bluuebunny/crossref_metadata_2025 huggingface dataset:
The Upholding of Beauty: A Reading of Anselm'sCur Deus Homo
Authors: Holmes Stephen R.
Published: January 2009

St Anselm of Canterbury is famous on two counts: he is the originator of the ontological argument for the existence of God and he is the source of the satisfaction theory of the atonement. These positions do not exhaust his theological contribution; he also wrote works defending and defining Western Trinitarian doctrine, against Sabellianism and tritheism, and arguing for the filioque; he wrote on the Incarnation; and was influential in modifying Augustine's account of the transmission of original sin. There is also a collection of meditations and prayers, traditionally attributed to St Anselm, which at their best rank alongside almost any devotional literature of the medieval period. His memory, however, is firmly attached today to just the two points with which I began. It would not be an exaggeration to claim that on both he has been fundamentally misunderstood by the popular accounts of his thought given in theological and philosophical introductions and histories; these misreadings have been pointed out often enough, but are still regularly repeated.
The Use and Abuse of Perichoresis in Recent Theology
Authors: Otto Randall E.
Published: January 2009

Perichoresis(perichoresis, circumincessio)is a theological term which describes the ‘necessary being-in-one-another or circumincession of the three divine Persons of the Trinity because of the single divine essence, the eternal procession of the Son from the Father and of the Spirit from the Father and (through) the Son, and the fact that the three Persons are distinguished solely by the relations of opposition between them.’ This term was popularized in the eighth century by John of Damascus who, in hisDe fide orthodoxa, said the three Persons of the Trinity ‘are made one not so as to commingle, but so as to cleave to each other, and they have their being in each other [kai ten en allelais perichoresin] without any coalescence or commingling.’ This important theological term, which Karl Barth rightly regarded 'as the one important form of the dialectic required to complete the concept of ‘three-in-oneness’ ‘from the side of the unity of the divine essence’ and ‘from the side of the original relations,’ has suffered in some recent theology from its appropriation to describe relationality apart from mutually shared being. For example, in his influential social doctrine of the Trinity, Jürgen Moltmann emphasizes the ‘relational, perichoretically consummated life processes’ of the three Persons who ‘cannot and must not be reduced to three modes of being of one and the same divine subject,’ whose unity ‘cannot and must not be seen in a general concept of divine substance.’
Karl Barth on Divine Command: A Jewish Response
Authors: Novak David
Published: January 2009

Usually one does not include Karl Barth in contemporary Jewish-Christian dialogue. Unlike his Protestant theological contemporaries, Paul Tillich and Reinhold Niebuhr, there in no evidence that during his long theological career Barth had any real contact with Jewish thinkers. The only contemporary Jewish thinker whom he engages, to my knowledge, is Martin Buber, but in his magnum opus,Church Dogmatics, Buber is discussed almosten passentand with a rather hurried dismissal. Barth's relations with Judaism are seriously complicated, but one gets the impression from reading what he says about Judaism that he is doing typology, engaging a type already created in his mind largely by Paul and those who followed in his path. He does not seem to be dealing with Judaism as a living tradition, indeed a current rival religious option to Christianity. After all, how can one engage Judaism as a living tradition, let alone as a current rival, if one has no serious contact with living Jews during the most productive years of one's thought? For that reason it would seem an engagement of Barth's thought by a contemporary Jewish theologian could only be, at most, an arcane academic exercise having no real Jewish significance.
Why was Jesus Crucified? Theology, History and the Story of Redemption
Authors: Brondos David
Published: January 2009

Why did Jesus die on the cross? Ask this question of a theologian, and the answer will likely be something to the effect that Jesus died so that our sins might be forgiven and the world might be saved from sin, death and evil eternally. Ask this question of a historian, however, and the answer will be quite different: Jesus died because his activity created conflict with the authorities of his time, and therefore they had him crucified.
The Early Reception of Karl Barth's Theology in Britain: A Supplementary View
Authors: Morgan D. Densil
Published: January 2009

One of the axioms of modern church history in Britain is that whereas Anglo-Saxon thought was on the whole impervious to the appeal and achievement of Karl Barth, it was among the Scots alone that the Swiss theologian's theories found any real resonance and creative response. Stephen Sykes in a 1979 volume of studies in Barth's theological method, mentions the somewhat bewildered response to his publications in Britain and the United States between 1925 and the mid-1980s and goes on to say that ‘from now onwards it is in Scotland that Barth is taken with the greatest seriousness in the English speaking world’. In a later volume of centenary essays, R. H. Roberts traced the reception of the theology of Karl Barth ‘in the Anglo-Saxon world’ by quoting the evidence of such late 1920s and early 1930s figures as J. H. Morrison, John McConnachie, H. R. Mackintosh, Norman Porteous and A. J. MacDonald to claim that ‘it is clear from an early stage that enthusiasm for Barth's work … was primarily a Scottish attribute’. In another essay in the same volume, Colin Gunton contrasted the usual English attitude to Barth with that of theologians from other lands: ‘For the most part and despite exceptions’, he claimed, ‘the English find it difficult to come to terms with the theology of Karl Barth’, while in a companion volume Geoffrey Bromiley noted that this was hardly the case for theologians and pastors ‘in such diverse lands as Switzerland, Germany, France, Holland, Hungary, and Scotland’. Again and again, it is Scotland which is emphasised as being the place within the British Isles where Barth's ideals took root.
The Exodus Tradition and Israelite Psalmody
Authors: Gillingham Susan
Published: January 2009

