bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrated cluster- and case-based surveillance for detecting stage III zoonotic pathogens: an example of Nipah virus surveillance in Bangladesh
Authors: NASER A. M. , HOSSAIN M. J. , SAZZAD H. M. S. , HOMAIRA N. , GURLEY E. S. , PODDER G. , AFROJ S. , BANU S. , ROLLIN P. E. , DASZAK P. , AHMED B.-N. , RAHMAN M. , LUBY S. P. 
Published: October 2014

SUMMARYThis paper explores the utility of cluster- and case-based surveillance established in government hospitals in Bangladesh to detect Nipah virus, a stage III zoonotic pathogen. Physicians listed meningo-encephalitis cases in the 10 surveillance hospitals and identified a cluster when ⩾2 cases who lived within 30 min walking distance of one another developed symptoms within 3 weeks of each other. Physicians collected blood samples from the clustered cases. As part of case-based surveillance, blood was collected from all listed meningo-encephalitis cases in three hospitals during the Nipah season (January–March). An investigation team visited clustered cases’ communities to collect epidemiological information and blood from the living cases. We tested serum using Nipah-specific IgM ELISA. Up to September 2011, in 5887 listed cases, we identified 62 clusters comprising 176 encephalitis cases. We collected blood from 127 of these cases. In 10 clusters, we identified a total of 62 Nipah cases: 18 laboratory-confirmed and 34 probable. We identified person-to-person transmission of Nipah virus in four clusters. From case-based surveillance, we identified 23 (4%) Nipah cases. Faced with thousands of encephalitis cases, integrated cluster surveillance allows targeted deployment of investigative resources to detect outbreaks by stage III zoonotic pathogens in resource-limited settings.
Gene expression analysis of E. coli strains provides insights into the role of gene regulation in diversification
Authors: Vital Marius , Chai Benli , Østman Bjørn , Cole James , Konstantinidis Konstantinos T , Tiedje James M 
Published: October 2014

Abstract
Escherichia coli spans a genetic continuum from enteric strains to several phylogenetically distinct, atypical lineages that are rare in humans, but more common in extra-intestinal environments. To investigate the link between gene regulation, phylogeny and diversification in this species, we analyzed global gene expression profiles of four strains representing distinct evolutionary lineages, including a well-studied laboratory strain, a typical commensal (enteric) strain and two environmental strains. RNA-Seq was employed to compare the whole transcriptomes of strains grown under batch, chemostat and starvation conditions. Highly differentially expressed genes showed a significantly lower nucleotide sequence identity compared with other genes, indicating that gene regulation and coding sequence conservation are directly connected. Overall, distances between the strains based on gene expression profiles were largely dependent on the culture condition and did not reflect phylogenetic relatedness. Expression differences of commonly shared genes (all four strains) and E. coli core genes were consistently smaller between strains characterized by more similar primary habitats. For instance, environmental strains exhibited increased expression of stress defense genes under carbon-limited growth and entered a more pronounced survival-like phenotype during starvation compared with other strains, which stayed more alert for substrate scavenging and catabolism during no-growth conditions. Since those environmental strains show similar genetic distance to each other and to the other two strains, these findings cannot be simply attributed to genetic relatedness but suggest physiological adaptations. Our study provides new insights into ecologically relevant gene-expression and underscores the role of (differential) gene regulation for the diversification of the model bacterial species.
Equilibrium Statistical Mechanics of Long-Range Interactions
Authors: Campa A. , Dauxois T. , Fanelli D. , Ruffo S. 
Published: October 2014

