bluuebunny/crossref_metadata_2025 huggingface dataset:
Building the Nation, Instrumentalizing Nationalism: Revisiting Romanian National-Communism, 1956–1989
Authors: Petrescu Dragoş
Published: June 2009

When approaching the issue of Romanian national-communism, it is Nicolae Ceauşescu's flamboyant display of chauvinistic nationalism that comes immediately to mind. Thus, it may come as a surprise for many to learn that it was in fact Gheorghe Gheorghiu-Dej, the Stalinist leader of the Romanian Workers’ Party (RWP) and Ceauşescu's predecessor, who initiated in the mid-1950s a return to the local traditions and subsequently to an ethnic understanding of the Romanian nation. True, under the reign of Ceauşescu, the communist regime engaged in sustained policies aimed at reinforcing the ethnic ties among the Romanian majority and assimilating the historic ethnic minorities. But, in the case of Romanian communism, a nationalistic turn had already been initiated during the year 1956, under the rule of Gheorghiu-Dej. At the same time, it took a rather long period, i.e. 1956–1968, for Romanian national-communism to mature.
School regimes and education equity: Some insights based on PISA 2006
Authors: Alegre Miquel Àngel , Ferrer Gerard
Published: June 2009

This paper aims to analyze the effects of certain characteristics of the educational systems on the social composition of schools. After accounting for significant effects of schools’ social composition on student outcomes (this is confirmed on the basis of a multilevel analysis), we explore the impacts of distinct components of what we name ‘school regimes’ on measures of school social segregation (Hutchens indices) across countries and regions. The PISA 2006 database has been used as the main source of information for such measures. Our analysis considers data for 32 OECD educational systems. Certain characteristics of school regimes are specially assessed: the level of institutional differentiation existing in the educational career; the presence of private schools in compulsory education; the level of school autonomy as regards the process of student admission; and the models and criteria defining public regulation of school access processes. Results of the regression analyses suggest that more market‐oriented school regimes tend to increase schools’ social segregation, whilst those characterised as more comprehensive and publicly regulated tend to reduce it.
Learning in the home and at school: How working class children ‘succeed against the odds’
Authors: Siraj‐Blatchford Iram
Published: June 2009

This paper presents data collected in individual case studies that aimed to investigate children and their families who succeeded against the usual ‘odds’ of disadvantage. Funded as an extension of EPPE 3–11 by the Cabinet Office for the Equalities Review, the study focused particularly closely upon the performance of disadvantaged children from White and minority ethnic groups. The study found that disadvantaged families often have high aspirations for their children and provide significant educational support through ‘concerted cultivation’. The paper discusses the implications for policy and for practice and argues that much of the popular criticism of state policies related to social exclusion fail to acknowledge the need to engage with the policy in action as well as in theory. It is also argued that these policies offer significant and valuable contexts for supporting efforts on the part of families and individuals to achieve success in education ‘against the odds’.
‘To benefit the world by whatever means possible’: Adolescents' constructed meanings for global citizenship
Authors: Myers John P.
Published: June 2009

This article reports on the ways that 77 students in an international studies programme constructed meanings for global citizenship. The focus was on their personal meanings for the topic and how they articulated a global identity with their national civic beliefs. Data were collected from online discussion boards, written essays and 20 interviews. A key finding was that the students' political language for global citizenship, examined here in terms of purpose, membership and relationship with national citizenship, was predominantly a moral commitment framed in universal language. A second finding was that the students understood global citizenship as a heterogeneous and complex affiliation shaped by a range of sources. The implication is that citizenship education emphasizing a narrow notion of patriotism may encourage students to disengage from civic life because it does not represent their lived experiences and identities. Insights for making citizenship education practices more inclusive are discussed.
Digital natives: Where is the evidence?
Authors: Helsper Ellen Johanna , Eynon Rebecca
Published: June 2009

Generational differences are seen as the cause of wide shifts in our ability to engage with technologies and the concept of the digital native has gained popularity in certain areas of policy and practice. This paper provides evidence, through the analysis of a nationally representative survey in the UK, that generation is only one of the predictors of advanced interaction with the Internet. Breadth of use, experience, gender and educational levels are also important, indeed in some cases more important than generational differences, in explaining the extent to which people can be defined as a digital native. The evidence provided suggests that it is possible for adults to become digital natives, especially in the area of learning, by acquiring skills and experience in interacting with information and communication technologies. This paper argues that we often erroneously presume a gap between educators and students and that if such a gap does exist, it is definitely possible to close it.
Normative cruelties and gender deviants: The performative effects of bully discourses for girls and boys in school
Authors: Ringrose Jessica , Renold Emma
Published: June 2009

Since the 1990s the educational community has witnessed a proliferation of ‘bullying’ discourses, primarily within the field of educational developmental social psychology. Drawing on ethnographic and qualitative interview data of primary and secondary school girls and boys, this article argues that the discourse ‘bullying’ operates to simplify and individualise complex gendered/classed/sexualised/racialised power relations embedded in children's school‐based cultures. Using a feminist post‐structural approach, this article critically traces the discursive production of how the signifiers ‘bully’ and ‘victim’ are implicated in the ‘normative cruelties’ of performing and policing ‘intelligible’ heteronormative masculinities and femininities. It shows how these everyday gender performances are frequently passed over by staff and pupils as ‘natural’. The analysis also illustrates how bully discourses operate in complex racialised and classed ways that mark children out as either gender deviants, or as not adequately performing normative ideals of masculinity and femininity. In conclusion, it is argued that bully discourses offer few symbolic resources and/or practical tools for addressing and coping with everyday school‐based gender violence, and some new research directions are suggested.
The assessment revolution that has passed England by: Rasch measurement
Authors: Panayides Panayiotis , Robinson Colin , Tymms Peter
Published: June 2009

