A scheme for multiple sequences alignment optimization-an improvement based on family representative mechanics features

As a basic tool of modern biology, sequence alignment can provide us useful information in fold, function, and active site of protein. For many cases, the increased quality of sequence alignment means a better performance. The motivation of present work is to increase ability of the existing scoring scheme/algorithm by considering residue–residue correlations better. Based on a coarse-grained approach, the hydrophobic force between each pair of residues is written out from protein sequence. It results in the construction of an intramolecular hydrophobic force network that describes the whole residue–residue interactions of each protein molecule, and characterizes protein's biological properties in the hydrophobic aspect. A former work has suggested that such network can characterize the top weighted feature regarding hydrophobicity. Moreover, for each homologous protein of a family, the corresponding network shares some common and representative family characters that eventually govern the conservation of biological properties during protein evolution. In present work, we score such family representative characters of a protein by the deviation of its intramolecular hydrophobic force network from that of background. Such score can assist the existing scoring schemes/algorithms, and boost up the ability of multiple sequences alignment, e.g. achieving a prominent increase (50%) in searching the structurally alike residue segments at a low identity level. As the theoretical basis is different, the present scheme can assist most existing algorithms, and improve their efficiency remarkably.

An in vivo approach to tRNA identity

A leucine-inserting tRNA has been transformed into a serine-inserting tRNA by changing 12 nucleotides. Only 8 of the 12 changes are required to effect the conversion of the leucine tRNA to serine tRNA identity. The 8 essential changes reside in basepair 11-24 in the D stem, basepairs 3-70, 2-71 and nucleotides 72 and 73, all of the acceptor stem.

Functional amber suppressor tRNA genes were generated for 14 species of tRNA in E. coli, and their amino acid specificities determined. The suppressors can be classified into three groups, based upon their specificities. Class I suppressors, tRNA^(Ala2)_(CUA), tRNA^(GlyU)_(CUA), tRNA^(HisA)_(CUA), tRNA^(Lys)_(CUA), and tRNA^(ProH)_(CUA), inserted the predicted amino acid. The Class II suppressors, tRNA^(GluA)_(CUA) , tRNA^(GlyT)_(CUA), and tRNA^(Ile1)_(CUA) were either partially or predominantly mischarged by the glutamine aminoacyl tRNA synthetase (AAS). The Class III suppressors, tRNA^(Arg)_(CUA), tRNA^(AspM)_(CUA), tRNA^(Ile2)_(CUA), tRNA^(Thr2)_(CUA), tRNA^(Met(m))_(CUA) and tRNA^(Val)_(CUA) inserted predominantly lysine.

BRST quantization and canonical Ward identity of the supersymmetric electromagnetic interaction system

According to the method of path integral quantization for the canonical constrained system in Becchi-Rouet-Stora-Tyutin scheme, the supersymmetric electromagnetic interaction system was quantized. Both the Hamiltonian of the supersymmetric electromagnetic interaction system in phase space and the quantization procedure were simplified. The BRST generator was constructed, and the BRST transformations of supersymmetric fields were gotten; the effective action was calculated, and the generating functional for the Green function was achieved; also, the gauge generator was constructed, and the gauge transformation of the system was obtained. Finally, the Ward-Takahashi identities based on the canonical Noether theorem were calculated, and two relations between proper vertices and propagators were obtained.

Detecting False Identity through Behavioural Patterns

T. Boongoen and Q. Shen. 'Detecting False Identity through Behavioural Patterns', In Proceedings of International Crime Science Conference, British Library, London UK, 2008. Publisher's online version forthcoming.;The full text is currently unavailable in CADAIR pending approval by the publisher. Sponsorship: UK EPSRC grant EP/D057086

