bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unraveling assembly of stream biofilm communities
Authors: Besemer Katharina , Peter Hannes , Logue Jürg B , Langenheder Silke , Lindström Eva S , Tranvik Lars J , Battin Tom J 
Published: January 2012

Abstract
Microbial biofilms assemble from cells that attach to a surface, where they develop into matrix-enclosed communities. Mechanistic insights into community assembly are crucial to better understand the functioning of natural biofilms, which drive key ecosystem processes in numerous aquatic habitats. We studied the role of the suspended microbial community as the source of the biofilm community in three streams using terminal-restriction fragment length polymorphism and 454 pyrosequencing of the 16S ribosomal RNA (rRNA) and the 16S rRNA gene (as a measure for the active and the bulk community, respectively). Diversity was consistently lower in the biofilm communities than in the suspended stream water communities. We propose that the higher diversity in the suspended communities is supported by continuous inflow from various sources within the catchment. Community composition clearly differed between biofilms and suspended communities, whereas biofilm communities were similar in all three streams. This suggests that biofilm assembly did not simply reflect differences in the source communities, but that certain microbial groups from the source community proliferate in the biofilm. We compared the biofilm communities with random samples of the respective community suspended in the stream water. This analysis confirmed that stochastic dispersal from the source community was unlikely to shape the observed community composition of the biofilms, in support of species sorting as a major biofilm assembly mechanism. Bulk and active populations generated comparable patterns of community composition in the biofilms and the suspended communities, which suggests similar assembly controls on these populations.
First evidence for the existence of pennate diatom viruses
Authors: Tomaru Yuji , Toyoda Kensuke , Kimura Kei , Hata Naotsugu , Yoshida Mikihide , Nagasaki Keizo 
Published: January 2012

Abstract
Diatoms are considered the most successful and widespread group of photosynthetic eukaryotes. Their contribution to primary production is remarkably significant to the earth's ecosystems. Diatoms are composed of two orders: Centrales and Pennales. Thus far, viruses infecting centric diatom species have been isolated and characterized; however, viruses infecting pennates have not been reported. Here, we describe the first isolations and preliminary characterizations of two distinct pennate diatom viruses, AglaRNAV (31 nm in diameter, accumulates in the host cytoplasm) and TnitDNAV (35 nm in diameter, accumulates in the host nuclei) infecting Asterionellopsis glacialis and Thalassionema nitzschioides, respectively. Their genomes contain a single-stranded RNA of approximately 9.5 kb, and a closed, circular single-stranded DNA of approximately 5.5 kb harboring a partially double-stranded region, respectively. Further analysis of these viruses may elucidate many aspects of diatom host–virus relationships.
Is an elevated submaximal heart rate associated with psychomotor slowness in young elite soccer players?
Authors: Brink Michel S. , Visscher Chris , Schmikli Sandor L. , Nederhof E. , Lemmink Koen A. P. M. 
Published: January 2012

AbstractThe aim of the present study was to find early markers for overreaching that are applicable in sport practice. In a group of elite soccer players aged 15–18, the stress–recovery balance and reaction times before and after exercise were assessed. Overreaching was indicated by an elevated submaximal heart rate during a sport‐specific field test. Submaximal changes in heart rate were prospectively monitored by means of monthly Interval Shuttle Run Tests during two competitive seasons. Out of 94 players, seven players with an elevated heart rate of at least one month could be included in the study, together with seven controls, matched for age, body composition, training and performance level. The stress–recovery balance was assessed with the Dutch version of the Recovery Stress Questionnaire (RESTQ‐Sport). The soccer players with an elevated heart rate reported a disturbed stress–recovery balance (Mann–Whitney test, P<0.05). An ANOVA for repeated measures of reaction times revealed a significant main effect of time (F 1,12=13.87, P<0.01) indicating an improvement of psychomotor speed. No differences between groups were found. We conclude that soccer players with an elevated submaximal heart rate of at least one month share a disturbed stress–recovery balance, but they could not be distinguished from controls based on reaction time after strenuous exercise.
CHROMATRA: a Galaxy tool for visualizing genome-wide chromatin signatures
Authors: Hentrich Thomas , Schulze Julia M. , Emberly Eldon , Kobor Michael S. 
Published: January 2012

