bluuebunny/crossref_metadata_2025_split huggingface dataset:
Embedding stock assessment within an integrated hierarchical Bayesian life cycle modelling framework: an application to Atlantic salmon in the Northeast Atlantic
Authors: Massiot-Granier Félix , Prévost Etienne , Chaput Gérald , Potter Ted , Smith Gordon , White Jonathan , Mäntyniemi Samu , Rivot Etienne 
Published: February 2014

AbstractWe developed a hierarchical Bayesian integrated life cycle model for Atlantic salmon that improves on the stock assessment approach currently used by ICES and provides some interesting insights about the population dynamics of a stock assemblage. The model is applied to the salmon stocks in eastern Scotland. It assimilates a 40-year (1971–2010) time-series of data compiled by ICES, including the catches in the distant water fisheries at Faroes and West Greenland and estimates of returning fish abundance. Our model offers major improvements in terms of statistical methodology for A. salmon stock assessment. Uncertainty about inferences is readily quantified in the form of Bayesian posterior distributions for parameters and abundance at all life stages, and the model could be adapted to provide projections based on the uncertainty derived from the estimation phase. The approach offers flexibility to improve the ecological realism of the model. It allows the introduction of density dependence in the egg-to-smolt transition, which is not considered in the current ICES assessment method. The results show that this modifies the inferences on the temporal dynamics of the post-smolt marine survival. In particular, the overall decrease in the marine survival between 1971 and 2010 and the sharp decline around 1988–1990 are dampened when density dependence is considered. The return rates of smolts as two-sea-winter (2SW) fish has declined in a higher proportion than return rates as one-sea-winter (1SW) fish. Our results indicate that this can be explained either by an increase in the proportion maturing as 1SW fish or by an increase in the mortality rate at sea of 2SW fish, but the data used in our analyses do not allow the likelihood of these two hypotheses to be gauged.
Revisiting the concept of Beverton­­–Holt life-history invariants with the aim of informing data-poor fisheries assessment
Authors: Prince Jeremy , Hordyk Adrian , Valencia Sarah R. , Loneragan Neil , Sainsbury Keith 
Published: February 2014

AbstractThe complexity and cost of assessment techniques prohibits their application to 90% of fisheries. Simple generic approaches are needed for the world's small-scale and data-poor fisheries. This meta-analysis of the relationship between spawning potential and the normalized size and age of 123 marine species suggests that the so-called Beverton–Holt life-history invariants (BH-LHI; Lm/L∞, M/k, M × Agem) actually vary together in relation to life-history strategy, determining the relationship between size, age, and reproductive potential for each species. Although little realized, the common assumption of unique values for the BH-LHI also implies that all species share the same relationship between size, age, and reproductive potential. This implicit assumption is not supported by this meta-analysis, which suggests that there is considerable but predictable natural variation in the BH-LHI ratios and the relationships between size, age, and reproductive potential that they determine. We believe that this reconceptualization of the BH-LHI has potential to provide a theoretical framework for “borrowing” knowledge from well-studied species to apply to related, unstudied species and populations, and when applied together with the assessment technique described by Hordyk et al. (2015b), could make simple forms of size-based assessment possible for many currently unassessable fish stocks.
50 picoarcsec astrometry of pulsar emission
Authors: Pen Ue-Li , Macquart Jean-Pierre , Deller Adam T. , Brisken Walter 
Published: February 2014

Abstract
We use very long baseline interferometry (VLBI) imaging of the interstellar scattering speckle pattern associated with the pulsar PSR 0834+06 to measure the astrometric motion of its emission. The D ∼ 5 au interstellar baselines, provided by interference between speckles spanning the scattering disc, enable us to detect motions with subnanoarcsecond accuracy. We measure a small pulse deflection of ∼18 ± 2 km (not including geometric uncertainties), which is 100 times smaller than the characteristic resolution (λ/D) of this interstellar interferometer. This implies that the emission region is small, and at an altitude of a few hundred km, with the exact value depending on field geometry. This is substantially closer to the star than to the light cylinder. Future VLBI measurements can improve on this finding. This new regime of ultraprecise astrometry may enable precision parallax distance determination of pulsar binary displacements.
Star formation in the ultraluminous infrared galaxy F00183-7111
Authors: Mao Minnie Y. , Norris Ray P. , Emonts Bjorn , Sharp Rob , Feain Ilana , Chow Kate , Lenc Emil , Stevens Jamie 
Published: February 2014