Assessment has been dominated by Classical Test Theory for the last half century although the radically different approach known as Rasch measurement briefly blossomed in England during the 1960s and 1970s. Its open development was stopped dead in the 1980s, whilst some work has continued almost surreptitiously. Elsewhere Rasch has assumed dominance. The purpose of this article is to discuss the major criticisms of the Rasch model, which led to its rejection by some, and to give responses to these criticisms whilst encouraging social scientists to appreciate its strengths. The original breakthrough by Georg Rasch in 1960 has been developed and extended to address every reasonable observational situation in the social sciences.
Preparation, crystal structure, and characterization of a polymeric phenol-bridged potassium compound with 2-bromo-4,6-dinitrophenolate
Authors: Najafpour Mohammad Mahdi , Boghaei Davar M. , Mckee Vickie
Published: June 2009

A polymeric phenolato-bridged potassium compound, K(2-bromo-4,6 dinitrophenolate) (H2O), was obtained by reaction of methylammonium 2-bromo-4,6-dinitrophenolate and potassium chloride in water. 2-bromo-4,6 dinitrophenolate co-ordinates to the metal ion by phenolic O atom, Br, and O atoms of the nitro groups. K+ ion is eleven-coordinate in the compound. Single-crystal X-ray diffraction for methylammonium 2-bromo-4,6-dinitrophenolate and single-crystal X-ray diffraction, elemental analysis, IR, UV-Vis spectra, and fluorescence emission spectra for the complex have also been determined. Methylammonium 2-bromo-4,6-dinitrophenolate was solved in the monoclinic system, space group P21/c, with the following unit-cell parameters: a = 4.7038(2) Å, b = 20.5427(1) Å, c = 10.5799(6) Å, β = 101.127(5)°, Z = 4, V = 1003.10(9) Å3. The final R value was R1 = 0.0206 for 12,732 measured reflections. The phenolato-bridged potassium compound was solved in the monoclinic system, space group P21/c, with the following unit-cell parameters: a = 9.8278(7) Å, b = 14.566(1) Å, c = 6.8007(5) Å, β = 94.754(1)°, Z = 2, V = 970.20(12) Å3. The final R value was R1 = 0.0319 for 9774 measured reflections.
Facile synthesis of novel 2-(4′-N,N-dimethylbenzylidenoimino)-6-substituted-1,3-benzothiazoles and crystal structures of 2-(4′-N,N-dimethylbenzylidenoimino)-6-chloro-1,3-benzothiazole and the co-crystal of 2-amino-6-nitro-1,3-benzothiazole and 4-(N,N-dimethylamino)benzaldehyde
Authors: Drake John E. , Hursthouse Michael B. , Kriplani Prashant , Light Mark E. , Mithlesh  , Ojha Krishan G. , Pareek Pawan K. , Ratnani Raju
Published: June 2009

2-Amino-6-substituted-1,3-benzothiazoles were condensed with N,N-dimethylaminobenzaldehyde to give novel 2-(4′-N,N-dimethylbenzylidenoimino)-6-substituted-1,3-benzothiazoles in good yields. However, in the case of 2-amino-6-nitro-1,3-benzothiazole, the desired product 2-(4′-N,N-dimethylbenzylidenoimino)-6-nitro-1,3-benzothiazole was not observed. Products were characterized by elemental analysis and infrared (IR) and 1H NMR spectroscopy. Two crystal structures were determined. ClC6H3(SCN)N == CHC6H4N(CH3)2 crystallizes as triclinic, P-1, a = 5.8799(2), b = 15.9279(4), c = 16.7264(4) Å, α = 64.769(1)°, β = 89.729(2)°, γ = 88.047(1)°, V = 1416.15(7) Å3, Z = 4, R = 0.0430, Rw = 0.1035. O2NC6H3(SCN)NH2·OCHC6H4N(CH3)2 crystallizes as monoclinic, P2/c, a = 18.7645(7), b = 3.8048(1), c = 22.0141(7) Å, β = 94.743(2)°, V = 1566.32(9) Å3, Z = 4, R = 0.0398, Rw = 0.0919.
Studies on DNA-binding and plasmid-cleavage of cobalt (III) mixed ligand complexes
Authors: Shilpa Mynam , Nagababu Penumaka , Satyanarayana S.
Published: June 2009

