Mind change complexity of learning logic programs

The present paper motivates the study of mind change complexity for learning minimal models of length-bounded logic programs. It establishes ordinal mind change complexity bounds for learnability of these classes both from positive facts and from positive and negative facts. Building on Angluin’s notion of finite thickness and Wright’s work on finite elasticity, Shinohara defined the property of bounded finite thickness to give a sufficient condition for learnability of indexed families of computable languages from positive data. This paper shows that an effective version of Shinohara’s notion of bounded finite thickness gives sufficient conditions for learnability with ordinal mind change bound, both in the context of learnability from positive data and for learnability from complete (both positive and negative) data. Let Omega be a notation for the first limit ordinal. Then, it is shown that if a language defining framework yields a uniformly decidable family of languages and has effective bounded finite thickness, then for each natural number m >0, the class of languages defined by formal systems of length <= m: • is identifiable in the limit from positive data with a mind change bound of Omega (power)m; • is identifiable in the limit from both positive and negative data with an ordinal mind change bound of Omega × m. The above sufficient conditions are employed to give an ordinal mind change bound for learnability of minimal models of various classes of length-bounded Prolog programs, including Shapiro’s linear programs, Arimura and Shinohara’s depth-bounded linearly covering programs, and Krishna Rao’s depth-bounded linearly moded programs. It is also noted that the bound for learning from positive data is tight for the example classes considered.

Molecular epidemiology of respiratory viruses in a paediatric cohort from Indonesia

Acute lower respiratory tract infections (ALRTIs) are a common cause of morbidity and mortality among children under 5 years of age and are found worldwide, with pneumonia as the most severe manifestation. Although the incidence of severe disease varies both between individuals and countries, there is still no clear understanding of what causes this variation. Studies of community-acquired pneumonia (CAP) have traditionally not focused on viral causes of disease due to a paucity of diagnostic tools. However, with the emergence of molecular techniques, it is now known that viruses outnumber bacteria as the etiological agents of childhood CAP, especially in children under 2 years of age. The main objective of this study was to investigate viruses contributing to disease severity in cases of childhood ALRTI, using a two year cohort study following 2014 infants and children enrolled in Bandung, Indonesia. A total of 352 nasopharyngeal washes collected from 256 paediatric ALRTI patients were used for analysis. A subset of samples was screened using a novel microarray pathogen detection method that identified respiratory syncytial virus (RSV), human metapneumovirus (hMPV) and human rhinovirus (HRV) in the samples. Real-time RT-PCR was used both for confirming and quantifying viruses found in the nasopharyngeal samples. Viral copy numbers were determined and normalised to the numbers of human cells collected with the use of 18S rRNA. Molecular epidemiology was performed for RSV A and hMPV using sequences to the glycoprotein gene and nucleoprotein gene respectively, to determine genotypes circulating in this Indonesian paediatric cohort. This study found that HRV (119/352; 33.8%) was the most common virus detected as the cause of respiratory tract infections in this cohort, followed by the viral pathogens RSV A (73/352; 20.7%), hMPV (30/352; 8.5%) and RSV B (12/352; 3.4%). Co-infections of more than two viruses were detected in 31 episodes (defined as an infection which occurred more than two weeks apart), accounting for 8.8% of the 352 samples tested or 15.4% of the 201 episodes with at least one virus detected. RSV A genotypes circulating in this population were predominantly GA2, GA5 and GA7, while hMPV genotypes circulating were mainly A2a (27/30; 90.0%), B2 (2/30; 6.7%) and A1 (1/30; 3.3%). This study found no evidence of disease severity associated either with a specific virus or viral strain, or with viral load. However, this study did find a significant association with co-infection of RSV A and HRV with severe disease (P = 0.006), suggesting that this may be a novel cause of severe disease.

