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.

Space division multiple access for wireless sensor networks

This dissertation proposed a self-organizing medium access control protocol (MAC) for wireless sensor networks (WSNs). The proposed MAC protocol, space division multiple access (SDMA), relies on sensor node position information and provides sensor nodes access to the wireless channel based on their spatial locations. SDMA divides a geographical area into space divisions, where there is one-to-one map between the space divisions and the time slots. Therefore, the MAC protocol requirement is the sensor node information of its position and a prior knowledge of the one-to-one mapping function. The scheme is scalable, self-maintaining, and self-starting. It provides collision-free access to the wireless channel for the sensor nodes thereby, guarantees delay-bounded communication in real time for delay sensitive applications. This work was divided into two parts: the first part involved the design of the mapping function to map the space divisions to the time slots. The mapping function is based on a uniform Latin square. A Uniform Latin square of order k = m 2 is an k x k square matrix that consists of k symbols from 0 to k-1 such that no symbol appears more than once in any row, in any column, or in any m x in area of main subsquares. The uniqueness of each symbol in the main subsquares presents very attractive characteristic in applying a uniform Latin square to time slot allocation problem in WSNs. The second part of this research involved designing a GPS free positioning system for position information. The system is called time and power based localization scheme (TPLS). TPLS is based on time difference of arrival (TDoA) and received signal strength (RSS) using radio frequency and ultrasonic signals to measure and detect the range differences from a sensor node to three anchor nodes. TPLS requires low computation overhead and no time synchronization, as the location estimation algorithm involved only a simple algebraic operation.

A fresh look at decision making in international investment choices: Firm international coherence and home-host country relatedness

Understanding how decisions for international investments are made and how this affects the overall pattern of investments and firm’s performance is of particular importance both in strategy and international business research. This dissertation introduced first home-host country relatedness (HHCR) as the degree to which countries are efficiently combined within the investment portfolios of firms. It theorized and demonstrated that HHCR will vary with the motivation for investments along at least two key dimensions: the nature of foreign investments and the connectedness of potential host countries to the rest of the world. Drawing on cognitive psychology and decision-making research, it developed a theory of strategic decision making proposing that strategic solutions are chosen close to a convenient anchor. Building on research on memory imprinting, it also proposed that managers tend to rely on older knowledge representation. In the context of international investment decisions, managers use their home countries as an anchor and are more likely to choose as a site for foreign investments host countries that are ‘close’ to the home country. These decisions are also likely to rely more strongly on closeness to time invariant country factors of historic and geographic nature rather than time-variant institutions. Empirical tests using comprehensive investments data by all public multinational companies (MNC) worldwide, or over 15,000 MNCs with over half a million subsidiaries, support the claims. Finally, the dissertation introduced the concept of International Coherence (IC) defined as the degree to which an MNE’s network comprises countries that are related. It was hypothesized that maintaining a high level of coherence is important for firm performance and will enhance it. Also, the presence of international coherence mitigates some of the negative effects of unrelated product diversification. Empirical tests using data on foreign investments of over 20,000 public firms, while also developing a home-host country relatedness index for up to 24,300 home-host pairs, provided support for the theory advanced.

Modelagem numérica de uma estrutura de contenção de estacas espaçadas atirantadas em areia

Retaining walls design involves factors such as plastification, loading and unloading, pre-stressing, excessive displacements and earth and water thrust. Furthermore, the interaction between the retained soil and the structure is rather complex and hard to predict. Despite the advances in numerical simulation techniques and monitoring of forces and displacements with field instrumentation, design projects are still based on classical methods, whose simplifying assumptions may overestimate structural elements of the retaining wall. This dissertation involves a three-dimensional numerical study on the behavior of a retaining wall using the finite element method (FEM). The retaining wall structure is a contiguous bored pile wall with tie-back anchors. The numerical results were compared to data obtained from field instrumentation. The influence of the position of one or two layers of anchors and the effects of the construction of a slab bounded at the top of the retaining wall was evaluated. Furthermore, this study aimed at investigating the phenomenon of arching in the soil behind the wall. Arching was evaluated by analyzing the effects of pile spacing on horizontal stresses and displacements. Parametric analysis with one layers of anchors showed that the smallest horizontal displacements of the structure were achieved for between 0.3 and 0.5 times the excavation depth. Parametric analyses with two anchor layers showed that the smallest horizontal displacements were achieve for anchors positioned in depths of 0.4H and 0.7H. The construction of a slab at the top of the retaining wall decreased the horizontal displacements by 0.14% times the excavation depth as compared to analyses without the slab. With regard to the arching , analyzes showed an optimal range of spacing between the faces of the piles between 0.4 and 0.6 times the diameter of the pile

Querido diário: a construção identitária de alunos da EJA em diários pessoais

This study aims to present analyses of our research, documentary type, which investigates the construction of cultural identities of the Youth and Adults Education (Educação de Jovens e Adultos – EJA), level III, in a public school in the city of Natal/RN, through personal diaries produced in the school environment. In a qualitative-interpretive approach, we anchor our identity studies (BAUMAN, 2001, 2005, 2006; HALL, 1987, 1997, 2011, 2012) that bring us the idea that identities are built and rebuilt by social relations that we do. To this end, we start from a conception of language that does not require pre-conceptions because they are based on the utterance itself. Therefore, we have analyzed the utterances produced by these students from the perspective of Bakhtin Circle (BAKHTIN, 1988, 1993, 1998, 2002, 2010, 2012), which deals with the discursive construction emerging from intersubjective processes of verbal interaction, in a dialogical relationship of the self to the other, by the otherness and the heteroglossia. Moreover, our study is also guided by the guidance on speech genres (BAKHTIN, 2010) and personal journal (LEJEUNE, 2008; MACHADO, 1998, 2009). We join to Applied Linguistics (MOITA LOPES, 2006, 2009) because we believe that this research focuses on a social practice in which language plays a central role and seeks to demonstrate how the speeches of the subject students of EJA, in personal journals, are building tools not only of their identities, but also knowledge and social life of the position that this subject student takes. We conclude this work in a perception of cultural identities that are built by the subject students of EJA, because the results suggest that the identities of these students are fluidly constructed by the representation that the student makes of his or her school, of being student of EJA and how he or she is a student of this educational modality. Thus, through our work, we plan to present another look about the identity or identities of a student of EJA, pointing an insight of this subject.

Characterisation of the oxysterol metabolising enzyme pathway in mismatch repair proficient and deficient colorectal cancer

ACKNOWLEDGMENTS The immunohistochemistry was performed with the support of the Grampian Biorepository. GRANT SUPPORT Rebecca Swan was supported by the Jean Shanks Foundation. This study was supported by funding from Friends of Anchor and the Encompass kick start and SMART:Scotland award schemes of Scottish Enterprise.

A Sting in the Tail : The N-Terminal Domain of the Androgen Receptor as a Drug Target

AEM was supported by a BBSRC-CASE studentship award. Research in the IJM laboratory is currently supported by the Chief Scientist's Office of the Scottish Government and the charity Friends of Anchor.

The expression and prognostic significance of bcl-2-associated transcription factor 1 in rectal cancer following neoadjuvant therapy

Date of Acceptance: 12/07/2015 © 2015 John Wiley & Sons Ltd. Acknowledgements This study was supported by funding from the Encompass kick start and SMART:Scotland award schemes of Scottish Enterprise and Friends of Anchor. The Grampian Biorepository assisted with the immunohistochemical investigations.