bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sequential acquisition of virulence and fluoroquinolone resistance has shaped the evolution ofEscherichia coliST131
Authors: Ben Zakour Nouri L. , Alsheikh-Hussain Areej S. , Ashcroft Melinda M. , Nhu Nguyen Thi Khanh , Roberts Leah W. , Stanton-Cook Mitchell , Schembri Mark A. , Beatson Scott A. 
Published: February 2016

AbstractEscherichia coliST131 is the most frequently isolated fluoroquinolone resistant (FQR)E. coliclone worldwide and a major cause of urinary tract and bloodstream infections. Although originally identified through its association with the CTX-M-15 extended-spectrum β-lactamase resistance gene, global genomic epidemiology studies have failed to resolve the geographical and temporal origin of the ST131 ancestor. Here, we developed a framework for the reanalysis of publicly available genomes from different sources and used this dataset to reconstruct the evolutionary steps that led to the emergence of FQR ST131. Using Bayesian estimation, we show that point mutations in chromosomal genes that confer FQR coincide with the first clinical use of fluoroquinolone in 1986, and illustrate the impact of this pivotal event in the rapid population expansion of ST131 worldwide from an apparent origin in North America. Furthermore, we identify key virulence factor acquisition events that predate the development of FQR, suggesting that the gain of virulence-associated genes followed by the tandem development of antibiotic resistance primed the successful global dissemination of ST131.
FRETBursts: An Open Source Toolkit for Analysis of Freely-Diffusing Single-Molecule FRET
Authors: Ingargiola Antonino , Lerner Eitan , Chung SangYoon , Weiss Shimon , Michalet Xavier 
Published: February 2016

AbstractSingle-molecule Förster Resonance Energy Transfer (smFRET) allows probing intermolecular interactions and conformational changes in biomacromolecules, and represents an invaluable tool for studying cellular processes at the molecular scale. smFRET experiments can detect the distance between two fluorescent labels (donor and acceptor) in the 3–10 nm range. In the commonly employed confocal geometry, molecules are free to diffuse in solution. When a molecule traverses the excitation volume, it emits a burst of photons, which can be detected by single-photon avalanche diode (SPAD) detectors. The intensities of donor and acceptor fluorescence can then be related to the distance between the two fluorophores.While recent years have seen a growing number of contributions proposing improvements or new techniques in smFRET data analysis, rarely have those publications been accompanied by so.ware implementation. In particular, despite the widespread application of smFRET, no complete so.ware package for smFRET burst analysis is freely available to date.In this paper, we introduce FRETBursts, an open source software for analysis of freely-diffusing smFRET data. FRETBursts allows executing all the fundamental steps of smFRET bursts analysis using state-of-the-art as well as novel techniques, while providing an open, robust and welldocumented implementation. Therefore, FRETBursts represents an ideal platform for comparison and development of new methods in burst analysis.We employ modern software engineering principles in order to minimize bugs and facilitate long-term maintainability. Furthermore, we place a strong focus on reproducibility by relying on Jupyter notebooks for FRETBursts execution. Notebooks are executable documents capturing all the steps of the analysis (including data files, input parameters, and results) and can be easily shared to replicate complete smFRET analyzes. Notebooks allow beginners to execute complex workflows and advanced users to customize the analysis for their own needs. By bundling analysis description, code and results in a single document, FRETBursts allows to seamless share analysis workflows and results, encourages reproducibility and facilitates collaboration among researchers in the single-molecule community.
Singing above the chorus: cooperative Princess cichlid fish (Neolamprologus pulcher) has high pitch
Authors: Spinks Rachel K. , Muschick Moritz , Salzburger Walter , Gante Hugo F. 
Published: February 2016

