Development of a Multiplexed Bead-Based Suspension Array for the Detection and Discrimination of Pospiviroid Plant Pathogens

Efficient and reliable diagnostic tools for the routine indexing and certification of clean propagating material are essential for the management of pospiviroid diseases in horticultural crops. This study describes the development of a true multiplexed diagnostic method for the detection and identification of all nine currently recognized pospiviroid species in one assay using Luminex bead-based suspension array technology. In addition, a new data-driven, statistical method is presented for establishing thresholds for positivity for individual assays within multiplexed arrays. When applied to the multiplexed array data generated in this study, the new method was shown to have better control of false positives and false negative results than two other commonly used approaches for setting thresholds. The 11-plex Luminex MagPlex-TAG pospiviroid array described here has a unique hierarchical assay design, incorporating a near-universal assay in addition to nine species-specific assays, and a co-amplified plant internal control assay for quality assurance purposes. All assays of the multiplexed array were shown to be 100% specific, sensitive and reproducible. The multiplexed array described herein is robust, easy to use, displays unambiguous results and has strong potential for use in routine pospiviroid indexing to improve disease management strategies.

A quantum chemical investigation of the metal centres in cytochrome c oxidase

Quantum effects are often of key importance for the function of biological systems at molecular level. Cellular respiration, where energy is extracted from the reduction of molecular oxygen to water, is no exception. In this work, the end station of the electron transport chain in mitochondria, cytochrome c oxidase, is investigated using quantum chemical methodology. Cytochrome c oxidase contains two haems, haem a and haem a3. Haem a3, with its copper companion, CuB, is involved in the final reduction of oxygen into water. This binuclear centre receives the necessary electrons from haem a. Haem a, in turn, receives its electrons from a copper ion pair in the vicinity, called CuA. Density functional theory (DFT) has been used to clarify the charge and spin distributions of haem a, as well as changes in these during redox activity. Upon reduction, the added electron is shown to be evenly distributed over the entire haem structure, important for the accommodation of the prosthetic group within the protein. At the same time, the spin distribution of the open-shell oxidised state is more localised to the central iron. The exact spin density distribution has been disputed in the literature, however, different experiments indicating different distributions of the unpaired electron. The apparent contradiction is shown to be due to the false assumption of a unit amount of unpaired electron density; in fact, the oxidised state has about 1.3 unpaired electrons. The validity of the DFT results have been corroborated by wave function based coupled cluster calculations. Point charges, for use in classical force field based simulations, have been parameterised for the four metal centres, using a newly developed methodology. In the procedure, the subsystem for which point charges are to be obtained, is surrounded by an outer region, with the purpose of stabilising the inner region, both electronically and structurally. Finally, the possibility of vibrational promotion of the electron transfer step between haem a and a3 has been investigated. Calculating the full vibrational spectra, at DFT level, of a combined model of the two haems, revealed several normal modes that do shift electron density between the haems. The magnitude of the shift was found to be moderate, at most. The proposed mechanism could have an assisting role in the electron transfer, which still seems to be dominated by electron tunnelling.

FreeS: A fast algorithm to discover frequent free subtrees using a novel canonical form

Web data can often be represented in free tree form; however, free tree mining methods seldom exist. In this paper, a computationally fast algorithm FreeS is presented to discover all frequently occurring free subtrees in a database of labelled free trees. FreeS is designed using an optimal canonical form, BOCF that can uniquely represent free trees even during the presence of isomorphism. To avoid enumeration of false positive candidates, it utilises the enumeration approach based on a tree-structure guided scheme. This paper presents lemmas that introduce conditions to conform the generation of free tree candidates during enumeration. Empirical study using both real and synthetic datasets shows that FreeS is scalable and significantly outperforms (i.e. few orders of magnitude faster than) the state-of-the-art frequent free tree mining algorithms, HybridTreeMiner and FreeTreeMiner.