It is impossible to read the first fifteen chapters of Exodus alongside the royal psalms and Zion hymns in the Psalter without noticing that very different perceptions of Israel's beginnings co-existed in the pre-exilic period. The Moses-Egypt tradition is about a wandering people, deprived of land and status, living under the promise of the protection offered by a nomadic clan-god; whilst the David-Zion tradition, fundamental to so many psalmists, concerns an established nation, a royal state cult which ratifies claims to land and status through its deity ‘housed’ in a Temple. And yet the Exodus tradition is used in a handful of psalms: the question thus arises — what purpose does it serve? Furthermore, why should the psalmists use such an anomalous tradition in this way?
Christian Morality?
Authors: Harvey Nicholas Peter
Published: January 2009

What follows is a set of reflections on the nature of Christian morality. Having been reared on and given allegiance to a morality which claimed to be rigorous, comprehensive and distinctively Christian, I have spent at least the last thirty years unlearning this in the light of experience and observation. The morality of my youth now appears as an ethics of boundaries rather than of transformation.
Johann Philipp Gabler and the Delineation of Biblical Theology
Authors: Stuckenbruck Loren T.
Published: January 2009

It has now been over 160 years since Johann philipp Gabler (1753–1826) was first credited with having ‘founded’ biblical theology as a discipline in its own right. Some ten years ago, as his 1787 inaugural address at Altdorf was being remembered, several scholars wrote articles which attempted to explore ways in which Gabler's proposals for biblical theology may be retained or, at least, may be interpreted as still relevant for current reflection. As these publications demonstrate, Gabler's methodological proposals have been capable of being interpreted with differing shades of emphasis. Behind such variance may well lie the likelihood that in coming to terms with the significance of forebearers out of the past, contemporaries in the biblical disciplines have found themselves articulating their own nuanced understandings concerning what ‘biblical theology’, if it denotes a task at all, should involve. The present article is no exception, as here I would like to propose a particular way of understanding Gabler. I shall thus (1) rehearse briefly some of the more basic antecedents to Gabler's formulations; (2) describe the contours of his proposals, beginning with his Altdorf address (Antrittsrede); (3) attempt to situate him within the context of late 18th-century German theology; and (4) comment briefly on the significance of his ideas in relation to the task of biblical theology.
New Testament Studies at the Turn of the Millennium: Questions for the Discipline
Authors: Hurtado Larry W.
Published: January 2009

In choosing the title for these reflections, I have attempted to note not only a transition in the occupant of the Chair of New Testament Language, Literature & Theology in the University of Edinburgh, but also the historic period in which this transition takes place, in the closing years of one millennium, approaching the threshold of a new one. In an effort to engage the interests of a wide circle of readers in various scholarly specialities, I have also chosen to discuss (though only in very limited depth) several major questions, each of which could occupy us for much longer than space here permits. I hope at least to underline their importance, and to sketch a rationale for the positions I shall advocate. I cannot hope that this sketch will persuade anyone not already inclined to my views, but I can perhaps indicate that they are not without reason. If a thorough treatment is not possible here, I shall at least endeavour to be clear, and this may better stimulate the reflections of others.
New Testament Interpretation as Performance
Authors: Barton Stephen C.
Published: January 2009

In recent study of the nature of NT interpretation, considerable attention in certain circles has been given to the possibility that there is one metaphor that is particularly appropriate for articulating what NT interpretation involves. It is the metaphor ofperformance. The purpose of this paper is to describe and develop this proposal and to give an assessment of it. To my knowledge, this is a task in biblical hermeneutics that has only just begun. If we ask why this is so, one possible answer lies in the fact that the proposal comes in the main from systematic and patristic theologians and therefore from outside the guild of biblical scholars. The consequence is that our customary division of labour inhibits us from attending with sufficient care to what our neighbours are saying even when it bears directly on our own work.
The Moral Crisis of the West: The Judaeo-Christian Response
Authors: Novak David
Published: January 2009

To speak of Jewish-Christian relations at the present time requires one to immediately recognise how different these relations are in this more secular period of the history of Western Civilisation than they were in earlier, more religious periods of that history. Jewish-Christian relations today are certainly different in character from the way they were during much of the past two millennia, when ‘Western Civilisation’ was very much a ‘Christian’ civilisation. Throughout this very long, earlier period of history, Jews related to Christians as the masters of the world in which we were continually struggling to survive and maintain our communal life.
Why Church?
Authors: Ford David F.
Published: January 2009

