Efficient computation of causal behavioural profiles using structural decomposition

Identification of behavioural contradictions is an important aspect of software engineering, in particular for checking the consistency between a business process model used as system specification and a corresponding workflow model used as implementation. In this paper, we propose causal behavioural profiles as the basis for a consistency notion, which capture essential behavioural information, such as order, exclusiveness, and causality between pairs of activities. Existing notions of behavioural equivalence, such as bisimulation and trace equivalence, might also be applied as consistency notions. Still, they are exponential in computation. Our novel concept of causal behavioural profiles provides a weaker behavioural consistency notion that can be computed efficiently using structural decomposition techniques for sound free-choice workflow systems if unstructured net fragments are acyclic or can be traced back to S- or T-nets.

CoRE : a context-aware relation extraction method for relation completion

We identify relation completion (RC) as one recurring problem that is central to the success of novel big data applications such as Entity Reconstruction and Data Enrichment. Given a semantic relation, RC attempts at linking entity pairs between two entity lists under the relation. To accomplish the RC goals, we propose to formulate search queries for each query entity α based on some auxiliary information, so that to detect its target entity β from the set of retrieved documents. For instance, a pattern-based method (PaRE) uses extracted patterns as the auxiliary information in formulating search queries. However, high-quality patterns may decrease the probability of finding suitable target entities. As an alternative, we propose CoRE method that uses context terms learned surrounding the expression of a relation as the auxiliary information in formulating queries. The experimental results based on several real-world web data collections demonstrate that CoRE reaches a much higher accuracy than PaRE for the purpose of RC.

Genetic aspects of the organization of legumin genes in pea

We have compared physical and genetic maps of the region around the legJ gene in pea. In this vicinity there are four B-type legumin genes, arranged as two close pairs. The detection of a recombination event within this gene cluster allows the orientation of this group of genes within the surrounding linkage group to be determined. The relationship between physical and genetic distances in this region is discussed, as are the implications of this for relating physical and genetic maps elsewhere in the pea genome.

Effects of small field output factors on IMRT optimisation and dose calculation

Introduction Given the known challenges of obtaining accurate measurements of small radiation fields, and the increasing use of small field segments in IMRT beams, this study examined the possible effects of referencing inaccurate field output factors in the planning of IMRT treatments. Methods This study used the Brainlab iPlan treatment planning system to devise IMRT treatment plans for delivery using the Brainlab m3 microMLC (Brainlab, Feldkirchen, Germany). Four pairs of sample IMRT treatments were planned using volumes, beams and prescriptions that were based on a set of test plans described in AAPM TG 119’s recommendations for the commissioning of IMRT treatment planning systems [1]: • C1, a set of three 4 cm volumes with different prescription doses, was modified to reduce the size of the PTV to 2 cm across and to include an OAR dose constraint for one of the other volumes. • C2, a prostate treatment, was planned as described by the TG 119 report [1]. • C3, a head-and-neck treatment with a PTV larger than 10 cm across, was excluded from the study. • C4, an 8 cm long C-shaped PTV surrounding a cylindrical OAR, was planned as described in the TG 119 report [1] and then replanned with the length of the PTV reduced to 4 cm. Both plans in each pair used the same beam angles, collimator angles, dose reference points, prescriptions and constraints. However, one of each pair of plans had its beam modulation optimisation and dose calculation completed with reference to existing iPlan beam data and the other had its beam modulation optimisation and dose calculation completed with reference to revised beam data. The beam data revisions consisted of increasing the field output factor for a 0.6 9 0.6 cm2 field by 17 % and increasing the field output factor for a 1.2 9 1.2 cm2 field by 3 %. Results The use of different beam data resulted in different optimisation results with different microMLC apertures and segment weightings between the two plans for each treatment, which led to large differences (up to 30 % with an average of 5 %) between reference point doses in each pair of plans. These point dose differences are more indicative of the modulation of the plans than of any clinically relevant changes to the overall PTV or OAR doses. By contrast, the maximum, minimum and mean doses to the PTVs and OARs were smaller (less than 1 %, for all beams in three out of four pairs of treatment plans) but are more clinically important. Of the four test cases, only the shortened (4 cm) version of TG 119’s C4 plan showed substantial differences between the overall doses calculated in the volumes of interest using the different sets of beam data and thereby suggested that treatment doses could be affected by changes to small field output factors. An analysis of the complexity of this pair of plans, using Crowe et al.’s TADA code [2], indicated that iPlan’s optimiser had produced IMRT segments comprised of larger numbers of small microMLC leaf separations than in the other three test cases. Conclusion: The use of altered small field output factors can result in substantially altered doses when large numbers of small leaf apertures are used to modulate the beams, even when treating relatively large volumes.

An instrument to assess the obesogenic environment of child care centers

OBJECTIVES To describe protocol and interobserver agreements of an instrument to evaluate nutrition and physical activity environments at child care. METHODS Interobserver data were collected from 9 child care centers, through direct observation and document review (17 observer pairs). RESULTS Mean agreement between observer pairs was 87.26% and 79.29% for the observation and document review, respectively. Items with lower agreement were primarily staff behavior, counting across the day/week, and policy classifications. CONCLUSIONS Although some revisions are required, the interobserver agreement for the environment and policy assessment and observation (EPAO instrument) appears to be quite good for assessing the nutrition and physical activity environment of child care centers.

