LVB: parsimony and simulated annealing in the search for phylogenetic trees

Summary: The program LVB seeks parsimonious phylogenies from nucleotide alignments, using the simulated annealing heuristic. LVB runs fast and gives high quality results.

Argon predissociation spectroscopy of the OH-center dot H2O and Cl-center dot H2O complexes in the 1000-1900 cm(-1) region: Intramolecular bending transitions and the search for the shared-proton fundamental in the hydroxide monohydrate

We present argon predissociation vibrational spectra of the OH-.H2O and Cl-.H2O complexes in the 1000-1900 cm(-1) energy range, far below the OH stretching region reported in previous studies. This extension allows us to explore the fundamental transitions of the intramolecular bending vibrations associated with the water molecule, as well as that of the shared proton inferred from previous assignments of overtones in the higher energy region. Although the water bending fundamental in the Cl-.H2O spectrum is in very good agreement with expectations, the OH-.H2O spectrum is quite different than anticipated, being dominated by a strong feature at 1090 cm(-1). New full-diniensionality calculations of the OH-.H2O vibrational level structure using diffusion Monte Carlo and the VSCF/CI methods indicate this band arises from excitation of the shared proton.

Synthesis of heterosulfamates. Search for structure-taste relationships

Thirty one new sodium heterosulfamates, RNHSO3Na, where the R portion contains mainly thiazole, benzothiazole, thiadiazole and pyridine ring structures, have been synthesized and their taste portfolios have been assessed. A database of 132 heterosulfamates ( both open-chain and cyclic) has been formed by combining these new compounds with an existing set of 101 heterosulfamates which were previously synthesized and for which taste data are available. Simple descriptors have been obtained using (i) measurements with Corey-Pauling-Koltun (CPK) space- filling models giving x, y and z dimensions and a volume VCPK, (ii) calculated first order molecular connectivities ((1)chi(v)) and (iii) the calculated Spartan program parameters to obtain HOMO, LUMO energies, the solvation energy E-solv and V-SPART AN. The techniques of linear (LDA) and quadratic (QDA) discriminant analysis and Tree analysis have then been employed to develop structure-taste relationships (SARs) that classify the sweet (S) and non-sweet (N) compounds into separate categories. In the LDA analysis 70% of the compounds were correctly classified ( this compares with 65% when the smaller data set of 101 compounds was used) and in the QDA analysis 68% were correctly classified ( compared to 80% previously). TheTree analysis correctly classified 81% ( compared to 86% previously). An alternative Tree analysis derived using the Cerius2 program and a set of physicochemical descriptors correctly classified only 54% of the compounds.

The human thalamus processes syntactic and semantic language violations

Numerous linguistic operations have been assigned to cortical brain areas, but the contributions of subcortical structures to human language processing are still being discussed. Using simultaneous EEG recordings directly from deep brain structures and the scalp, we show that the human thalamus systematically reacts to syntactic and semantic parameters of auditorily presented language in a temporally interleaved manner in coordination with cortical regions. In contrast, two key structures of the basal ganglia, the globus pallidus internus and the subthalamic nucleus, were not found to be engaged in these processes. We therefore propose that syntactic and semantic language analysis is primarily realized within cortico-thalamic networks, whereas a cohesive basal ganglia network is not involved in these essential operations of language analysis.

Neural mechanisms of visual object priming: evidence for perceptual and semantic distinctions in fusiform cortex

Previous functional imaging studies have shown that facilitated processing of a visual object on repeated, relative to initial, presentation (i.e., repetition priming) is associated with reductions in neural activity in multiple regions, including fusiforin/lateral occipital cortex. Moreover, activity reductions have been found, at diminished levels, when a different exemplar of an object is presented on repetition. In one previous study, the magnitude of diminished priming across exemplars was greater in the right relative to the left fusiform, suggesting greater exemplar specificity in the right. Another previous study, however, observed fusiform lateralization modulated by object viewpoint, but not object exemplar. The present fMRI study sought to determine whether the result of differential fusiform responses for perceptually different exemplars could be replicated. Furthermore, the role of the left fusiform cortex in object recognition was investigated via the inclusion of a lexical/semantic manipulation. Right fusiform cortex showed a significantly greater effect of exemplar change than left fusiform, replicating the previous result of exemplar-specific fusiform lateralization. Right fusiform and lateral occipital cortex were not differentially engaged by the lexical/semantic manipulation, suggesting that their role in visual object recognition is predominantly in the. C visual discrimination of specific objects. Activation in left fusiform cortex, but not left lateral occipital cortex, was modulated by both exemplar change and lexical/semantic manipulation, with further analysis suggesting a posterior-to-anterior progression between regions involved in processing visuoperceptual and lexical/semantic information about objects. The results are consistent with the view that the right fusiform plays a greater role in processing specific visual form information about objects, whereas the left fusiform is also involved in lexical/semantic processing. (C) 2003 Elsevier Science (USA). All rights reserved.

