bluuebunny/crossref_metadata_2025_split huggingface dataset:
Earthquake‐volcano interaction imaged by coda wave interferometry
Authors: Battaglia Jean , Métaxian Jean‐Philippe , Garaebiti Esline 
Published: May 2012

Large earthquakes are often assumed to influence the eruptive activity of volcanoes. A major challenge to better understand the causal relationship between these phenomena is to detect and image, in detail, all induced changes, including subtle, non‐eruptive responses. We show that coda wave interferometry can be used to image such earthquake‐induced responses, as recorded at Yasur volcano (Vanuatu) following a magnitude 7.3 earthquake which occurred 80 km from its summit. We use repeating Long‐Period events to show that the earthquake caused a sudden seismic velocity drop, followed by a slow partial recovery process. The spatial distribution of the response amplitude indicates an effect centered on the volcano. Our result demonstrates that, even if no major change in eruptive activity is observed, volcanoes will be affected by the propagation of large amplitude seismic waves through their structure, suggesting that Earthquake‐volcano interaction is likely a more common phenomenon than previously believed.
High‐resolution comparison of sediment dynamics under different forcing conditions in the bottom boundary layer of a shallow, micro‐tidal estuary
Authors: Ha Ho Kyung , Park Kyeong 
Published: May 2012

Data for high‐resolution profiles of current velocity and suspended sediment concentration (SSC) were collected in bottom boundary layer (BBL) of Mobile Bay, Alabama. The data were used to study the vertical and temporal variability in SSC under various forcing conditions of tide, wind and freshwater discharge. During the winter stormy season, the background SSC was low (0.015–0.03 g l−1). An episodic storm‐induced erosion/resuspension was responsible for the short‐lasting high SSC in BBL. During the spring flooding period, the background SSC was relatively high (0.04–0.07 g l−1) likely due to the large amount of suspended sediment from the fluvial input and bed softening, and the contribution of wind forcing to sediment resuspension was somewhat enhanced by the destratification in BBL. When the freshwater discharge was extremely high (>5000 m3 s−1), the entire water column in shallow areas of the Bay was influenced by freshwater input. Therefore, the thermohaline anomaly's contribution to the stratification considerably weakened, while the SSC's contribution strengthened. When the freshwater discharge was relatively low (<5000 m3 s−1), a critical wind stress for sediment erosion (0.08–0.1 Pa) was observed to abruptly increase the SSC. Despite a micro‐tidal regime, Mobile Bay exhibited the cyclic erosion and deposition pattern induced by the tidal acceleration and deceleration.
Stratospheric water vapor and climate: Sensitivity to the representation in radiation codes
Authors: Maycock A. C. , Shine K. P. 
Published: May 2012

There has been considerable interest in the climate impact of trends in stratospheric water vapor (SWV). However, the representation of the radiative properties of water vapor under stratospheric conditions remains poorly constrained across different radiation codes. This study examines the sensitivity of a detailed line‐by‐line (LBL) code, a Malkmus narrow‐band model and two broadband GCM radiation codes to a uniform perturbation in SWV in the longwave spectral region. The choice of sampling rate in wave number space (Δν) in the LBL code is shown to be important for calculations of the instantaneous change in heating rate (ΔQ) and the instantaneous longwave radiative forcing (ΔFtrop). ΔQ varies by up to 50% for values of Δν spanning 5 orders of magnitude, and ΔFtrop varies by up to 10%. In the three less detailed codes, ΔQdiffers by up to 45% at 100 hPa and 50% at 1 hPa compared to a LBL calculation. This causes differences of up to 70% in the equilibrium fixed dynamical heating temperature change due to the SWV perturbation. The stratosphere‐adjusted radiative forcing differs by up to 96% across the less detailed codes. The results highlight an important source of uncertainty in quantifying and modeling the links between SWV trends and climate.
Legal norms as objects of (non-)commitment
Authors: Deschamps Karen 
Published: May 2012