Comparison of surveys used to measure physical activity

Objective To compare the level of agreement in results obtained from four physical activity (PA) measurement instruments that are in use in Australia and around the world. Methods 1,280 randomly selected participants answered two sets of PA questions by telephone. 428 answered the Active Australia (AA) and National Health Surveys, 427 answered the AA and CDC Behavioural Risk Factor Surveillance System surveys (BRFSS), and 425 answered the AA survey and the short International Physical Activity Questionnaire (IPAQ). Results Among the three pairs of survey items, the difference in mean total PA time was lowest when the AA and NHS items were asked (difference=24) (SE:17) minutes, compared with 144 (SE:21) mins for AA/BRFSS and 406 (SE:27) mins for AA/IPAQ). Correspondingly, prevalence estimates for 'sufficiently active' were similar for AA and NHS (56% and 55% respectively), but about 10% higher when BRFSS data were used, and about 26% higher when the IPAQ items were used, compared with estimates from the AA survey. Conclusions The findings clearly demonstrate that there are large differences in reported PA times and hence in prevalence estimates of 'sufficient activity' from these four measures. Implications It is important to consistently use the same survey for population monitoring purposes. As the AA survey has now been used three times in national surveys, its continued use for population surveys is recommended so that trend data ever a longer period of time can be established.

Detection of object onset and offset in naturalistic scenes

The present study was conducted to investigate whether ob- servers are equally prone to overlook any kinds of visual events in change blindness. Capitalizing on the finding from visual search studies that abrupt appearance of an object effectively captures observers' attention, the onset of a new object and the offset of an existing object were contrasted regarding their detectability when they occurred in a naturalistic scene. In an experiment, participants viewed a series of photograph pairs in which layouts of seven or eight objects were depicted. One object either appeared in or disappeared from the layout, and participants tried to detect this change. Results showed that onsets were detected more quickly than offsets, while they were detected with equivalent ac- curacy. This suggests that the primacy of onset over offset is a robust phenomenon that likely makes onsets more resistant to change blindness under natural viewing conditions.

Polarization of forecast densities : a new approach to time series classification

Time series classification has been extensively explored in many fields of study. Most methods are based on the historical or current information extracted from data. However, if interest is in a specific future time period, methods that directly relate to forecasts of time series are much more appropriate. An approach to time series classification is proposed based on a polarization measure of forecast densities of time series. By fitting autoregressive models, forecast replicates of each time series are obtained via the bias-corrected bootstrap, and a stationarity correction is considered when necessary. Kernel estimators are then employed to approximate forecast densities, and discrepancies of forecast densities of pairs of time series are estimated by a polarization measure, which evaluates the extent to which two densities overlap. Following the distributional properties of the polarization measure, a discriminant rule and a clustering method are proposed to conduct the supervised and unsupervised classification, respectively. The proposed methodology is applied to both simulated and real data sets, and the results show desirable properties.

Tunable “Nano-Shearing” : A physical mechanism to displace nonspecific cell adhesion during rare cell detection

We report a tunable alternating current electrohydrodynamic (ac-EHD) force which drives lateran fluid motion within a few nanometers of an electrode surface. Because the magnitude of this fluid shear force can be tuned externally (e.g., via the application of an ac electric field), it provides a new capability to physically displace weakly (nonspecifically) bound cellular analytes. To demonstrate the utility of the tunable nanoshearing phenomenon, we present data on purpose-built microfluidic devices that employ ac-EHD force to remove nonspecific adsorption of molecular and cellular species. Here, we show that an ac-EHD device containing asymmetric planar and microtip electrode pairs resulted in a 4-fold reduction in nonspecific adsorption of blood cells and also captured breast cancer cells in blood, with high efficiency (approximately 87%) and specificity. We therefore feel that this new capability of externally tuning and manipulating fluid flow could have wide applications as an innovative approach to enhance the specific capture of rare cells such as cancer cells in blood.

Alternating current electrohydrodynamics induced nanoshearing and fluid micromixing for specific capture of cancer cells

We report a new tuneable alternating current (ac) electrohydrodynamics (ac-EHD) force referred to as “nanoshearing” which involves fluid flow generated within a few nanometers of an electrode surface. This force can be externally tuned via manipulating the applied ac-EHD field strength. The ability to manipulate ac-EHD induced forces and concomitant fluid micromixing can enhance fluid transport within the capture domain of the channel (e.g., transport of analytes and hence increase target–sensor interactions). This also provides a new capability to preferentially select strongly bound analytes over onspecifically bound cells and molecules. To demonstrate the utility and versatility of nanoshearing phenomenon to specifically capture cancer cells, we present proof-of-concept data in lysed blood using two microfluidic devices containing a long array of asymmetric planar electrode pairs. Under the optimal experimental conditions, we achieved high capture efficiency (e.g., approximately 90%; %RSD=2, n=3) with a 10-fold reduction in nonspecific dsorption of non-target cells for the detection of whole cells expressing Human Epidermal Growth Factor Receptor 2 (HER2). We believe that our ac-EHD devices and the use of tuneable nanoshearing phenomenon may find relevance in a wide variety of biological and medical applications.