Mixed ligand cobalt (III) complexes of [Co(phen)2nip]3+, [Co(phen)2apip]3+, [Co(bpy)2nip]3+, [Co(bpy)2apip]3+ where [apip = 2(4-aminophenyl)imidazo[4,5f] [1,10] [phenanthroline], [nip = 2(2-napthyl) l4-midazo[4,5-f][1,10]phenanthroline] have been synthesized and characterized. The interaction of these complexes with calf thymus DNA was investigated by absorption (UV/Vis), emission spectroscopy, viscosity measurements, and DNA melting. The results suggest that the complexes bind to DNA via the intercalative mode with complexes 1 > 2 > 3 > 4 binding more strongly to CT DNA. Moreover, these complexes have been found to promote the photocleavage of plasmid DNA pBR322.
Spectral studies and antimicrobial activities of organosilicon(IV) and organotin(IV) complexes of nitrogen and sulfur donor Schiff bases derived from 4-amino-5-mercapto-3-methyl-s-triazole
Authors: Singh Kiran , Dharampal  , Dhiman Saurabh Sudha
Published: June 2009

Some new organosilicon(IV) and organotin(IV) complexes formulated as R2SiCl[L1], R2SiCl[L2], R2Si[L1]2, R2Si[L2]2, R2SnCl[L1], R2SnCl[L2], R2Sn[L1]2, and R2Sn[L2]2 have been synthesized by the reactions of Me2SiCl2 and Me2SnCl2 with Schiff bases in 1:1 and 1:2 molar ratios. L1 [2-(chlorobenzylidineamino)-5-mercapto-3-methyl-s-triazole] and L2[4-(flourobenzylidineamino)-5-mercapto-3-methyl-s-triazole] have been synthesized by the condensation of 2-chlorobenzaldehyde and 4-flourobenzaldehyde with 4-amino-5-mercapto-3-methyl-s-triazole. Newly synthesized organosilicon and organotin complexes have been characterized by elemental analysis, molar conductance measurements, spectral studies, including UV, IR, 1H, 13C, 29Si, and 119Sn NMR. The nature of these complexes is non-electrolytic. With the help of these techniques, trigonal bipyramidal and octahedral geometries are proposed for the newly synthesized complexes. The biological activity of these complexes against various bacteria and fungi has been investigated and then compared with free ligands.
Interaction studies on the binary mixture of formamide with 2-butoxyethanol, 2-ethyl-1-hexanol, and isopropanol at 303 K
Authors: Sankar U. , Parthipan G. , Undre P. , Khirade P.W. , Thenappan T. , Mehrotra S.C.
Published: June 2009

A molecular interaction study for binary mixture of 2-butoxyethanol, 2-ethyl-1-hexanol, and isopropanol with formamide has been carried out over the frequency range of 10 MHz–20 GHz at 303 K using time domain reflectometry method for 16 concentrations. The bilinear calibration method on least-square method has been used to obtain the static permittivity, relaxation time, and the permittivity at high frequency. The excess permittivity and excess relaxation time have been calculated, which provide information regarding the interaction among the molecules in the mixtures. Short-range interaction and alignment of the dipoles in the mixtures are studied using Kirkwood factors. The dielectric parameters are found to vary with concentration randomly.
Role of aniline in destructing the 1-propanol + toluene azeotrope
Authors: Palaniappan Lakshmanan , Jaafar Mohamad Suhaimi
Published: June 2009

The separation of azeotropes is a major task in petrochemical industries. The role of aniline in destructing the toluene–1-propanol azeotrope is analyzed in the present work. Sound velocity and density values have been measured at 303 K in the binary and ternary systems containing aniline, 1-propanol, and toluene. From these data, adiabatic compressibility and its excess values have been estimated and used as the key parameter to analyze the ternary situation that exists in the system. The results are interpreted in terms of molecular interaction between the components of the mixtures that can ascertain the role of aniline in this process.
Synthesis, characterization, electrochemical studies, DNA binding, and cleavage activity of mixed copper(II)oxime DMSO complexes
Authors: Surendra Babu M.S. , Krishna Pitchika G. , Hussain Reddy K. , Philip G.H.
Published: June 2009

Mixed ligand complexes having molecular formulae Cu(L)2(DMSO)2 [where L = salicylaldoxime (SAO), 2-hydroxyacetophenone oxime (HAO), and resacetophenone oxime (RPO)] have been synthesized and characterized by molar conductivity, magnetic susceptibility, UV–vis, IR, and ESR methods. The electronic and ESR spectra suggest distorted octahedral geometry for mixed ligand complexes. From ESR data all the complexes follow the order g‖ > g⊥ > 2.003– showing covalent bonding nature and copper(II) (d9) ion in axial symmetry with unpaired electron in dx2–y2 orbital. Cyclic voltammetric studies show quasi-reversible reduction attributable to Cu2+/Cu+. Absorption titration studies revealed that each complex is an avid binder of CT DNA. The apparent binding constants are in the range 3.2 × 105 to 2.4 × 106. The cleavage activity of complexes was carried out on double-stranded pBR322 circular plasmid DNA using gel electrophoresis. All complexes show increased nuclease activity in the presence of oxidant (H2O2) and cleavage is strongly dependent on time of incubation and concentration of complex. Control cleavage experiment carried out in the presence of potential inhibitors, viz. dimethyl sulfoxide, tert-Butyl alcohol, ethylenediaminetetraacetic acid and NaN3, inhibits cleavage activity suggesting an oxidative mechanism with major active species involving •OH in cleavage of plasmid DNA.
Ligand design and metal ion recognition: comparison of the interaction of zinc(II) and cadmium(II) with 17- and 18-membered N3O2 donor macrocycles
Authors: Nasman Omar S.M.
Published: June 2009