In linguistics, the notion of commitment is associated with a range of other notions, such as belief (Dendale & Coltier 2005: 127), will (Palmer 1998: 102) and responsibility (Nølke et al. 2004: 44). Belief and will are examples of psychological states the speaker has towards a certain proposition – they are also known as propositional attitudes – while responsibility has to do with the speaker being the source of a certain proposition. The aim of this article is to examine the relation between these different notions. I will do this by analysing the use of deontic sentences in different types of legal and administrative texts in Dutch.
The article is organised as follows. In section 1, I will provide some background on deontic sentences (§1.1), on legal and administrative discourse (§1.2) and on the notion of commitment (§1.3). In section 2, the notion of commitment will be applied to deontic sentences, both in terms of responsibility (§2.1) and propositional attitudes (§2.2).
Temporal and Spatial Genetic Consistency of Walleye Spawning Groups
Authors: Stepien Carol A. , Banda Jo Ann , Murphy Douglas M. , Haponski Amanda E. 
Published: May 2012

AbstractPopulation genetic compositions of the three largest spawning groups of Lake Erie walleyes Sander vitreus (Maumee River, Sandusky River, and Van Buren Bay reefs) were tested for temporal and spatial consistency across 14 years using nine nuclear DNA microsatellite loci from 726 adult walleyes collected in 1995, 1998, 2003, 2007, and 2008. Previous genetic work focused on a one‐time “snapshot”; an earlier study by our laboratory found genetic connectivity among the three spawning groups in 2003, whereas most other spawning runs across Lake Erie were genetically distinct. Present results show overall year‐to‐year genetic consistency of walleye spawning groups; no significant differences were found among collection dates within an annual run, between sexes, or among age‐cohorts. Overall, walleyes spawning at the Van Buren Bay reefs were genetically divergent from those spawning in the Maumee and Sandusky rivers, reflecting geographic distance; the latter two groups were genetically closer, with slight differences that suggested more recent divergence, higher gene flow, or both. Individual year comparisons among the three sites showed some stochasticity, and the spawning groups appeared to be more similar in some years than in others. The Van Buren Bay spawning group in 1995 was the most divergent sample and had the greatest genetic self‐assignment (100%); this may reflect some changes over time. Results demonstrate the importance of sampling over several years of spawning runs to understand overall patterns of walleye genetic stock structure, which show remarkable genetic consistency across an open‐lake system.
Reflective listening and open‐ended questions in counselling: Preferences moderated by social skills and cognitive ability
Authors: Rautalinko Erik 
Published: May 2012

AbstractAims: We examined how nondirective counselling skills affect the evaluation of counsellors and the observed working alliance, and how evaluators' social skills and cognitive ability moderate evaluations. Method: In a first analogue experiment, counselling transcripts containing more or less restatements, reflections and open‐ended questions were audio‐taped and rated by evaluators (n=52) who self‐reported social skills. In a second experiment, a different sample of evaluators (n=63) rated transcripts and self‐reported social skills and were tested on cognitive ability. Results: Restatements and reflections improved ratings of the counsellors and the observed working alliance, but open‐ended questions did not. Ratings were moderated by evaluators' social skills and cognitive ability. Discussion: The results agree with previous evidence on restating–reflecting and open‐ended questions. That certain evaluators preferred open‐ended questions more than others can be understood as an issue of matching between conceptual level, social skills, and counselling structure.
MotifSuite: workflow for probabilistic motif detection and assessment
Authors: Claeys Marleen , Storms Valerie , Sun Hong , Michoel Tom , Marchal Kathleen 
Published: May 2012

Abstract
Motivation: Probabilistic motif detection requires a multi-step approach going from the actual de novo regulatory motif finding up to a tedious assessment of the predicted motifs. MotifSuite, a user-friendly web interface streamlines this analysis flow. Its core consists of two post-processing procedures that allow prioritizing the motif detection output. The tools offered by MotifSuite are built around the well-established motif detection tool MotifSampler and can also be used in combination with any other probabilistic motif detection tool. Elaborate guidelines on each of its applications have been provided.
Availability: http://homes.esat.kuleuven.be/bioi_marchal/MotifSuite/Index.htm
Contact: kamar@psb.ugent.be
OSA: a fast and accurate alignment tool for RNA-Seq
Authors: Hu Jun , Ge Huanying , Newman Matt , Liu Kejun 
Published: May 2012