An evaluation of the components of a proposed perimeter baiting system for cucumber fly, Bactrocera cucumis

Management of cucumber fly (Bactrocera cucumis) has relied heavily on cover sprays of broad spectrum insecticides such as dimethoate and fenthion. Long term access to these insecticides is uncertain, and their use can disrupt integrated pest management programs for other pests such as whitefly, aphids and mites. Application of a protein bait spray for fruit fly control is common practice in tree crops. However, vegetable crops present different challenges as fruit flies are thought to enter these crops only to oviposit, spending the majority of their time in roosting sites outside of the cropping area. Perimeter baiting of non-crop vegetation was developed overseas as a technique for control of melon fly (B. cucurbitae) in cucurbits in Hawaii. More recent work has refined the technique further, with certain types of perimeter vegetation proving more attractive to melon fly than the sorghum or corn crops which are commonly utilised. Trials were performed to investigate the potential of developing a similar system for cucumber fly. Commercially available fruit fly baits were compared for attractiveness to cucumber fly. Eight plant species were evaluated for their relative attractiveness to cucumber flies as roosting sites. Differences were observed in the number of flies feeding at protein bait applied to each of the plants. Results are discussed in the context of the development of a perimeter baiting system for cucumber fly in cucurbit crops.

The role of spiders as predators of two lepidopteran Brassica pests

Spiders are thought to play a significant role in limiting pest outbreaks in agroecosystems such as vineyards, orchards and cotton. The diversity and impact of spiders in vegetable crops are less well understood, although there is evidence that predators may be important for suppression of lepidopteran pests in Brassica crops, particularly early in the season before parasitoids become established. Sampling was conducted in early season plantings of Brassicas in the Lockyer Valley (South East Queensland, Australia) in order to determine the most commonly occurring spider families. The most numerous were Theridiidae, which were more strongly associated with cauliflower and poorly associated with cabbage. The Lycosidae and Clubionidae/Miturgidae (formerly in the ‘catch-all’ family Clubionidae) also occurred commonly. Lycosidae (and to a lesser extent Salticidae) had above average abundance in Chinese cabbage and below average abundance in broccoli compared with average abundance for these spider families; Clubionidae/Miturgidae had above average abundance in cauliflower. Laboratory studies were then conducted to explore the predatory capacity of these three most commonly occurring spider families. All three were capable of feeding on larvae of the diamondback moth, Plutella xylostella (Linnaeus), and cabbage cluster caterpillar, Crocidolomia pavonana (Fabricius), under laboratory conditions. Theridiidae, which are thought to prey on small pests such as leafhoppers and aphids, were able to successfully attack larvae up to five times their body size. Predation rates varied from an average of 1.7 (SE = 0.47) (1.6 control corrected) larvae consumed over a 24 h period in the case of the Theridiidae, to 3.3 (SE = 0.60) larvae for the Clubionidae/Miturgidae.

Head motion and Inattention/Hyperactivity share common genetic influences: Implications for fMRI studies of ADHD

Head motion (HM) is a well known confound in analyses of functional MRI (fMRI) data. Neuroimaging researchers therefore typically treat HM as a nuisance covariate in their analyses. Even so, it is possible that HM shares a common genetic influence with the trait of interest. Here we investigate the extent to which this relationship is due to shared genetic factors, using HM extracted from resting-state fMRI and maternal and self report measures of Inattention and Hyperactivity-Impulsivity from the Strengths and Weaknesses of ADHD Symptoms and Normal Behaviour (SWAN) scales. Our sample consisted of healthy young adult twins (N = 627 (63% females) including 95 MZ and 144 DZ twin pairs, mean age 22, who had mother-reported SWAN; N = 725 (58% females) including 101 MZ and 156 DZ pairs, mean age 25, with self reported SWAN). This design enabled us to distinguish genetic from environmental factors in the association between head movement and ADHD scales. HM was moderately correlated with maternal reports of Inattention (r = 0.17, p-value = 7.4E-5) and Hyperactivity-Impulsivity (r = 0.16, p-value = 2.9E-4), and these associations were mainly due to pleiotropic genetic factors with genetic correlations [95% CIs] of rg = 0.24 [0.02, 0.43] and rg = 0.23 [0.07, 0.39]. Correlations between self-reports and HM were not significant, due largely to increased measurement error. These results indicate that treating HM as a nuisance covariate in neuroimaging studies of ADHD will likely reduce power to detect between-group effects, as the implicit assumption of independence between HM and Inattention or Hyperactivity-Impulsivity is not warranted. The implications of this finding are problematic for fMRI studies of ADHD, as failing to apply HM correction is known to increase the likelihood of false positives. We discuss two ways to circumvent this problem: censoring the motion contaminated frames of the RS-fMRI scan or explicitly modeling the relationship between HM and Inattention or Hyperactivity-Impulsivity

