialed colleagues. Conclusions The credentialing process itself may assist in supporting ICP development by providing an opportunity for reflection and feedback from peer review. Further, the process may assist ICPs in being flexible and adaptable to the challenging and ever-changing environment that is infection control.

Intensive versus conventional glycaemic control for treating diabetic foot ulcers

Background The estimated likelihood of lower limb amputation is 10 to 30 times higher amongst people with diabetes compared to those without diabetes. Of all non-traumatic amputations in people with diabetes, 85% are preceded by a foot ulcer. Foot ulceration associated with diabetes (diabetic foot ulcers) is caused by the interplay of several factors, most notably diabetic peripheral neuropathy (DPN), peripheral arterial disease (PAD) and changes in foot structure. These factors have been linked to chronic hyperglycaemia (high levels of glucose in the blood) and the altered metabolic state of diabetes. Control of hyperglycaemia may be important in the healing of ulcers. Objectives To assess the effects of intensive glycaemic control compared to conventional control on the outcome of foot ulcers in people with type 1 and type 2 diabetes. Search methods In December 2015 we searched: The Cochrane Wounds Specialised Register; The Cochrane Central Register of Controlled Trials (CENTRAL) (The Cochrane Library); Ovid MEDLINE; Ovid MEDLINE (In-Process & Other Non-Indexed Citations); Ovid EMBASE; EBSCO CINAHL; Elsevier SCOPUS; ISI Web of Knowledge Web of Science; BioMed Central and LILACS. We also searched clinical trial databases, pharmaceutical trial databases and current international and national clinical guidelines on diabetes foot management for relevant published, non-published, ongoing and terminated clinical trials. There were no restrictions based on language or date of publication or study setting. Selection criteria Published, unpublished and ongoing randomised controlled trials (RCTs) were considered for inclusion where they investigated the effects of intensive glycaemic control on the outcome of active foot ulcers in people with diabetes. Non randomised and quasi-randomised trials were excluded. In order to be included the trial had to have: 1) attempted to maintain or control blood glucose levels and measured changes in markers of glycaemic control (HbA1c or fasting, random, mean, home capillary or urine glucose), and 2) documented the effect of these interventions on active foot ulcer outcomes. Glycaemic interventions included subcutaneous insulin administration, continuous insulin infusion, oral anti-diabetes agents, lifestyle interventions or a combination of these interventions. The definition of the interventional (intensive) group was that it should have a lower glycaemic target than the comparison (conventional) group. Data collection and analysis All review authors independently evaluated the papers identified by the search strategy against the inclusion criteria. Two review authors then independently reviewed all potential full-text articles and trials registry results for inclusion. Main results We only identified one trial that met the inclusion criteria but this trial did not have any results so we could not perform the planned subgroup and sensitivity analyses in the absence of data. Two ongoing trials were identified which may provide data for analyses in a later version of this review. The completion date of these trials is currently unknown. Authors' conclusions The current review failed to find any completed randomised clinical trials with results. Therefore we are unable to conclude whether intensive glycaemic control when compared to conventional glycaemic control has a positive or detrimental effect on the treatment of foot ulcers in people with diabetes. Previous evidence has however highlighted a reduction in risk of limb amputation (from various causes) in people with type 2 diabetes with intensive glycaemic control. Whether this applies to people with foot ulcers in particular is unknown. The exact role that intensive glycaemic control has in treating foot ulcers in multidisciplinary care (alongside other interventions targeted at treating foot ulcers) requires further investigation.

Boarding control system for improved accessibility to offshore wind turbines: Full-scale testing

This paper considers the dynamic modelling and motion control of a Surface Effect Ship (SES) for safer transfer of personnel and equipment from vessel to-and-from an offshore wind-turbine. The control system designed is referred to as Boarding Control System (BCS). The performance of this system is investigated for a specific wind-farm service vessel—The Wave Craft. On a SES, the pressurized air cushion supports the majority of the weight of the vessel. The control problem considered relates to the actuation of the pressure such that wave-induced vessel motions are minimized. Results are given through simulation, model- and full-scale experimental testing.

Ship collision avoidance and COLREGS compliance using simulation-based control behavior selection with predictive hazard assessment

This paper describes a concept for a collision avoidance system for ships, which is based on model predictive control. A finite set of alternative control behaviors are generated by varying two parameters: offsets to the guidance course angle commanded to the autopilot and changes to the propulsion command ranging from nominal speed to full reverse. Using simulated predictions of the trajectories of the obstacles and ship, compliance with the Convention on the International Regulations for Preventing Collisions at Sea and collision hazards associated with each of the alternative control behaviors are evaluated on a finite prediction horizon, and the optimal control behavior is selected. Robustness to sensing error, predicted obstacle behavior, and environmental conditions can be ensured by evaluating multiple scenarios for each control behavior. The method is conceptually and computationally simple and yet quite versatile as it can account for the dynamics of the ship, the dynamics of the steering and propulsion system, forces due to wind and ocean current, and any number of obstacles. Simulations show that the method is effective and can manage complex scenarios with multiple dynamic obstacles and uncertainty associated with sensors and predictions.