AbstractThis chapter deals with the peculiarities that are present in the statistical mechanics treatment and in the equilibrium properties of system with long-range interactions. In dimension d they are characterized at large distance r by a decay slower than 1/rd. The important concepts of additivity and extensivity are analysed. It is shown that long-range systems are intrinsically nonadditive: the interaction energy between macroscopic subsystems is not negligible with respect to the total energy of the system. This can often give rise to ensemble inequivalence. In particular, also with the help of a simple model, the possibility to have convex regions in the entropy is demonstrated. These regions can cause a negative specific heat in the microcanonical ensemble, while in the canonical ensemble this quantity is always positive. A negative magnetic susceptibility is possible, as well, in the microcanonical ensemble.
The Large Deviations Method and Its Applications
Authors: Campa A. , Dauxois T. , Fanelli D. , Ruffo S. 
Published: October 2014

AbstractThis chapter is devoted to the study of a very useful mathematical tool for the computation of the entropy in long-range systems. The method is based on large deviation theory, and it is very well suited for purely mean-field systems, in which the interaction does not decay at all with the distance. However, it can be applied also to the other long-range systems. The three steps of the method are described: the expression of the energy in terms of global variables, the mean fields; the computation of the entropy of the macrostates, defined by given values of the mean fields; the computation of the entropy, maximizing on the macrostates. Finally, the method is illustrated by applying it to two simple models.
Solutions of Mean Field Models
Authors: Campa A. , Dauxois T. , Fanelli D. , Ruffo S. 
Published: October 2014

AbstractIn this chapter the theory and the tools described in the previous two chapters are applied to several simple mean-field models, computing both the microcanonical and the canonical partition functions. It is shown that in the first model, the Hamiltonian Mean Field model, ensembles are equivalent, while in the others, the generalized XY model, the phi-4 model and the Self-Gravitating Ring model, ensembles are nonequivalent, with the occurrence of negative specific heat or negative susceptibility in the microcanonical ensemble. A feature that can appear in long-range systems is presented, namely the occurrence of ergodicity breaking. Mentioned in chapter 2 as a consequence of the possibility to have not connected regions in the thermodynamic parameter space, it is here explicitly shown in the XY model. Ergodicity breaking clearly manifests itself in the dynamical behaviour.
Beyond Mean-Field Models
Authors: Campa A. , Dauxois T. , Fanelli D. , Ruffo S. 
Published: October 2014

AbstractThis chapter aims at showing that the features occurring in mean-field models, described in the previous chapters, can be found also in the other long-range systems. The first four sections are dedicated to generalizations of the models of chapter 4, in which either the mean-field interaction is augmented with a nearest neighbour interaction, or it is replaced by a slowly decaying interaction. It is shown that the long-range characteristics of the associated mean-field models are preserved, and in addition ensemble inequivalence, microcanonical negative specific heat and ergodicity breaking are induced in some cases. The final section introduces the dipolar interaction, a marginal long-range system. Dipolar systems are treated in details in chapter 15, and in this chapter few relevant properties are presented, focussing in particular on elongated ferromagnets and on ergodicity breaking.
Kinetic Theory of Long-Range Systems: Klimontovich, Vlasov and Lenard–Balescu Equations
Authors: Campa A. , Dauxois T. , Fanelli D. , Ruffo S. 
Published: October 2014

AbstractThis chapter describes the derivation of kinetic equations for long-range systems. This is done on the basis of the Klimontovich equation, following an approach which is alternative but equivalent to the BBGKY hierarchy. After the derivation of the Klimontovich equation, that mathematically is equivalent to the full equations of motion, the Vlasov and the Lenard-Balescu equations are obtained. The former approximates the interaction in the system with a mean-field force, and for this it is considered a collisionless approximation; the latter takes into account the collisional corrections to the Vlasov equation. In the last section, with the background of the general theory presented in chapter 2 and in this chapter, there is a description of the physical meaning of the Kac’s prescription, often used as a convenient tool for the study of long-range systems.
Dipolar Systems
Authors: Campa A. , Dauxois T. , Fanelli D. , Ruffo S. 
Published: October 2014