Irish neo-paganism: worldview, ritual and identity

Neo-paganism is a vibrant, dynamic global movement, which has had a significant cultural impact. Neo-paganism is an umbrella term for a wide range of spiritual practices, often described as nature- or earth-based spirituality. There are different “paths” or spiritual traditions within this movement, of which Druidry, Wicca and other forms of Pagan Witchcraft are included in this research. The present work is an ethnographic study of the worldview and ritual practices of the Irish neo-pagan community. It is an enquiry into (a) what characterises the neo-pagan worldview and (b) how this worldview is expressed through ritual behaviour. In order to collect data, the methodology of participant observation and ethnographic interviewing was employed. The thesis comprises a collection of “insider” accounts of what it is like to be a neo-pagan in Ireland and analysis of these narratives, which gives insight into different aspects of neopagan culture. In the discussion, the use of mythology is examined in regard to how mythic narrative is connected to identity formation. Irish cultural symbols are observed as resources utilised in the construction of the movement’s overall character. The interconnectedness of the natural landscape, the numinous and mythology gives rise to creative expression through various forms of neo-pagan artworks, which are discussed herein. The identifying features and key issues of Irish neo-pagan culture are addressed. These key issues are expressed as prominent themes and symbols of their discourse. Neo-pagan dialogue often features discussion of the relationship that this cultural group has with the Irish landscape, history, and indigenous and popular Irish religion. Some of the specific aspects of neo-pagan culture examined are magical worldview, the notion of holism, different types of ritual practices (festivals, life cycle rituals, healing), and material culture. The thesis presents an in-depth analysis of neopagan cultural expressions and their significance as cultural processes

The double bind for non-traditional families in post-primary settings; to tell or not to tell their family identity

This thesis involved researching normative family discourses which are mediated through educational settings. The traditional family, consisting of father, mother and children all living together in one house is no longer reflective of the home situation of many Irish students (Lunn and Fahey, 2011). My study problematizes the dominant discourses which reflect how family differences are managed and recognised in schools. A framework using Foucauldian post structural critical analysis traces family stratification through the organisation of institutional and interpersonal relations at micro level in four post-primary schools. Standardising procedures such as the suppression of intimate relations between and among teacher and student, as well as the linear ordering of intergenerational relations, such as teacher/student and adult/child are critiqued. Normalising discourses operate in practices such as notes home which presume two parents together. Teacher assumptions about heterosexual two-parent families make it difficult for students to be open about a family setup that is constructed as different to the rest of the schools'. The management of family difference and deficit through pastoral care structures suggests a school-based politics of family adjustment. These practices beg the question whether families are better off not telling the school about their family identity. My thesis will be of interest to educational research and educational policy because it highlights how changing demographics such as family compositions are mis-conceptualised in schools, as well as revealing the changing forms of family governance through regimes such as pastoral care. This analysis allows for the existence of, and a valuing for, alternative modes of family existence, so that future curricular and legal discourses can be challenged in the interest of equity and social justice.

Beginning primary teachers’ perspectives on becoming a teacher in the workplace: Contextual, emotional, and temporo-spatial dimensions of identity shaping

The issue, with international and national overtones, of direct relevance to the present study, relates to the shaping of beginning teachers’ identities in the workplace. As the shift from an initial teacher education programme into initial practice in schools is a period of identity change worthy of investigation, this study focuses on the transformative search by nine beginning primary teachers for their teaching identities, throughout the course of their initial year of occupational experience, post-graduation. The nine beginning teacher participants work in a variety of primary school settings, thus strengthening the representativeness of the research cohort. Privileging ‘insider’ perspectives, the research goal is to understand the complexities of lived experience from the viewpoints of the participating informants. The shaping of identity is conceived of in dimensional terms. Accordingly, a framework composed of three dimensions of beginning teacher experience is devised, namely: contextual; emotional; temporo-spatial. Data collection and analysis is informed by principles derived from sociocultural theories; activity theory; figured worlds theory; and, dialogical self theory. Individual, face-to-face semi-structured interviews, and the maintenance of solicited digital diaries, are the principal methods of data collection employed. The use of a dimensional model fragments the integrated learning experiences of beginning teachers into constituent parts for the purpose of analysis. While acknowledging that the actual journey articulated by each participant is a more complex whole than the sum of its parts, key empirically-based claims are presented as per the dimensional framework employed: contextuality; emotionality; temporo-spatiality. As a result of applying the foci of an international literature to an under-researched aspect of Irish education, this study is offered as a context-specific contribution to the knowledge base on beginning teaching. As the developmental needs of beginning teachers constitute an emerging area of intense policy focus in Ireland, this research undertaking is both relevant and timely.