Fuzzy logic power system stabilizer in multimachine stability studies

Power system stabilizers (PSS) work well at the particular network configuration and steady state conditions for which they were designed. Once conditions change, their performance degrades. This can be overcome by an intelligent nonlinear PSS based on fuzzy logic. Such a fuzzy logic power system stabilizer (FLPSS) is developed, using speed and power deviation as inputs, and provides an auxiliary signal for the excitation system of a synchronous motor in a multimachine power system environment. The FLPSS's effect on the system damping is then compared with a conventional power system stabilizer's (CPSS) effect on the system. The results demonstrate an improved system performance with the FLPSS and also that the FLPSS is robust

Fuzzy logic traffic control at a road junction with time-varying flow rates

Fuzzy logic has been applied to control traffic at road junctions. A simple controller with one fixed rule-set is inadequate to minimise delays when traffic flow rate is time-varying and likely to span a wide range. To achieve better control, fuzzy rules adapted to the current traffic conditions are used.

Hierarchical fuzzy logic traffic control at a road junction

Traffic control at road junctions is one of the major concerns in most metropolitan cities. Controllers of various approaches are available and the required control action is the effective green-time assigned to each traffic stream within a traffic-light cycle. The application of fuzzy logic provides the controller with the capability to handle uncertain natures of the system, such as drivers’ behaviour and random arrivals of vehicles. When turning traffic is allowed at the junction, the number of phases in the traffic-light cycle increases. The additional input variables inevitably complicate the controller and hence slow down the decision-making process, which is critical in this real-time control problem. In this paper, a hierarchical fuzzy logic controller is proposed to tackle this traffic control problem at a 2-way road junction with turning traffic. The two levels of fuzzy logic controllers devise the minimum effective green-time and fine-tune it respectively at each phase of a traffic-light cycle. The complexity of the controller at each level is reduced with smaller rule-set. The performance of this hierarchical controller is examined by comparison with a fixed-time controller under various traffic conditions. Substantial delay reduction has been achieved as a result and the performance and limitation of the controller will be discussed.

Hierarchical fuzzy logic traffic control at a road junction using genetic algorithms

Traffic control at a road junction by a complex fuzzy logic controller is investigated. The increase in the complexity of junction means more number of input variables must be taken into account, which will increase the number of fuzzy rules in the system. A hierarchical fuzzy logic controller is introduced to reduce the number of rules. Besides, the increase in the complexity of the controller makes formulation of the fuzzy rules difficult. A genetic algorithm based off-line leaning algorithm is employed to generate the fuzzy rules. The learning algorithm uses constant flow-rates as training sets. The system is tested by both constant and time-varying flow-rates. Simulation results show that the proposed controller produces lower average delay than a fixed-time controller does under various traffic conditions.

Molecular characterisation of six badnavirus species associated with leaf streak disease of banana in East Africa

Banana leaf streak disease, caused by several species of Banana streak virus (BSV), is widespread in East Africa. We surveyed for this disease in Uganda and Kenya, and used rolling-circle amplification (RCA) to detect the presence of BSV in banana. Six distinct badnavirus sequences, three from Uganda and three from Kenya, were amplified for which only partial sequences were previously available. The complete genomes were sequenced and characterised. The size and organisation of all six sequences was characteristic of other badnaviruses, including conserved functional domains present in the putative polyprotein encoded by open reading frame (ORF) 3. Based on nucleotide sequence analysis within the reverse transcriptase/ribonuclease H-coding region of open reading frame 3, we propose that these sequences be recognised as six new species and be designated as Banana streak UA virus, Banana streak UI virus, Banana streak UL virus, Banana streak UM virus, Banana streak CA virus and Banana streak IM virus. Using PCR and species-specific primers to test for the presence of integrated sequences, we demonstrated that sequences with high similarity to BSIMV only were present in several banana cultivars which had tested negative for episomal BSV sequences.