Abstract
Summary: Accurately mapping RNA-Seq reads to the reference genome is a critical step for performing downstream analysis such as transcript assembly, isoform detection and quantification. Many tools have been developed; however, given the huge size of the next generation sequencing datasets and the complexity of the transcriptome, RNA-Seq read mapping remains a challenge with the ever-increasing amount of data. We develop Omicsoft sequence aligner (OSA), a fast and accurate alignment tool for RNA-Seq data. Benchmarked with existing methods, OSA improves mapping speed 4–10-fold with better sensitivity and less false positives.
Availability: OSA can be downloaded from http://omicsoft.com/osa. It is free to academic users. OSA has been tested extensively on Linux, Mac OS X and Windows platforms.
Contact: john.hu@omicsoft.com; jhu7@ncsu.edu; jack.liu@omicsoft.com
Supplementary information: Supplementary data are available at Bioinformatics online.
Drosophilaas a model system to unravel the layers of innate immunity to infection
Authors: Kounatidis Ilias , Ligoxygakis Petros 
Published: May 2012

SummaryInnate immunity relies entirely upon germ-line encoded receptors, signalling components and effector molecules for the recognition and elimination of invading pathogens. The fruit flyDrosophila melanogasterwith its powerful collection of genetic and genomic tools has been the model of choice to develop ideas about innate immunity and host–pathogen interactions. Here, we review current research in the field, encompassing all layers of defence from the role of the microbiota to systemic immune activation, and attempt to speculate on future directions and open questions.
Miocene sedimentation, volcanism and deformation in the Eastern Cordillera (24°30′ S, NW Argentina): tracking the evolution of the foreland basin of the Central Andes
Authors: Vezzoli Luigina , Acocella Valerio , Omarini Ricardo , Mazzuoli Roberto 
Published: May 2012

AbstractUnderstanding the relationships between sedimentation, tectonics and magmatism is crucial to defining the evolution of orogens and convergent plate boundaries. Here, we consider the lithostratigraphy, clastic provenance, syndepositional deformation and volcanism of the Almagro‐El Toro basin of NW Argentina (24°30′ S, 65°50′ W), which experienced eruptive and depositional episodes between 14.3 and 6.4 Ma. Our aims were to elucidate the spatial and temporal record of the onset and style of the shortening and exhumation of the Eastern Cordillera in the frame of the Miocene evolution of the Central Andes foreland basin. The volcano‐sedimentary sequence of the Almagro‐El Toro basin consists of lower red floodplain sandstones and siltstones, medial non‐volcanogenic conglomerates with localised volcanic centres and upper volcanogenic coarse conglomerates and breccia. Coarse, gravity flow‐dominated (debris‐flow and sheet‐flow) alluvial fan systems developed proximal to the source area in the upper and medial sequence. Growing frontal and intrabasinal structures suggest that the Almagro‐El Toro portion of the foreland basin accumulated on top of the eastward‐propagating active thrust front of the Eastern Cordillera. Synorogenic deposits indicate that the shortening of the foreland deposits was occurring by 11.1 Ma, but conglomerates derived from the erosion of western sources suggest that the uplift and erosion of this portion of the Eastern Cordillera has occurred since ca.12.5 Ma. An unroofing reconstruction suggests that 6.5 km of rocks were exhumed. A tectono‐sedimentary model of an episodically evolving thick‐skinned foreland basin is proposed. In this frame, the NW‐trending, transtensive Calama–Olacapato–El Toro (COT) structures interacted with the orogen, influencing the deposition and deformation of synorogenic conglomerates, the location of volcanic centres and the differential tilt and exhumation of the foreland.
Late Cenozoic tectono‐stratigraphic sequences of theCrotoneBasin: insights on the geodynamic history of theCalabrian arc andTyrrhenian Sea
Authors: Massari F. , Prosser G. 
Published: May 2012

