HLA-DP2 binding prediction by molecular dynamics simulations

Major histocompatibility complex (MHC) II proteins bind peptide fragments derived from pathogen antigens and present them at the cell surface for recognition by T cells. MHC proteins are divided into Class I and Class II. Human MHC Class II alleles are grouped into three loci: HLA-DP, HLA-DQ, and HLA-DR. They are involved in many autoimmune diseases. In contrast to HLA-DR and HLA-DQ proteins, the X-ray structure of the HLA-DP2 protein has been solved quite recently. In this study, we have used structure-based molecular dynamics simulation to derive a tool for rapid and accurate virtual screening for the prediction of HLA-DP2-peptide binding. A combinatorial library of 247 peptides was built using the "single amino acid substitution" approach and docked into the HLA-DP2 binding site. The complexes were simulated for 1 ns and the short range interaction energies (Lennard-Jones and Coulumb) were used as binding scores after normalization. The normalized values were collected into quantitative matrices (QMs) and their predictive abilities were validated on a large external test set. The validation shows that the best performing QM consisted of Lennard-Jones energies normalized over all positions for anchor residues only plus cross terms between anchor-residues.

Ethnic groups as market segments: implications of the demand structure

Ethnic market potential in Britain has not yet been thoroughly researched. Important recent trends have focused mainly on the affective and emotional aspects of ethnicity, and included deliberations on the emergence of a revitalised neo-ethnic consciousness; its identification; politicisation, and the impact on it; of a rising third-world consciousness. This investigation attempts to take cognizance of the consuner demand of the ethnic Asian and West Indian groups, as specific market segments. It discusses the rationale for ethnic segmentation on the underlying premise, that the starting point for all product marketing is a response to perceived market opportunities. On the basis of this approach, the UK laundry detergent and automobile markets were investigated; as being representative of product categories constitutirg extremes along the purchase-search-time continuun in consuner decision-making. Ethnic groups were further analysed for their retail patronage patterns; media usage, and the differential effectiveness of alternative advertisirg strategies. The basic technique of marketing research namely the sample survey, was used with the aim of applying scientific techniques in obtaining information on ethnic groups. The integrated marketirg framework utilised allowed, moreover, for the collection of market research data on the specific issues of ethnic product penetration dealing with retailing, advertising and product promotion. The evidence highlights the fact that the cultural orientations of ethnic groups are instrunental in providing for differential demand structures. It points to the answer that ethnicity is an anchor not only for a deeper sense of identity; but also serves as a focus for the economic interests of ethnic groups. On this basis it is argued here, that since cultural levelling would eventually produce stagnation; current marketing strategies should utilise ethnic diversity as an econanic artifact; which; per se is necessary for profitability and growth; especially in innovative product design and development.

