Immersive Projection for biochemical pattern matching

In all biological processes, protein molecules and other small molecules interact to function and form transient macromolecular complexes. This interaction of two or more molecules can be described by a docking event. Docking is an important phase for structure-based drug design strategies, as it can be used as a method to simulate protein-ligand interactions. Various docking programs exist that allow automated docking, but most of them have limited visualization and user interaction. It would be advantageous if scientists could visualize the molecules participating in the docking process, manipulate their structures and manually dock them before submitting the new conformations to an automated docking process in an immersive environment, which can help stimulate the design/docking process. This also could greatly reduce docking time and resources. To achieve this, we propose a new virtual modelling/docking program, whereby the advantages of virtual modelling programs and the efficiency of the algorithms in existing docking programs will be merged.

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.

Tests of syntactic comprehension in aphasia: an investigation of task effects

Background: Consistency of performance across tasks that assess syntactic comprehension in aphasia has clinical and theoretical relevance. In this paper we add to the relatively sparse previous work on how sentence comprehension abilities are influenced by the nature of the assessment task. Aims: Our aims are: (1) to compare linguistic performance across sentence-picture matching, enactment, and truth-value judgement tasks; (2) to investigate the impact of pictorial stimuli on syntactic comprehension. Methods Procedures: We tested a group of 10 aphasic speakers (3 with fluent and 7 with non-fluent aphasia) in three tasks (Experiment 1): (i) sentence-picture matching with four pictures, (ii) sentence-picture matching with two pictures, and (iii) enactment. A further task of truth-value judgement was given to a subgroup of those speakers (n=5, Experiment 2). Similar sentence types across all tasks were used and included canonical (actives, subject clefts) and non-canonical (passives, object clefts) sentences. We undertook two types of analyses: (a) we compared canonical and non-canonical sentences in each task; (b) we compared performance between (i) actives and passives, (ii) subject and object clefts in each task. We examined the results of all participants as a group and as case-series. Outcomes Results: Several task effects emerged. Overall, the two-picture sentence-picture matching and enactment tasks were more discriminating than the four-picture condition. Group performance in the truth-value judgement task was similar to two-picture sentence-picture matching and enactment. At the individual level performance across tasks contrasted to some group results. Conclusions: Our findings revealed task effects across participants. We discuss reasons that could explain the diverse profiles of performance and the implications for clinical practice.

Unifying syntactic theory and sentence processing difficulty through a connectionist minimalist parser

Syntactic theory provides a rich array of representational assumptions about linguistic knowledge and processes. Such detailed and independently motivated constraints on grammatical knowledge ought to play a role in sentence comprehension. However most grammar-based explanations of processing difficulty in the literature have attempted to use grammatical representations and processes per se to explain processing difficulty. They did not take into account that the description of higher cognition in mind and brain encompasses two levels: on the one hand, at the macrolevel, symbolic computation is performed, and on the other hand, at the microlevel, computation is achieved through processes within a dynamical system. One critical question is therefore how linguistic theory and dynamical systems can be unified to provide an explanation for processing effects. Here, we present such a unification for a particular account to syntactic theory: namely a parser for Stabler's Minimalist Grammars, in the framework of Smolensky's Integrated Connectionist/Symbolic architectures. In simulations we demonstrate that the connectionist minimalist parser produces predictions which mirror global empirical findings from psycholinguistic research.

The application of affine projection to the development of a siren noise cancellation system

Emergency vehicles use high-amplitude sirens to warn pedestrians and other road users of their presence. Unfortunately, the siren noise enters the vehicle and corrupts the intelligibility of two-way radio voice com-munications from the emergency vehicle to a control room. Often the siren has to be turned off to enable the control room to hear what is being said which subsequently endangers people's lives. A digital signal processing (DSP) based system for the cancellation of siren noise embedded within speech is presented. The system has been tested with the least mean square (LMS), normalised least mean square (NLMS) and affine projection algorithm (APA) using recordings from three common types of sirens (two-tone, wail and yelp) from actual test vehicles. It was found that the APA with a projection order of 2 gives comparably improved cancellation over the LMS and NLMS with only a moderate increase in algorithm complexity and code size. Therefore, this siren noise cancellation system using the APA offers an improvement in cancellation achieved by previous systems. The removal of the siren noise improves the response time for the emergency vehicle and thus the system can contribute to saving lives. The system also allows voice communication to take place even when the siren is on and as such the vehicle offers less risk of danger when moving at high speeds in heavy traffic.

