bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dissident writings as political theory on civil society and democracy
Authors: GLASIUS MARLIES 
Published: May 2011

AbstractThis article offers an analysis of precisely how civil society and its relation to democracy were conceptualised by its East European and South American proponents in their pre-democratic contexts, through an examination of declarations, newspaper articles, samizdat essays, diaries, letters from prison, academic articles and prize acceptance speeches written at the time. The analysis of these source materials is organised under three main themes: the first concerns activists' understanding of the nature of the regime, its aims and its relation to society; the second relates to the features of the emergent civil society the writers of these documents desired, observed, and helped to create; and the final section discusses their strategies and aspirations in relation to ‘democratisation’. On the basis of an analysis of commonalities in ideas across these two very different regional and ideological contexts, hypotheses are formulated as building blocks for a political theory of civil society under authoritarian rule, which may apply in yet other, contemporary contexts.
Quality/control: international peace interventions and ‘the everyday’
Authors: MITCHELL AUDRA 
Published: May 2011

AbstractCurrent discourses about the everyday in relation to international peace interventions focus on two main aspects. First, the perceived quality or qualities of everyday life tend to be attributed to ‘local’ organisations or actors and assessed positively. Second, the control of life (including bio-political control and governance) tends to be associated with ‘international’ actors and viewed negatively. This article challenges these key assumptions by contextualising them in social and political theories of the everyday and in two key examples: ‘affective’ peacebuilding in Bosnia-Herzegovina, and ‘threatworks’ in Northern Ireland. It also calls for an approach to the ‘everyday’ in international interventions which moves beyond local/international power dynamics and is attentive to the pluralities of power and practice that emerge in these settings.
Learning Bayesian networks: approaches and issues
Authors: Daly Rónán , Shen Qiang , Aitken Stuart 
Published: May 2011

AbstractBayesian networks have become a widely used method in the modelling of uncertain knowledge. Owing to the difficulty domain experts have in specifying them, techniques that learn Bayesian networks from data have become indispensable. Recently, however, there have been many important new developments in this field. This work takes a broad look at the literature on learning Bayesian networks—in particular their structure—from data. Specific topics are not focused on in detail, but it is hoped that all the major fields in the area are covered. This article is not intended to be a tutorial—for this, there are many books on the topic, which will be presented. However, an effort has been made to locate all the relevant publications, so that this paper can be used as a ready reference to find the works on particular sub-topics.
Delimiting tropical mountain ecoregions for conservation
Authors: PLATTS PHILIP J. , BURGESS NEIL D. , GEREAU ROY E. , LOVETT JON C. , MARSHALL ANDREW R. , McCLEAN COLIN J. , PELLIKKA PETRI K.E. , SWETNAM RUTH D. , MARCHANT ROB 
Published: May 2011

SUMMARYEcological regions aggregate habitats with similar biophysical characteristics within well-defined boundaries, providing spatially consistent platforms for monitoring, managing and forecasting the health of interrelated ecosystems. A major obstacle to the implementation of this approach is imprecise and inconsistent boundary placement. For globally important mountain regions such as the Eastern Arc (Tanzania and Kenya), where qualitative definitions of biophysical affinity are well established, rule-based methods for landform classification provide a straightforward solution to ambiguities in region extent. The method presented in this paper encompasses the majority of both contemporary and estimated preclearance forest cover within strict topographical limits. Many of the species here tentatively considered ‘near-endemic’ could be reclassified as strictly endemic according to the derived boundaries. LandScan and census data show population density inside the ecoregion to be higher than in rural lowlands, and lowland settlement to be most probable within 30 km. This definition should help to align landscape scale conservation strategies in the Eastern Arc and promote new research in areas of predicted, but as yet undocumented, biological importance. Similar methods could work well in other regions where mountain extent is poorly resolved. Spatial data accompany the online version of this article.
Tunnel effect and symmetries for Kramers–Fokker–Planck type operators
Authors: Hérau Frédéric , Hitrik Michael , Sjöstrand Johannes 
Published: May 2011