Tense, aspect and modality in first and second language

Time after time… and aspect and mood. Over the last twenty five years, the study of time, aspect and - to a lesser extent - mood acquisition has enjoyed increasing popularity and a constant widening of its scope. In such a teeming field, what can be the contribution of this book? We believe that it is unique in several respects. First, this volume encompasses studies from different theoretical frameworks: functionalism vs generativism or function-based vs form-based approaches. It also brings together various sub-fields (first and second language acquisition, child and adult acquisition, bilingualism) that tend to evolve in parallel rather than learn from each other. A further originality is that it focuses on a wide range of typologically different languages, and features less studied languages such as Korean and Bulgarian. Finally, the book gathers some well-established scholars, young researchers, and even research students, in a rich inter-generational exchange, that ensures the survival but also the renewal and the refreshment of the discipline. The book at a glance The first part of the volume is devoted to the study of child language acquisition in monolingual, impaired and bilingual acquisition, while the second part focuses on adult learners. In this section, we will provide an overview of each chapter. The first study by Aviya Hacohen explores the acquisition of compositional telicity in Hebrew L1. Her psycholinguistic approach contributes valuable data to refine theoretical accounts. Through an innovating methodology, she gathers information from adults and children on the influence of definiteness, number, and the mass vs countable distinction on the constitution of a telic interpretation of the verb phrase. She notices that the notion of definiteness is mastered by children as young as 10, while the mass/count distinction does not appear before 10;7. However, this does not entail an adult-like use of telicity. She therefore concludes that beyond definiteness and noun type, pragmatics may play an important role in the derivation of Hebrew compositional telicity. For the second chapter we move from a Semitic language to a Slavic one. Milena Kuehnast focuses on the acquisition of negative imperatives in Bulgarian, a form that presents the specificity of being grammatical only with the imperfective form of the verb. The study examines how 40 Bulgarian children distributed in two age-groups (15 between 2;11-3;11, and 25 between 4;00 and 5;00) develop with respect to the acquisition of imperfective viewpoints, and the use of imperfective morphology. It shows an evolution in the recourse to expression of force in the use of negative imperatives, as well as the influence of morphological complexity on the successful production of forms. With Yi-An Lin’s study, we concentrate both on another type of informant and of framework. Indeed, he studies the production of children suffering from Specific Language Impairment (SLI), a developmental language disorder the causes of which exclude cognitive impairment, psycho-emotional disturbance, and motor-articulatory disorders. Using the Leonard corpus in CLAN, Lin aims to test two competing accounts of SLI (the Agreement and Tense Omission Model [ATOM] and his own Phonetic Form Deficit Model [PFDM]) that conflicts on the role attributed to spellout in the impairment. Spellout is the point at which the Computational System for Human Language (CHL) passes over the most recently derived part of the derivation to the interface components, Phonetic Form (PF) and Logical Form (LF). ATOM claims that SLI sufferers have a deficit in their syntactic representation while PFDM suggests that the problem only occurs at the spellout level. After studying the corpus from the point of view of tense / agreement marking, case marking, argument-movement and auxiliary inversion, Lin finds further support for his model. Olga Gupol, Susan Rohstein and Sharon Armon-Lotem’s chapter offers a welcome bridge between child language acquisition and multilingualism. Their study explores the influence of intensive exposure to L2 Hebrew on the development of L1 Russian tense and aspect morphology through an elicited narrative. Their informants are 40 Russian-Hebrew sequential bilingual children distributed in two age groups 4;0 – 4;11 and 7;0 - 8;0. They come to the conclusion that bilingual children anchor their narratives in perfective like monolinguals. However, while aware of grammatical aspect, bilinguals lack the full form-function mapping and tend to overgeneralize the imperfective on the principles of simplicity (as imperfective are the least morphologically marked forms), universality (as it covers more functions) and interference. Rafael Salaberry opens the second section on foreign language learners. In his contribution, he reflects on the difficulty L2 learners of Spanish encounter when it comes to distinguishing between iterativity (conveyed with the use of the preterite) and habituality (expressed through the imperfect). He examines in turn the theoretical views that see, on the one hand, habituality as part of grammatical knowledge and iterativity as pragmatic knowledge, and on the other hand both habituality and iterativity as grammatical knowledge. He comes to the conclusion that the use of preterite as a default past tense marker may explain the impoverished system of aspectual distinctions, not only at beginners but also at advanced levels, which may indicate that the system is differentially represented among L1 and L2 speakers. Acquiring the vast array of functions conveyed by a form is therefore no mean feat, as confirmed by the next study. Based on the prototype theory, Kathleen Bardovi-Harlig’s chapter focuses on the development of the progressive in L2 English. It opens with an overview of the functions of the progressive in English. Then, a review of acquisition research on the progressive in English and other languages is provided. The bulk of the chapter reports on a longitudinal study of 16 learners of L2 English and shows how their use of the progressive expands from the prototypical uses of process and continuousness to the less prototypical uses of repetition and future. The study concludes that the progressive spreads in interlanguage in accordance with prototype accounts. However, it suggests additional stages, not predicted by the Aspect Hypothesis, in the development from activities and accomplishments at least for the meaning of repeatedness. A similar theoretical framework is adopted in the following chapter, but it deals with a lesser studied language. Hyun-Jin Kim revisits the claims of the Aspect Hypothesis in relation to the acquisition of L2 Korean by two L1 English learners. Inspired by studies on L2 Japanese, she focuses on the emergence and spread of the past / perfective marker ¬–ess- and the progressive – ko iss- in the interlanguage of her informants throughout their third and fourth semesters of study. The data collected through six sessions of conversational interviews and picture description tasks seem to support the Aspect Hypothesis. Indeed learners show a strong association between past tense and accomplishments / achievements at the start and a gradual extension to other types; a limited use of past / perfective marker with states and an affinity of progressive with activities / accomplishments and later achievements. In addition, - ko iss– moves from progressive to resultative in the specific category of Korean verbs meaning wear / carry. While the previous contributions focus on function, Evgeniya Sergeeva and Jean-Pierre Chevrot’s is interested in form. The authors explore the acquisition of verbal morphology in L2 French by 30 instructed native speakers of Russian distributed in a low and high levels. They use an elicitation task for verbs with different models of stem alternation and study how token frequency and base forms influence stem selection. The analysis shows that frequency affects correct production, especially among learners with high proficiency. As for substitution errors, it appears that forms with a simple structure are systematically more frequent than the target form they replace. When a complex form serves as a substitute, it is more frequent only when it is replacing another complex form. As regards the use of base forms, the 3rd person singular of the present – and to some extent the infinitive – play this role in the corpus. The authors therefore conclude that the processing of surface forms can be influenced positively or negatively by the frequency of the target forms and of other competing stems, and by the proximity of the target stem to a base form. Finally, Martin Howard’s contribution takes up the challenge of focusing on the poorer relation of the TAM system. On the basis of L2 French data obtained through sociolinguistic interviews, he studies the expression of futurity, conditional and subjunctive in three groups of university learners with classroom teaching only (two or three years of university teaching) or with a mixture of classroom teaching and naturalistic exposure (2 years at University + 1 year abroad). An analysis of relative frequencies leads him to suggest a continuum of use going from futurate present to conditional with past hypothetic conditional clauses in si, which needs to be confirmed by further studies. Acknowledgements The present volume was inspired by the conference Acquisition of Tense – Aspect – Mood in First and Second Language held on 9th and 10th February 2008 at Aston University (Birmingham, UK) where over 40 delegates from four continents and over a dozen countries met for lively and enjoyable discussions. This collection of papers was double peer-reviewed by an international scientific committee made of Kathleen Bardovi-Harlig (Indiana University), Christine Bozier (Lund Universitet), Alex Housen (Vrije Universiteit Brussel), Martin Howard (University College Cork), Florence Myles (Newcastle University), Urszula Paprocka (Catholic University of Lublin), †Clive Perdue (Université Paris 8), Michel Pierrard (Vrije Universiteit Brussel), Rafael Salaberry (University of Texas at Austin), Suzanne Schlyter (Lund Universitet), Richard Towell (Salford University), and Daniel Véronique (Université d’Aix-en-Provence). We are very much indebted to that scientific committee for their insightful input at each step of the project. We are also thankful for the financial support of the Association for French Language Studies through its workshop grant, and to the Aston Modern Languages Research Foundation for funding the proofreading of the manuscript.