Some uniform stability and convergence results for integral equations on the real line and projection methods for their solution

The paper considers second kind equations of the form (abbreviated x=y + K2x) in which and the factor z is bounded but otherwise arbitrary so that equations of Wiener-Hopf type are included as a special case. Conditions on a set are obtained such that a generalized Fredholm alternative is valid: if W satisfies these conditions and I − Kz, is injective for each z ε W then I − Kz is invertible for each z ε W and the operators (I − Kz)−1 are uniformly bounded. As a special case some classical results relating to Wiener-Hopf operators are reproduced. A finite section version of the above equation (with the range of integration reduced to [−a, a]) is considered, as are projection and iterated projection methods for its solution. The operators (where denotes the finite section version of Kz) are shown uniformly bounded (in z and a) for all a sufficiently large. Uniform stability and convergence results, for the projection and iterated projection methods, are obtained. The argument generalizes an idea in collectively compact operator theory. Some new results in this theory are obtained and applied to the analysis of projection methods for the above equation when z is compactly supported and k(s − t) replaced by the general kernel k(s,t). A boundary integral equation of the above type, which models outdoor sound propagation over inhomogeneous level terrain, illustrates the application of the theoretical results developed.

Projection of global wave climate change towards the end of the 21st century

Wind generated waves at the sea surface are of outstanding importance for both their practical relevance in many aspects, such as coastal erosion, protection, or safety of navigation, and for their scientific relevance in modifying fluxes at the air-sea interface. So far long-term changes in ocean wave climate have been studied mostly from a regional perspective with global dynamical studies emerging only recently. Here a global wave climate study is presented, in which a global wave model (WAM) is driven by atmospheric forcing from a global climate model (ECHAM5) for present day and potential future climate conditions represented by the IPCC (Intergovernmental Panel for Climate Change) A1B emission scenario. It is found that changes in mean and extreme wave climate towards the end of the twenty-first century are small to moderate, with the largest signals being a poleward shift in the annual mean and extreme significant wave heights in the mid-latitudes of both hemispheres, more pronounced in the Southern Hemisphere, and most likely associated with a corresponding shift in mid-latitude storm tracks. These changes are broadly consistent with results from the few studies available so far. The projected changes in the mean wave periods, associated with the changes in the wave climate in the mid to high latitudes, are also shown, revealing a moderate increase in the equatorial eastern side of the ocean basins. This study presents a step forward towards a larger ensemble of global wave climate projections required to better assess robustness and uncertainty of potential future wave climate change.

L3 syntactic transfer selectivity and typological determinacy: the typological primacy model

The present article addresses the following question: what variables condition syntactic transfer? Evidence is provided in support of the position that third language (L3) transfer is selective, whereby, at least under certain conditions, it is driven by the typological proximity of the target L3 measured against the other previously acquired linguistic systems (cf. Rothman and Cabrelli Amaro, 2007, 2010; Rothman, 2010; Montrul et al., 2011). To show this, we compare data in the domain of adjectival interpretation between successful first language (L1) Italian learners of English as a second language (L2) at the low to intermediate proficiency level of L3 Spanish, and successful L1 English learners of L2 Spanish at the same levels for L3 Brazilian Portuguese. The data show that, irrespective of the L1 or the L2, these L3 learners demonstrate target knowledge of subtle adjectival semantic nuances obtained via noun-raising, which English lacks and the other languages share. We maintain that such knowledge is transferred to the L3 from Italian (L1) and Spanish (L2) respectively in light of important differences between the L3 learners herein compared to what is known of the L2 Spanish performance of L1 English speakers at the same level of proficiency (see, for example, Judy et al., 2008; Rothman et al., 2010). While the present data are consistent with Flynn et al.’s (2004) Cumulative Enhancement Model, we discuss why a coupling of these data with evidence from other recent L3 studies suggests necessary modifications to this model, offering in its stead the Typological Primacy Model (TPM) for multilingual transfer.

On the typological economy of syntactic transfer: word order and relative clause high/low attachment preference in L3 Brazilian Portuguese

One central question in the formal linguistic study of adult multilingual morphosyntax (i.e., L3/Ln acquisition) involves determining the role(s) the L1 and/or the L2 play(s) at the L3 initial state (e.g., Bardel & Falk, Second Language Research 23: 459–484, 2007; Falk & Bardel, Second Language Research: forthcoming; Flynn et al., The International Journal of Multilingualism 8: 3–16, 2004; Rothman, Second Language Research: forthcoming; Rothman & Cabrelli, On the initial state of L3 (Ln) acquisition: Selective or absolute transfer?: 2007; Rothman & Cabrelli Amaro, Second Language Research 26: 219–289, 2010). The present article adds to this general program, testing Rothman's (Second Language Research: forthcoming) model for L3 initial state transfer, which when relevant in light of specific language pairings, maintains that typological proximity between the languages is the most deterministic variable determining the selection of syntactic transfer. Herein, I present empirical evidence from the later part of the beginning stages of L3 Brazilian Portuguese (BP) by native speakers of English and Spanish, who have attained an advanced level of proficiency in either English or Spanish as an L2. Examining the related domains of syntactic word order and relative clause attachment preference in L3 BP, the data clearly indicate that Spanish is transferred for both experimental groups irrespective of whether it was the L1 or L2. These results are expected by Rothman's (Second Language Research: forthcoming) model, but not necessarily predicted by other current hypotheses of multilingual syntactic transfer; the implications of this are discussed.