AbstractThis chapter is devoted to studying systems with magnetic dipolar interactions. After a general introduction, the origin of the so called demagnetized field arising in the interior of magnetized bodies, is discussed. Then, the existence of a thermodynamic limit for systems of dipoles coupled via a dipole-dipole interaction, is shown. Importantly, the free energy of the system is independent on the sample shape. The physical consequences of this result are thoroughly analyzed. Finally, recent experimental studies aimed at investigating both equilibrium and dynamical properties of dipolar systems are reviewed and discussed.
The cost-effectiveness of radiofrequency catheter ablation as
first-line treatment for paroxysmal atrial fibrillation: results from a
MANTRA-PAF substudy
Authors: Aronsson Mattias , Walfridsson Håkan , Janzon Magnus , Walfridsson Ulla , Nielsen Jens Cosedis , Hansen Peter Steen , Johannessen Arne , Raatikainen Pekka , Hindricks Gerhard , Kongstad Ole , Pehrson Steen , Englund Anders , Hartikainen Juha , Mortensen Leif Spange , Levin Lars-Åke 
Published: October 2014

Aim
The aim of this prospective substudy was to estimate the cost-effectiveness of treating paroxysmal atrial fibrillation (AF) with radiofrequency catheter ablation (RFA) compared with antiarrhythmic drugs (AADs) as first-line treatment.

Methods and results
A decision-analytic Markov model, based on MANTRA-PAF (Medical Antiarrhythmic Treatment or Radiofrequency Ablation in Paroxysmal Atrial Fibrillation) study data, was developed to study long-term effects and costs of RFA compared with AADs as first-line treatment. Positive clinical effects were found in the overall population, a gain of an average 0.06 quality-adjusted life years (QALYs) to an incremental cost of €3033, resulting in an incremental cost-effectiveness ratio of €50 570/QALY. However, the result of the subgroup analyses showed that RFA was less costly and more effective in younger patients. This implied an incremental cost-effectiveness ratio of €3434/QALY in ≤50-year-old patients respectively €108 937/QALY in >50-year-old patients.

Conclusion
Radiofrequency catheter ablation as first-line treatment is a cost-effective strategy for younger patients with paroxysmal AF. However, the cost-effectiveness of using RFA as first-line therapy in older patients is uncertain, and in most of these AADs should be attempted before RFA (MANTRA-PAF ClinicalTrials.gov number; NCT00133211).
Chromosome conformation maps in fission yeast reveal cell cycle dependent sub nuclear structure
Authors: Grand Ralph S. , Pichugina Tatyana , Gehlen Lutz R. , Jones M. Beatrix , Tsai Peter , Allison Jane R. , Martienssen Robert , O'Sullivan Justin M. 
Published: October 2014

Abstract
Successful progression through the cell cycle requires spatial and temporal regulation of gene transcript levels and the number, positions and condensation levels of chromosomes. Here we present a high resolution survey of genome interactions in Schizosaccharomyces pombe using synchronized cells to investigate cell cycle dependent changes in genome organization and transcription. Cell cycle dependent interactions were captured between and within S. pombe chromosomes. Known features of genome organization (e.g. the clustering of telomeres and retrotransposon long terminal repeats (LTRs)) were observed throughout the cell cycle. There were clear correlations between transcript levels and chromosomal interactions between genes, consistent with a role for interactions in transcriptional regulation at specific stages of the cell cycle. In silico reconstructions of the chromosome organization within the S. pombe nuclei were made by polymer modeling. These models suggest that groups of genes with high and low, or differentially regulated transcript levels have preferred positions within the S. pombe nucleus. We conclude that the S. pombe nucleus is spatially divided into functional sub-nuclear domains that correlate with gene activity. The observation that chromosomal interactions are maintained even when chromosomes are fully condensed in M phase implicates genome organization in epigenetic inheritance and bookmarking.
Bayesian analyses of Yemeni mitochondrial genomes suggest multiple migration events with Africa and Western Eurasia
Authors: Vyas Deven N. , Kitchen Andrew , Miró-Herrans Aida T. , Pearson Laurel N. , Al-Meeri Ali , Mulligan Connie J. 
Published: October 2014