It is an honour and a delight to be this Society's President and I am immensely grateful for the privilege. I have been coming to the Society's Annual Meetings for about twenty-five years and I owe it more than I can express. It has acted as a basic network of colleagues which I have valued more and more as our conversations have been renewed year by year. It has been my main theological community beyond my church and the institutions in which I have studied and taught: it has been so good to have this broad, ecumenical intellectual community. It has offered a rich theological life, a diversity of theological positions and arguments, and a place where I have regularly engaged with the different generations in our field.
Baptismal Fluid
Authors: Loughlin Gerard
Published: January 2009

There is neither Jew nor Greek, there is neither bond nor free, there is neither male nor female; for ye are all one in Christ Jesus. (Galatians 3:28)
The Parable of the Rebellious Son(s)
Authors: Brown Colin
Published: January 2009

The parable which we know as as ‘The Parable of the Prodigal Son’ and which the Germans call ‘Das Gleichnis vom verlorenen Sohn’ is the best loved of all Jesus' parables. It has given inspiration to Rembrandt and countless other artists. It has provided the theme for novels, ballet and film. It touches the human condition like no other story. It holds a mirror up to ourselves, whether we identify ourselves with the returning prodigal or see those around us unmasked as the elder brother. The parable has been examined by the best exegetes of the past and present.
Theology and Music
Authors: Watson Francis
Published: January 2009

Our topic is theology and music — the conjunction expressing the modest hope that some useful demarcations and interactions maybe identifiable here. We are in no position to attempt, even in outline, a theology of music. Theologies of lay claim to a non-theological field in its entirety; they attempt to annex it, to re-establish it on what are taken to be its authentic theological foundations. They tend to find their most congenial subject-matter outside the normal sphere of the theological disciplines. But no theological annexation of music is conceivable or desirable. The question is rather whether any theologically worthwhile relationship between the two disciplines can be established at all. To pose this problem in its strongest form, I shall have little to say here about the use of music within the Christian community and its worship, confining myself to the more-or-less ‘secularized’ music of the European classical tradition of the past three hundred years or so. And I shall omit all consideration of the broader topic of ‘theology and the arts’. It does not seem particularly helpful to assume that such diverse practices as music, sculpture and drama are best considered in parallel to one another.
Faithful Dissenters? Feminist Ecclesiologies and Dissent
Authors: Watson Natalie
Published: January 2009

The title of this article contains a paradox which I have chosen deliberately and the meaning of which will become clear during the course of it. The topic is ‘Women in Dissent’. A number of meanings could be attributed to this title. It could either be understood as ‘Women in the dissenting or non-conformist tradition’ or it could mean ‘dissenting women’ which is the option I have chosen. I want to discuss whether or not feminism, or to be more precise, feminist theology, can be understood as a form of dissent or in what respects it differs from the forms of dissent that would normally be studied in the dissenting or non-conformist tradition.
On the Way from Schleiermacher to Barth: A Critical Reappraisal of Isaak August Dorner's Essay on Divine Immutability
Authors: Gockel Matthias
Published: January 2009

The theme of this article is the reconstruction of the doctrine of God offered by the German theologian and historian of doctrine Isaak August Dorner (1809–84), in his treatise ‘On the Proper Conception of the Doctrine of God's Immutability, with Special Reference to the Reciprocal Relation between God's Suprahistorical and Historical Life.’ Although the theme of God's immutability has received wide attention in the last years, Dorner's essay has gone largely unnoticed, and its contribution to the current debate still awaits appreciation. The following argument shall provide some building-blocks for this goal. It presupposes that Dorner's theology was shaped in dialogue with the thought of Schelling, Hegel, and Schleiermacher, but it will extend this perspective and ask for the particular systematic-theological link between Schleiermacher and Karl Barth that Dorner's essay represents.
Pneumatologia Crucis: Reclaiming Theologia Crucis for a Theology of the Spirit Today
Authors: Dabney D. Lyle
Published: January 2009

Of what are we speaking when we speak of the Holy Spirit? This most fundamental of all the questions asked in the field of Pneumatology has not received an answer widely accepted in the theology of the twentieth century. Karl Barth could write that the ‘Holy Spirit is nothing else than a certain relation of the Word to man’; while to Rudolph Bultmann, the Spirit was ‘the power of futurity,’ and was to be counted among the mythological forms of New Testament speech. Heribert Mühlen, on the other hand, interpreting the Latin pneumatological tradition in terms of the personalism of Ebner and Bubner, calls the Spirit ‘we,’ the unity of T and ‘thou.’ And David Gelpi reflects current feminist concerns when he designates God's Spirit as ‘The Divine Mother,’ the feminine in God. Finally, most recendy, Michael Welker has adopted the language of the natural sciences mediated through process thought and calls the Holy Spirit a ‘force field,’ while Jürgen Moltmann terms God's Spirit ‘the Spirit of Life’; a notion echoed in Mark Wallace's thesis that the Spirit is ‘the power of life-giving breath (r¨ah) within the cosmos who continually works to transform and renew all forms of life—both human and nonhuman.‘
UNIT ROOT TESTING IN PRACTICE: DEALING WITH UNCERTAINTY OVER THE TREND AND INITIAL CONDITION
Authors: Harvey David I. , Leybourne Stephen J. , Taylor A.M. Robert
Published: January 2009

