A Bayesian approach for estimating the probability of trigger failures in the stop-signal paradigm

Response inhibition is frequently investigated using the stop-signal paradigm, where participants perform a two-choice response time task that is occasionally interrupted by a stop signal instructing them to withhold their response. Stop-signal performance is formalized as a race between a go and a stop process. If the go process wins, the response is executed; if the stop process wins, the response is inhibited. Successful inhibition requires fast stop responses and a high probability of triggering the stop process. Existing methods allow for the estimation of the latency of the stop response, but are unable to identify deficiencies in triggering the stop process. We introduce a Bayesian model that addresses this limitation and enables researchers to simultaneously estimate the probability of trigger failures and the entire distribution of stopping latencies. We demonstrate that trigger failures are clearly present in two previous studies, and that ignoring them distorts estimates of stopping latencies. The parameter estimation routine is implemented in the BEESTS software (Matzke et al., Front. Quantitative Psych. Measurement, 4, 918; 2013a) and is available at http://dora.erbe-matzke.com/software.html

A key to selected rockfishes (Sebastes spp.) based on mitochondrial DNA restriction fragment analysis

Larval and juvenile rockfishes (Sebastes spp.) are difficult to identify using morphological characters. We developed a key based on sizes of restriction endonuclease fragments of the NADH dehydrogenase-3 and -4 (ND3/ND4) and 12S and 16S ribosomal RNA (12S/16S) mitochondrial regions. The key makes use of variation in the ND3/ND4 region. Restriction endonuclease Dde I variation can corroborate identifications, as can 12S/16S variation. The key, based on 71 species, includes most North American taxa, several Asian species, and Sebastolobus alascanus and Helicolenus hilgendorfi that are closely related to rockfishes. Fifty-eight of 71 rockfish species in our database can be distinguished unequivocally, using one to five restriction enzymes; identities of the remaining species are narrowed to small groups: 1) S. polyspinis, S. crameri, and S. ciliatus or variabilis (the two species could not be distinguished and were considered as a single species) ; 2) S. chlorostictus, S. eos, and S. rosenblatti; 3) S. entomelas and S. mystinus; 4)S. emphaeus, S. variegatus, and S. wilsoni; and 5) S. carnatus and S. chrysomelas

Host responses to infection by Cauliflower mosaic virus

The role of soluble sugars in the development of symptoms in compatible virus infection was examined in turnip and several Arabidopsis thaliana lines infected with Cauliflower mosaic virus CaMV. In turnip (Brassica campestris cv. Just Right) infected with four CaMV isolates that induced symptoms of differing severity, there were changes in levels of free soluble sugars in infected plants, but the changes showed no direct correlation with either the level of virus replication or symptom severity. This implies that in CaMV-infected turnip, changes in sugar levels probably do not act directly as elicitors of symptom development. CaMV infection in wildtype and putative Arabidopsis sugar signalling mutants had little effect on levels of free soluble sugar during symptom development. Again this observation does not support a role for changes in sugar levels in potentiating the development of symptoms. However on infection, the mutants developed a range of unusual symptom phenotypes and showed differences in level of virus accumulation, when compared with wildtype plants. This suggested a possible link between sugar signalling pathways and symptom development and viral pathogenesis. Soluble sugars have been reported to act as signalling molecules in defence responses. To test this the expression of three PR protein genes, which are reported to be modulatable by sugars and the SA defence pathway, were analysed in infected Arabidopsis. In infected plants, the expression of these genes was greatly elevated, whereas uninfected plants had undetectable levels of expression. Since sugar levels were unaffected during virus infection this suggests that sugars are probably not involved in the invocation of PR defence genes. The temporal and spatial activation of three defence pathways was investigated using defence marker gene promoter::Luciferase reporter plants. Ambidopsis thaliana GST1::Luciferase was used in the analysis of the oxidative burst, Arabidopsis thaliana PDF1.2::Luciferase for the JA/ethylene pathway and tobacco PR-1::Luciferase for the SA pathway. Systemic activation of the JA/ethylene pathway and oxidative burst was detectable two hours after virus inoculation, and continued until 5 dpi. In contrast activation of the SA-mediated defence pathway was first detected 8 days after infection, continuing strongly until at least 19 dpi. The timing of the SA pathway activation coincided with a second burst of increased AtGST1:;Luciferase. However plants stained for H2O2, a product of the oxidative burst, demonstrated that the oxidative burst occurred only in the very early stages of virus infection (3.5 hours- 4 days after inoculation). This suggested that the second phase of G5T7::Luciferase activity is perhaps regulated by other pathways, in the absence of the oxidative burst. The invocation of defence responses during compatible interactions has often been overlooked since the pathogen appears to replicate and move freely in the plant. These results provide strong evidence for a co-ordinated activation of defence pathways in response to infection by a compatible virus pathogen

A framework for design engineering education in a global context

This paper presents a framework for teaching design engineering in a global context using innovative technologies to enable distributed teams to work together effectively across international and cultural boundaries. The DIDET Framework represents the findings of a 5-year project conducted by the University of Strathclyde, Stanford University and Olin College which enhanced student learning opportunities by enabling them to partake in global, team based design engineering projects, directly experiencing different cultural contexts and accessing a variety of digital information sources via a range of innovative technology. The use of innovative technology enabled the formalization of design knowledge within international student teams as did the methods that were developed for students to store, share and reuse information. Coaching methods were used by teaching staff to support distributed teams and evaluation work on relevant classes was carried out regularly to allow ongoing improvement of learning and teaching and show improvements in student learning. Major findings of the 5 year project include the requirement to overcome technological, pedagogical and cultural issues for successful eLearning implementations. The DIDET Framework encapsulates all the conclusions relating to design engineering in a global context. Each of the principles for effective distributed design learning is shown along with relevant findings and suggested metrics. The findings detailed in the paper were reached through a series of interventions in design engineering education at the collaborating institutions. Evaluation was carried out on an ongoing basis and fed back into project development, both on the pedagogical and the technological approaches

A comparison of the Bravyi-Kitaev and Jordan-Wigner transformations for the quantum simulation of quantum chemistry

The ability to perform classically intractable electronic structure calculations is often cited as one of the principal applications of quantum computing. A great deal of theoretical algorithmic development has been performed in support of this goal. Most techniques require a scheme for mapping electronic states and operations to states of and operations upon qubits. The two most commonly used techniques for this are the Jordan-Wigner transformation and the Bravyi-Kitaev transformation. However, comparisons of these schemes have previously been limited to individual small molecules. In this paper we discuss resource implications for the use of the Bravyi-Kitaev mapping scheme, specifically with regard to the number of quantum gates required for simulation. We consider both small systems which may be simulatable on near-future quantum devices, and systems sufficiently large for classical simulation to be intractable. We use 86 molecular systems to demonstrate that the use of the Bravyi-Kitaev transformation is typically at least approximately as efficient as the canonical Jordan-Wigner transformation, and results in substantially reduced gate count estimates when performing limited circuit optimisations.Comment: 46 pages, 11 figure