Abstract
Summary: CHROMATRA (CHROmatin Mapping Across TRAnscripts) is a visualization tool available as plug-in for the Galaxy platform. It allows detailed yet concise presentations of data derived from ChIP-chip or ChIP-seq experiments by visualizing enrichment scores across genes or other genomic features while accounting for their length and additional characteristics such as gene expression. It integrates into typical analysis workflows and enables rapid graphical assessment and comparison of genome-wide data at a glance.
Availability: https://github.com/cmmt/chromatra
Contact: msk@cmmt.ubc.ca; eemberly@sfu.ca
MSY-orientated management of Baltic Sea herring (Clupea harengus) during different ecosystem regimes
Authors: Holmgren Noel M. A. , Norrström Niclas , Aps Robert , Kuikka Sakari 
Published: January 2012

Abstract
Holmgren, N. M. A., Norrström, N., Aps, R., and Kuikka, S. 2012. MSY-orientated management of Baltic Sea herring (Clupea harengus) during different ecosystem regimes. – ICES Journal of Marine Science, 69: 257–266. The Baltic Sea ecosystem has undergone dramatic changes, so-called ecosystem regime shifts, during the past four decades. Baltic Sea herring (Clupea harengus) spawning-stock biomass has declined to a third, and weight-at-age has halved as a result of food shortages and competition with sprat (Sprattus sprattus). The management objective for the herring stock is currently in transition from precautionary to maximum sustainable yield (MSY). The main basin Baltic Sea herring was modelled under the current ecosystem regime and the effect of a recovery of the cod (Gadus morhua) stock and the availability of planktonic food to levels found in the early 1980s analysed. A target of FMSY = 0.16 for herring, which should decline to FMSY = 0.10 with recovery of the cod stock, is proposed. An increase in the availability of planktonic food is estimated to more than double the yield at FMSY = 0.27, overriding the negative effects of cod predation should there be a simultaneous increase in both cod and availability of planktonic food. The estimated net increase in yield is 40% at FMSY = 0.20. Functions are presented to calculate FMSY and to estimate the expected yield depending on the abundance of cod and food availability. Retrospective application of the functions is indicative of overfishing of herring in the 1990s and early 2000s, and a net loss in yield, with a landing value of some €440 million.
Beyond the God/Man Duo: Globalization, Feminist Theology, and Religious Subjectivity
Authors: Armour Ellen T. 
Published: January 2012

Abstract
This chapter considers analyses offered by three important feminist scholars, working in different religious traditions, who attend to specific forms of women's religiosity. In Changing the Subject: Women's Discourses and Feminist Theology, Mary McClintock Fulkerson attempts to carve out a place within feminist theology for Christian women who do not consider themselves feminist. In The Hammer and the Flute: Women, Power and Spirit Possession, Mary Keller's analysis of the phenomenon of spirit possession, which affects many more women than men, becomes a site in which to reflect anew on questions of gender and religious subjectivity. In Politics of Piety: The Islamic Revival and the Feminist Subject, anthropologist Saba Mahmood finds that the issues raised by her study of Egyptian women involved in an Islamic renewal movement challenge certain feminist orthodoxies. Taking each author in turn, the chapter first traces the particular contours of the religious phenomenon each analyzes and shows how they reframe religious subjectivity. The final section brings the three essays together and describes what avenues they open up for constructive feminist theology in a global context.
Doing a Theology from Disappeared Bodies: Theology, Sexuality, and the Excluded Bodies of the Discourses of Latin American Liberation Theology
Authors: Althaus‐Reid Marcella 
Published: January 2012