In this paper we focus on two major issues that surround testing for a unit root in practice, namely, (i) uncertainty as to whether or not a linear deterministic trend is present in the data and (ii) uncertainty as to whether the initial condition of the process is (asymptotically) negligible or not. In each case simple testing procedures are proposed with the aim of maintaining good power properties across such uncertainties. For the first issue, if the initial condition is negligible, quasi-differenced (QD) detrended (demeaned) Dickey–Fuller-type unit root tests are near asymptotically efficient when a deterministic trend is (is not) present in the data generating process. Consequently, we compare a variety of strategies that aim to select the detrended variant when a trend is present, and the demeaned variant otherwise. Based on asymptotic and finite-sample evidence, we recommend a simple union of rejections-based decision rule whereby the unit root null hypothesis is rejected whenever either of the detrended or demeaned unit root tests yields a rejection. Our results show that this approach generally outperforms more sophisticated strategies based on auxiliary methods of trend detection. For the second issue, we again recommend a union of rejections decision rule, rejecting the unit root null if either of the QD or ordinary least squares (OLS) detrended/demeaned Dickey–Fuller-type tests rejects. This procedure is also shown to perform well in practice, simultaneously exploiting the superior power of the QD (OLS) detrended/demeaned test for small (large) initial conditions.
ALMOST SURE BOUNDS ON THE ESTIMATION ERROR FOR OLS ESTIMATORS WHEN THE REGRESSORS INCLUDE CERTAIN MFI(1) PROCESSES
Authors: Bauer Dietmar
Published: January 2009

Lai and Wei (1983, Annals of Statistics 10, 154–166) state in their Theorem 1 that the estimators of the regression coefficients in the regression $y_t = x_t^' \beta + \varepsilon _{\rm{t}} $, t ∈ ℕ are almost surely (a.s.) consistent under the assumption that the minimum eigenvalue λmin(T) of $\sum\nolimits_{t = 1}^T {x_t } x'_t $ tends to infinity (a.s.) and log(λmax(T))/λmin(T) → 0 (a.s.) where λmax(T) denotes the maximal eigenvalue. Moreover the rate of convergence in this case equals $O(\root \of {\log (\lambda _{max} (T))/\lambda _{min} (T)})$. In this note xt is taken to be a particular multivariate multifrequency I(1) processes, and almost sure rates of convergence for least squares estimators are established.
Justifications for logic programs under answer set semantics
Authors: PONTELLI ENRICO , SON TRAN CAO , ELKHATIB OMAR
Published: January 2009

The paper introduces the notion of offline justification for answer set programming (ASP). Justifications provide a graph-based explanation of the truth value of an atom with respect to a given answer set. The paper extends also this notion to provide justification of atoms during the computation of an answer set (on-line justification) and presents an integration of online justifications within the computation model of Smodels. Offline and online justifications provide useful tools to enhance understanding of ASP, and they offer a basic data structure to support methodologies and tools for debugging answer set programs. A preliminary implementation has been developed in – .
Interprétation de l'arithmétique dans certains groupes de permutations affines par morceaux d'un intervalle
Authors: Altinel Tuna , Muranov Alexey
Published: January 2009

L'arithmétique est interprétée dans tous les groupes de Richard Thompson et de Graham Higman, aussi bien que dans d'autres groupes des permutations affines par morceaux d'un intervalle qui généralisent les groupes de Thompson et de Higman. En particulier, les théories élémentaires de tous ces groupes sont indécidables. De plus, le groupeFde Thompson et certaines de ses généralisations interprètent l'arithmétique sans paramètres.
PresqueCp-représentations et (ϕ,Γ)-modules
Authors: Berger Laurent
Published: January 2009

On associe deuxyy presqueCp-représentations à un (ϕΓ)-module, et on en calcule les dimensions et les hauteurs. Comme corollaire, on obtient un résultat de pleine fidélité pour lesBe-représentations.
Triggering the formation of tasiRNAs in Arabidopsis thaliana: the role of microRNA miR173
Authors: Felippes Felipe F , Weigel Detlef
Published: January 2009

Trans‐acting small interfering RNAs (tasiRNAs) comprise a class of endogenous small RNAs that are generated from TAS gene‐derived transcripts after these are cleaved at a microRNA (miRNA) target site. Arabidopsis thaliana has four families of TAS genes: miR173 triggers tasiRNA production from TAS1 and TAS2, miR390 from TAS3 and miR828 from TAS4. The two‐hit trigger model postulates that dual target sites in the same transcript are often sufficient to initiate tasiRNA production, but two hits are not always required for tasiRNA formation. Here, we characterize the function of miR173 in the formation of tasiRNAs from TAS1 transcripts, as well as the importance of the TAS1 and TAS3 transcript sequences outside the miRNA‐targeting sites for tasiRNA production. We show that tasiRNAs can be produced from heterologous transcripts containing miR173 or miR390 target sites, indicating that these trigger sequences are the only cis sequences essential for tasiRNA formation.
Action to Reduce Worklessness: What Works?
Authors: Green Anne E. , Hasluck Chris
Published: January 2009