Effects of lithium and valproic acid on gene expression and phenotypic markers in an NT2 neurosphere model of neural development

Mood stabilising drugs such as lithium (LiCl) and valproic acid (VPA) are the first line agents for treating conditions such as Bipolar disorder and Epilepsy. However, these drugs have potential developmental effects that are not fully understood. This study explores the use of a simple human neurosphere-based in vitro model to characterise the pharmacological and toxicological effects of LiCl and VPA using gene expression changes linked to phenotypic alterations in cells. Treatment with VPA and LiCl resulted in the differential expression of 331 and 164 genes respectively. In the subset of VPA targeted genes, 114 were downregulated whilst 217 genes were upregulated. In the subset of LiCl targeted genes, 73 were downregulated and 91 were upregulated. Gene ontology (GO) term enrichment analysis was used to highlight the most relevant GO terms associated with a given gene list following toxin exposure. In addition, in order to phenotypically anchor the gene expression data, changes in the heterogeneity of cell subtype populations and cell cycle phase were monitored using flow cytometry. Whilst LiCl exposure did not significantly alter the proportion of cells expressing markers for stem cells/undifferentiated cells (Oct4, SSEA4), neurons (Neurofilament M), astrocytes (GFAP) or cell cycle phase, the drug caused a 1.4-fold increase in total cell number. In contrast, exposure to VPA resulted in significant upregulation of Oct4, SSEA, Neurofilament M and GFAP with significant decreases in both G2/M phase cells and cell number. This neurosphere model might provide the basis of a human-based cellular approach for the regulatory exploration of developmental impact of potential toxic chemicals.