Abstract
This chapter begins by considering the contributions of feminist theologies. It then discusses Liberation Theology, a theology reflecting on the concrete site of bodies in suffering, and looks at what a Queer Liberation Theology, concerned with issues of politics and sexuality, can contribute both to the Liberation Theology project and to the Feminist Liberation Theology movement. This is followed by a discussion of bisexuality and Latin American liberation spirituality, and the so-called “the postcolonial queer twist.” It is argued that the unveiling of ideology in theology also applies to Feminist Liberation Theology itself, and to its own ideological presuppositions. If our theological projects are nurtured by the understanding that theology is a second act, then Feminist Liberation Theology needs to take more seriously the fact that a critical reflection on women's material lives and experiences is the starting point and the only valid agenda of our theological reflections; this includes women's sexualities. Feminist Liberation Theology's own poiesis (or sense of creation) should come from that. In a way, this is the kind of theology that allows God to be God, by allowing people “to come as they are,” too, beyond the politics of ideal theological constructions.
Wittgenstein and Infinity
Authors: Moore Adrian W. 
Published: January 2012

Abstract
The aim of this paper is to give an overview of Wittgenstein’s conception of the infinite. One focus of the paper is Wittgenstein’s rejection of what is dubbed a ‘realist’ model of our idea of the infinite. On this model our idea is the source of beliefs that we have about an independent reality. Another focus is the way in which Wittgenstein’s rejection of this model leads him to reject the idea of the infinite itself as it appears in certain mathematical contexts. I argue that these two rejections can be uncoupled: abandonment of the realist model of our idea of the infinite is consonant with full endorsement of the use to which mathematicians put the idea. There remains scope for Wittgenstein to take issue, if not with the use to which mathematicians put the idea, then with their choice of language in doing so, something that he has reason to do precisely because this choice encourages adoption of the realist model.
Logical Atomism in Russell and Wittgenstein
Authors: Proops Ian 
Published: January 2012

Abstract
Bertrand Russell and Ludwig Wittgenstein developed different, though closely related, versions of logical atomism. Wittgenstein's version is presented in Tractatus Logico-Philosophicus, and discussed in the various pre-Tractatus manuscripts. For Russell, analytical realism is a form of atomism because it maintains that the existence of the complex depends on the existence of the simple and not vice versa, and that the atomic entities in its ontology (universals and particulars) have their nature quite independently of the relations they bear to one another. The core tenets of Wittgenstein's logical atomism may be summarised as follows: Every proposition has a unique final analysis that reveals it to be a truth-function of elementary propositions; These elementary propositions assert the existence of atomic states of affairs; Elementary propositions are mutually independent — each one can be true or false independently of the truth or falsity of the others; Elementary propositions are immediate combinations of semantically simple symbols or ‘names’; Names refer to items wholly devoid of complexity, so-called ‘objects’; Atomic states of affairs are combinations of these simple objects.
Private Language
Authors: Stern David 
Published: January 2012

Abstract
Ludwig Wittgenstein's treatment of private language has received more attention than any other aspect of his philosophy. Yet, for more than fifty years, a remarkably self-contained exegetical tradition has defined the terms of debate and the principal positions that are discussed. Orthodox interpreters hold that the proof that a private language is impossible turns on showing it is ruled out by some set of systematic philosophical commitments about logic, meaning, and knowledge. Leading candidates for this ground on which the argument depends have included the analysis of concepts, the grammar of our everyday language, the logic of criteria, or the nature of our rule-following, practical activity, or form of life. This article introduces an alternative interpretive tradition, which not only rejects the orthodox methodology, but also rejects the presupposition that Wittgenstein's principal aim is to provide a deductive proof that the idea of a private language leads to contradiction. Finally, it examines some of the leading readings of Philosophical Investigations §258, the passage most frequently discussed by orthodox interpreters.
Wittgenstein's Methods
Authors: Conant James 
Published: January 2012