Addressing local concentrations of worklessness is an ongoing challenge for policy at national, regional and local levels. The paper outlines the changing nature of worklessness, the rationale for supply-side and demand-side interventions to address it and the balance between people- and place-based policies. It discusses the issues involved in assessing the contribution of interventions to reduce worklessness and highlights key lessons emerging from a review of the evidence on ‘what works’. While no single model of successful intervention is identified, the importance of outreach, holistic approaches, individualisation and the position of personal advisers, continuing support, flexibility, motivation and aspirations, partnership working and the role of employers is highlighted.
Governing the Skills Agenda: Insights from the Sheffield City-Region
Authors: Jones Martin , Etherington David
Published: January 2009

Skills are currently riding high on the political agenda and major changes are underway with respect to regulation and governance. We explore developments taking place in the Sheffield city-region, particularly the ‘skills strategy for Sheffield’ and its governance. We suggest that city-regions reinforce, and have the potential to increase, rather than resolve, the uneven development of labour markets and interlinked socio-spatial inequalities.
SECISaln, a web-based tool for the creation of structure-based alignments of eukaryotic SECIS elements
Authors: Chapple Charles E. , Guigó Roderic , Krol Alain
Published: January 2009

Summary: Selenoproteins contain the 21st amino acid selenocysteine which is encoded by an inframe UGA codon, usually read as a stop. In eukaryotes, its co-translational recoding requires the presence of an RNA stem–loop structure, the SECIS element in the 3 untranslated region of (UTR) selenoprotein mRNAs. Despite little sequence conservation, SECIS elements share the same overall secondary structure. Until recently, the lack of a significantly high number of selenoprotein mRNA sequences hampered the identification of other potential sequence conservation. In this work, the web-based tool SECISaln provides for the first time an extensive structure-based sequence alignment of SECIS elements resulting from the well-defined secondary structure of the SECIS RNA and the increased size of the eukaryotic selenoproteome. We have used SECISaln to improve our knowledge of SECIS secondary structure and to discover novel, conserved nucleotide positions and we believe it will be a useful tool for the selenoprotein and RNA scientific communities.

Availability: SECISaln is freely available as a web-based tool at http://genome.crg.es/software/secisaln/.

Contact:  charles.chapple@crg.es

Supplementary information:  Supplementary data are available at Bioinformatics online.
‘Double water exclusion’: a hypothesis refining the O-ring theory for the hot spots at protein interfaces
Authors: Li Jinyan , Liu Qian
Published: January 2009

Motivation: The O-ring theory reveals that the binding hot spot at a protein interface is surrounded by a ring of residues that are energetically less important than the residues in the hot spot. As this ring of residues is served to occlude water molecules from the hot spot, the O-ring theory is also called ‘water exclusion’ hypothesis. We propose a ‘double water exclusion’ hypothesis to refine the O-ring theory by assuming the hot spot itself is water-free. To computationally model a water-free hot spot, we use a biclique pattern that is defined as two maximal groups of residues from two chains in a protein complex holding the property that every residue contacts with all residues in the other group.

Methods and Results: Given a chain pair A and B of a protein complex from the Protein Data Bank (PDB), we calculate the interatomic distance of all possible pairs of atoms between A and B. We then represent A and B as a bipartite graph based on these distance information. Maximal biclique subgraphs are subsequently identified from all of the bipartite graphs to locate biclique patterns at the interfaces. We address two properties of biclique patterns: a non-redundant occurrence in PDB, and a correspondence with hot spots when the solvent-accessible surface area (SASA) of a biclique pattern in the complex form is small. A total of 1293 biclique patterns are discovered which have a non-redundant occurrence of at least five, and which each have a minimum two and four residues at the two sides. Through extensive queries to the HotSprint and ASEdb databases, we verified that biclique patterns are rich of true hot residues. Our algorithm and results provide a new way to identify hot spots by examining proteins' structural data.

Availability: The biclique mining algorithm is available at http://www.ntu.edu.sg/home/jyli/dwe.html.

Contact:  jyli@ntu.edu.sg

Supplementary information:  Supplementary data are available at Bioinformatics online.
Computing Response Metrics for Online Panels
Authors: Callegaro Mario , DiSogra Charles
Published: January 2009

As more researchers use online panels for studies, the need for standardized rates to evaluate these studies becomes paramount. There are currently many different ways and conflicting terminology used to compute various metrics for online panels. This paper discusses the sparse literature on how to compute response, refusal, and other rates and proposes a set of formulas and a standardized terminology that can be used to calculate and interpret these metrics for online panel studies. A description of and distinction between probability-based and volunteer opt-in panels is made since not all metrics apply to both types. A review of the existing discussion and recommendations, mostly from international organizations, is presented for background and context. In order to propose response and other metrics, the different stages involved in building an online panel are delineated. Metrics associated with these stages contribute to cumulative response rate formulas that can be used to evaluate studies using online probability-based panels. (Only completion rates can be calculated with opt-in panels.) We conclude with a discussion of the meaning of the different metrics proposed and what we think should be reported for which type of panel.
Integrating computing, data and collaboration grids: the RMCS tool
Authors: Walker A.M , Bruin R.P , Dove M.T , White T.O.H , Kleese van Dam K , Tyer R.P
Published: January 2009