AbstractWe study operators of Kramers–Fokker–Planck type in the semiclassical limit, assuming that the exponent of the associated Maxwellian is a Morse function with a finite number n0 of local minima. Under suitable additional assumptions, we show that the first n0 eigenvalues are real and exponentially small, and establish the complete semiclassical asymptotics for these eigenvalues.
Instantons beyond topological theory. I
Authors: Frenkel E. , Losev A. , Nekrasov N. 
Published: May 2011

AbstractMany quantum field theories in one, two and four dimensions possess remarkable limits in which the instantons are present, the anti-instantons are absent, and the perturbative corrections are reduced to one-loop. We analyse the corresponding models as full quantum field theories, beyond their topological sector. We show that the correlation functions of all, not only topological (or BPS), observables may be studied explicitly in these models, and the spectrum may be computed exactly. An interesting feature is that the Hamiltonian is not always diagonalizable, but may have Jordan blocks, which leads to the appearance of logarithms in the correlation functions. We also find that in the models defined on Kähler manifolds the space of states exhibits holomorphic factorization. We conclude that in dimensions two and four our theories are logarithmic conformal field theories.In Part I we describe the class of models under study and present our results in the case of one-dimensional (quantum mechanical) models, which is quite representative and at the same time simple enough to analyse explicitly. Part II will be devoted to supersymmetric two-dimensional sigma models and four-dimensional Yang–Mills theory. In Part III we will discuss non-supersymmetric models.
Compact dual-band axially corrugated profiled horn for prime-focus reflector antenna
Authors: Gupta Ramesh Chandra , Pandya Jigar , Sood Khagindra K. , Jyoti Rajeev 
Published: May 2011

This paper reports a new compact dual-band axially corrugated profiled horn feed (DBCPH) for prime-focus reflector antenna at C-band (uplink and downlink frequency bands with bandwidth ratio of 1.6). DBPCH consists of one sinusoid profiled section and two internal axial corrugations (internal short-circuited ring slots), for obtaining a multimode horn feed. Such a blended structure is optimized over the specified frequency bands (3.68–3.70 and 5.865–5.915 GHz) to achieve various performance objectives (such as compactness, return loss, polarization purity, etc.). Measured and predicted results show that DBCPH provides better return loss >18.6 dB, low cross-polarization (better than −32 dB), and adequate edge taper at ±48° (8.5–11.7 dB) along with compact size (1.3λ aperture diameter and 0.88λ length at lower frequency). The horn would be used as a feed element for front-fed prime-focus reflector for pencil beam spacecraft antenna application.
Transcriptome response of high- and low-light-adapted Prochlorococcus strains to changing iron availability
Authors: Thompson Anne W , Huang Katherine , Saito Mak A , Chisholm Sallie W 
Published: May 2011

Abstract
Prochlorococcus contributes significantly to ocean primary productivity. The link between primary productivity and iron in specific ocean regions is well established and iron limitation of Prochlorococcus cell division rates in these regions has been shown. However, the extent of ecotypic variation in iron metabolism among Prochlorococcus and the molecular basis for differences is not understood. Here, we examine the growth and transcriptional response of Prochlorococcus strains, MED4 and MIT9313, to changing iron concentrations. During steady state, MIT9313 sustains growth at an order-of-magnitude lower iron concentration than MED4. To explore this difference, we measured the whole-genome transcriptional response of each strain to abrupt iron starvation and rescue. Only four of the 1159 orthologs of MED4 and MIT9313 were differentially expressed in response to iron in both strains. However, in each strain, the expression of over a hundred additional genes changed, many of which are in labile genomic regions, suggesting a role for lateral gene transfer in establishing diversity of iron metabolism among Prochlorococcus. Furthermore, we found that MED4 lacks three genes near the iron-deficiency-induced gene (idiA) that are present and induced by iron stress in MIT9313. These genes are interesting targets for studying the adaptation of natural Prochlorococcus assemblages to local iron conditions as they show more diversity than other genomic regions in environmental metagenomic databases.
Metabolic diversity among main microorganisms inside an arsenic-rich ecosystem revealed by meta- and proteo-genomics
Authors: Bertin Philippe N , Heinrich-Salmeron Audrey , Pelletier Eric , Goulhen-Chollet Florence , Arsène-Ploetze Florence , Gallien Sébastien , Lauga Béatrice , Casiot Corinne , Calteau Alexandra , Vallenet David , Bonnefoy Violaine , Bruneel Odile , Chane-Woon-Ming Béatrice , Cleiss-Arnold Jessica , Duran Robert , Elbaz-Poulichet Françoise , Fonknechten Nuria , Giloteaux Ludovic , Halter David , Koechler Sandrine , Marchal Marie , Mornico Damien , Schaeffer Christine , Smith Adam Alexander Thil , Van Dorsselaer Alain , Weissenbach Jean , Médigue Claudine , Le Paslier Denis 
Published: May 2011