AbstractTeleost fishes not only communicate with well-known visual cues, but also olfactory and acoustic signals. Communicating with sound has advantages, as signals propagate fast, omnidirectionally, around obstacles, and over long distances. Heterogeneous environments might favour multimodal communication, especially in socially complex species, as combination of modalities’ strengths helps overcome their individual limitations. Cichlid fishes are known to be vocal, but a recent report suggests that this is not the case for the socially complex Princess cichlidNeolamprologus pulcherfrom Lake Tanganyika. Here we further investigated acoustic communication in this species. Wild and captiveN. pulcherproduced high frequency sounds (mean: 12 kHz), when stimulated by mirror images. In laboratory experiments,N. pulcherproduced distinct two-pulsed calls mostly, but not exclusively, associated with agonistic displays. Our results suggest that maleN. pulcherproduce more sounds at greater durations than females. Thus, we confirm that the Princess cichlid does not produce low frequency sounds, but does produce high frequency sounds, both in combination with and independent from visual displays, suggesting that sounds are not a by-product of displays. Further studies on the hearing abilities ofN. pulcherare needed to clarify if the high-frequency sounds are used in intra-or inter-specific communication.
Audit quality within adverse selection markets
Authors: Sarath Bharat 
Published: February 2016

Purpose
– Auditing may be viewed as an arrangement for reducing inefficiencies arising from the fundamental market conflict between a seller who wants as high a price as possible and a buyer who wants to pay as low a price as possible. In more general terms, sellers prefer policies that boost the stock price in the short run whereas buyers would prefer the price to peak when they are ready to sell some time in the future. By framing audited financial reports within this context, the purpose of this paper is to provide some insights regarding both audit institutions and audit regulation.

Design/methodology/approach
– This paper relies on conceptual arguments and a simple analytical model.

Findings
– The basic findings are that a unique definition of audit quality is not compatible with the economics of a market where there are conflicts across traders as well a possibility that some traders hold superior information to others. Even an identification of quality with accuracy fails in this setting of conflict. The inference is that audit quality should be approached from a multi-dimensional perspective rather than a unique measure.

Research limitations/implications
– While the paper points out difficulties in constructing measures of audit quality extant in the literature, it does not provide any clear empirical suggestions for better measures.

Originality/value
– The paper brings back into focus issues from information economics that form the bedrock for the study of audited financial statements in equity markets. While the paper is partially a survey and synthesis of some of the latest empirical findings, it describes them within the context of a rational economic market where traders may possess private information. Within such a market, the paper outlines both the conflicts and the benefits inherent to the current institutional arrangements where auditors are paid by incumbent shareholders and overseen by regulators.
The mediating effects of customers’ intimacy perceptions on the trust-commitment relationship
Authors: Ponder Nicole , Bugg Holloway Betsy , Hansen John D. 
Published: February 2016

Purpose
This paper aims to draw from intimacy theory in examining the mediating effects of interactive communication and social bonds on the trust–commitment relationship.

Design/methodology/approach
The study is conducted in the professional services context. Qualitative and quantitative data are gathered from respondents engaged in attorney–client and real estate–client relationships. Unstructured, in-depth interviews are first conducted for use in model development. Study hypotheses are examined and mediation tests are conducted utilizing the serial multiple mediator model proposed by Hayes (2013).

Findings
Study findings indicate that intimate relationships in the professional services context are characterized by interactive communication and social bonds, and that the variables act as full mediators of the trust–commitment relationship. Though trust has a positive and significant effect on commitment in isolation, this relationship becomes nonsignificant when simultaneously accounting for the effects of the two variables.

Practical/implications
Study findings suggest a need for programs designed to assist professional service providers in the development of intimate customer relationships. The importance of interactive communications and social bonding should be emphasized in these programs.

Originality/value
The study is one of the few empirical papers to investigate the role of intimacy in service relationships and the first to illustrate its mediating effects on the trust–commitment relationship.
Revisiting “big ideas in services marketing” 30 years later
Authors: Berry Leonard L. 
Published: February 2016

Purpose
“Big Ideas in Services Marketing”, published in 1987, identified seven precepts fundamental to the just emerging field; this paper aims to explore the relevance of these ideas three decades later and discuss what should be changed and what should be added.