We describe RMCS as one of the first tools for grid computing that integrates data and metadata management into a single job submission system. The system is easy to use, with client tools that are easy to install. Although the RMCS system was developed as a prototype, it is now in production use and a number of scientific studies have been completed using it.
Using GENIE to study a tipping point in the climate system
Authors: Lenton Timothy M , Myerscough Richard J , Marsh Robert , Livina Valerie N , Price Andrew R , Cox Simon J ,   the GENIE Team
Published: January 2009

We have used the Grid ENabled Integrated Earth system modelling framework to study the archetypal example of a tipping point in the climate system; a threshold for the collapse of the Atlantic thermohaline circulation (THC). eScience has been invaluable in this work and we explain how we have made it work for us. Two stable states of the THC have been found to coexist, under the same boundary conditions, in a hierarchy of models. The climate forcing required to collapse the THC and the reversibility or irreversibility of such a collapse depends on uncertain model parameters. Automated methods have been used to assimilate observational data to constrain the pertinent parameters. Anthropogenic climate forcing leads to a robust weakening of the THC and increases the probability of crossing a THC tipping point, but some ensemble members collapse readily, whereas others are extremely resistant. Hence, we test general methods that have been developed to directly diagnose, from time-series data, the proximity of a ‘tipping element’, such as the THC to a bifurcation point. In a three-dimensional ocean–atmosphere model exhibiting THC hysteresis, despite high variability in the THC driven by the dynamical atmosphere, some early warning of an approaching tipping point appears possible.
Decadal climate prediction (project GCEP)
Authors: Haines Keith , Hermanson Leon , Liu Chunlei , Putt Debbie , Sutton Rowan , Iwi Alan , Smith Doug
Published: January 2009

Decadal prediction uses climate models forced by changing greenhouse gases, as in the International Panel for Climate Change, but unlike longer range predictions they also require initialization with observations of the current climate. In particular, the upper-ocean heat content and circulation have a critical influence. Decadal prediction is still in its infancy and there is an urgent need to understand the important processes that determine predictability on these timescales. We have taken the first Hadley Centre Decadal Prediction System (DePreSys) and implemented it on several NERC institute compute clusters in order to study a wider range of initial condition impacts on decadal forecasting, eventually including the state of the land and cryosphere. The eScience methods are used to manage submission and output from the many ensemble model runs required to assess predictive skill. Early results suggest initial condition skill may extend for several years, even over land areas, but this depends sensitively on the definition used to measure skill, and alternatives are presented. The Grid for Coupled Ensemble Prediction (GCEP) system will allow the UK academic community to contribute to international experiments being planned to explore decadal climate predictability.
Running climate models on grids using G-R
ex
Authors: Bretherton D.A , Blower J.D , Haines K , Smith G.C
Published: January 2009

Compute grids are used widely in many areas of environmental science, but there has been limited uptake of grid computing by the climate modelling community, partly because the characteristics of many climate models make them difficult to use with popular grid middleware systems. In particular, climate models usually produce large volumes of output data, and running them also involves complicated workflows implemented as shell scripts. A new grid middleware system that is well suited to climate modelling applications is presented in this paper.
Grid Remote Execution
(G-
Rex
) allows climate models to be deployed as Web services on remote computer systems and then launched and controlled as if they were running on the user's own computer. Output from the model is transferred back to the user while the run is in progress, to prevent it from accumulating on the remote system and to allow the user to monitor the model. G-
Rex
has a representational state transfer (REST) architectural style, featuring a Java client program that can easily be incorporated into existing scientific workflow scripts. Some technical details of G-
Rex
are presented, with examples of its use by climate modellers.
Land surface anomaly simulations and predictions with a climate model: an El Niño Southern Oscillation case study
Authors: Putt Debbie , Haines Keith , Gurney Robert , Liu Chunlei
Published: January 2009

The ability of climate models to reproduce and predict land surface anomalies is an important but little-studied topic. In this study, an atmosphere and ocean assimilation scheme is used to determine whether HadCM3 can reproduce and predict snow water equivalent and soil moisture during the 1997–1998 El Niño Southern Oscillation event. Soil moisture is reproduced more successfully, though both snow and soil moisture show some predictability at 1- and 4-month lead times. This result suggests that land surface anomalies may be reasonably well initialized for climate model predictions and hydrological applications using atmospheric assimilation methods over a period of time.
Storm tracking and eScience
Authors: Froude Lizzie
Published: January 2009