Religion Explained? : A Philosophical Appraisal of the Cognitive Science of Religion

This study examines philosophically the main theories and methodological assumptions of the field known as the cognitive science of religion (CSR). The study makes a philosophically informed reconstruction of the methodological principles of the CSR, indicates problems with them, and examines possible solutions to these problems. The study focuses on several different CSR writers, namely, Scott Atran, Justin Barrett, Pascal Boyer and Dan Sperber. CSR theorising is done in the intersection between cognitive sciences, anthropology and evolutionary psychology. This multidisciplinary nature makes CSR a fertile ground for philosophical considerations coming from philosophy of psychology, philosophy of mind and philosophy of science. The study begins by spelling out the methodological assumptions and auxiliary theories of CSR writers by situating these theories and assumptions in the nexus of existing approaches to religion. The distinctive feature of CSR is its emphasis on information processing: CSR writers claim that contemporary cognitive sciences can inform anthropological theorising about the human mind and offer tools for producing causal explanations. Further, they claim to explain the prevalence and persistence of religion by cognitive systems that undergird religious thinking. I also examine the core theoretical contributions of the field focusing mainly on the (1) “minimally counter-intuitiveness hypothesis” and (2) the different ways in which supernatural agent representations activate our cognitive systems. Generally speaking, CSR writers argue for the naturalness of religion: religious ideas and practices are widespread and pervasive because human cognition operates in such a way that religious ideas are easy to acquire and transmit. The study raises two philosophical problems, namely, the “problem of scope” and the “problem of religious relevance”. The problem of scope is created by the insistence of several critics of the CSR that CSR explanations are mostly irrelevant for explaining religion. Most CSR writers themselves hold that cognitive explanations can answer most of our questions about religion. I argue that the problem of scope is created by differences in explanation-begging questions: the former group is interested in explaining different things than the latter group. I propose that we should not stick too rigidly to one set of methodological assumptions, but rather acknowledge that different assumptions might help us to answer different questions about religion. Instead of adhering to some robust metaphysics as some strongly naturalistic writers argue, we should adopt a pragmatic and explanatory pluralist approach which would allow different kinds of methodological presuppositions in the study of religion provided that they attempt to answer different kinds of why-questions, since religion appears to be a multi-faceted phenomenon that spans over a variety of fields of special sciences. The problem of religious relevance is created by the insistence of some writers that CSR theories show religious beliefs to be false or irrational, whereas others invoke CSR theories to defend certain religious ideas. The problem is interesting because it reveals the more general philosophical assumptions of those who make such interpretations. CSR theories can (and have been) interpreted in terms of three different philosophical frameworks: strict naturalism, broad naturalism and theism. I argue that CSR theories can be interpreted inside all three frameworks without doing violence to the theories and that these frameworks give different kinds of results regarding the religious relevance of CSR theories.