Design/methodology/approach
Deep reflection on the central ideas proposed in a paper written 30 years ago through the lens of the author’s personal research and learning journey was the basis for preparing this retrospective essay.

Findings
The seven ideas presented in the original paper have stood the test of time although one of the seven “services branding” was incompletely developed. After 30 years, four more ideas need to be added, i.e. competing on value, meeting and exceeding customers’ expectations, saving customers’ time and effort, and generosity.

Originality/value
The proposals in the 1987 paper offered an early framework for consideration by scholars who have produced a worthy body of work and brought services marketing into its own as a legitimate discipline.
Retrospective: compatibility management: customer-to-customer relationships in service environments
Authors: Martin Charles L. 
Published: February 2016

Purpose
This paper aims to revisit Martin and Pranter’s (1989) Journal of Services Marketing article, “Compatibility Management […]”, and by doing so, heighten service scholars’ and practitioners’ awareness of the historical and ongoing relevance of customer-to-customer (C2C) encounters, the challenges C2C encounters pose and the opportunities for future research.

Design/methodology/approach
A combination of review and commentary approaches is taken to summarize the 1989 article, the circumstances of its conception, the topic’s intersection with contemporary service topics and to illustrate the multi-faceted nature of C2C encounters and the challenges faced in their management.

Findings
Investigated in a number of service contexts, C2C encounters continue to be relevant in a multitude of service environments where customers converge.

Research limitations/implications
Because the evolution of service scholarship and practice is collectively shaped by an infinite number of people, events and sources, the attribution of effects to only one or a few influences is a highly subjective matter of interpretation.

Practical implications
Because C2C encounters are part of customers’ service experiences and can affect their satisfaction and patronage behaviors, service organizations can benefit by their efforts to influence C2C encounters.

Social implications
The criteria customers use to react to other customers and the bases used by service organizations/personnel to manage C2C encounters may not always be morally, ethically or legally defensible. For example, the Napa Valley Wine Train incident of 2015 involved allegations of racial discrimination and intentional infliction of emotional distress.

Originality/value
The retrospective analysis contributes to the field’s understanding of the historical development of services marketing and provides fodder for future research.
Nitrogen loads influence trophic organization of estuarine fish assemblages
Authors: Warry Fiona Y. , Reich Paul , Cook Perran L. M. , Mac Nally Ralph , Thomson James R. , Woodland Ryan J. 
Published: February 2016

Summary

Nutrient (N and P) loading may affect functioning in aquatic ecosystems by restructuring producer assemblages with flow‐on effects to consumers. Trophic niche occupancy and trophic organization of consumers are key components of ecosystem function that have been increasingly investigated using quantitative isotopic niche indices. These indices are based on the premise that the isotopic values of consumer tissues indicate their assimilated diet. Typically, isotopic niche indices are calculated using only consumer isotope data, which limit their application for spatial and temporal comparisons because consumer isotopic niches depend on isotopic variability of available autotrophs.

We used measures of isotopic variability of autotrophs to standardize isotopic niche indices, which enabled us to compare trophic organization of fish assemblages in nine estuaries spanning a broad range of nutrient loading. We related standardized isotopic niche indices of fish assemblages to nitrogen and phosphorous loads and hydrological flushing of the estuaries in autumn and spring.

The estuarine fish assemblages studied here showed greater trophic diversity and less redundancy given moderate to high inorganic nitrogen loading. Taxonomic richness partly influenced three isotopic niche indices measuring trophic diversity, but not measures of redundancy. Similar patterns may occur in other systems in which nitrogen loads have increased but the diversity of primary producers has not been reduced to a single dominant source.