Abstract
By their metabolic activities, microorganisms have a crucial role in the biogeochemical cycles of elements. The complete understanding of these processes requires, however, the deciphering of both the structure and the function, including synecologic interactions, of microbial communities. Using a metagenomic approach, we demonstrated here that an acid mine drainage highly contaminated with arsenic is dominated by seven bacterial strains whose genomes were reconstructed. Five of them represent yet uncultivated bacteria and include two strains belonging to a novel bacterial phylum present in some similar ecosystems, and which was named ‘Candidatus Fodinabacter communificans.’ Metaproteomic data unravelled several microbial capabilities expressed in situ, such as iron, sulfur and arsenic oxidation that are key mechanisms in biomineralization, or organic nutrient, amino acid and vitamin metabolism involved in synthrophic associations. A statistical analysis of genomic and proteomic data and reverse transcriptase–PCR experiments allowed us to build an integrated model of the metabolic interactions that may be of prime importance in the natural attenuation of such anthropized ecosystems.
Population genomics of Sinorhizobium medicae based on low-coverage sequencing of sympatric isolates
Authors: Bailly Xavier , Giuntini Elisa , Sexton M Connor , Lower Ryan P J , Harrison Peter W , Kumar Nitin , Young J Peter W 
Published: May 2011

Abstract
We investigated the genomic diversity of a local population of the symbiotic bacterium Sinorhizobium medicae, isolated from the roots of wild Medicago lupulina plants, in order to assess genomic diversity, to identify genomic regions influenced by duplication, deletion or strong selection, and to explore the composition of the pan-genome. Partial genome sequences of 12 isolates were obtained by Roche 454 shotgun sequencing (average 5.3 Mb per isolate) and compared with the published sequence of S. medicae WSM 419. Homologous recombination appears to have less impact on the polymorphism patterns of the chromosome than on the chromid pSMED01 and megaplasmid pSMED02. Moreover, pSMED02 is a hot spot of insertions and deletions. The whole chromosome is characterized by low sequence polymorphism, consistent with the high density of housekeeping genes. Similarly, the level of polymorphism of symbiosis genes (low) and of genes involved in polysaccharide synthesis (high) may reflect different selection. Finally, some isolates carry genes that may confer adaptations that S. medicae WSM 419 lacks, including homologues of genes encoding rhizobitoxine synthesis, iron uptake, response to autoinducer-2, and synthesis of distinct polysaccharides. The presence or absence of these genes was confirmed by PCR in each of these 12 isolates and a further 27 isolates from the same population. All isolates had rhizobitoxine genes, while the other genes were co-distributed, suggesting that they may be on the same mobile element. These results are discussed in relation to the ecology of Medicago symbionts and in the perspective of population genomics studies.
Enrichment and characterization of ammonia-oxidizing archaea from the open ocean: phylogeny, physiology and stable isotope fractionation
Authors: Santoro Alyson E , Casciotti Karen L 
Published: May 2011