AbstractTheCrotoneBasin was generated in the lateCenozoic as a forearc basin of theIonian arc‐trench system. New data are gained through detailed field mapping, high‐resolution stratigraphic analysis of a key area and examination of offshore well data and seismic reflection profiles. Major unconformities divide the basin fill into major sequences, which reveal a three‐stage internal organization thought to reflect geodynamic events of theCalabrian arc and backarc area closely. Thefirst stageis characterized by extensional block faulting and uplift followed by rapid drowning during high subsidence and transtension in the basin along a major NNW‐ to NW‐striking fault system. This stage is interpreted to reflect resumption of rollback after an episode of slab tearing triggered by transitory docking of continental lithosphere in the trench. The initial uplift is inferred to reflect decoupling and rebound after the transitory coupling phase. Thesecond stageis characterized by increased subsidence and continued extension/transtension. This trend presumably reflects a decreasing rate of rollback resulting from a tendency towards viscous coupling after acceleration of slab downwelling. Thethird stageis characterized by short‐lived transpression along major shear zones and local inversion of former basins. This is inferred to reflect entrance into the trench of buoyant continental lithosphere, resulting in significant deceleration of slab rollback and consequently a break in, or slowing of, backarc extension, and predominance of the effects of compression related toAfrica–Europe convergence. Overall, the above evolution resulted in the formation of a progressively narrower and rapidly retreating slab, inducing extreme rates of backarc extension, and may have played a critical role in determining the intermittent nature of the backarc rifting.
Carbon outcomes of major land‐cover transitions in SE Asia: great uncertainties and REDD+ policy implications
Authors: Ziegler Alan D. , Phelps Jacob , Yuen Jia QI , Webb Edward L. , Lawrence Deborah , Fox Jeff M. , Bruun Thilde B. , Leisz Stephen J. , Ryan Casey M. , Dressler Wolfram , Mertz Ole , Pascual Unai , Padoch Christine , Koh Lian Pin 
Published: May 2012

AbstractPolicy makers across the tropics propose that carbon finance could provide incentives for forest frontier communities to transition away from swidden agriculture (slash‐and‐burn or shifting cultivation) to other systems that potentially reduce emissions and/or increase carbon sequestration. However, there is little certainty regarding the carbon outcomes of many key land‐use transitions at the center of current policy debates. Our meta‐analysis of over 250 studies reporting above‐ and below‐ground carbon estimates for different land‐use types indicates great uncertainty in the net total ecosystem carbon changes that can be expected from many transitions, including the replacement of various types of swidden agriculture with oil palm, rubber, or some other types of agroforestry systems. These transitions are underway throughout Southeast Asia, and are at the heart of REDD+ debates. Exceptions of unambiguous carbon outcomes are the abandonment of any type of agriculture to allow forest regeneration (a certain positive carbon outcome) and expansion of agriculture into mature forest (a certain negative carbon outcome). With respect to swiddening, our meta‐analysis supports a reassessment of policies that encourage land‐cover conversion away from these [especially long‐fallow] systems to other more cash‐crop‐oriented systems producing ambiguous carbon stock changes – including oil palm and rubber. In some instances, lengthening fallow periods of an existing swidden system may produce substantial carbon benefits, as would conversion from intensely cultivated lands to high‐biomass plantations and some other types of agroforestry. More field studies are needed to provide better data of above‐ and below‐ground carbon stocks before informed recommendations or policy decisions can be made regarding which land‐use regimes optimize or increase carbon sequestration. As some transitions may negatively impact other ecosystem services, food security, and local livelihoods, the entire carbon and noncarbon benefit stream should also be taken into account before prescribing transitions with ambiguous carbon benefits.
Maintaining the ‘good maternal body’: expressing milk as a way of negotiating the demands and dilemmas of early infant feeding
Authors: Johnson Sally , Leeming Dawn , Williamson Iain , Lyttle Steven 
Published: May 2012