Our results demonstrate bottom‐up controls of estuarine food webs. Effects of inorganic nitrogen loading were transmitted upwards through the food web to affect the trophic organization of higher trophic levels, demonstrating the crucial role of nitrogen for estuarine trophic dynamics.
Fungal effects on plant–plant interactions contribute to grassland plant abundances: evidence from the field
Authors: Bennett Jonathan A. , Cahill James F. 
Published: February 2016

Summary

Plant–fungal interactions can have strong effects on plant abundances, both through direct effects on plant performance and indirect effects on competition and facilitation. Most evidence linking fungi to plant abundances derives from direct fungal effects on initial growth, with little evidence linking fungal effects on plant–plant interactions in intact communities to plant abundances for any plant life‐history stage.

We transplanted 4320 individuals belonging to 18 plant species into plots where we removed neighbouring vegetation and suppressed fungi using fungicide in a factorial design. We monitored plant survival and growth for 3 years, using these data to test whether fungi had net effects on how plant–plant interactions affected different plant life‐history components (initial survival/growth, adult survival/growth). We then tested whether these indirect fungal effects or direct fungal effects on plant performance best explained plant commonness (frequency of occurrence) and local density (per cent cover). Finally, we measured differences in root‐associated fungi following fungal suppression and associated these differences with fungal effects on plant performance.

Overall, fungi increased competitive effects on survival (i.e. lower survival with fungi intact), but reduced competitive effects on growth of adult plants (i.e. higher growth when fungi intact). Among the focal species, these indirect fungal effects increased survival for more common species relative to rarer species. However, indirect fungal effects on adult growth benefitted rarer species more than common species. Local plant densities were unassociated with indirect fungal effects, but were negatively associated with direct fungal effects on survival and adult growth. This suggests that fungi limit local dominance, thereby indirectly increasing the establishment of common species and the growth of rare species.

Synthesis. Using a variety of plant species and suppressing both fungi and neighbours, we show that fungi have net indirect effects, through plant–plant interactions, within intact plant communities. Variation among species in both direct and indirect fungal effects contributed to plant abundances, yet fungal effects did not consistently benefit either common or rare species. However, regardless of commonness, fungi directly reduced growth and survival for species with high local densities, consistent with plant–soil feedbacks limiting species dominance.
A non‐invasive magnetic resonance imaging‐based model predicts portal venous pressure
Authors: Zhang Qian Wen , Wang Yi , Wang Jian , Zhao Hong Bo , Yu Hong , Liu Shi Yuan , Zeng Xin , Chen Qi , Hu Zhi Qian , Guo Wen Yuan , Fu Zhi Ren , Ding Guo Shan , Shi Xue Yin , Xie Wei Fen 
Published: February 2016

ObjectiveTo establish a non‐invasive model for the assessment of portal venous pressure (PVP) based on the magnetic resonance (MR) parameters.MethodsIn this prospective study, contrast‐enhanced magnetic resonance imaging (MRI) scan was performed in 109 patients indicated for upper abdominal surgeries after their written consents were obtained, and intraoperative PVP measurements were completed in 92 patients. Altogether 17 patients were excluded for not undergoing surgery or unsuccessful catheterization. A linear model was constructed for estimating PVP levels in 56 patients and further validation was conducted in the other 36 patients.ResultsThe PVP levels were significantly correlated with MR parameters, including splenic volume (SV), splenic venous diameter (SVD), liver/splenic volume ratio, portal venous diameter, hepatic diameter, portal venous cross‐sectional area, ascites, varices and arterial portal shunts. A linear model was established as follows: PVP (mmHg) = 2.529 + 1.572 × SVD (mm) + 0.231 × SV/body mass index (× 104 cm5/kg) + 3.44 × aspartate aminotransferase‐to‐platelet ratio index. This model showed excellent accuracy in the detection of portal hypertension, with the area under the receiver operating characteristic curve (AUROC) of 0.945 (95% CI 0.867–1.000), with the sensitivity and specificity of 91.7% and 93.7%, respectively. The agreement analysis revealed that the predictive value using this formula closely reflected the patients’ actual PVP level. Moreover, the validation confirmed the accuracy of this model for the assessment of portal hypertension [AUROC 0.935 (95% CI 0.856–1.000)].ConclusionsThe MRI‐based formula has great potential for detecting portal hypertension. As a non‐invasive measurement, it may be clinically accepted for the replacement of invasive modalities after further refinement.
Methylene blue attenuates mitochondrial dysfunction of rat kidney during experimental acute pancreatitis
Authors: Kuliaviene Irma , Baniene Rasa , Virketyte Simona , Kincius Marius , Jansen Eugene , Gulbinas Antanas , Kupcinskas Limas , Trumbeckaite Sonata , Borutaite Vilmante 
Published: February 2016