Nonresonant power transfer in plasma-surface interactions via two-surface wave decay

The excitation of pairs of electron surface waves via nonresonant decay of plasma waves incident onto a solid surface is studied in the context of controlling the interaction of pulsed electromagnetic radiation with plasma-exposed solid surfaces. The role of the plasma-exposed surfaces in nonlinear heating of the plasma edge and related power transfer is discussed. It is shown that the maximum efficiency of the power transfer at solid surfaces with dielectric permittivity εd <3 corresponds to the resonant two-surface wave decay. On the other hand, for solids with εd >3 the maximum power transfer efficiency is achieved through nonresonant excitation of the quasistatic surface waves. In this case the plasma waves generated by external radiation dissipate their energy into the plasma periphery most effectively.

Semantic interference in object naming : an fMRI study of the postcue naming paradigm

It is well established that the time to name target objects can be influenced by the presence of categorically related versus unrelated distractor items. A variety of paradigms have been developed to determine the level at which this semantic interference effect occurs in the speech production system. In this study, we investigated one of these tasks, the postcue naming paradigm, for the first time with fMRI. Previous behavioural studies using this paradigm have produced conflicting interpretations of the processing level at which the semantic interference effect takes place, ranging from pre- to post-lexical. Here we used fMRI with a sparse, event-related design to adjudicate between these competing explanations. We replicated the behavioural postcue naming effect for categorically related target/distractor pairs, and observed a corresponding increase in neuronal activation in the right lingual and fusiform gyri-regions previously associated with visual object processing and colour-form integration. We interpret these findings as being consistent with an account that places the semantic interference effect in the postcue paradigm at a processing level involving integration of object attributes in short-term memory.

Weaknesses in the initialisation process of the Common Scrambling Algorithm Stream Cipher

The Common Scrambling Algorithm Stream Cipher (CSASC) is a shift register based stream cipher designed to encrypt digital video broadcast. CSA-SC produces a pseudo-random binary sequence that is used to mask the contents of the transmission. In this paper, we analyse the initialisation process of the CSA-SC keystream generator and demonstrate weaknesses which lead to state convergence, slid pairs and shifted keystreams. As a result, the cipher may be vulnerable to distinguishing attacks, time-memory-data trade-off attacks or slide attacks.

Reducing bubble defect on the outsole production process in the footwear manufacturing industry

The purpose of this study is to discover the significant factors causing the bubble defect on the outsoles manufactured by the Case Company. The bubble defect occurs approximately 1.5 per cent of the time or in 36 pairs per day. To understand this problem, experimental studies are undertaken to identify various factors such as injector temperature, mould temperature; that affects the production of waste. The work presented in this paper comprises a review of the relevant literature on the Six Sigma DMAIC improvement process, quality control tools, and the design of the experiments. After the experimentation following the Six Sigma process, the results showed that the defect occurred in approximately 0.5 per cent of the products or in 12 pairs per day; this decreased the production cost from 6,120 AUD per month to 2,040 AUD per month. This research aimed to reduce the amount of waste in men’s flat outsoles. Hence, the outcome of research presented in this paper should be used as a guide for applying the appropriate process for each type of outsole.

Assembly and annotation of a non-model gastropod (Nerita melanotragus) transcriptome: a comparison of De novo assemblers

Background The sequencing, de novo assembly and annotation of transcriptome datasets generated with next generation sequencing (NGS) has enabled biologists to answer genomic questions in non-model species with unprecedented ease. Reliable and accurate de novo assembly and annotation of transcriptomes, however, is a critically important step for transcriptome assemblies generated from short read sequences. Typical benchmarks for assembly and annotation reliability have been performed with model species. To address the reliability and accuracy of de novo transcriptome assembly in non-model species, we generated an RNAseq dataset for an intertidal gastropod mollusc species, Nerita melanotragus, and compared the assembly produced by four different de novo transcriptome assemblers; Velvet, Oases, Geneious and Trinity, for a number of quality metrics and redundancy. Results Transcriptome sequencing on the Ion Torrent PGM™ produced 1,883,624 raw reads with a mean length of 133 base pairs (bp). Both the Trinity and Oases de novo assemblers produced the best assemblies based on all quality metrics including fewer contigs, increased N50 and average contig length and contigs of greater length. Overall the BLAST and annotation success of our assemblies was not high with only 15-19% of contigs assigned a putative function. Conclusions We believe that any improvement in annotation success of gastropod species will require more gastropod genome sequences, but in particular an increase in mollusc protein sequences in public databases. Overall, this paper demonstrates that reliable and accurate de novo transcriptome assemblies can be generated from short read sequencers with the right assembly algorithms. Keywords: Nerita melanotragus; De novo assembly; Transcriptome; Heat shock protein; Ion torrent