Molecular analysis of the myosin gene family in Arabidopsis thaliana

Myosin is believed to act as the molecular motor for many actin-based motility processes in eukaryotes. It is becoming apparent that a single species may possess multiple myosin isoforms, and at least seven distinct classes of myosin have been identified from studies of animals, fungi, and protozoans. The complexity of the myosin heavy-chain gene family in higher plants was investigated by isolating and characterizing myosin genomic and cDNA clones from Arabidopsis thaliana. Six myosin-like genes were identified from three polymerase chain reaction (PCR) products (PCR1, PCR11, PCR43) and three cDNA clones (ATM2, MYA2, MYA3). Sequence comparisons of the deduced head domains suggest that these myosins are members of two major classes. Analysis of the overall structure of the ATM2 and MYA2 myosins shows that they are similar to the previously-identified ATM1 and MYA1 myosins, respectively. The MYA3 appears to possess a novel tail domain, with five IQ repeats, a six-member imperfect repeat, and a segment of unique sequence. Northern blot analyses indicate that some of the Arabidopsis myosin genes are preferentially expressed in different plant organs. Combined with previous studies, these results show that the Arabidopsis genome contains at least eight myosin-like genes representing two distinct classes.

A coupled meshless technique/molecular dynamics approach for deformation characterization of monocrystalline metal

This paper presents a multiscale study using the coupled Meshless technique/Molecular Dynamics (M2) for exploring the deformation mechanism of mono-crystalline metal (focus on copper) under uniaxial tension. In M2, an advanced transition algorithm using transition particles is employed to ensure the compatibility of both displacements and their gradients, and an effective local quasi-continuum approach is also applied to obtain the equivalent continuum strain energy density based on the atomistic poentials and Cauchy-Born rule. The key parameters used in M2 are firstly investigated using a benchmark problem. Then M2 is applied to the multiscale simulation for a mono-crystalline copper bar. It has found that the mono-crystalline copper has very good elongation property, and the ultimate strength and Young's modulus are much higher than those obtained in macro-scale.

Molecular evolutionary dynamics of Ross River virus and implications for vaccine efficacy

Ross River virus (RRV) is a mosquito-borne member of the genus Alphavirus that causes epidemic polyarthritis in humans, costing the Australian health system at least US$10 million annually. Recent progress in RRV vaccine development requires accurate assessment of RRV genetic diversity and evolution, particularly as they may affect the utility of future vaccination. In this study, we provide novel RRV genome sequences and investigate the evolutionary dynamics of RRV from time-structured E2 gene datasets. Our analysis indicates that, although RRV evolves at a similar rate to other alphaviruses (mean evolutionary rate of approx. 8x10(-4) nucleotide substitutions per site year(-1)), the relative genetic diversity of RRV has been continuously low through time, possibly as a result of purifying selection imposed by replication in a wide range of natural host and vector species. Together, these findings suggest that vaccination against RRV is unlikely to result in the rapid antigenic evolution that could compromise the future efficacy of current RRV vaccines.

Molecular structure of Mg-Al, Mn-Al and Zn-Al halotrichites : an infrared spectroscopic study

Near infrared (NIR), X-ray diffraction (XRD) and infrared (IR) spectroscopy have been applied to halotrichites of the formula MgAl2(SO4)4∙22H2O, MnAl2(SO4)4∙22H2O and ZnAl2(SO4)4∙22H2O. Comparison of the halotrichites in different spectral regions has shown that the incorporation of a divalent transition metal into the halotrichite structure causes a shift in OH stretching band positions to lower wavenumbers. Therefore, an increase in hydrogen bonded water is observed for divalent cations with a larger molecular mass. XRD has confirmed the formation of halotrichite for all three samples and characteristic peaks of halotrichite have been identified at 18.5 and 24.5° 2θ, along with a group of six peaks between 5 and 15° 2θ. It has been observed that Mg-Al and Mn-Al halotrichite are very similar in structure, while Zn-Al showed several differences particularly in the NIR spectra. This work has shown that halotrichite structures can be synthesised and characterised by infrared and NIR spectroscopy.