ARAB MUSICIANS IN WASHINGTON, D.C. AREA: ETHNICITY AND IDENTITY

Musicians living in the Arab Diaspora around the Washington, D.C. metro area are a small group of multi-faceted individuals with significant contributions and intentions to propagate and disseminate their music. Various levels of identity are discussed and analyzed, including self-identity, group/ collective identity, and Arab ethnic identity. The performance and negotiation of Arab ethnic identity is apparent in selected repertoire, instrumentation, musical style, technique and expression, shared conversations about music, worldview on Arabic music and its future. For some musicians, further evidence of self-construction of one's ethnic identity entails choice of name, costume, and venue. Research completed is based on fieldwork, observations, participant-observations, interviews, and communications by phone and email. This thesis introduces concepts of Arabic music, discusses recent literature, reveals findings from case studies on individual Arab musicians and venues, and analyzes Arab identity and ethnicity in relation to particular definitions of identity found in anthropological and ethnomusicological writings. Musical lyrics, translations, transcriptions, quotes, discussions, analyses, as well as charts and diagrams of self-identity analyses are provided as evidence of the performance and negotiation of Arab identity.

Accurate localized resolution of identity approach for linear-scaling hybrid density functionals and for many-body perturbation theory

© 2015 IOP Publishing Ltd and Deutsche Physikalische Gesellschaft.A key component in calculations of exchange and correlation energies is the Coulomb operator, which requires the evaluation of two-electron integrals. For localized basis sets, these four-center integrals are most efficiently evaluated with the resolution of identity (RI) technique, which expands basis-function products in an auxiliary basis. In this work we show the practical applicability of a localized RI-variant ('RI-LVL'), which expands products of basis functions only in the subset of those auxiliary basis functions which are located at the same atoms as the basis functions. We demonstrate the accuracy of RI-LVL for Hartree-Fock calculations, for the PBE0 hybrid density functional, as well as for RPA and MP2 perturbation theory. Molecular test sets used include the S22 set of weakly interacting molecules, the G3 test set, as well as the G2-1 and BH76 test sets, and heavy elements including titanium dioxide, copper and gold clusters. Our RI-LVL implementation paves the way for linear-scaling RI-based hybrid functional calculations for large systems and for all-electron many-body perturbation theory with significantly reduced computational and memory cost.

Biodiversity loss and ecosystem functioning: Distinguishing between number and identity of species

Given currently high rates of extinction, it is critical to be able to predict how ecosystems will respond to loss of species and consequent changes in community structure. Much previous research in this area has been based on terrestrial systems, using synthetically assembled communities. There has beer! much less research on inter-trophic effects in different systems, using in situ removal experiments. Problems with the design of early experiments have made it difficult to determine whether reductions in ecosystem functioning in low diversity treatments were due to the number of species present or merely to the reduced likelihood of including particular (

Simulated predator extinctions: Predator identity affects survival and recruitment of oysters

The rate of species loss is increasing at a global scale, and human-induced extinctions are biased toward predator species. We examined the effects of predator extinctions on a foundation species, the eastern oyster (Crassostrea virginica). We performed a factorial experiment manipulating the presence and abundance of three of the most common predatory crabs, the blue crab (Callinectes sapidus), stone crab (Menippe mercenaria), and mud crab (Panopeus herbstii) in estuaries in the eastern United States. We tested the effects of species richness and identity of predators on juvenile oyster survival, oyster recruitment, and organic matter content of sediment. We also manipulated the density of each of the predators and controlled for the loss of biomass of species by maintaining a constant mass of predators in one set of treatments and simultaneously using an additive design. This design allowed us to test the density dependence of our results and test for functional compensation by other species. The identity of predator species, but not richness, affected oyster populations. The loss of blue crabs, alone or in combination with either of the other species, affected the survival rate of juvenile oysters. Blue crabs and stone crabs both affected oyster recruitment and sediment organic matter negatively. Mud crabs at higher than ambient densities, however, could fulfill some of the functions of blue and stone crabs, suggesting a level of ecological redundancy. Importantly, the strong effects of blue crabs in all processes measured no longer occurred when individuals were present at higher-than-ambient densities. Their role as dominant predator is, therefore, dependent on their density within the system and the density of other species within their guild (e.g., mud crabs). Our findings support the hypothesis that the effects of species loss at higher trophic levels are determined by predator identity and are subject to complex intraguild interactions that are largely density dependent. Understanding the role of biodiversity in ecosystem functioning or addressing practical concerns, such as loss of predators owing to overharvesting, remains complicated because accurate predictions require detailed knowledge of the system and should be drawn from sound experimental evidence, not based on observations or generalized models.