Policing online fraud in Australia: The emergence of a victim‐oriented approach

Online fraud is a global problem. Millions of individuals worldwide are losing money and experiencing the devastation associated with becoming a victim of online fraud. In 2014, Australians reported losses of $82 million as a result of online fraud to the Australian Competition and Consumer Commission (ACCC). Given that the ACCC is one of many agencies that receives victim complaints, and the extent of under‐reporting of online fraud, this figure is likely to represent only a fraction of the actual monetary losses incurred. The successful policing of online fraud is hampered by its transnational nature, the prevalence of false/stolen identities used by offenders, and a lack of resources available to investigate offences. In addition, police are restricted by the geographical boundaries of their own jurisdictions which conflicts with the lack of boundaries afforded to offenders by the virtual world. In response to this, Australia is witnessing the emergence of victim‐oriented policing approaches to counter online fraud victimisation. This incorporates the use of financial intelligence as a tool to proactively notify potential victims of online fraud. Using a variety of Australian examples, this paper documents the history to this new approach and considers the significance that such a shift represents to policing in a broader context. It also details the value that this approach can have to both victims and law enforcement agencies. Overall, it is argued that a victim‐oriented approach to policing online fraud can have substantial benefits to police and victims alike.

Short-term effects of variable retention on epigaeic spiders and carabid beetles in Finland

Forestry has influenced forest dwelling organisms for centuries in Fennoscandia. For example, in Finland ca. 30% of the threatened species are threatened because of forestry. Nowadays forest management recommendations include practices aimed at maintaining biodiversity in harvesting, such as green-tree retention. However, the effects of these practices have been little studied. In variable retention, different numbers of trees are retained, varying from green-tree retention (at least a few live standing trees in clear-cuts) to thinning (only individual trees removed). I examined the responses of ground-dwelling spiders and carabid beetles to green-tree retention (with small and large tree groups), gap felling and thinning aimed at an uneven age structure of trees. The impacts of these harvesting methods were compared to those of clear-cutting and uncut controls. I aimed to test the hypothesis that retaining more trees positively affects populations of those species of spiders and carabids that were present before harvesting. The data come from two studies. First, spiders were collected with pitfall traps in south-central Finland in 1995 (pre-treatment) and 1998 (after-treatment) in order to examine the effects of clear-cutting, green-tree retention (with 0.01-0.02-ha sized tree groups), gap felling (with three 0.16-ha sized openings in a 1-ha stand), thinning aiming at an uneven age structure of trees and uncut control. Second, spiders and carabids were caught with pitfall traps in eastern Finland in 1998-2001 (pre-treatment and three post-treatment years) in eleven 0.09-0.55-ha sized retention-tree groups and clear-cuts adjacent to them. Original spider and carabid assemblages were better maintained after harvests that retained more trees. Thinning maintained forest spiders well. However, gap felling and large retention-tree groups maintained some forest spider and carabid species in the short-term, but negatively affected some species over time. However, use of small retention-tree groups was associated with negative effects on forest spider populations. Studies are needed on the long-term effects of variable retention on terrestrial invertebrates; especially those directed at defining appropriate retention patch size and on the importance of structural diversity provided by variable retention for invertebrate populations. However, the aims of variable retention should be specified first. For example, are retention-tree groups planned to constitute life-boats , stepping-stones or to create structural diversity? Does it suffice that some species are maintained, or do we want to preserve the most sensitive ones, and how are these best defined? Moreover, the ecological benefits and economic costs of modified logging methods should be compared to other approaches aimed at maintaining biodiversity.

Numerical study of heat transfer in laminar film boiling by the finite-difference method

The finite-difference form of the basic conservation equations in laminar film boiling have been solved by the false-transient method. By a judicious choice of the coordinate system the vapour-liquid interface is fitted to the grid system. Central differencing is used for diffusion terms, upwind differencing for convection terms, and explicit differencing for transient terms. Since an explicit method is used the time step used in the false-transient method is constrained by numerical instability. In the present problem the limits on the time step are imposed by conditions in the vapour region. On the other hand the rate of convergence of finite-difference equations is dependent on the conditions in the liquid region. The rate of convergence was accelerated by using the over-relaxation technique in the liquid region. The results obtained compare well with previous work and experimental data available in the literature.