Abstract
This article explores the relation between the philosophies of the early and the later Ludwig Wittgenstein as they are standardly distinguished, with the aim of raising some questions about whether that standard distinction might not obstruct our view of certain significant aspects of the development of Wittgenstein's thought. Drawing on the work of Marie McGinn and Warren Goldfarb, it also distinguishes two senses in which these two commentators have been moved to call upon the expression ‘piecemeal’ in their respective attempts to characterise an important feature of Wittgenstein's conception of philosophical method. In August 1936, Wittgenstein withdrew to a tiny hut in Skjolden, Norway, in order to be able to continue his work on the Philosophical Investigations in complete solitude. His conception of method in philosophy underwent more than one Kehre, more than one revolution. It therefore precludes the possibility that his conception of philosophy itself could have undergone significant further metamorphosis while he was in Norway in 1937.
Wittgenstein's Use of Examples
Authors: Savickey Beth 
Published: January 2012

Abstract
As Ludwig Wittgenstein moves from Tractatus Logico-Philosophicus to Philosophical Investigations, he dramatically alters his use of examples. His early work, almost entirely devoid of examples, gives way to later writings that could be described (with little exaggeration) as nothing but examples. Tractatus becomes an important example in the later writings, which Wittgenstein characterises as the description of ‘a field of varying examples by means of centers of variation’. The dramatic shift in Wittgenstein's use of examples expresses a new understanding of language, and enacts a new method of philosophical investigation. The use of examples becomes an important method of conceptual imagination. There are approximately three dozen examples in the Notebooks and Tractatus. These include examples of propositions and examples of systems of representation. In his later writings, Wittgenstein's focus shifts from logic to grammar. This is evident in remarks concerning ‘essence’.
Working the ‘spaces’ between policy and practice: the contributions offered by resilience theory and action research
Authors: Hendrick Antonia S. , Young Susan 
Published: January 2012

ABSTRACTThe policy‐practice dimension often presents challenges particularly in the policy arena of child well‐being. Policy designers identify risk factors and design programmes intended to develop protective factors in areas of need. The 2004 Australian Communities for Children (CfC) initiative aimed to improve the social, health and educational outcomes for young children living in socio‐economically disadvantaged localities. Its method was to engage local community members to contribute towards developing protective factors. Rather than considering this national–local arrangement, an unworkable alliance, we examine the performance of CfC through three examples and demonstrate how resilience theory and action research can assist this programme achieve its social inclusion aims and well‐being outcomes. We choose not to disregard policy programmes like CfC, rather we emphasize the possibilities offered when working these complex spaces involving multiple and inherent contradictions. The spaces that often exist between the policy and its implementation are rethought to allow a greater opportunity for the growth of innovation and change.
Daphnia in tadpole mesocosms: trophic links and interactions with Batrachochytrium dendrobatidis
Authors: HAMILTON PHINEAS T. , RICHARDSON JEAN M. L. , ANHOLT BRADLEY R. 
Published: January 2012