The molecular mechanisms utilised by mesenchymal stem cells in migration to acute myocardial infarction

Heart damage caused by acute myocardial infarction (AMI) is a leading cause of death and disability in Australia. Novel therapies are still required for the treatment of this condition due to the poor reparative ability of the heart. As such, cellular therapies that assist in the recovery of heart muscle are of great current interest. Culture expanded mesenchymal stem cells (MSC) represent a stem and progenitor cell population that has been shown to promote tissue recovery in pre-clinical studies of AMI. For MSC-based therapies in the clinic, an intravenous route of administration would ideally be used due to the low cost, ease of delivery and relative safety. The study of MSC migration is therefore clinically relevant for a minimally invasive cell therapy to promote regeneration of damaged tissue. C57BL/6, UBI-GFP-BL/6 and CD44-/-/GFP+/+ mice were utilised to investigate mMSC migration. To assist in murine models of MSC migration, a novel method was used for the isolation of murine MSC (mMSC). These mMSC were then expanded in culture and putative mMSC were positive for Sca-1, CD90.2, and CD44 and were negative for CD45 and CD11b. Furthermore, mMSC from C57BL/6 and UBI-GFP-BL/6 mice were shown to differentiate into cells of the mesodermal lineage. Cells from CD44-/-/GFP+/+ mice were positive for Sca-1 and CD90.2, and negative for CD44, CD45 and CD11b however, these cells were unable to differentiate into adipocytes and chondrocytes and express lineage specific genes, PLIN and ACAN. Analysis of mMSC chemokine receptor (CR) expression showed that although mMSC do express chemokine receptors, (including those specific for chemokines released after AMI), these were low or undetectable by mRNA. However, protein expression could be detected, which was predominantly cytoplasmic. It was further shown that in both healthy (unperturbed) and inflamed tissues, mMSC had very little specific migration and engraftment after intravenous injection. To determine if poor mMSC migration was due to the inability of mMSC to respond to chemotactic stimuli, chemokine expression in bone marrow, skin injury and hearts (healthy and after AMI) was analysed at various time points by quantitative real-time PCR (qRT PCR). Many chemokines were up-regulated after skin biopsy and AMI, but the highest acute levels were found for CXCL12 and CCL7. Due to their high expression in infarcted hearts, the chemokines CXCL12 and CCL7 were tested for their effect on mMSC migration. Despite CR expression at both protein and mRNA levels, migration in response to CXCL12 and CCL7 was low in mMSC cultured on Nunclon plastic. A novel tissue culture plastic technology (UpCellTM) was then used that allowed gentle non-enzymatic dissociation of mMSC, thus preserving surface expression of the CRs. Despite this the in vitro data indicated that CXCL12 fails to induce significant migration ability of mMSC, while CCL7 induces significant, but low-level migration. We speculated this may be because of low levels of surface expression of chemokine receptors. In a strategy to increase cell surface expression of mMSC chemokine receptors and enhance their in vitro and in vivo migration capacity, mMSC were pre-treated with pro-inflammatory cytokines. Increased levels of both mRNA and surface protein expression were found for CRs by pre-treating mMSC with pro-inflammatory cytokines including TNF-á, IFN-ã, IL-1á and IL-6. Furthermore, the chemotactic response of mMSC to CXCL12 and CCL7 was significantly higher with these pretreated cells. Finally, the effectiveness of this type of cell manipulation was demonstrated in vivo, where mMSC pre-treated with TNF-á and IFN-ã showed significantly increased migration in skin injury and AMI models. Therefore this thesis has demonstrated, using in vitro and in vivo models, the potential for prior manipulation of MSC as a possible means for increasing the utility of intravenously delivery for MSC-based cellular therapies.

Molecular dynamics study of dynamic buckling properties of nanowires with defects

Based on the embedded atom method (EAM) and molecular dynamics (MD) method, the deformation properties of Cu nanowires with different single defects under dynamic compression have been studied. The mechanical behaviours of the perfect nanowire are first studied, and the critical stress decreases with the increase of the nanowire’s length, which is well agreed with the modified Euler theory. We then consider the effects to the buckling phenomenon resulted from different defects. It is found that obvious decrease of the critical stress is resulted from different defects, and the largest decrease is found in nanowire with the surface vertical defect. Surface defects are found exerting larger influence than internal defects. The buckling duration is found shortened due to different defects except the nanowire with surface horizon defect, which is also found possessing the largest deflection. Different deflections are also observed for different defected nanowires. It is find that due to surface defects, only deflection in one direction is happened, but for internal defects, more complex deflection circumstances are observed.