johnson s., leeming d., williamson i. & lyttle s. (2013) Maintaining the ‘good maternal body’: expressing milk as a way of negotiating the demands and dilemmas of early infant feeding. Journal of Advanced Nursing69(3), 590–599. doi: 10.1111/j.1365‐2648.2012.06035.xAbstractAim.  To report a descriptive study of early infant feeding experiences focusing on accounts of women who expressed milk extensively in the first few weeks postpartum.Background.  Relatively little is known about the reasons for expressing milk following healthy term births. Evidence indicates it is an increasingly common practice during early infant feeding in Westernized countries. A more comprehensive understanding of this practice will help midwives and nurses assist mothers negotiate early feeding challenges.Design.  Qualitative data were collected in two phases in the first few weeks postpartum.Method.  Audio‐diary and semi‐structured interview data from seven British women who extensively expressed milk in the first month postpartum were analysed. These data were drawn from a larger qualitative longitudinal study which took place in 2006–2007. Themes, discursive constructions and discourses are identified through the use of a feminist informed analysis.Findings.  The practice of expressing was employed as a solution to managing the competing demands and dilemmas of early breastfeeding and ensuring the continued provision of breast milk, thereby deflecting potential accusations of poor mothering. In addition, the practice may afford a degree of freedom to new mothers.Conclusions.  The need to maintain the ‘good maternal body’ can account for the motivation to express milk, although there may be reasons to be cautious about promoting expression as a solution to breastfeeding difficulties. Education for health professionals, which emphasizes the complexities and contradictions of mothering and which challenges prescriptive notions of ‘good mothering’ could better support new mothers in their feeding ‘choices’.
Literature search strategies for conducting knowledge‐building and theory‐generating qualitative systematic reviews
Authors: Finfgeld‐Connett Deborah , Johnson E. Diane 
Published: May 2012

AbstractAim.  To report literature search strategies for the purpose of conducting knowledge‐building and theory‐generating qualitative systematic reviews.Background.  Qualitative systematic reviews lie on a continuum from knowledge‐building and theory‐generating to aggregating and summarizing. Different types of literature searches are needed to optimally support these dissimilar reviews.Data sources.  Articles published between 1989–Autumn 2011. These documents were identified using a hermeneutic approach and multiple literature search strategies.Discussion.  Redundancy is not the sole measure of validity when conducting knowledge‐building and theory‐generating systematic reviews. When conducting these types of reviews, literature searches should be consistent with the goal of fully explicating concepts and the interrelationships among them. To accomplish this objective, a ‘berry picking’ approach is recommended along with strategies for overcoming barriers to finding qualitative research reports.Implications.  To enhance integrity of knowledge‐building and theory‐generating systematic reviews, reviewers are urged to make literature search processes as transparent as possible, despite their complexity. This includes fully explaining and rationalizing what databases were used and how they were searched. It also means describing how literature tracking was conducted and grey literature was searched. In the end, the decision to cease searching also needs to be fully explained and rationalized.Conclusion.  Predetermined linear search strategies are unlikely to generate search results that are adequate for purposes of conducting knowledge‐building and theory‐generating qualitative systematic reviews. Instead, it is recommended that iterative search strategies take shape as reviews evolve.
The Pseudomonas syringae HrpJ protein controls the secretion of type III translocator proteins and has a virulence role inside plant cells
Authors: Crabill Emerson , Karpisek Andrew , Alfano James R. 
Published: May 2012

SummaryThe bacterial plant pathogen Pseudomonas syringae injects effector proteins into plant cells via a type III secretion system (T3SS), which is required for pathogenesis. The protein HrpJ is secreted by P. syringae and is required for a fully functional T3SS. A hrpJ mutant is non‐pathogenic and cannot inject effectors into plant cells or secrete the harpin HrpZ1. Here we show that the hrpJ mutant also cannot secrete the harpins HrpW1 and HopAK1 or the translocator HrpK1, suggesting that these proteins are required in the translocation (injection) of effectors into plant cells. Complementation of the hrpJ mutant with secretion incompetent HrpJ derivatives restores the secretion of HrpZ1 and HrpW1 and the ability to elicit a hypersensitive response, a measure of translocation. However, growth in planta and disease symptom production is only partially restored, suggesting that secreted HrpJ may have a direct role in virulence. Transgenic Arabidopsis plants expressing HrpJ‐HA complemented the virulence phenotype of the hrpJ mutant expressing a secretion incompetent HrpJ derivative and were reduced in their immune responses. Collectively, these data indicate that HrpJ has a dual role in P. syringae: inside bacterial cells HrpJ controls the secretion of translocator proteins and inside plant cells it suppresses plant immunity.