Abstract
Archaeal genes for ammonia oxidation are widespread in the marine environment, but direct physiological evidence for ammonia oxidation by marine archaea is limited. We report the enrichment and characterization of three strains of pelagic ammonia-oxidizing archaea (AOA) from the North Pacific Ocean that have been maintained in laboratory culture for over 3 years. Phylogenetic analyses indicate the three strains belong to a previously identified clade of water column-associated AOA and possess 16S ribosomal RNA genes and ammonia monooxygenase subunit a (amoA) genes highly similar (98–99% identity) to those recovered in DNA and complementary DNA clone libraries from the open ocean. The strains grow in natural seawater-based liquid medium while stoichiometrically converting ammonia (NH3) to nitrite (NO2−). Ammonia oxidation by the enrichments is only partially inhibited by allylthiourea at concentrations known to completely inhibit cultivated ammonia-oxidizing bacteria. The three strains were used to determine the nitrogen stable isotope effect (15ɛNH3) during archaeal ammonia oxidation, an important parameter for interpreting stable isotope ratios in the environment. Archaeal 15ɛNH3 ranged from 13‰ to 41‰, within the range of that previously reported for ammonia-oxidizing bacteria. Despite low amino acid identity between the archaeal and bacterial Amo proteins, their functional diversity as captured by 15ɛNH3 is similar.
Electrokinetic trapping at the one nanometer limit
Authors: Fields Alexander P. , Cohen Adam E. 
Published: May 2011

Anti-Brownian electrokinetic traps have been used to trap and study the free-solution dynamics of large protein complexes and long chains of DNA. Small molecules in solution have thus far proved too mobile to trap by any means. Here we explore the ultimate limits on trapping single molecules. We developed a feedback-based anti-Brownian electrokinetic trap in which classical thermal noise is compensated to the maximal extent allowed by quantum measurement noise. We trapped single fluorophores with a molecular weight of < 1 kDa and a hydrodynamic radius of 6.7 Å for longer than one second, in aqueous buffer at room temperature. This achievement represents an 800-fold decrease in the mass of objects trapped in solution, and opens the possibility to trap and manipulate any soluble molecule that can be fluorescently labeled. To illustrate the use of this trap, we studied the binding of unlabeled RecA to fluorescently labeled single-stranded DNA. Binding of RecA induced changes in the DNA diffusion coefficient, electrophoretic mobility, and brightness, all of which were measured simultaneously and on a molecule-by-molecule basis. This device greatly extends the size range of molecules that can be studied by room temperature feedback trapping, and opens the door to further studies of the binding of unmodified proteins to DNA in free solution.
Measurement of protein unfolding/refolding kinetics and structural characterization of hidden intermediates by NMR relaxation dispersion
Authors: Meinhold Derrick W. , Wright Peter E. 
Published: May 2011

Detailed understanding of protein function and malfunction hinges on the ability to characterize transiently populated states and the transitions between them. Here, we use
15
N,

, and
13
CO NMR
R
2
relaxation dispersion to investigate spontaneous unfolding and refolding events of native apomyoglobin. Above pH 5.0, dispersion is dominated by processes involving fluctuations of the F-helix region, which is invisible in NMR spectra. Measurements of
R
2
dispersion for residues contacted by the F-helix region in the native (N) structure reveal a transient state formed by local unfolding of helix F and undocking from the protein core. A similar state was detected at pH 4.75–4.95 and determined to be an on-pathway intermediate (I1) in a linear three-state unfolding scheme (N⇆I1⇆MG) leading to a transiently populated molten globule (MG) state. The slowest steps in unfolding and refolding are N → I1 (36 s
-1
) and MG → I1 (26 s
-1
), respectively. Differences in chemical shift between N and I1 are very small, except in regions adjacent to helix F, showing that their core structures are similar. Chemical shift changes between the N and MG states, obtained from
R
2
dispersion, reveal that the transient MG state is structurally similar to the equilibrium MG observed previously at high temperature and low pH. Analysis of MG state chemical shifts shows the location of residual helical structure in the transient intermediate and identifies regions that unfold or rearrange into nonnative structure during the N → MG transition. The experiments also identify regions of energetic frustration that “crack” during unfolding and impede the refolding process.
Modular model of TNFα cytotoxicity
Authors: Chignola Roberto , Vyshemirsky Vladislav , Farina Marcello , Del Fabbro Alessio , Milotti Edoardo 
Published: May 2011