The interaction of zinc(II) and cadmium(II) with 17- and 18-membered ring macrocycles incorporating nitrogen and oxygen hetero-atoms is reported. These ligands constitute an array of related macrocyclic structures in which the position of the donor atoms, their spacing and the macrocyclic ring size all vary in a systematic manner. Physical measurements confirm the 1:1 metal to ligand stoichiometry of the respective complexes. The complexes, [ML 1–2H2O] X2; [M = Zn(II) or Cd(II); X = Cl or NO3], have been synthesized via the templated cyclocondensation reactions of salicylaldehyde with 1,2-dibromoethane or 1,3-dibromopropane and diethylenetriamine in 2:1:1 molar ratio. The stoichiometries and coordination modes of the complexes have been deduced from IR, 1H, and 13C NMR, conductivity and microanalytical data. Tetrahedral geometry is suggested for Zn(II) compounds, where three nitrogen atoms are coordinated to the metal and the fourth being occupied by a water molecule, while octahedral geometry is suggested for Cd(II) where three nitrogen and two oxygen atoms are coordinated to the metal, the sixth being occupied by a water molecule.
WHO CHOOSES THE WEDDING GUESTS, THE COUPLE OR THE FAMILY?
Authors: Castrén Anna-Maija , Maillochon Florence
Published: June 2009

Marriage has become an individual choice in most European countries. In this article we study entry into marriage, i.e., weddings, which in the contemporary research literature are often presented with an emphasis on modernity: consumerism, celebration of romance, and the experience of a unique and individual occasion. The wedding guests are an important part in the making of ‘the perfect day’ but the topic has largely been neglected in the literature. In this study we analyse the selection of wedding guests in 12 weddings (six French and six Finnish) to investigate the dynamics of the interplay between individual preferences and the determinants that are more relational in origin. Three empirical questions are presented: first, who is responsible for choosing the guests? Second, what is the distribution of wedding guests between kin and non-kin? And third, who are the non-kin guests: are they friends first met by the couple alone, or also by the wider family? The results show that despite the predominantly individualistic discourse expressed by the couples, a wedding is still a familial affair: the configurations of family ties are influential in constraining as well as enabling the choices available to the couple.
NARRATIVES OF SELF AND RELATEDNESS IN ECO-COMMUNES
Authors: Eräranta Kirsi , Moisander Johanna , Pesonen Sinikka
Published: June 2009

This paper focuses on eco-communes as sites of resistance and political activism. Based on a post-structuralist narrative analysis of interview materials, this paper elaborates on the ways in which life in a commune is narrated and represented as an identity project with a mission to bring about social change. The environmentalists studied make sense of their choice to live in an eco-commune as something that was triggered and facilitated by important crossroads and fateful moments that they had encountered in their past life. They also work on their identity as eco-communards by discursively problematizing their personal relation to themselves (self) and to others (spouse and family), as well as by constructing new forms of subjectivity, intimacy, and relatedness through communal life. Life in the eco-commune thus represents a form of resistance and political struggle that Michel Foucault has referred to as politics of self; it represents not only direct opposition against the social order of contemporary Western consumer society but also more subtle resistance against the normalized forms of subjectivity that it entails.
GAINING PERSPECTIVE ON CHOICE AND FATE
Authors: Holland Janet , Thomson Rachel
Published: June 2009

The idea of epiphanies, turning points and critical biographical moments is a central analytic category of life history research in general, and of youth studies in particular. In this paper we explore how we have engaged with ideas of ‘fatefulness’ (Giddens 1991) and biographical ‘choice’ in a longitudinal qualitative study of young people's transitions to adulthood, tracing the employment of theoretical and analytical devices through time to assess their usefulness in this context. We attempted to operationalise Giddens’ idea of the fateful moment in relation to biographical data asking how the analysis of a formal narrative device (critical moments, turning points) might play a part in mapping and theorising the configuration of structural conditions, individual responses, timing and chance. We reviewed earlier analyses, and the changes of interpretation brought about by the accumulation of biographical data through time, recognising the provisional nature of interpretation in longitudinal research and analysis. The process of revisiting and revising our deliberations over the meaning and significance of the critical moments within biographical narratives confirms the interpretative value of focussing on these narrative forms, yet suggests that late modern theoretical frameworks with their emphasis on reflexivity may have a limited contribution to make to understanding the configuration of biography and history. We suggest that this makes a theoretical and methodological contribution to biographical and narrative approaches to the study of young people's lives, transitions to adulthood and trajectories.
SHARING THE SAME FATE
Authors: Ketokivi Kaisa
Published: June 2009

Peer support has become a growing source of consolation for individuals in contemporary social life. This article examines the social bond between selves and their fellow sufferers ‘sharing the same fate’ in support groups and personal networks. Analyzed fateful conditions include serious illness, premature loss of a spouse through death or abandonment, infertility and family disruptions. The results show that selves colonized by agonizing life experiences confront social isolation and turn to their fellow sufferers in order to find understanding. A distinct kind of social bond is proposed between fellow sufferers involving sharing at the level of generalized experiences. Further analysis of different states of the bonds and their consequences is drawn from Thomas Scheff's distinction of the social bond as one of three states: attuned, engulfed or isolated. When attuned to fellow sufferers, peer support can be genuinely self-empowering and healing, but also other consequences emerge. In engulfed bonds with fellow sufferers, the particular self stands at risk of being overpowered by others. Isolated bonds with fellow sufferers may not be capable of breaking the lonely state of suffering. This paper provides an elaborate empirical understanding of the interplay between fate, the social and the individual in the context of peer support. The data is made up of repeated in-depth interviews with 22 Finnish women and men that contain narrated life stories, accompanied by information about their network, of significant others and support contacts.
HAUNTING IN AN AGE OF INDIVIDUALIZATION
Authors: Roseneil Sasha
Published: June 2009