Evaluation of methods and applications for behavioural profiling of transgenic mice

During the last 10-15 years interest in mouse behavioural analysis has evolved considerably. The driving force is development in molecular biological techniques that allow manipulation of the mouse genome by changing the expression of genes. Therefore, with some limitations it is possible to study how genes participate in regulation of physiological functions and to create models explaining genetic contribution to various pathological conditions. The first aim of our study was to establish a framework for behavioural phenotyping of genetically modified mice. We established comprehensive battery of tests for the initial screening of mutant mice. These included tests for exploratory and locomotor activity, emotional behaviour, sensory functions, and cognitive performance. Our interest was in the behavioural patterns of common background strains used for genetic manipulations in mice. Additionally we studied the behavioural effect of sex differences, test history, and individual housing. Our findings highlight the importance of careful consideration of genetic background for analysis of mutant mice. It was evident that some backgrounds may mask or modify the behavioural phenotype of mutants and thereby lead to false positive or negative findings. Moreover, there is no universal strain that is equally suitable for all tests, and using different backgrounds allows one to address possible phenotype modifying factors. We discovered that previous experience affected performance in several tasks. The most sensitive traits were the exploratory and emotional behaviour, as well as motor and nociceptive functions. Therefore, it may be essential to repeat some of the tests in naïve animals for assuring the phenotype. Social isolation for a long time period had strong effects on exploratory behaviour, but also on learning and memory. All experiments revealed significant interactions between strain and environmental factors (test history or housing condition) indicating genotype-dependent effects of environmental manipulations. Several mutant line analyses utilize this information. For example, we studied mice overexpressing as well as those lacking extracellular matrix protein heparin-binding growth-associated molecule (HB-GAM), and mice lacking N-syndecan (a receptor for HB-GAM). All mutant mice appeared to be fertile and healthy, without any apparent neurological or sensory defects. The lack of HB-GAM and N-syndecan, however, significantly reduced the learning capacity of the mice. On the other hand, overexpression of HB-GAM resulted in facilitated learning. Moreover, HB-GAM knockout mice displayed higher anxiety-like behaviour, whereas anxiety was reduced in HB-GAM overexpressing mice. Changes in hippocampal plasticity accompanied the behavioural phenotypes. We conclude that HB-GAM and N-syndecan are involved in the modulation of synaptic plasticity in hippocampus and play a role in regulation of anxiety- and learning-related behaviour.

Conservation of Atlantic salmon by supplementary stocking of juvenile fish

Wild salmon stocks in the northern Baltic rivers became endangered in the second half of the 20th century, mainly due to recruitment overfishing. As a result, supplementary stocking was widely practised, and supplementation of the Tornionjoki salmon stock took place over a 25 year period until 2002. The stock has been closely monitored by electrofishing, smolt trapping, mark-recapture studies, catch samples and catch surveys. Background information on hatchery-reared stocked juveniles was also collected for this study. Bayesian statistics was applied to the data as this method offers the possibility of bringing prior information into the analysis and an advanced ability for incorporating uncertainty, and also provides probabilities for a multitude of hypotheses. Substantial divergences between reared and wild Tornionjoki salmon were identified in both demographic and phenological characteristics. The divergences tended to be larger the longer the duration spent in hatchery and the more favourable the hatchery conditions were for fast growth. Differences in environment likely induced most of the divergences, but selection of brood fish might have resulted in genotypic divergence in maturation age of reared salmon. Survival of stocked 1-year old juveniles to smolt varied from about 10% to about 25%. Stocking on the lower reach of the river seemed to decrease survival, and the negative effect of stocking volume on survival raises the concern of possible similar effects on the extant wild population. Post-smolt survival of wild Tornionjoki smolts was on average two times higher than that of smolts stocked as parr and 2.5 times higher than that of stocked smolts. Smolts of different groups showed synchronous variation and similar long-term survival trends. Both groups of reared salmon were more vulnerable to offshore driftnet and coastal trapnet fishing than wild salmon. Average survival from smolt to spawners of wild salmon was 2.8 times higher than that of salmon stocked as parr and 3.3 times higher than that of salmon stocked as smolts. Wild salmon and salmon stocked as parr were found to have similar lifetime survival rates, while stocked smolts have a lifetime survival rate over 4 times higher than the two other groups. If eggs are collected from the wild brood fish, stocking parr would therefore not be a sensible option. Stocking smolts instead would create a net benefit in terms of the number of spawners, but this strategy has serious drawbacks and risks associated with the larger phenotypic and demographic divergences from wild salmon. Supplementation was shown not to be the key factor behind the recovery of the Tornionjoki and other northern Baltic salmon stocks. Instead, a combination of restrictions in the sea fishery and simultaneous occurrence of favourable natural conditions for survival were the main reasons for the revival in the 1990 s. This study questions the effectiveness of supplementation as a conservation management tool. The benefits of supplementation seem at best limited. Relatively high occurrences of reared fish in catches may generate false optimism concerning the effects of supplementation. Supplementation may lead to genetic risks due to problems in brood fish collection and artificial rearing with relaxed natural selection and domestication. Appropriate management of fisheries is the main alternative to supplementation, without which all other efforts for long-term maintenance of a healthy fish resource fail.

