Modelling of the lignin peroxidase LIII of Phlebia radiata: use of a sequence template generated from a 3-D structure

A model of the lignin peroxidase LIII of Phlebia radiata wasconstructed on the basis of the structure of cytochrome c peroxidase(CCP). Because of the low percentage of amino acid identitybetween the CCP and the lignin peroxidase LIII of Phlebia radiata,alignment of the sequences was based on the generation of atemplate from a knowledge of the 3-D structure of CCP and consensussequences of lignin peroxidases. This approach gave an alignmentin which all the insertions in the lignin peroxidase were placedat loop regions of CCP, with a 21.1% identity for these twoproteins. The model was constructed using this alignment andthe computer program COMPOSER, which assembles the model asa series of rigid fragments derived from CCP and other proteins.Manual intervention was required for some of the longer loopregions. The -helices forming the structural framework, andespecially the haem environment of CCP, are conserved in theLIII model and the core is close packed without holes. A possiblesite of the substrate oxidation at the haem edge of LIII isdiscussed.     

On reducing the number of states in a PDA

A transformation is presented which converts any pushdown automaton (PDA)M ₀ withn ₀ states andp ₀ stack symbols into an equivalent PDAM withn states and n ₀ /n² p ₀ stack symbols into an equivalent ofn, 1n ₀. This transformation preserves realtime behavior but not derterminism. The transformation is proved to be the best possible one in the following sense: for each choice of the parametersn ₀ + 1 stack symbols for any desired value realtime PDAM ₀ such that any equivalent PDAM (whether realtime or not) havingn states must have at least (n ₀ /n)² p₀ stack symbols. Furthermore, the loss of deterministic behavior cannot be avoided, since for each choice ofn ₀ andp ₀, there is a deterministic PDAM ₀ such that no equivalent PDAM with fewer states can be deterministic.This research was supported in part by the National Science Foundation under Grants MCS76-10076 and MCS76-10076A01.     

Sparse coding on the spot: spontaneous retinal waves suffice for orientation selectivity

Ohshiro, Hussain, and Weliky (2011) recently showed that ferrets reared with exposure to flickering spot stimuli, in the absence of oriented visual experience, develop oriented receptive fields. They interpreted this as refutation of efficient coding models, which require oriented input in order to develop oriented receptive fields. Here we show that these data are compatible with the efficient coding hypothesis if the influence of spontaneous retinal waves is considered. We demonstrate that independent component analysis learns predominantly oriented receptive fields when trained on a mixture of spot stimuli and spontaneous retinal waves. Further, we show that the efficient coding hypothesis provides a compelling explanation for the contrast between the lack of receptive field changes seen in animals reared with spot stimuli and the significant cortical reorganisation observed in stripe-reared animals.     

Intrinsically universal n-dimensional quantum cellular automata

Several non-axiomatic approaches have been taken to define Quantum Cellular Automata (QCA); Partitioned QCA (PQCA) are the most canonical. Here we show any QCA can be put into PQCA form. Our construction reconciles the non-axiomatic definitions of QCA, showing that they can all simulate one another, thus they are all equivalent to the axiomatic definition. A simple n-dimensional QCA capable of simulating all others to arbitrary precision is described, where the initial configuration and the evolution of any QCA can be encoded within the initial configuration of the intrinsically universal QCA. Several steps then correspond to one step of the simulated QCA, achieved via a non-trivial reduction of the problem to universality in quantum circuits. Results are formalised by defining generalised n-dimensional intrinsic simulation, preserving topology in that each cell of the simulated QCA is encoded as a group of adjacent cells in the universal QCA. Implications are discussed.     

AH-64D main transmission accessory drive spur gear installation fault detections

The US Army has launched an aggressive program to implement condition based maintenance on its rotary wing assets. Condition Based Maintenance takes advantage of technology developments in the areas of machinery monitoring, signal processing and fault modeling to reduce the cost of ownership through improved maintenance procedures. Documenting the reduction in maintenance burden, cost savings and increased safety through early detection of helicopter faults is an important step in justifying the program. This paper describes a novel technique used to detect a serious fault in the accessory section of the AH-64D Apache main transmission. The technique determines if the primary or secondary clutch system is driving the aircraft accessories through a tachometer speed ratio. The method has identified three aircraft operating on the secondary system allowing Army maintenance crews to replace the affected transmissions and quickly restore the aircraft to operational status.     

BCI Meeting 2005--workshop on signals and recording methods.

This paper describes the highlights of presentations and discussions during the Third International BCI Meeting in a workshop that evaluated potential brain-computer interface (BCI) signals and currently available recording methods. It defined the main potential user populations and their needs, addressed the relative advantages and disadvantages of noninvasive and implanted (i.e., invasive) methodologies, considered ethical issues, and focused on the challenges involved in translating BCI systems from the laboratory to widespread clinical use. The workshop stressed the critical importance of developing useful applications that establish the practical value of BCI technology.     

Development and evaluation of the Air Travel Stress Scale.

Despite anecdotal evidence suggesting that air travel is personally demanding, little research has examined air travel stress. To address these issues, the author developed and evaluated the 1st known measure of air travel stress--the Air Travel Stress Scale--in 3 studies. Exploratory and confirmatory factor analysis indicated 3 components: (a) anxious reactions to adverse air travel events, (b) angry reactions to other passengers as well as an antecedent of air travel stress, and (c) the lack of trust that the airlines/airports will ensure one's comfort and safety. Each component had good internal reliability and test-retest reliability over a 6- to 7-week interval. Each component showed evidence for discriminant and convergent validity. Implications for research into understanding and intervening on air travel stress are discussed. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Dissociating Processes Supporting Causal Perception and Causal Inference in the Brain.

An understanding of relations between causes and effects is essential for making sense of the dynamic physical world. It has been argued that this understanding of causality depends on both perceptual and inferential components. To investigate whether causal perception and causal inference rely on common or on distinct processes, the authors tested 2 callosotomy (split-brain) patients and a group of neurologically intact participants. The authors show that the direct perception of causality and the ability to infer causality depend on different hemispheres of the divided brain. This finding implies that understanding causality is not a unitary process and that causal perception and causal inference can proceed independently. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Construct validation of the Rorschach Reality-Fantasy Scale in alexithymia.

The study applies Winnicott's conceptualization of potential space to the alexithymia construct by using a new Rorschach index, the Reality-Fantasy Scale (RFS). The scale uses variables derived from the Rorschach Comprehensive System (Exner, 2000, 2001) to detect different types of psychopathological manifestations conceptualized as forms of collapse of potential space. Following previous research, the present study further evaluates the construct validity of the RFS in a sample of 92 patients with inflammatory bowel disease, categorized on the basis of the Toronto Alexithymia Scale (TAS-20) as alexithymic, indeterminate alexithymia, and nonalexithymic groups. As hypothesized, the RFS significantly correlated with the TAS-20, discriminated among the 3 groups, and showed incremental validity in detecting alexithymia over isolated Rorschach markers. The study supports the exploration of psychoanalytic ideas by empirical, statistically based methods. (PsycINFO Database Record (c) 2010 APA, all rights reserved)