What variables condition syntactic transfer? A look at the L3 initial state

This study investigates transfer at the third-language (L3) initial state, testing between the following possibilities: (1) the first language (L1) transfer hypothesis (an L1 effect for all adult acquisition), (2) the second language (L2) transfer hypothesis, where the L2 blocks L1 transfer (often referred to in the recent literature as the ‘L2 status factor’; Williams and Hammarberg, 1998), and (3) the Cumulative Enhancement Model (Flynn et al., 2004), which proposes selective transfer from all previous linguistic knowledge. We provide data from successful English-speaking learners of L2 Spanish at the initial state of acquiring L3 French and L3 Italian relating to properties of the Null-Subject Parameter (e.g. Chomsky, 1981; Rizzi, 1982). We compare these groups to each other, as well as to groups of English learners of L2 French and L2 Italian at the initial state, and conclude that the data are consistent with the predictions of the ‘L2 status factor’. However, we discuss an alternative possible interpretation based on (psycho)typologically-motivated transfer (borrowing from Kellerman, 1983), providing a methodology for future research in this domain to meaningfully tease apart the ‘L2 status factor’ from this alternative account.

Pragmatic deficits with syntactic consequences?: L2 pronominal subjects and the syntax–pragmatics interface

Contemporary acquisition theorizing has placed a considerable amount of attention on interfaces, points at which different linguistic modules interact. The claim is that vulnerable interfaces cause particular difficulties in L1, bilingual and adult L2 acquisition (e.g. Platzack, 2001; Montrul, 2004; Müller and Hulk, 2001; Sorace, 2000, 2003, 2004, 2005). Accordingly, it is possible that deficits at the syntax–pragmatics interface cause what appears to be particular non-target-like syntactic behavior in L2 performance. This syntax-before-discourse hypothesis is examined in the present study by analyzing null vs. overt subject pronoun distribution in L2 Spanish of English L1 learners. As ultimately determined by L2 knowledge of the Overt Pronoun Constraint (OPC) (Montalbetti, 1984), the data indicate that L2 learners at the intermediate and advanced levels reset the Null Subject Parameter (NSP), but only advanced learners have acquired a more or less target null/overt subject distribution. Against the predictions of Sorace (2004) and in line with Montrul and Rodríguez-Louro (2006), the data indicate an overuse of both overt and null subject pronouns. As a result, this behavior cannot be from L1 interference alone, suggesting that interface-conditioned properties are simply more complex and therefore, harder to acquire. Furthermore, the data from the advanced learners demonstrate that the syntax–pragmatics interface is not a predetermined locus for fossilization (in contra e.g. Valenzuela, 2006).

Interface vulnerability and knowledge of the subjunctive/indicative distinction with negated epistemic predicates in L2 Spanish.

Much recent research in SLA is guided by the hypothesis of L2 interface vulnerability (see Sorace 2005). This study contributes to this general project by examining the acquisition of two classes of subjunctive complement clauses in L2 Spanish: subjunctive complements of volitional predicates (purely syntactic) and subjunctive vs. indicative complements with negated epistemic matrix predicates, where the mood distinction is discourse dependent (thus involving the syntax-discourse interface). We provide an analysis of the volitional subjunctive in English and Spanish, suggesting that English learners of L2 Spanish need to access the functional projection Mood P and an uninterpretable modal feature on the Force head available to them from their formal English register grammar, and simultaneously must unacquire the structure of English for-to clauses. For negated epistemic predicates, our analysis maintains that they need to revalue the modal feature on the Force head from uninterpretable to interpretable, within the L2 grammar.With others (e.g. Borgonovo & Prévost 2003; Borgonovo, Bruhn de Garavito & Prévost 2005) and in line with Sorace's (2000, 2003, 2005) notion of interface vulnerability, we maintain that the latter case is more difficult for L2 learners, which is borne out in the data we present. However, the data also show that the indicative/subjunctive distinction with negated epistemics can be acquired by advanced stages of acquisition, questioning the notion of obligatory residual optionality for all properties which require the integration of syntactic and discourse information.

Optimal convergence estimates for the trace of the polynomial L2-projection operator on a simplex

In this paper we study convergence of the L2-projection onto the space of polynomials up to degree p on a simplex in Rd, d >= 2. Optimal error estimates are established in the case of Sobolev regularity and illustrated on several numerical examples. The proof is based on the collapsed coordinate transform and the expansion into various polynomial bases involving Jacobi polynomials and their antiderivatives. The results of the present paper generalize corresponding estimates for cubes in Rd from [P. Houston, C. Schwab, E. Süli, Discontinuous hp-finite element methods for advection-diffusion-reaction problems. SIAM J. Numer. Anal. 39 (2002), no. 6, 2133-2163].