Re-examination of the anion derivatives of isoflavones by radical fragmentation in negative electrospray ionization tandem mass spectrometry: experimental and computational studies

This paper reports theoretical and experimental studies of gas-phase fragmentation reactions of four naturally occurring isoflavones. The samples were analyzed in negative ion mode by direct infusion in ESI-QqQ, ESI-QqTOF and ESI-Orbitrap systems. The MS/MS and MS(n) spectra are in agreement with the fragmentation proposals and high-resolution analyses have confirmed the formulae for each ion observed. As expected, compounds with methoxyl aromatic substitution have showed a radical elimination of center dot CH(3) as the main fragmentation pathway. A second radical loss (center dot H) occurs as previously observed for compounds which exhibit a previous homolytic center dot CH(3) cleavage (radical anion) and involves radical resonance to stabilize the anion formed. However, in this study we suggest another mechanism for the formation of the main ions, on the basis of the enthalpies for each species. Compounds without methoxy substituent dissociate at the highest energies and exhibit the deprotonated molecule as the most intense ion. Finally, energy-resolved experiments were carried out to give more details about the gas-phase dissociation reaction of the isoflavones and the results are in agreement with the theoretical approaches. Copyright (C) 2011 John Wiley & Sons, Ltd.

Ca(2+) binding to c-state of adenine nucleotide translocase (ANT)-surrounding cardiolipins enhances (ANT)-Cys(56) relative mobility: A computational-based mitochondrial permeability transition study

The oxidation of critical cysteines/related thiols of adenine nucleotide translocase (ANT) is believed to be an important event of the Ca(2+)-induced mitochondrial permeability transition (MPT), a process mediated by a cyclosporine A/ADP-sensitive permeability transition pores (PTP) opening. We addressed the ANT-Cys(56) relative mobility status resulting from the interaction of ANT/surrounding cardiolipins with Ca(2+) and/or ADP by means of computational chemistry analysis (Molecular Interaction Fields and Molecular Dynamics studies), supported by classic mitochondrial swelling assays. The following events were predicted: (i) Ca(2+) interacts preferentially with the ANT surrounding cardiolipins bound to the H4 helix of translocase, (ii) weakens the cardiolipins/ANT interactions and (iii) destabilizes the initial ANT-Cys(56) residue increasing its relative mobility. The binding of ADP that stabilizes the conformation ""m"" of ANT and/or cardiolipin, respectively to H5 and H4 helices, could stabilize their contacts with the short helix h56 that includes Cys(56), accounting for reducing its relative mobility. The results suggest that Ca(2+) binding to adenine nucleotide translocase (ANT)-surrounding cardiolipins in c-state of the translocase enhances (ANT)-Cys(56) relative mobility and that this may constitute a potential critical step of Ca(2+)-induced PTP opening. (C) 2009 Elsevier B.V. All rights reserved.

A Computational Framework for Institutional Agency

This paper provides a computational framework, based on Defeasible Logic, to capture some aspects of institutional agency. Our background is Kanger-Lindahl-P\"orn account of organised interaction, which describes this interaction within a multi-modal logical setting. This work focuses in particular on the notions of counts-as link and on those of attempt and of personal and direct action to realise states of affairs. We show how standard Defeasible Logic can be extended to represent these concepts: the resulting system preserves some basic properties commonly attributed to them. In addition, the framework enjoys nice computational properties, as it turns out that the extension of any theory can be computed in time linear to the size of the theory itself.