A new ‘storm-tracking approach’ to analysing the prediction of storms by different forecast systems has recently been developed. This paper provides a brief illustration of the type of results/information that can be obtained using the approach. It also describes in detail how eScience methodologies have been used to help apply the storm-tracking approach to very large datasets.
Computational provenance in hydrologic science: a snow mapping example
Authors: Dozier Jeff , Frew James
Published: January 2009

Computational provenance—a record of the antecedents and processing history of digital information—is key to properly documenting computer-based scientific research. To support investigations in hydrologic science, we produce the daily fractional snow-covered area from NASA's moderate-resolution imaging spectroradiometer (MODIS). From the MODIS reflectance data in seven wavelengths, we estimate the fraction of each 500 m pixel that snow covers. The daily products have data gaps and errors because of cloud cover and sensor viewing geometry, so we interpolate and smooth to produce our best estimate of the daily snow cover. To manage the data, we have developed the Earth System Science Server (ES
3
), a software environment for data-intensive Earth science, with unique capabilities for automatically and transparently capturing and managing the provenance of arbitrary computations. Transparent acquisition avoids the scientists having to express their computations in specific languages or schemas in order for provenance to be acquired and maintained. ES
3
models provenance as relationships between processes and their input and output files. It is particularly suited to capturing the provenance of an evolving algorithm whose components span multiple languages and execution environments.
Modelling the global coastal ocean
Authors: Holt Jason , Harle James , Proctor Roger , Michel Sylvain , Ashworth Mike , Batstone Crispian , Allen Icarus , Holmes Robert , Smyth Tim , Haines Keith , Bretherton Dan , Smith Gregory
Published: January 2009

Shelf and coastal seas are regions of exceptionally high biological productivity, high rates of biogeochemical cycling and immense socio-economic importance. They are, however, poorly represented by the present generation of Earth system models, both in terms of resolution and process representation. Hence, these models cannot be used to elucidate the role of the coastal ocean in global biogeochemical cycles and the effects global change (both direct anthropogenic and climatic) are having on them. Here, we present a system for simulating all the coastal regions around the world (the Global Coastal Ocean Modelling System) in a systematic and practical fashion. It is based on automatically generating multiple nested model domains, using the Proudman Oceanographic Laboratory Coastal Ocean Modelling System coupled to the European Regional Seas Ecosystem Model. Preliminary results from the system are presented. These demonstrate the viability of the concept, and we discuss the prospects for using the system to explore key areas of global change in shelf seas, such as their role in the carbon cycle and climate change effects on fisheries.
The computational future for climate and Earth system models: on the path to petaflop and beyond
Authors: Washington Warren M , Buja Lawrence , Craig Anthony
Published: January 2009

The development of the climate and Earth system models has had a long history, starting with the building of individual atmospheric, ocean, sea ice, land vegetation, biogeochemical, glacial and ecological model components. The early researchers were much aware of the long-term goal of building the Earth system models that would go beyond what is usually included in the climate models by adding interactive biogeochemical interactions. In the early days, the progress was limited by computer capability, as well as by our knowledge of the physical and chemical processes. Over the last few decades, there has been much improved knowledge, better observations for validation and more powerful supercomputer systems that are increasingly meeting the new challenges of comprehensive models. Some of the climate model history will be presented, along with some of the successes and difficulties encountered with present-day supercomputer systems.
Information in environmental data grids
Authors: Lawrence B.N , Lowry R , Miller P , Snaith H , Woolf A
Published: January 2009

Providing homogeneous access (‘services’) to heterogeneous environmental data distributed across heterogeneous computing systems on a wide area network requires a robust information paradigm that can mediate between differing storage and information formats. While there are a number of ISO standards that provide some guidance on how to do this, the information landscape within domains is not well described. In this paper, we present an information taxonomy and two information components, which have been built for a specific application. These two components, one to aid data understanding and the other to aid data manipulation, are both deployed in the UK NERC DataGrid as described elsewhere.
Dentate gyrus-specific knockdown of adult neurogenesis impairs spatial and object recognition memory in adult rats
Authors: Jessberger Sebastian , Clark Robert E. , Broadbent Nicola J. , Clemenson Gregory D. , Consiglio Antonella , Lie D. Chichung , Squire Larry R. , Gage Fred H.
Published: January 2009

New granule cells are born throughout life in the dentate gyrus of the hippocampal formation. Given the fundamental role of the hippocampus in processes underlying certain forms of learning and memory, it has been speculated that newborn granule cells contribute to cognition. However, previous strategies aiming to causally link newborn neurons with hippocampal function used ablation strategies that were not exclusive to the hippocampus or that were associated with substantial side effects, such as inflammation. We here used a lentiviral approach to specifically block neurogenesis in the dentate gyrus of adult male rats by inhibiting WNT signaling, which is critically involved in the generation of newborn neurons, using a dominant-negative WNT (dnWNT). We found a level-dependent effect of adult neurogenesis on the long-term retention of spatial memory in the water maze task, as rats with substantially reduced levels of newborn neurons showed less preference for the target zone in probe trials >2 wk after acquisition compared with control rats. Furthermore, animals with strongly reduced levels of neurogenesis were impaired in a hippocampus-dependent object recognition task. Social transmission of food preference, a behavioral test that also depends on hippocampal function, was not affected by knockdown of neurogenesis. Here we identified a role for newborn neurons in distinct aspects of hippocampal function that will set the ground to further elucidate, using experimental and computational strategies, the mechanism by which newborn neurons contribute to behavior.
Boundary conditions for the maintenance of memory by PKMζ in neocortex
Authors: Shema Reut , Hazvi Shoshi , Sacktor Todd C. , Dudai Yadin
Published: January 2009

