Ferric and ferrous iron in nitroso-myoglobin: computer simulations of stable and metastable states and their infrared spectra

The binding of NO to iron is involved in the biological function of many heme proteins. Contrary to ligands like CO and O-2, which only bind to ferrous (Fe-II) iron, NO binds to both ferrous and ferric (Fe-II) iron. In a particular protein, the natural oxidation state can therefore be expected to be tailored to the required function. Herein, we present an ob initio potential-energy surface for ferric iron interacting with NO. This potential-energy surface exhibits three minima corresponding to eta'-NO coordination (the global minimum), eta(1)-ON coordination and eta(2) coordination. This contrasts with the potential-energy surface for Fe-II-NO, which ex- hibits only two minima (the eta(2) coordination mode for Fe-II is a transition state, not a minimum). In addition, the binding energies of NO are substantially larger for Fe-III than for Fe-II. We have performed molecular dynamics simulations for NO bound to ferric myoglobin (Mb(III)) and compare these with results obtained for Mb(II). Over the duration of our simulations (1.5 ns), all three binding modes are found to be stable at 200 K and transiently stable at 300 K, with eventual transformation to the eta(1)-NO global-minimum conformation. We discuss the implication of these results related to studies of rebinding processes in myoglobin.

Computer simulations of structures, energetics and dynamics of myoglobin center dot center dot center dot ligand complexes

Myoglobin has been studied in considerable detail using different experimental and computational techniques over the past decades. Recent developments in time-resolved spectroscopy have provided experimental data amenable to detailed atomistic simulations. The main theme of the present review are results on the structures, energetics and dynamics of ligands ( CO, NO) interacting with myoglobin from computer simulations. Modern computational methods including free energy simulations, mixed quantum mechanics/molecular mechanics simulations, and reactive molecular dynamics simulations provide insight into the dynamics of ligand dynamics in confined spaces complementary to experiment. Application of these methods to calculate and understand experimental observations for myoglobin interacting with CO and NO are presented and discussed.

Loss of language in early development of autism and specific language impairment

Background:  Several authors have highlighted areas of overlap in symptoms and impairment among children with autism spectrum disorder (ASD) and children with specific language impairment (SLI). By contrast, loss of language and broadly defined regression have been reported as relatively specific to autism. We compare the incidence of language loss and language progression of children with autism and SLI. Methods:  We used two complementary studies: the Special Needs and Autism Project (SNAP) and the Manchester Language Study (MLS) involving children with SLI. This yielded a combined sample of 368 children (305 males and 63 females) assessed in late childhood for autism, history of language loss, epilepsy, language abilities and nonverbal IQ. Results:  language loss occurred in just 1% of children with SLI but in 15% of children classified as having autism or autism spectrum disorder. Loss was more common among children with autism rather than milder ASD and is much less frequently reported when language development is delayed. For children who lost language skills before their first phrases, the phrased speech milestone was postponed but long-term language skills were not significantly lower than children with autism but without loss. For the few who experienced language loss after acquiring phrased speech, subsequent cognitive performance is more uncertain. Conclusions:  Language loss is highly specific to ASD. The underlying developmental abnormality may be more prevalent than raw data might suggest, its possible presence being hidden for children whose language development is delayed.

Digital signal processing of optical monitoring by means of a Kalman filter

A Kalman filter algorithm has been applied to interpret the optical reflectance excursions during vacuum deposition of infrared coatings and multilayer thin-film filters. The application has been described in detail elsewhere and this paper now reports on-line experience for estimating deposition rate and thickness. The estimation proved sufficiently reliable to firstly 'navigate' regular manufacture (as controlled by a skilled operator) and to subsequently reproduce the skill without interpretation or intervention whilst maintaining exemplary product quality. Optical control by means of this Kalman filter application is therefore considered suitable as a basis for the automated manufacture of infrared coatings and multilayer thin-film filters.

Research review: reading comprehension in developmental disorders of language and communication

Background: Deficits in reading airment (SLI), Down syndrome (DS) and autism spectrum disorders (ASD). Methods: In this review (based on a search of the ISI Web of Knowledge database to 2011), the Simple View of Reading is used as a framework for considering reading comprehension in these groups. Conclusions: There is substantial evidence for reading comprehension impairments in SLI and growing evidence that weaknesses in this domain are common in DS and ASD. Further, in these groups reading comprehension is typically more impaired than word recognition. However, there is also evidence that some children and adolescents with DS, ASD and a history of SLI develop reading comprehension and word recognition skills at or above the age appropriate level. This review of the literature indicates that factors including word recognition, oral language, nonverbal ability and working memory may explain reading comprehension difficulties in SLI, DS and ASD. In addition, it highlights methodological issues, implications of poor reading comprehension and fruitful areas for future research.