This paper uses the notion of ‘haunting’ to explore how even those who might be considered to be particularly individualized are inhabited by the traces of the lives of others. The paper works with a single detailed case study taken from UK based research on the personal lives and values of people living outside the conventional cohabiting couple. It develops a psycho-social-analysis of interviews with Ben, a black English man in his 50s who is a ‘strong’ case of the individualization of personal life. Ben represents himself as highly self-reliant and self-sufficient, yet his narratives repeatedly return to the central importance of his long dead father; the paper suggests that his interviews, and his subjectivity, are ‘haunted’ by the ghost of his father. It explores the ways in which conflicted issues of gendered and racialized belonging and identification, and questions of ethical subjectivity, are worked out in relation to his dead father. The paper is informed by psychoanalytic and sociological writing on psychic and socio-cultural processes of haunting, particularly the work of Christopher Bollas and Avery Gordon. It contributes to the re-thinking of sociological theories of individualization, challenging sociology to take seriously a psychoanalytically inspired ontology of relationality, and the impacts of past relationships on subjectivity.
REFLEXIVE SELF-TALK AND SITUATED FREEDOM IN THE CONTEXT OF SOCIABILITY
Authors: Törrönen Jukka , Maunu Antti
Published: June 2009

This paper analyses narratives in drinking and pub diaries written by young Finns aged 23–35. Drinking occasions in Finland are highly sociable gatherings in which one is oriented towards intensive interaction with one's friends. Thus, in the diaries the writers also reflect upon their expectations, descriptions and evaluations of these gatherings and the sociability they offer. In the analysis we focus on how during these occasions the writers adapt themselves to the perceived expectations of others, integrate these expectations with their own aspirations, or are sometimes compelled to change their aspirations. On this basis, we also pay attention to how this work of reflexive orientation functions to strengthen the expected course of one's own life, or as implying fateful moments, that is, transitions or turning points in the life course. In the analysis we apply G.H. Mead's concepts of ‘I’ and ‘me’. The paper identifies three different kinds of ‘I–me dialogues’. First, loosening oneself momentarily from reflexivity to the collective body of friends; second, binding oneself reflexively to the common will of the group; and third, loosening oneself from group commitments, that is moving towards individual reflexivity and desires. Of these dialogues, the last mentioned contributes most often to fateful activity in which the writers’ life course is at stake. By contrast, the other two more collectively oriented self-talks rather refer to positive peak experiences that give emotional momentum to continue with one's existing life plans.
THE NEXT EUROPEAN EMPIRE?
Authors: Gravier Magali
Published: June 2009

This paper proposes to use the concept of empire for the analysis the European integration process. From a methodological point of view, this concept is an invitation to reintroduce in EU studies the comparative approach as well as long-term history. This paper also leads to a detailed reflection on the concept of empire itself and proposes a modernized definition of it. The use of this concept enables to shed a new light on the EU and some of its policies. If the EU cannot be considered an empire, it can nonetheless be said that it is undergoing a process of imperialization. This raises the question of the transformation of the European project and to the consequences of this transformation.
CIVIC STRATIFICATION AND THE COSMOPOLITAN IDEAL
Authors: Morris Lydia
Published: June 2009

Beck (2006) has suggested that trans-national migration and the consolidation of human rights are features of an emergent cosmopolitan society in which we see a blurring of distinctions with respect to the rights of citizens and non-citizens. This paper argues that the presence of noncitizens on national territory has rather been accompanied by an expansion of distinctions in a system of civic stratification. It outlines the construction of asylum seekers as a ‘target group’ within this complex, and the withdrawal of welfare support from ‘late claimers’. However, the paper also considers the limits placed on the erosion of rights through the human rights challenge that followed, in which the European Convention on Human Rights played a central role. Finally, the paper elaborates the interplay of formal entitlement and informal status in the process of change, and examines the implications of the whole account for cosmopolitan thinking.
The effect of predictive history on the learning of sub-sequence contingencies
Authors: Beesley T. , Le Pelley M. E.
Published: June 2009

Two experiments demonstrated that the prior predictive history of a cue governs the extent to which that cue engages in sequence learning. Using a serial reaction time task, we manipulated the predictiveness of the stimulus locations (cues) with respect to the location of the stimulus on the next trial (outcome), such that half of the cues were good predictors of their outcomes, whilst the other half were poorer predictors. Following this, all cues were then paired with novel outcomes. Learning about those cues that were previously established as good predictors proceeded more rapidly than learning for those cues previously established as poor predictors. When the simple recurrent network is modified to include a variable associability parameter, the effects are easily modelled.
The influence of temporal factors on automatic priming and conscious expectancy in a simple reaction time task
Authors: Destrebecqz Arnaud , Perruchet Pierre , Cleeremans Axel , Laureys Steven , Maquet Pierre , Peigneux Philippe
Published: June 2009