We report here that ZIP, a selective inhibitor of the atypical protein kinase C isoform PKMζ, abolishes very long-term conditioned taste aversion (CTA) associations in the insular cortex of the behaving rat, at least 3 mo after encoding. The effect of ZIP is not replicated by a general serine/threonine protein kinase inhibitor that is relatively ineffective toward PKMζ, is independent of the intensity of training and the perceptual quality of the taste saccharin (conditioned stimulus, CS), and does not affect the ability of the insular cortex to re-encode the same specific CTA association again. The memory trace is, however, insensitive to ZIP during or immediately after training. This implies that the experience-dependent cellular plasticity mechanism targeted by ZIP is established following a brief time window after encoding, consistent with the standard period of cellular consolidation, but then, once established, does not consolidate further to gain immunity to the amnesic agent. Hence, we conclude that PKMζ is not involved in short-term CTA memory, but is a critical component of the cortical machinery that stores long- and very long-term CTA memories.
Stress disrupts context-dependent memory
Authors: Schwabe Lars , Böhringer Andreas , Wolf Oliver T.
Published: January 2009

Memory is facilitated when the retrieval context resembles the learning context. The brain structures underlying contextual influences on memory are susceptible to stress. Whether stress interferes with context-dependent memory is still unknown. We exposed healthy adults to stress or a control procedure before they learned an object-location task in a room scented with vanilla. Memory was tested 24 h later, either in the same or in a different context (unfamiliar room without the odor). Stress administered prior to encoding abolished the context-dependent memory enhancement found in the control group. Thus, these findings represent the first demonstration of impaired context-dependent memory following stress.
Activity-dependent calpain activation plays a critical role in synaptic facilitation and post-tetanic potentiation
Authors: Khoutorsky Arkady , Spira Micha E.
Published: January 2009

Synaptic facilitation and post-tetanic potentiation (PTP) are believed to necessitate active regeneration of the release machinery and supply of synaptic vesicles to a ready-releasable site. The prevailing hypothesis assumes that synapsins play pivotal roles in these processes. Using a cholinergic synapse formed between cultured Aplysia neurons (B2 and MCn), we demonstrate here that the calcium-activated protease-calpain serves as a major regulating element in the cascade that links electrical activity, elevation of the free intracellular calcium concentration, and short-term synaptic enhancements such as facilitation and PTP. Our study revealed that calpain inhibitors (calpeptin and MG132) transform a facilitating synapse into a depressing one, and reduce its PTP by 80.6%. Inhibition of CaM kinases, PKA, and MAPK also reduced PTP at this synapse. When inhibitors of these kinases were applied together with calpeptin, tetanic stimuli led to synaptic depression. We concluded that at this synapse facilitation and PTP are mediated mainly by the calpain-dependent processes and to a smaller extent by the CaMKs/PKA/MAPK-dependent cascades.
Evaluation of the continuum of gambling problems using the DSM‐IV
Authors: Strong David R. , Kahler Christopher W.
Published: January 2009

Aims  To assess the measurement properties of the 10 symptoms of pathological gambling defined by the Diagnostic and Statistical Manual of Mental Disorders, fourth edition (DSM‐IV) in a general population survey, including examination of unidimensionality and relative severity of the symptoms and their typical patterning.

Design  We conducted a Rasch model item–response analysis of data from the National Epidemiologic Survey on Alcohol and Related Conditions (NESARC).

Setting  The NESARC surveyed a nationally representative sample from the United States.

Participants  Participants were 11 153 individuals who reported gambling more than five times in a single year.

Measurements  The NESARC survey employed the Alcohol Use Disorder and Associated Disability Interview Schedule‐DSM‐IV version (AUDADIS‐IV).

Findings and conclusions  DSM‐IV problem gambling symptoms were strongly unidimensional and maintained a reliable ordering across a broad range of the problem gambling continuum, indicating that the 10 symptoms can be used to create an additive index of problem severity. The DSM‐IV‐based symptom index appeared to have sufficient reliability to separate life‐time pathological gamblers from other gamblers using the current diagnostic threshold of five or more symptoms. However, the DSM‐IV symptom index did not have sufficient reliability to separate further among groups of gamblers who reported fewer than five symptoms. After equating for the level of gambling problem severity, the likelihood of reporting certain symptoms was biased across groups characterized by their age and gender. Implications for understanding the construct of gambling problems severity and use of symptom counts as a continuous index are discussed.