Measuring lexical diversity among L2 learners of French: an exploration of the validity of D, MTLD and HD-D as measures of language ability

In this study two new measures of lexical diversity are tested for the first time on French. The usefulness of these measures, MTLD (McCarthy and Jarvis (2010 and this volume) ) and HD-D (McCarthy and Jarvis 2007), in predicting different aspects of language proficiency is assessed and compared with D (Malvern and Richards 1997; Malvern, Richards, Chipere and Durán 2004) and Maas (1972) in analyses of stories told by two groups of learners (n=41) of two different proficiency levels and one group of native speakers of French (n=23). The importance of careful lemmatization in studies of lexical diversity which involve highly inflected languages is also demonstrated. The paper shows that the measures of lexical diversity under study are valid proxies for language ability in that they explain up to 62 percent of the variance in French C-test scores, and up to 33 percent of the variance in a measure of complexity. The paper also provides evidence that dependence on segment size continues to be a problem for the measures of lexical diversity discussed in this paper. The paper concludes that limiting the range of text lengths or even keeping text length constant is the safest option in analysing lexical diversity.

The shape and tempo of language evolution

There are approximately 7000 languages spoken in the world today. This diversity reflects the legacy of thousands of years of cultural evolution. How far back we can trace this history depends largely on the rate at which the different components of language evolve. Rates of lexical evolution are widely thought to impose an upper limit of 6000-10,000 years on reliably identifying language relationships. In contrast, it has been argued that certain structural elements of language are much more stable. Just as biologists use highly conserved genes to uncover the deepest branches in the tree of life, highly stable linguistic features hold the promise of identifying deep relationships between the world's languages. Here, we present the first global network of languages based on this typological information. We evaluate the relative evolutionary rates of both typological and lexical features in the Austronesian and Indo-European language families. The first indications are that typological features evolve at similar rates to basic vocabulary but their evolution is substantially less tree-like. Our results suggest that, while rates of vocabulary change are correlated between the two language families, the rates of evolution of typological features and structural subtypes show no consistent relationship across families.

Auditory distraction eliminates retrieval induced forgetting: implications for the processing of unattended sound

The Retrieval-Induced Forgetting (RIF) paradigm includes three phases: (a) study/encoding of category exemplars, (b) practicing retrieval of a sub-set of those category exemplars, and (c) recall of all exemplars. At the final recall phase, recall of items that belong to the same categories as those items that undergo retrieval-practice, but that do not undergo retrieval-practice, is impaired. The received view is that this is because retrieval of target category-exemplars (e.g., ‘Tiger’ in the category Four-legged animal) requires inhibition of non-target category-exemplars (e.g., ‘Dog’ and ‘Lion’) that compete for retrieval. Here, we used the RIF paradigm to investigate whether ignoring auditory items during the retrieval-practice phase modulates the inhibitory process. In two experiments, RIF was present when retrieval-practice was conducted in quiet and when conducted in the presence of spoken words that belonged to a category other than that of the items that were targets for retrieval-practice. In contrast, RIF was abolished when words that either were identical to the retrieval-practice words or were only semantically related to the retrieval-practice words were presented as background speech. The results suggest that the act of ignoring speech can reduce inhibition of the non-practiced category-exemplars, thereby eliminating RIF, but only when the spoken words are competitors for retrieval (i.e., belong to the same semantic category as the to-be-retrieved items).

L2 performance and context of language learning: a comparative study of learners in Tehran and London

The importance of learning context has stirred debates in the field of second language acquisition over the past two decades since studying a second language (L2) abroad is believed to provide authentic opportunities that facilitate L2 acquisition and development. The present paper examines whether language performance of learners studying English in a formal language classroom context at home (AH) is different from performance of learners who study English abroad (SA) where they would have to use English for a range of communicative purposes. The data for this comparative study is part of a larger corpus of L2 performance of 100 learners of English, 60 in Tehran and 40 in London, on four oral narrative tasks. The two groups’ performances are compared on a range of different measures of fluency, accuracy, syntactic complexity and lexical diversity. The results of the analyses indicate that learners in the two contexts are very similar with respect to the grammatical accuracy and aspects of the oral fluency of their performance. However, the SA group appears to have benefited from living and studying abroad in producing language of higher syntactic complexity and lexical diversity. These results have significant implications for language teaching in AH contexts.

Femto-chemometrics: the signal processing of fast pulse transients

Traditional chemometrics techniques are augmented with algorithms tailored specifically for the de-noising and analysis of femtosecond duration pulse datasets. The new algorithms provide additional insights on sample responses to broadband excitation and multi-moded propagation phenomena.