ABSTRACTAnatomically modern humans (AMHs) left Africa ˜60,000 years ago, marking the first of multiple dispersal events by AMH between Africa and the Arabian Peninsula. The southern dispersal route (SDR) out of Africa (OOA) posits that early AMHs crossed the Bab el-Mandeb strait from the Horn of Africa into what is now Yemen and followed the coast of the Indian Ocean into eastern Eurasia. If AMHs followed the SDR and left modern descendantsin situ, Yemeni populations should retain old autochthonous mitogenome lineages. Alternatively, if AMHs did not follow the SDR or did not leave modern descendants in the region, only young autochthonous lineages will remain as evidence of more recent dispersals. We sequenced 113 whole mitogenomes from multiple Yemeni regions with a focus on haplogroups M, N, and L3(xM,N) as they are considered markers of the initial OOA migrations. We performed Bayesian evolutionary analyses to generate time-measured phylogenies calibrated by Neanderthal and Denisovan mitogenome sequences in order to determine the age of Yemeni-specific clades in our dataset. Our results indicate that the M1, N1, and L3(xM,N) sequences in Yemen are the product of recent migration from Africa and western Eurasia. Although these data suggest that modern Yemeni mitogenomes are not markers of the original OOA migrants, we hypothesize that recent population dynamics may obscure any genetic signature of an ancient SDR migration.
The MaizeDWARF1Encodes a Gibberellin 3-Oxidase and Is Dual Localized to the Nucleus and Cytosol
Authors: Chen Yi , Hou Mingming , Liu Lijuan , Wu Shan , Shen Yun , Ishiyama Kanako , Kobayashi Masatomo , McCarty Donald R. , Tan Bao-Cai 
Published: October 2014

AbstractThe maize (Zea mays) gibberellin (GA)-deficient mutant dwarf1 (d1) displays dwarfism and andromonoecy (i.e. forming anthers in the female flower). Previous characterization indicated that the d1 mutation blocked three steps in GA biosynthesis; however, the locus has not been isolated and characterized. Here, we report that D1 encodes a GA 3-oxidase catalyzing the final step of bioactive GA synthesis. Recombinant D1 is capable of converting GA20 to GA1, GA20 to GA3, GA5 to GA3, and GA9 to GA4 in vitro. These reactions are widely believed to take place in the cytosol. However, both in vivo GFP fusion analysis and western-blot analysis of organelle fractions using a D1-specific antibody revealed that the D1 protein is dual localized in the nucleus and cytosol. Furthermore, the upstream gibberellin 20-oxidase1 (ZmGA20ox1) protein was found dual localized in the nucleus and cytosol as well. These results indicate that bioactive GA can be synthesized in the cytosol and the nucleus, two compartments where GA receptor Gibberellin-insensitive dwarf protein1 exists. Furthermore, the D1 protein was found to be specifically expressed in the stamen primordia in the female floret, suggesting that the suppression of stamen development is mediated by locally synthesized GAs.
Smart specialisation in the tangled web of European inter-regional trade
Authors: Gianelle Carlo , Goenaga Xabier , González Vázquez Ignacio , Thissen Mark 
Published: October 2014