All in Good Time: Exploring Change in Neanderthal Behavioural Complexity

Since their discovery 150 years ago, Neanderthals have been considered incapable of behavioural change and innovation. Traditional synchronic approaches to the study of Neanderthal behaviour have perpetuated this view and shaped our understanding of their lifeways and eventual extinction. In this thesis I implement an innovative diachronic approach to the analysis of Neanderthal faunal extraction, technology and symbolic behaviour as contained in the archaeological record of the critical period between 80,000 and 30,000 years BP. The thesis demonstrates patterns of change in Neanderthal behaviour which are at odds with traditional perspectives and which are consistent with an interpretation of increasing behavioural complexity over time, an idea that has been suggested but never thoroughly explored in Neanderthal archaeology. Demonstrating an increase in behavioural complexity in Neanderthals provides much needed new data with which to fuel the debate over the behavioural capacities of Neanderthals and the first appearance of Modern Human Behaviour in Europe. It supports the notion that Neanderthal populations were active agents of behavioural innovation prior to the arrival of Anatomically Modern Humans in Europe and, ultimately, that they produced an early Upper Palaeolithic cultural assemblage (the Châtelperronian) independent of modern humans. Overall, this thesis provides an initial step towards the development of a quantitative approach to measuring behavioural complexity which provides fresh insights into the cognitive and behavioural capabilities of Neanderthals.

Exploring Change in Neanderthal Behavioural Complexity: An Innovative Approach to the Study of Neanderthal Behaviour

Diachronic approaches provide potential for a more sophisticated framework within which to examine change in Neanderthal behavioural complexity using archaeological proxies such as symbolic artefacts, faunal assemblages and technology. Analysis of the temporal appearance and distribution of such artefacts and assemblages provide the basis for identifying changes in Neanderthal behavioural complexity in terms of symbolism, faunal extraction and technology respectively. Although changes in technology and faunal extraction were examined in the wider study, only the results of the symbolic study are presented below to illustrate the potential of the approach.

Two times three little pigs: Dysfluency, cognitive complexity and autism

This paper presents an analysis of dysfluencies in two oral tellings of a familiar children's story by a young boy with autism. Thurber & Tager-Flusberg (1993) postulate a lower degree of cognitive and communicative investment to explain a lower frequency of non-grammatical pauses observed in elicited narratives of children with autism in comparison to typically developing and intellectually disabled controls. we also found a very low frequency of non-grammatical pauses in our data, but indications of high engagement and cognitive and communicative investment. We point to a wider range of disfluencies as indicators of cognitive load, and show that the kind and location of dysfluencies produced may reveal which aspects of the narrative task are creating the greatest cognitive demand: here, mental state ascription, perspectivization, and adherence to story schema. This paper thus generates analytical options and hypotheses that can be explored further in a larger population of children with autism and typically developing controls.

A matching pursuit-based signal complexity measure for the analysis of newborn EEG

This paper presents a new relative measure of signal complexity, referred to here as relative structural complexity, which is based on the matching pursuit (MP) decomposition. By relative, we refer to the fact that this new measure is highly dependent on the decomposition dictionary used by MP. The structural part of the definition points to the fact that this new measure is related to the structure, or composition, of the signal under analysis. After a formal definition, the proposed relative structural complexity measure is used in the analysis of newborn EEG. To do this, firstly, a time-frequency (TF) decomposition dictionary is specifically designed to compactly represent the newborn EEG seizure state using MP. We then show, through the analysis of synthetic and real newborn EEG data, that the relative structural complexity measure can indicate changes in EEG structure as it transitions between the two EEG states; namely seizure and background (non-seizure).

BIO Logical Agents: Norms, Beliefs, Intentions in Defeasible Logic

In this paper we follow the BOID (Belief, Obligation, Intention, Desire) architecture to describe agents and agent types in Defeasible Logic. We argue, in particular, that the introduction of obligations can provide a new reading of the concepts of intention and intentionality. Then we examine the notion of social agent (i.e., an agent where obligations prevail over intentions) and discuss some computational and philosophical issues related to it. We show that the notion of social agent either requires more complex computations or has some philosophical drawbacks.