Summary1. Amphibians are in decline, and the disease chytridiomycosis, caused by the chytrid fungus Batrachochytrium dendrobatidis (Bd), has been repeatedly implicated throughout the world. This chytrid reproduces via an infectious, motile zoospore stage that remains viable for weeks in the water column.2. Daphnia is a keystone zooplankton grazer in intact freshwater ecosystems, whose importance to amphibians may be overlooked. As an efficient grazer, Daphnia can suppress chytrid epidemics by consuming zoospores and may therefore play a role in Bd infection dynamics. Daphnia may also have important effects on tadpoles by mediating the properties of pond food webs. We tested the role of Daphnia in outdoor mesocosms containing the tadpoles of red‐legged frogs (Rana aurora) infected with Bd. We also tested the ability of Daphnia to filter Bd from the water column in laboratory microcosms.3. In the water of microcosms, Daphnia dramatically decreased the number of Bd genomic equivalents detectable using quantitative PCR. Bd genomic equivalents fell below the limit of detection at very high (>1 Daphnia mL−1) Daphnia densities.4. In mesocosms, Daphnia was critical to the development of tadpoles: in the presence of Daphnia, tadpoles were twofold heavier at metamorphosis than in their absence. Daphnia and Bd interacted to affect the tadpole survival: survival was highest in the presence of Daphnia and in the absence of Bd. We were unable to detect an effect of Daphnia on the transmission of Bd in mesocosms. However, Bd transmission among the tadpoles in mesocosms was unexpectedly low, limiting our power to detect an effect of Daphnia on transmission.5. Tadpole dissection showed that tadpoles also consumed large numbers of Daphnia. Current models of mesocosm food webs that assume no predation by tadpoles on zooplankton therefore probably overlook important features of both natural and experimental systems.
Increased interleukin‐1β levels are associated with left ventricular hypertrophy and remodelling following acute ST segment elevation myocardial infarction treated by primary percutaneous coronary intervention
Authors: Ørn S. , Ueland T. , Manhenke C. , Sandanger Ø. , Godang K. , Yndestad A. , Mollnes T. E. , Dickstein K. , Aukrust P. 
Published: January 2012

Abstract.  Ørn S, Ueland T, Manhenke C, Sandanger Ø, Godang K, Yndestad A, Mollnes TE, Dickstein K, Aukrust P (Stavanger University Hospital, Stavanger; Oslo University Hospital Rikshospitalet; University of Bergen, Bergen; University of Oslo; Oslo; Norway). Increased interleukin‐1β levels are associated with left ventricular hypertrophy and remodelling following acute ST segment elevation myocardial infarction treated by primary percutaneous coronary intervention. J Intern Med 2012; 272: 267–276.Objectives.  To assess the relationship between interleukin (IL)‐1‐related molecules, infarct size and left ventricular (LV) remodelling following acute myocardial infarction (MI).Methods.  Forty‐two patients with first‐time diagnosis of ST segment elevation MI (STEMI), with a single occluded vessel successfully revascularized by primary percutaneous coronary intervention (PCI), were recruited to this observational study conducted at a university teaching hospital and followed for 1 year.Main outcome measures.  Plasma levels of IL‐1β, IL‐1 receptor antagonist (IL‐1Ra), IL‐18 and caspase‐1 were analysed before and 2 days, 1 week and 2 months after PCI. Serial cardiac magnetic resonance imaging (CMR) was used for the assessment of infarct size and LV remodelling. CMR findings at 1 year was the primary outcome variable.Results.  Univariate analysis showed that IL‐1‐related mediators were strongly (IL‐1 β), moderately (caspase‐1) and weakly (IL‐1Ra) associated with impaired myocardial function and noninfarct mass, but not infarct size, 1 year after reperfused STEMI. In multivariate analyses, troponin T predicted LV ejection fraction (LVEF), infarct size and LV end‐diastolic (LVEDVi) and end‐systolic volume index (LVESVi). However, significant additional variance was explained by IL‐1β, IL‐18 and caspase‐1. IL‐1β levels at 2 months, IL‐18 at 2 days and pre‐PCI caspase‐1 were predictors of LVEF. Caspase‐1 and in particular IL‐1β at 2 days were the only predictors of noninfarct mass. IL‐1β and IL‐18 at 2 days were predictors of LVEDVi, whilst pre‐PCI levels of IL‐1β contributed to prediction of LVESVi. By contrast, pro‐B‐type natriuretic peptide, C‐reactive protein, IL‐6 and transforming growth factor‐β1 (TGF‐β1) had no or only a weak (TGF‐β1) association with these CMR parameters in multivariate analyses.Conclusions.  IL‐1β levels after STEMI were strongly associated with impaired myocardial function and noninfarct LV mass after 1 year, suggesting a potential role for IL‐1β as a predictor of maladaptive myocardial remodelling following reperfused MI.