In a previous study, we reported a dissociation between subjective expectancy and motor behaviour in a simple associative learning task (Perruchet, Cleeremans, & Destrebecqz, 2006). According to previous conditioning studies (Clark, Manns, & Squire, 2001), this dissociation is observed when the to-be-associated events coterminate and thus overlap in time (a training regimen called delay conditioning), but not when they are separated by a temporal delay (trace conditioning). In this latter situation indeed, there tends to be a direct relationship between subjective expectancy and behaviour. In this study, we further investigated this issue in a series of experiments where conscious and unconscious components of performance were pitted against each other. In Experiments 1–3, participants performed a simple reaction time task in which a preparatory signal (a tone) either overlapped with or terminated earlier than the imperative stimulus (a visual target presented in 50% of the trials). After each response, participants also had to state how much they expected the imperative stimulus to be displayed on the next trial. Results indicate that reaction times tend to decrease when the tone is consistently followed by the visual target across successive trials, whereas conscious expectancy for the target decreases at the same time. Importantly, we systematically found that the temporal relationship between the tone and the target failed to influence performance. In a fourth experiment, we examined whether these results extend to a two-choice reaction time task. To our surprise, we observed a direct relationship between subjective expectancies and reaction time in that situation. We nevertheless observed that the introduction of a delay between the tone and the target had, once again, no effect on performance.
Stimulus–response compatibility for mixed mappings and tasks with unique responses
Authors: Proctor Robert W. , Vu Kim-Phuong L.
Published: June 2009

For two stimulus locations mapped to two keypresses, reaction time is shorter when the mapping is compatible than when it is not (the stimulus–response compatibility, SRC, effect). A similar result, called the Simon effect, occurs when stimulus location is irrelevant, and colour is relevant. When compatibly mapped trials are intermixed with incompatibly mapped trials or Simon task trials, the compatibility effect is eliminated, and the Simon effect is influenced by the location mapping. In five experiments, we examined whether similar mixing effects occur when the two spatial mappings or location-relevant and location-irrelevant tasks use distinct keypresses on the left and right hands. Mixing had considerably less influence on the SRC and Simon effects than it does when the intermixed trial types or tasks share the same responses, even though response time was lengthened to a similar extent. Mixing two tasks for which stimulus location was irrelevant yielded no within-task Simon effect, but the effect was also absent when four stimuli were assigned to two responses on a single hand. The relative lack of influence of mixing on the SRC and Simon effects when the tasks have unique responses implies that suppression of direct activation of the corresponding response occurs primarily when the tasks share responses.
Copy number variation has little impact on bead-array-based measures of DNA methylation
Authors: Houseman E. Andrés , Christensen Brock C. , Karagas Margaret R. , Wrensch Margaret R. , Nelson Heather H. , Wiemels Joseph L. , Zheng Shichun , Wiencke John K. , Kelsey Karl T. , Marsit Carmen J.
Published: June 2009

Motivation: Integration of various genome-scale measures of molecular alterations is of great interest to researchers aiming to better define disease processes or identify novel targets with clinical utility. Particularly important in cancer are measures of gene copy number DNA methylation. However, copy number variation may bias the measurement of DNA methylation. To investigate possible bias, we analyzed integrated data obtained from 19 head and neck squamous cell carcinoma (HNSCC) tumors and 23 mesothelioma tumors.

Results: Statistical analysis of observational data produced results consistent with those anticipated from theoretical mathematical properties. Average beta value reported by Illumina GoldenGate (a bead-array platform) was significantly smaller than a similar measure constructed from the ratio of average dye intensities. Among CpGs that had only small variations in measured methylation across tumors (filtering out clearly biological methylation signatures), there were no systematic copy number effects on methylation for three and more than four copies; however, one copy led to small systematic negative effects, and no copies led to substantial significant negative effects.

Conclusions: Since mathematical considerations suggest little bias in methylation assayed using bead-arrays, the consistency of observational data with anticipated properties suggests little bias. However, further analysis of systematic copy number effects across CpGs suggest that though there may be little bias when there are copy number gains, small biases may result when one allele is lost, and substantial biases when both alleles are lost. These results suggest that further integration of these measures can be useful for characterizing the biological relationships between these somatic events.

Contact:  E_Andres_Houseman@brown.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
GR-Aligner: an algorithm for aligning pairwise genomic sequences containing rearrangement events
Authors: Chu Te-Chin , Liu Tsunglin , Lee D. T. , Lee Greg C. , Shih Arthur Chun-Chieh
Published: June 2009

Motivation: Homologous genomic sequences between species usually contain different rearrangement events. Whether some specific patterns existed in the breakpoint regions that caused such events to occur is still unclear. To resolve this question, it is necessary to determine the location of breakpoints at the nucleotide level. The availability of sequences near breakpoints would further facilitate the related studies. We thus need a tool that can identify breakpoints and align the neighboring sequences. Although local alignment tools can detect rearrangement events, they only report a set of discontinuous alignments, where the detailed alignments in the breakpoint regions are usually missing. Global alignment tools are even less appropriate for these tasks since most of them are designed to align the conserved regions between sequences in a consistent order, i.e. they do not consider rearrangement events.