ObjectiveThe disturbance of mitochondrial functions has been considered as one of the mechanisms of pathogenesis of acute pancreatitis (AP) followed by kidney failure. This study was aimed to investigate the effects of methylene blue (MB) on pancreas and kidney mitochondrial respiratory functions during experimental acute pancreatitis in rats.MethodsAP was induced by administrating sodium taurocholate into the pancreatic duct of male Wistar rats. The rats were divided into three groups: the MB group, MB (5 mg/kg) was injected intravenously 10 min prior to AP induction; the AP group, saline solution was injected intravenously 10 min prior to AP induction; and the sham operation group, isotonic sodium chlorine was used instead of sodium taurocholate. The animals were sacrificed after 24 h. The pancreas and kidney were removed for mitochondrial assay by oxygraphic and spectrophotometric methods.ResultsIntravenous injection of MB did not prevent AP‐induced inhibition of pancreatic mitochondrial respiration; however, MB significantly improved kidney mitochondrial respiratory functions with complex I‐dependent substrates glutamate and malate. The activity of complex I of mitochondria isolated from AP‐damaged kidney was increased after pretreatment with MB. However, MB did not affect AP‐inhibited kidney mitochondrial respiration with succinate. MB had no protective effects on amylase activity or on urea content in serum in AP.ConclusionThe disturbances of kidney mitochondrial energy metabolism in experimental model of severe AP can be ameliorated by MB administration.
Alcohol withdrawal induces long‐lasting spatial working memory impairments: relationship with changes in corticosterone response in the prefrontal cortex
Authors: Dominguez Gaelle , Belzung Catherine , Pierard Christophe , David Vincent , Henkous Nadia , Decorte Laurence , Mons Nicole , Beracochea Daniel 
Published: February 2016

AbstractThis study intends to determine whether long‐lasting glucocorticoids (GCs) dysregulation in the prefrontal cortex (PFC) or the dorsal hippocampus (dHPC) play a causal role in the maintenance of working memory (WM) deficits observed after alcohol withdrawal. Here, we report that C57/BL6 male mice submitted to 6 months alcohol consumption (12 percent v/v) followed by 1 (1W) or 6 weeks (6W) withdrawal periods exhibit WM deficits in a spatial alternation task and an exaggerated corticosterone rise during and after memory testing in the PFC but not the dHPC. In contrast, emotional reactivity evaluated in a plus‐maze is altered only in the 1W group. No behavioral alterations are observed in mice still drinking alcohol. To determine the causal role of corticosterone in the withdrawal‐associated long‐lasting WM deficits, we further show that a single intraperitoneal injection injection of metyrapone (an inhibitor of corticosterone synthesis) 30 minutes before testing, prevents withdrawal‐associated WM deficits and reestablishes PFC activity, as assessed by increased phosphorylated C‐AMP Response Element‐binding protein (CREB) immunoreactivity in withdrawn mice. Finally, we show that intra‐PFC blockade of mineralocorticoid receptors by infusion of spironolactone and, to a lesser extent, of GCs receptors by injection of mifepristone reverses the WM deficits induced by withdrawal whereas the same injections into the dHPC do not. Overall, our study evidences that long‐lasting GCs dysfunction selectively in the PFC is responsible for the emergence and maintenance of WM impairments after withdrawal and that blocking prefrontal mineralocorticoid receptors receptors restores WM in withdrawn animals.