Abstract
Motivation: Tumour Necrosis Factor alpha (TNF) initiates a complex series of biochemical events in the cell upon binding to its type R1 receptor (TNF-R1). Recent experimental work has unravelled the molecular regulation of the signalling complexes that lead either to cell survival or death. Survival signals are activated by direct binding of TNF to TNF-R1 at the cell membrane whereas apoptotic signals by endocytosed TNF/TNF-R1 complexes. Here we describe a reduced, effective model with few free parameters, where we group some intricate mechanisms into effective modules, that successfully describes this complex set of actions. We study the parameter space to show that the model is structurally stable and robust over a broad range of parameter values.
Results: We use state-of-the-art Bayesian methods (a Sequential Monte Carlo sampler) to perform inference of plausible values of the model parameters from experimental data. As a result, we obtain a robust model that can provide a solid basis for further modelling of TNF signalling. The model is also suitable for inclusion in multi-scale simulation programs that are presently under development to study the behaviour of large tumour cell populations.
Availability: We provide supplementary material that includes all mathematical details and all algorithms (Matlab code) and models (SBML descriptions).
Contact: edoardo.milotti@ts.infn.it
Supplementary information: Supplementary data are available at Bioinformatics online.
Long-term changes in trophic patterns of Iceland cod and linkages to main prey stock sizes
Authors: Pálsson Ólafur K. , Björnsson Höskuldur 
Published: May 2011

Abstract
Pálsson, Ó. K., and Björnsson, H. 2011. Long-term changes in trophic patterns of Iceland cod and linkages to main prey stock sizes. – ICES Journal of Marine Science, 68: 1488–1499. Data on the diet composition of Iceland cod (Gadus morhua) were collected in March of the years 1981–2010 and in autumn of the years 1988–2010. Capelin, northern shrimp, and euphausiids dominate the diet in all years and may be classified as the stable food of Iceland cod. Overall, total consumption by the smallest cod (20–29 cm) remained stable over the three decades, whereas that of larger fish has declined since the mid-1990s. This decline may explain the reduced growth rate of cod in recent years. Long-term, prey-specific patterns were identified in consumption, and significant trophic links were found between cod consumption and stock sizes of capelin and northern shrimp. In March, the correlation between cod consumption on capelin and capelin stock size was highly significant, a type I functional feeding response, but not significant in autumn. The correlation deteriorated in the early to mid-1990s and in the early 2000s. Increased inflow of Atlantic water into north Icelandic waters, and associated changes in capelin distribution, may have contributed to this trend. The interaction between cod consumption on northern shrimp and shrimp stock size showed a highly significant type I functional feeding response in both seasons.
Receptor-Like Activity Evoked by Extracellular ADP in Arabidopsis Root Epidermal Plasma Membrane
Authors: Demidchik Vadim , Shang Zhonglin , Shin Ryoung , Colaço Renato , Laohavisit Anuphon , Shabala Sergey , Davies Julia M. 
Published: May 2011

Abstract
Extracellular purine nucleotides are implicated in the control of plant development and stress responses. While extracellular ATP is known to activate transcriptional pathways via plasma membrane (PM) NADPH oxidase and calcium channel activation, very little is known about signal transduction by extracellular ADP. Here, extracellular ADP was found to activate net Ca2+ influx in roots of Arabidopsis (Arabidopsis thaliana) and transiently elevate cytosolic free Ca2+ in root epidermal protoplasts. An inward Ca2+-permeable conductance in root epidermal PM was activated within 1 s of ADP application and repeated application evoked a smaller current. Such response speed and densitization are consistent with operation of equivalents to animal ionotropic purine receptors, although to date no equivalent genes for such receptors have been identified in higher plants. In contrast to ATP, extracellular ADP did not evoke accumulation of intracellular reactive oxygen species. While high concentrations of ATP caused net Ca2+ efflux from roots, equivalent concentrations of ADP caused net influx. Overall the results point to a discrete ADP signaling pathway, reliant on receptor-like activity at the PM.