Who We Are and Who Can Join Us: National Identity Content and Entry Criteria for New Immigrants

We argue that attitudes about immigration can be better understood by paying closer attention to the various ways in which national group boundaries are demarcated. We describe two related lines of work that address this. The first deals with national group definitions and, based on evidence from studies carried out in England and analyses of international survey data, argues that the relationship between national identification and prejudice toward immigrants is contingent on the extent to which ethnic or civic definitions of nationality are endorsed. The second, which uses European survey data, examines support for ascribed and acquired criteria that can be applied when determining who is permitted to migrate to one's country, and the various forms of national and individual threat that affect support for these criteria. We explain how the research benefits from a multilevel approach and also suggest how these findings relate to some current policy debates.

The Evolution of European Identity: Using biographical methods to study the development of European identity

Based upon the original application to the European Commission, this article gives insights into the thinking of the Euroidentities team at the point that the project began. The question: “Is the European ‘identity project’ failing?” is posed in the sense that the political and economic attainments of the European Union have not been translated into a sense of identity with or commitment to Europe from the populaces that have benefited from them. The urgency of European ‘identity work’ is asserted with a number of levels for the construction of European identity being hypothesized. Euroidentities is intended to break conceptual ground by bringing together on an equal footing two apparently antagonistic views of identity -- the collective and institutional and the individual and biographical – to give a more anchored and nuanced view of identity formation and transformation than either can provide on its own. Rather than following the dominant approaches to research on European identity that have been macro-theoretical and ‘top-down’, retrospective in-depth qualitative biographical interviews are planned since they provide the ideal means of gaining insight into the formation of a European identity or multiple identities from the ‘bottom up’ perspective of non-elite groups. The reliability of analysis will be buttressed by the use of contrastive comparison between cases, culminating in contrastive comparison across the national project teams between cases drawn from different ‘sensitized groups’ that provide the fieldwork structure of the project. The paper concludes with a summary of some of the more significant findings.

Indigenous rights in Chile: National identity and majority group support for multicultural policies

We examine support for policies affecting indigenous ethnic minorities in Chile. Specifically, we examine the role of national group definitions that include the largest indigenous group—the Mapuche—in different ways. Based on questionnaire data from nonindigenous Chilean students (N = 338), we empirically distinguish iconic inclusion, whereby the Mapuche are seen as an important part of Chile's history and identity on the one hand, from egalitarian inclusion, which represents the Mapuche as citizens of equal importance to the nonindigenous majority on the other. Both forms of inclusion positively predict support for indigenous rights, independent of participants' political affiliation, strength of national identification, and social distance. A second study (N = 277) replicates this finding whilst controlling for right-wing authoritarianism, social dominance orientation, blind patriotism, and constructive patriotism. It also finds iconic inclusion to be predictive of a pro-Mapuche position regarding the unrest over the issue of ancestral land in 2009. We conclude that understanding how national identity affects attitudes about minority rights necessitates appreciating the importance of particular meanings of nationality, and not only the strength of identification.

Defending Identity and Ethos: an analysis of teacher perceptions of school collaboration in Northern Ireland

The purpose of this article is to examine the process of collaborative working between teachers located in separate faith-based schools in Northern Ireland. Drawing on theories of intergroup relations, and with reference to in-depth interviews with teachers in post-primary schools, the article shows that despite earlier research which identified a reluctance amongst teachers in the different sectors to work together, most Catholic and Protestant teachers are motivated to collaborate to develop a more broadly based curriculum for pupils. However, it has also been shown that teachers tend to studiously avoid discussing their differences in mixed-faith contexts, and it is argued that this may have the potential to constrain collaborative relations. It is concluded that without strategic direction from policy makers to assist teachers in negotiating and exploring their differences it will be difficult to build the trust which is likely to sustain collaborative relations.