The effect of learning condition on perceptual anticipation, awareness, and visual search

The efficacy of explicit and implicit learning paradigms was examined during the very early stages of learning the perceptual-motor anticipation task of predicting ball direction from temporally occluded footage of soccer penalty kicks. In addition, the effect of instructional condition on point-of-gaze during learning was examined. A significant improvement in horizontal prediction accuracy was observed in the explicit learning group; however, similar improvement was evident in a placebo group who watched footage of soccer matches. Only the explicit learning intervention resulted in changes in eye movement behaviour and increased awareness of relevant postural cues. Results are discussed in terms of methodological and practical issues regarding the employment of implicit perceptual training interventions. (c) 2005 Elsevier B.V. All rights reserved.

fMRI delineation of working memory for emotional prosody in the brain: commonalities with the lexico-semantic emotion network

Decoding emotional prosody is crucial for successful social interactions, and continuous monitoring of emotional intent via prosody requires working memory. It has been proposed by Ross and others that emotional prosody cognitions in the right hemisphere are organized in an analogous fashion to propositional language functions in the left hemisphere. This study aimed to test the applicability of this model in the context of prefrontal cortex working memory functions. BOLD response data were therefore collected during performance of two emotional working memory tasks by participants undergoing fMRI. In the prosody task, participants identified the emotion conveyed in pre-recorded sentences, and working memory load was manipulated in the style of an N-back task. In the matched lexico-semantic task, participants identified the emotion conveyed by sentence content. Block-design neuroimaging data were analyzed parametrically with SPM5. At first, working memory for emotional prosody appeared to be right-lateralized in the PFC, however, further analyses revealed that it shared much bilateral prefrontal functional neuroanatomy with working memory for lexico-semantic emotion. Supplementary separate analyses of males and females suggested that these language functions were less bilateral in females, but their inclusion did not alter the direction of laterality. It is concluded that Ross et al.'s model is not applicable to prefrontal cortex working memory functions, that evidence that working memory cannot be subdivided in prefrontal cortex according to material type is increased, and that incidental working memory demands may explain the frontal lobe involvement in emotional prosody comprehension as revealed by neuroimaging studies. (c) 2007 Elsevier Inc. All rights reserved.

How does the brain mediate interpretation of incongruent auditory emotions? The neural response to prosody in the presence of conflicting lexico-semantic cues

We frequently encounter conflicting emotion cues. This study examined how the neural response to emotional prosody differed in the presence of congruent and incongruent lexico-semantic cues. Two hypotheses were assessed: (i) decoding emotional prosody with conflicting lexico-semantic cues would activate brain regions associated with cognitive conflict (anterior cingulate and dorsolateral prefrontal cortex) or (ii) the increased attentional load of incongruent cues would modulate the activity of regions that decode emotional prosody (right lateral temporal cortex). While the participants indicated the emotion conveyed by prosody, functional magnetic resonance imaging data were acquired on a 3T scanner using blood oxygenation level-dependent contrast. Using SPM5, the response to congruent cues was contrasted with that to emotional prosody alone, as was the response to incongruent lexico-semantic cues (for the 'cognitive conflict' hypothesis). The right lateral temporal lobe region of interest analyses examined modulation of activity in this brain region between these two contrasts (for the 'prosody cortex' hypothesis). Dorsolateral prefrontal and anterior cingulate cortex activity was not observed, and neither was attentional modulation of activity in right lateral temporal cortex activity. However, decoding emotional prosody with incongruent lexico-semantic cues was strongly associated with left inferior frontal gyrus activity. This specialist form of conflict is therefore not processed by the brain using the same neural resources as non-affective cognitive conflict and neither can it be handled by associated sensory cortex alone. The recruitment of inferior frontal cortex may indicate increased semantic processing demands but other contributory functions of this region should be explored.

False recognition of abstract versus common objects in older and younger adults: testing the semantic categorization account

Older adults often demonstrate higher levels of false recognition than do younger adults. However, in experiments using novel shapes without preexisting semantic representations, this age-related elevation in false recognition was found to be greatly attenuated. Two experiments tested a semantic categorization account of these findings, examining whether older adults show especially heightened false recognition if the stimuli have preexisting semantic representations, such that semantic category information attenuates or truncates the encoding or retrieval of item-specific perceptual information. In Experiment 1, ambiguous shapes were presented with or without disambiguating semantic labels. Older adults showed higher false recognition when labels were present but not when labels were never presented. In Experiment 2, older adults showed higher false recognition for concrete but not abstract objects. The semantic categorization account was supported.

Search space pruning and global optimization of multiple gravity assist trajectories with deep space manoeuvres

This paper deals with the design of optimal multiple gravity assist trajectories with deep space manoeuvres. A pruning method which considers the sequential nature of the problem is presented. The method locates feasible vectors using local optimization and applies a clustering algorithm to find reduced bounding boxes which can be used in a subsequent optimization step. Since multiple local minima remain within the pruned search space, the use of a global optimization method, such as Differential Evolution, is suggested for finding solutions which are likely to be close to the global optimum. Two case studies are presented.