A hierarchical localization scheme for large scale underwater wireless sensor networks

In this paper, we study the localization problem in large-scale Underwater Wireless Sensor Networks (UWSNs). Unlike in the terrestrial positioning, the global positioning system (GPS) can not work efficiently underwater. The limited bandwidth, the severely impaired channel and the cost of underwater equipment all makes the localization problem very challenging. Most current localization schemes are not well suitable for deep underwater environment. We propose a hierarchical localization scheme to address the challenging problems. The new scheme mainly consists of four types of nodes, which are surface buoys, Detachable Elevator Transceivers (DETs), anchor nodes and ordinary nodes. Surface buoy is assumed to be equipped with GPS on the water surface. A DET is attached to a surface buoy and can rise and down to broadcast its position. The anchor nodes can compute their positions based on the position information from the DETs and the measurements of distance to the DETs. The hierarchical localization scheme is scalable, and can be used to make balances on the cost and localization accuracy. Initial simulation results show the advantages of our proposed scheme. © 2009 IEEE.

Molecular identification of 26 syntaxin genes and their assignment to the different trafficking pathways in Paramecium

SNARE proteins have been classified as vesicular (v)- and target (t)-SNAREs and play a central role in the various membrane interactions in eukaryotic cells. Based on the Paramecium genome project, we have identified a multigene family of at least 26 members encoding the t-SNARE syntaxin (PtSyx) that can be grouped into 15 subfamilies. Paramecium syntaxins match the classical build-up of syntaxins, being 'tail-anchored' membrane proteins with an N-terminal cytoplasmic domain and a membrane-bound single C-terminal hydrophobic domain. The membrane anchor is preceded by a conserved SNARE domain of approximately 60 amino acids that is supposed to participate in SNARE complex assembly. In a phylogenetic analysis, most of the Paramecium syntaxin genes were found to cluster in groups together with those from other organisms in a pathway-specific manner, allowing an assignment to different compartments in a homology-dependent way. However, some of them seem to have no counterparts in metazoans. In another approach, we fused one representative member of each of the syntaxin isoforms to green fluorescent protein and assessed the in vivo localization, which was further supported by immunolocalization of some syntaxins. This allowed us to assign syntaxins to all important trafficking pathways in Paramecium.

Statistical deconvolution of enthalpic energetic contributions to MHC-peptide binding affinity

Background - MHC Class I molecules present antigenic peptides to cytotoxic T cells, which forms an integral part of the adaptive immune response. Peptides are bound within a groove formed by the MHC heavy chain. Previous approaches to MHC Class I-peptide binding prediction have largely concentrated on the peptide anchor residues located at the P2 and C-terminus positions. Results - A large dataset comprising MHC-peptide structural complexes was created by re-modelling pre-determined x-ray crystallographic structures. Static energetic analysis, following energy minimisation, was performed on the dataset in order to characterise interactions between bound peptides and the MHC Class I molecule, partitioning the interactions within the groove into van der Waals, electrostatic and total non-bonded energy contributions. Conclusion - The QSAR techniques of Genetic Function Approximation (GFA) and Genetic Partial Least Squares (G/PLS) algorithms were used to identify key interactions between the two molecules by comparing the calculated energy values with experimentally-determined BL50 data. Although the peptide termini binding interactions help ensure the stability of the MHC Class I-peptide complex, the central region of the peptide is also important in defining the specificity of the interaction. As thermodynamic studies indicate that peptide association and dissociation may be driven entropically, it may be necessary to incorporate entropic contributions into future calculations.