Task Complexity and Variation in L2 Learner’s Oral Discourse

There are many factors which affect the L2 learner’s performance at the levels of phonology, morphology and syntax. Consequently when L2 learners attempt to communicate in the target language, their language production will show systematic variability across the above mentioned linguistic domains. This variation can be attributed to some factors such as interlocutors, topic familiarity, prior knowledge, task condition, planning time and tasks types. This paper reports the results of an on going research investigating the issue of variability attributed to the task type. It is hypothesized that the particular type of task learners are required to perform will result in variation in their performance. Results of the statistical analyses of this study investigating the issue of variation in the performance of twenty L2 learners at the English department of Tabriz University provided evidence in support of the hypothesis that performance of L2 learners show systematic variability attributed to task.

Two dimensional computational fluid dynamic models for waste stabilisation ponds

Traditional waste stabilisation pond (WSP) models encounter problems predicting pond performance because they cannot account for the influence of pond features, such as inlet structure or pond geometry, on fluid hydrodynamics. In this study, two dimensional (2-D) computational fluid dynamics (CFD) models were compared to experimental residence time distributions (RTD) from literature. In one of the-three geometries simulated, the 2-D CFD model successfully predicted the experimental RTD. However, flow patterns in the other two geometries were not well described due to the difficulty of representing the three dimensional (3-D) experimental inlet in the 2-D CFD model, and the sensitivity of the model results to the assumptions used to characterise the inlet. Neither a velocity similarity nor geometric similarity approach to inlet representation in 2-D gave results correlating with experimental data. However. it was shown that 2-D CFD models were not affected by changes in values of model parameters which are difficult to predict, particularly the turbulent inlet conditions. This work suggests that 2-D CFD models cannot be used a priori to give an adequate description of the hydrodynamic patterns in WSP. (C) 1998 Elsevier Science Ltd. All rights reserved.

A computational study of shock speeds in high-performance shock tubes

This paper describes U2DE, a finite-volume code that numerically solves the Euler equations. The code was used to perform multi-dimensional simulations of the gradual opening of a primary diaphragm in a shock tube. From the simulations, the speed of the developing shock wave was recorded and compared with other estimates. The ability of U2DE to compute shock speed was confirmed by comparing numerical results with the analytic solution for an ideal shock tube. For high initial pressure ratios across the diaphragm, previous experiments have shown that the measured shock speed can exceed the shock speed predicted by one-dimensional models. The shock speeds computed with the present multi-dimensional simulation were higher than those estimated by previous one-dimensional models and, thus, were closer to the experimental measurements. This indicates that multi-dimensional flow effects were partly responsible for the relatively high shock speeds measured in the experiments.

Computational binding assays of antigenic peptides

Computer models can be combined with laboratory experiments for the efficient determination of (i) peptides that bind MHC molecules and (ii) T-cell epitopes. For maximum benefit, the use of computer models must be treated as experiments analogous to standard laboratory procedures. This requires the definition of standards and experimental protocols for model application. We describe the requirements for validation and assessment of computer models. The utility of combining accurate predictions with a limited number of laboratory experiments is illustrated by practical examples. These include the identification of T-cell epitopes from IDDM-, melanoma- and malaria-related antigens by combining computational and conventional laboratory assays. The success rate in determining antigenic peptides, each in the context of a specific HLA molecule, ranged from 27 to 71%, while the natural prevalence of MHC-binding peptides is 0.1-5%.

Computational chemistry on Fujitsu vector-parallel processors: Development and performance of applications software

In this and a preceding paper, we provide an introduction to the Fujitsu VPP range of vector-parallel supercomputers and to some of the computational chemistry software available for the VPP. Here, we consider the implementation and performance of seven popular chemistry application packages. The codes discussed range from classical molecular dynamics to semiempirical and ab initio quantum chemistry. All have evolved from sequential codes, and have typically been parallelised using a replicated data approach. As such they are well suited to the large-memory/fast-processor architecture of the VPP. For one code, CASTEP, a distributed-memory data-driven parallelisation scheme is presented. (C) 2000 Published by Elsevier Science B.V. All rights reserved.