Results: We propose an effective and efficient pairwise sequence alignment algorithm, called GR-Aligner (Genomic Rearrangement Aligner), which can find breakpoints of rearrangement events by integrating the forward and reverse alignments of the breakpoint regions flanked by homologously rearranged sequences. In addition, GR-Aligner also provides an option to view the alignments of sequences extended to the breakpoints. These outputs provide materials for studying possible evolutionary mechanisms and biological functionalities of the rearrangement.

Availability:  http://biocomp.iis.sinica.edu.tw/new/GR_Aligner.htm

Contact:  arthur@iis.sinica.edu.tw
VarScan: variant detection in massively parallel sequencing of individual and pooled samples
Authors: Koboldt Daniel C. , Chen Ken , Wylie Todd , Larson David E. , McLellan Michael D. , Mardis Elaine R. , Weinstock George M. , Wilson Richard K. , Ding Li
Published: June 2009

Summary: Massively parallel sequencing technologies hold incredible promise for the study of DNA sequence variation, particularly the identification of variants affecting human disease. The unprecedented throughput and relatively short read lengths of Roche/454, Illumina/Solexa, and other platforms have spurred development of a new generation of sequence alignment algorithms. Yet detection of sequence variants based on short read alignments remains challenging, and most currently available tools are limited to a single platform or aligner type. We present VarScan, an open source tool for variant detection that is compatible with several short read aligners. We demonstrate VarScan's ability to detect SNPs and indels with high sensitivity and specificity, in both Roche/454 sequencing of individuals and deep Illumina/Solexa sequencing of pooled samples.

Availability and Implementation: Source code and documentation freely available at http://genome.wustl.edu/tools/cancer-genomics implemented as a Perl package and supported on Linux/UNIX, MS Windows and Mac OSX.

Contact:  dkoboldt@genome.wustl.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Reconstructing signaling pathways from RNAi data using probabilistic Boolean threshold networks
Authors: Kaderali Lars , Dazert Eva , Zeuge Ulf , Frese Michael , Bartenschlager Ralf
Published: June 2009

Motivation: The reconstruction of signaling pathways from gene knockdown data is a novel research field enabled by developments in RNAi screening technology. However, while RNA interference is a powerful technique to identify genes related to a phenotype of interest, their placement in the corresponding pathways remains a challenging problem. Difficulties are aggravated if not all pathway components can be observed after each knockdown, but readouts are only available for a small subset. We are then facing the problem of reconstructing a network from incomplete data.

Results: We infer pathway topologies from gene knockdown data using Bayesian networks with probabilistic Boolean threshold functions. To deal with the problem of underdetermined network parameters, we employ a Bayesian learning approach, in which we can integrate arbitrary prior information on the network under consideration. Missing observations are integrated out. We compute the exact likelihood function for smaller networks, and use an approximation to evaluate the likelihood for larger networks. The posterior distribution is evaluated using mode hopping Markov chain Monte Carlo. Distributions over topologies and parameters can then be used to design additional experiments. We evaluate our approach on a small artificial dataset, and present inference results on RNAi data from the Jak/Stat pathway in a human hepatoma cell line.

Availability: Software is available on request.

Contact:  lars.kaderali@bioquant.uni-heidelberg.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
Reconstruct modular phenotype-specific gene networks by knowledge-driven matrix factorization
Authors: Yang Xuerui , Zhou Yang , Jin Rong , Chan Christina
Published: June 2009

Motivation: Reconstructing gene networks from microarray data has provided mechanistic information on cellular processes. A popular structure learning method, Bayesian network inference, has been used to determine network topology despite its shortcomings, i.e. the high-computational cost when analyzing a large number of genes and the inefficiency in exploiting prior knowledge, such as the co-regulation information of the genes. To address these limitations, we are introducing an alternative method, knowledge-driven matrix factorization (KMF) framework, to reconstruct phenotype-specific modular gene networks.

Results: Considering the reconstruction of gene network as a matrix factorization problem, we first use the gene expression data to estimate a correlation matrix, and then factorize the correlation matrix to recover the gene modules and the interactions between them. Prior knowledge from Gene Ontology is integrated into the matrix factorization. We applied this KMF algorithm to hepatocellular carcinoma (HepG2) cells treated with free fatty acids (FFAs). By comparing the module networks for the different conditions, we identified the specific modules that are involved in conferring the cytotoxic phenotype induced by palmitate. Further analysis of the gene modules of the different conditions suggested individual genes that play important roles in palmitate-induced cytotoxicity. In summary, KMF can efficiently integrate gene expression data with prior knowledge, thereby providing a powerful method of reconstructing phenotype-specific gene networks and valuable insights into the mechanisms that govern the phenotype.

Contact:  krischan@msu.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
SHREC: a short-read error correction method
Authors: Schröder Jan , Schröder Heiko , Puglisi Simon J. , Sinha Ranjan , Schmidt Bertil
Published: June 2009

Motivation: Second-generation sequencing technologies produce a massive amount of short reads in a single experiment. However, sequencing errors can cause major problems when using this approach for de novo sequencing applications. Moreover, existing error correction methods have been designed and optimized for shotgun sequencing. Therefore, there is an urgent need for the design of fast and accurate computational methods and tools for error correction of large amounts of short read data.