"It's not the Jedi way!": Moral ambivalence and delivering the 'good' in Star Wars

This article examines the nature of good and evil through the prism of Star Wars, arguing that the ostensible dichotomy between the ‘good’ Jedi and the ‘evil’ Sith is false, and instead both the Jedi and the Sith engage in violence, which is evil. Anakin Skywalker then arrives as the Christ-figure who becomes evil and ‘dies’ to destroy the old rigid law of the letter adhered to by the Jedi, before resurrecting and sacrificing himself to defeat the Sith transgressors. As Milbank argues, the act of selfless love by Anakin as the Christ-figure therefore produces the good, the end of violent conflict which is ontological peace, and institutes the law of love which leads to life and peace.

Keeping kids sun safe: exploring parents' beliefs about their young child's sun-protective behaviours

Objectives Melanoma of the skin is the third most commonly diagnosed cancer in Australia. Given the high incidence of sunburn in children and the level of sun protection provided by parents is often infrequent and/or insufficient, this research employed qualitative methodology to examine parents' beliefs about their young child's sun safe behaviour. Methods Parents (N = 21; n = 14 mothers, n = 7 fathers) of children aged 2–5 years participated in focus groups to identify commonly held beliefs about their decision to sun protect their child. Data were analysed using thematic content analysis. Results Parents generally had knowledge of the broad sun safe recommendations; however, the specific details of the recommendations were not always known. Parents reported adopting a range of sun-protective measures for their child, which depended on the time of year. A range of advantages (e.g. reducing the risk of skin cancer, developing good habits early and parental peace of mind), disadvantages (e.g. false sense of safety and preventing vitamin D absorption), barriers (e.g. child refusal) and facilitators (e.g. routine and accessibility) to performing sun safe practices were identified. Normative pressures and expectations also affected parents' motivation to be sun safe for their child. Conclusions These identified beliefs can be used to inform interventions to improve sun safe behaviours in young children who reside in a region that has the highest skin cancer incidence in the world.

Automated feature engineering for HTTP tunnel detection

Generating discriminative input features is a key requirement for achieving highly accurate classifiers. The process of generating features from raw data is known as feature engineering and it can take significant manual effort. In this paper we propose automated feature engineering to derive a suite of additional features from a given set of basic features with the aim of both improving classifier accuracy through discriminative features, and to assist data scientists through automation. Our implementation is specific to HTTP computer network traffic. To measure the effectiveness of our proposal, we compare the performance of a supervised machine learning classifier built with automated feature engineering versus one using human-guided features. The classifier addresses a problem in computer network security, namely the detection of HTTP tunnels. We use Bro to process network traffic into base features and then apply automated feature engineering to calculate a larger set of derived features. The derived features are calculated without favour to any base feature and include entropy, length and N-grams for all string features, and counts and averages over time for all numeric features. Feature selection is then used to find the most relevant subset of these features. Testing showed that both classifiers achieved a detection rate above 99.93% at a false positive rate below 0.01%. For our datasets, we conclude that automated feature engineering can provide the advantages of increasing classifier development speed and reducing development technical difficulties through the removal of manual feature engineering. These are achieved while also maintaining classification accuracy.