Coupling in silico and in vitro analysis of peptide-MHC binding:a bioinformatic approach enabling prediction of superbinding peptides and anchorless epitopes

The ability to define and manipulate the interaction of peptides with MHC molecules has immense immunological utility, with applications in epitope identification, vaccine design, and immunomodulation. However, the methods currently available for prediction of peptide-MHC binding are far from ideal. We recently described the application of a bioinformatic prediction method based on quantitative structure-affinity relationship methods to peptide-MHC binding. In this study we demonstrate the predictivity and utility of this approach. We determined the binding affinities of a set of 90 nonamer peptides for the MHC class I allele HLA-A*0201 using an in-house, FACS-based, MHC stabilization assay, and from these data we derived an additive quantitative structure-affinity relationship model for peptide interaction with the HLA-A*0201 molecule. Using this model we then designed a series of high affinity HLA-A2-binding peptides. Experimental analysis revealed that all these peptides showed high binding affinities to the HLA-A*0201 molecule, significantly higher than the highest previously recorded. In addition, by the use of systematic substitution at principal anchor positions 2 and 9, we showed that high binding peptides are tolerant to a wide range of nonpreferred amino acids. Our results support a model in which the affinity of peptide binding to MHC is determined by the interactions of amino acids at multiple positions with the MHC molecule and may be enhanced by enthalpic cooperativity between these component interactions.

Maritime expressions:a corpus based exploration of maritime metaphors

This study uses a purpose-built corpus to explore the linguistic legacy of Britain’s maritime history found in the form of hundreds of specialised ‘Maritime Expressions’ (MEs), such as TAKEN ABACK, ANCHOR and ALOOF, that permeate modern English. Selecting just those expressions commencing with ’A’, it analyses 61 MEs in detail and describes the processes by which these technical expressions, from a highly specialised occupational discourse community, have made their way into modern English. The Maritime Text Corpus (MTC) comprises 8.8 million words, encompassing a range of text types and registers, selected to provide a cross-section of ‘maritime’ writing. It is analysed using WordSmith analytical software (Scott, 2010), with the 100 million-word British National Corpus (BNC) as a reference corpus. Using the MTC, a list of keywords of specific salience within the maritime discourse has been compiled and, using frequency data, concordances and collocations, these MEs are described in detail and their use and form in the MTC and the BNC is compared. The study examines the transformation from ME to figurative use in the general discourse, in terms of form and metaphoricity. MEs are classified according to their metaphorical strength and their transference from maritime usage into new registers and domains such as those of business, politics, sports and reportage etc. A revised model of metaphoricity is developed and a new category of figurative expression, the ‘resonator’, is proposed. Additionally, developing the work of Lakov and Johnson, Kovesces and others on Conceptual Metaphor Theory (CMT), a number of Maritime Conceptual Metaphors are identified and their cultural significance is discussed.

The HLA-A2-supermotif:a QSAR definition

Identification of epitopes capable of binding multiple HLA types will significantly rationalise the development of epitope-based vaccines. A quantitative method assessing the contribution of each amino acid at each position was applied to over 500 nonamer peptides binding to 5 MHC alleles — A*0201, A*0202, A*0203, A*0206 and A*6802 — which together define the HLA-A2-like supertype. FXIGXI (L)IFV was identified as a supermotif for the A2-supertype based on the contributions of the common preferred amino acids at each of the nine positions. The results indicate that HLA-A*6802 is an intermediate allele standing between A2 and A3 supertypes: at anchor position 2 it is closer to A3 and at anchor position 9 it is nearer to A2. Models are available free on-line at http://www.jenner.ac.uk/MHCPred and can be used for binding affinity prediction.

Cross-national differences in e-WOM influence

Purpose: This paper aims to present a cross-national study that investigates changes in purchase intentions of UK versus Chinese consumers following exposure to successive e-WOM comments in the form of positive and negative user reviews for experience versus search products. Design/methodology/approach: A 2(e-WOM valence and order: negative versus positive most recent)×2(product type: experience versus search)×3(purchase intentions at t 1, t 2, t 3) repeated-measures factorial design is used to test a set of hypotheses developed from the literature. Findings: Chinese consumers are susceptible to recent e-WOM comments regardless of their valence, while UK consumers anchor on negative information regardless of the order in which it is acquired. This holds particularly for experience products. Originality/value: This cross-national study contributes to the scarce literature on the impact of e-WOM on consumer purchase decisions by comparing UK and Chinese consumers. The authors suggest that culture moderates the development of product evaluations following exposure to e-WOM. © Emerald Group Publishing Limited.