Purpose– The purpose of this paper is to present a new methodology to assess the outward connectivity among regional economies in the European Union (EU) and derives policy lessons for the design of regional innovation and competitiveness-enhancing strategic frameworks, with particular reference to research and innovation strategies for smart specialisation (RIS3).Design/methodology/approach– The authors study the network of inter-regional trade flows in the EU25 in the year 2007. Trade data are taken from the PBL Netherlands Environmental Assessment Agency database and mapped onto weighted directed networks in which the nodes represent regions and the links are flows of goods. The authors measure several structural characteristics of the networks, both global properties and centrality indicators describing the position of individual regions within the system.Findings– European regions appear to be mostly integrated in the European single market. Strengths and weaknesses of individual regions are discussed based on rankings obtained from network centrality indicators. Specific policy implications in the context of RIS3 are derived in the case of the Spanish region of Andalusia.Practical implications– The authors show the potential of the methodology for providing a new family of indicators of the external connectivity of regional economies that can be used by regions wishing to develop their own RIS3 for 2014-2020, as required by the EU in the context of the new cohesion policy framework.Originality/value– The characteristics of a EU-wide inter-regional network of trade flows are obtained and thoroughly discussed for the first time. A unique and original instrument suitable for inter-regional comparison is developed and tested.
How has the French context shaped the organization of the Airbus Group?
Authors: Barmeyer Christoph , Mayrhofer Ulrike 
Published: October 2014

Purpose– The purpose of this paper is to examine whether characteristics of French organizations can be found in the Airbus Group, ancient European Aeronautic Defence and Space Company (EADS) Group, and how these characteristics have evolved over time in comparison to German ones.Design/methodology/approach– This article presents an in-depth case study by using a contextual approach, considering influential factors which are likely to influence the evolution of organizations.Findings– The analysis shows that the Airbus Group reflects characteristics of French organizations: the importance of strategy, the principle of honour, centralization of decision and power, the role of the state in the capital and its influence via professional networks of its elite coming from the Grandes Ecoles. These findings confirm a relative continuity of national peculiarities over time. The recent evolution of the company also highlights the German influence, notably in terms of shares and management positions.Research limitations/implications– The case study demonstrates that the Airbus Group has become a multinational company where contextual elements and organizational structures regulate intercultural relationships of interests, influence and power.Originality/value– Five contextual factors are proposed, which allow to understand and structure the peculiarities of French organizations, in comparison to German ones as well as power distribution within the Airbus Group.
Gestion & Société’s approach to cooperation of French firms
Authors: Segal Jean-Pierre 
Published: October 2014

Purpose– This paper aims to provide a more nuanced image of cooperation in France, first, insisting on the idiosyncratic conditions under which French will be likely to cooperate, and, second, pointing the importance of the local context, finally criticizing the average stereotyped image given by the intercultural management quantitative literature.Design/methodology/approach– The studies behind the article are based on qualitative data and on an interpretative analysis of culture, considered as a frame of meanings through which people read the organizational situation they are in.Findings– Advanced form of cooperation may be obtained when some balance can be established through subtle arrangement between organizational and cultural needs, i.e. allowing staff to escape from their founding fear of servility.Research limitations/implications– Such analysis of the conditions that can facilitate or hinder cooperation should not be limited to France. It may be applied to any other cultural area.Practical implications– Intercultural management training sessions for expatriates could benefit from this qualitative approach.Originality/value– This approach challenges the quantitative main Stream approach in cross-national studies on management.
Language and thinking in organization studies
Authors: Chanlat Jean-François 
Published: October 2014

Purpose– The purpose of this paper is to clarify the relationship between language, thinking and society for explaining the degree of visibility of the French organizational studies (OS) production.Design/methodology/approach– This paper proposes a sociological analysis based on Bourdieu field to understand the variation of reception the French OS production have had among the Anglo-Saxon field. The paper aims to underline some key elements, which can explain the differences of reception experienced by the French OS scientists. The paper opted for a general review using historical data; reviews of OS literature; and Google scholar, Web of Science and major OS Journal data.Findings– The paper provides some evidence about how the degree of visibility of the French OS production is related to translation, cognitive and social resonance, producer place in the scientific network and relationship between the fields. It suggests that the degree of visibility is the result of a complex set of socio-cognitive schemes, social issues raised by the scholar and the place occupied by the researcher in the field.Originality/value– The paper brings interesting ideas concerning the international development of the OS field, the degree of visibility of diverse contributions coming from non-English speaking researchers, notably the French ones, and how the dialogue between different linguistic and social universes can be ameliorated.