Results: We present SHREC, a new algorithm for correcting errors in short-read data that uses a generalized suffix trie on the read data as the underlying data structure. Our results show that the method can identify erroneous reads with sensitivity and specificity of over 99% and 96% for simulated data with error rates of up to 3% as well as for real data. Furthermore, it achieves an error correction accuracy of over 80% for simulated data and over 88% for real data. These results are clearly superior to previously published approaches. SHREC is available as an efficient open-source Java implementation that allows processing of 10 million of short reads on a standard workstation.

Availability: SHREC source code in JAVA is freely available at http://www.informatik.uni-kiel.de/∼jasc/Shrec/

Contact:  jasc@informatik.uni-kiel.de
Antihypertension Induced by Tanshinone IIA Isolated from the Roots of Salvia miltiorrhiza
Authors: Chan Paul , Liu I-Min , Li Ying-Xiao , Yu Wen-Jen , Cheng Juei-Tang
Published: June 2009

Tanshinone IIA is one of the active principles in danshen (Salvia miltiorrhiza Bge) widely used in treatment of cardiovascular disorders. We investigated the effect of danshen or tanshinone IIA on blood pressure and its possible mechanisms. An i.p. injection of danshen at 10 mg kg−1 significantly lowered systolic blood pressure (SBP) of spontaneously hypertensive rats (SHRs) but failed to modify the SBP in normotensive Wistar‐Kyoto rats (WKY). Oral administration of tanshinone IIA also decreased SBP in SHR but not in WKY. Tanshinone IIA produced a concentration‐dependent relaxation in isolated SHR aortic rings precontracted with phenylephrine (10 nmol l−1) or potassium chloride (KCl) (40 mmol l−1). The relaxing effect of tanshinone IIA on tonic contraction of phenylephrine in isolated aortic rings without endothelium remained produced. Glibenclamide at concentration sufficient to block adenosine triphosphatase (ATP)‐sensitive potassium (K+) channel attenuated this tanshinone IIA‐induced relaxation that was not influenced by other inhibitors. We further investigated the effect of tanshinone IIA on the changes of intracellular calcium concentration () in cultured aortic smooth muscle (A7r5) cells using fura‐2 as indicator. Tanshinone IIA decreased elicited by phenylephrine (10 nmol l−1) or KCl (40 mmol l−1) in a concentration‐dependent manner; glibenclamide, but not other inhibitors for K+ channel, abated this effect. Our results suggest that tanshinone IIA acts as an active principle of danshen showing vasodilation through ATP‐sensitive K+ channel to lower .
Different responses to area closures and effort controls for sedentary and migratory harvested species in a multispecies coral reef linefishery
Authors: Little L. Richard , Punt André E. , Mapstone Bruce D. , Begg Gavin A. , Goldman Barry , Ellis Nick
Published: June 2009

Little, L. R., Punt, A. E., Mapstone, B. D., Begg, G. A., Goldman, B., and Ellis, N. 2009. Different responses to area closures and effort controls for sedentary and migratory harvested species in a multispecies coral reef linefishery. – ICES Journal of Marine Science, 66: 1931–1941. We used a simulation model to examine the effect of area closures and fishing effort on the two main target species of the Great Barrier Reef Coral Reef Finfish Fishery: common coral trout (Plectropomus leopardus) and red throat emperor (Lethrinus miniatus). Area closures had greater effect on the more sedentary coral trout, in the areas outside the closures and accessible to the fishery, and little effect on red throat emperor, which was assumed to move among reefs. The effects of effort levels were greater than area closures on the harvest of both species and were seen not only in the areas accessible to the fishery, but also in the biomass of red throat emperor in the areas closed to the fishery. The catch and biomass resulting from a given effort level did not appear to have an equivalent effect attributable to any area closure. Although the effects of effort levels and area closures are confounded in reality by the coincidental implementation of area closures and restructuring of the fishery, the simulation model separated these factors to show that the closures under the 2004 rezoning should have had minimal effect on total-stock biomass and that a greater effect would result from changes in fishing effort.
Using stock assessment information to assess fishing capacity of tuna fisheries
Authors: Arrizabalaga Haritz , Restrepo Victor R. , Maunder Mark N. , Majkowski Jacek
Published: June 2009

Arrizabalaga, H., Restrepo, V. R., Maunder, M. N., and Majkowski, J. 2009. Using stock assessment information to assess fishing capacity of tuna fisheries. – ICES Journal of Marine Science, 66: 1959–1966. In tuna and tuna-like fisheries, there is a need for periodic assessments of fishing capacity to aid management. However, the nature and quantity of data needed to apply conventional methodologies for estimating fishing capacity are not usually available for tuna fisheries. We discuss simple alternative approaches to estimate fishing capacity and related quantities (i.e. capacity utilization, excess capacity, and overcapacity) directly from stock assessment inputs and outputs that are usually available for most tuna (and many other) stocks. Sensitivity analyses are performed to assess the effect of different levels of data aggregation and different assumptions made during the stock assessments on estimates of fishing capacity. Main advantages and disadvantages of the proposed methodologies are also illustrated using stock assessment information from different tuna stocks with different historical developments and trends in fishing mortality.