Cramer-Rao bound analysis of location estimation in multi-hop wireless sensor networks

Location estimation is important for wireless sensor network (WSN) applications. In this paper we propose a Cramer-Rao Bound (CRB) based analytical approach for two centralized multi-hop localization algorithms to get insights into the error performance and its sensitivity to the distance measurement error, anchor node density and placement. The location estimation performance is compared with four distributed multi-hop localization algorithms by simulation to evaluate the efficiency of the proposed analytical approach. The numerical results demonstrate the complex tradeoff between the centralized and distributed localization algorithms on accuracy, complexity and communication overhead. Based on this analysis, an efficient and scalable performance evaluation tool can be designed for localization algorithms in large scale WSNs, where simulation-based evaluation approaches are impractical. © 2013 IEEE.

Orthodox Christianity and Nationalism:an introduction

On the morning of January 5, 1859, at the end of the liturgy in the Orthodox cathedral in Iaşi, the capital of the principality of Moldavia, Father Neofit Scriban addressed the congregation. He had given many sermons in the cathedral; however, on this par tic u lar date Father Neofit faced an unusual audience. Among the faithful who regularly worshipped at the relics of Saint Parascheva, the protector of Moldavia, were the members of the assembly who would decide the future of the principality. They had a specific mission: to elect a new prince, a key figure in their plan to unite Moldavia with the neighboring principality of Wallachia. Father Neofit, a supporter of the unionist cause and fully aware of the significance of the moment, stated: Brethren, Jesus Christ has said that "For where two or three have gathered together in My name, I am there in their midst." You, Brethren, are not two, or three, but a real gathering in the name of God. God is in your midst. You are here in the name of the Romanian nation [and] the Romanian nation is in your midst. On the flag under which you have assembled, the flag of the Romanian nation, great events, the Romanian faith, unity, are written in large letters. The church, which is founded on faith, blesses the flag of this faith⋯. You, Brethren, through the faith of the Romanian nation, by remaining faithful to this flag, will find the same strength as the church [finds] in its own saints. The faith of the Romanian nation was not, is not, and will not be anything else, but the unity of all Romanians in a single state, the only anchor of salvation, the only port in which the national boat could be saved from surrounding waves. You, Brethren, have gathered here in the church of Stephen the Great; looking at the altar that he raised to the God of your parents, I think that, through this [altar], you will be able to enter into the wishes of this hero of our nation. You, [remember that] by leaving this place, you are leaving [in order to fulfill] a great gesture that for many centuries has been lost for us; you are about to elect a successor to this great hero; therefore, as his true sons, you could not be anything other than the true expression of his wishes. Myself, [as] last year, from this altar, I said and I will continue to say that this great hero has told us that "the God of our parents will send us a Redeemer who will heal our wounds and accomplish our wishes." May your chosen leader today be the redeemer expected by the Romanian nation. May he heal its wounds and achieve its wishes. Therefore, Brethren, may your election today be that of a real Messiah of Romania. God and the world are looking at you, the church is blessing you and the whole Romanian nation is waiting for you!1 A few hours after Father Neofit's sermon, the assembly elected Alexandru Ioan Cuza to be the prince of the principality of Moldavia; a few days later, on January 24, 1859, the assembly of the neighboring principality of Wallachia decided that Cuza should also be their prince, thus confirming the unification of the two states. A new country was inscribed on the map of Southeastern Europe, titled "The United Principalities of Wallachia and Moldavia," also known as "The United Romanian Principalities".

MHC class II binding prediction by molecular docking

Proteins of the Major Histocompatibility Complex (MHC) bind self and nonself peptide antigens or epitopes within the cell and present them at the cell surface for recognition by T cells. All T-cell epitopes are MHC binders but not all MCH binders are T-cell epitopes. The MHC class II proteins are extremely polymorphic. Polymorphic residues cluster in the peptide-binding region and largely determine the MHC's peptide selectivity. The peptide binding site on MHC class II proteins consist of five binding pockets. Using molecular docking, we have modelled the interactions between peptide and MHC class II proteins from locus DRB1. A combinatorial peptide library was generated by mutation of residues at peptide positions which correspond to binding pockets (so called anchor positions). The binding affinities were assessed using different scoring functions. The normalized scoring functions for each amino acid at each anchor position were used to construct quantitative matrices (QM) for MHC class II binding prediction. Models were validated by external test sets comprising 4540 known binders. Eighty percent of the known binders are identified in the best predicted 15% of all overlapping peptides, originating from one protein. © 2011 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.