Abstract
We report the detection of molecular CO(1–0) gas in F00183-7111, one of the most extreme ultraluminous infrared galaxies (ULIRGs) known, with the Australia Telescope Compact Array. We measure a redshift of 0.3292 for F00183-7111 from the CO(1–0) line and estimate the mass of the molecular gas in 00183 to be 1 × 1010 M⊙. We find that F00183-7111 is predominately powered by the active galactic nucleus (AGN) and only ∼14 per cent of the total luminosity is contributed by star formation (SFR ∼220 M⊙ yr−1). We also present an optical image of F00183-7111, which shows an extension to the east. We searched for star formation in this extension using radio continuum observations but do not detect any. This suggests that the star formation is likely to be predominately nuclear. These observations provide additional support for a model in which the radio emission from ULIRGs is powered by an intense burst of star formation and by a radio-loud AGN embedded in its nucleus, both triggered by a merger of gas-rich galaxies.
A reassessment of consensus clustering for class discovery
Authors: Senbabaoglu Yasin , Michailidis George , Li Jun Z. 
Published: February 2014

AbstractConsensus clustering (CC) is an unsupervised class discovery method widely used to study sample heterogeneity in high-dimensional datasets. It calculates “consensus rate” between any two samples as how frequently they are grouped together in repeated clustering runs under a certain degree of random perturbation. The pairwise consensus rates form a between-sample similarity matrix, which has been used (1) as a visual proof that clusters exist, (2) for comparing stability among clusters, and (3) for estimating the optimal number (K) of clusters. However, the sensitivity and specificity of CC have not been systemically studied. To assess its performance, we investigated the most common implementations of CC; and compared CC with other popular methods that also focus on cluster stability and estimation of K. We evaluated these methods using simulated datasets with either known structure or known absence of structure. Our results showed that (1) CC was able to divide randomly generated unimodal data into pre-specified numbers of clusters, and was able to show apparent stability of these chance partitions of known cluster-less data; (2) for data with known structure, the proportion of ambiguously clustered (PAC) pairs infers the known number of clusters more reliably than several commonly used K estimating methods; and (3) validation of the optimal K by choosing the most discriminant genes from the discovery cohort and applying them in an independent cohort often exaggerates the confidence in K due to inherent gene-gene correlations among the selected genes. While these results do not yet prove that any of the published studies using CC has generated false positive findings, they show that datasets with subtle or no structure are fully capable of producing strong evidence of consensus clustering. We therefore recommend caution is using CC in class discovery and validation.
Spectacle: Faster and more accurate chromatin state annotation using spectral learning
Authors: Song Jimin , Chen Kevin C. 
Published: February 2014

AbstractRecently, a wealth of epigenomic data has been generated by biochemical assays and next-generation sequencing (NGS) technologies. In particular, histone modification data generated by the ENCODE project and other large-scale projects show specific patterns associated with regulatory elements in the human genome. It is important to build a unified statistical model to decipher the patterns of multiple histone modifications in a cell type to annotate chromatin states such as transcription start sites, enhancers and transcribed regions rather than to map histone modifications individually to regulatory elements.Several genome-wide statistical models have been developed based on hidden Markov models (HMMs). These methods typically use the Expectation-Maximization (EM) algorithm to estimate the parameters of the model. Here we used spectral learning, a state-of-the-art parameter estimation algorithm in machine learning. We found that spectral learning plus a few (up to five) iterations of local optimization of the likelihood outper-forms the standard EM algorithm. We also evaluated our software implementation calledSpectacleon independent biological datasets and found thatSpectacleannotated experimentally defined functional elements such as enhancers significantly better than a previous state-of-the-art method.Spectaclecan be downloaded fromhttps://github.com/jiminsong/Spectacle.
Imaging of Endogenous Messenger RNA Splice Variants in Living Cells Reveals Nuclear Retention of Transcripts Inaccessible to Nonsense-Mediated Decay in Arabidopsis
Authors: Göhring Janett , Jacak Jaroslaw , Barta Andrea 
Published: February 2014

Abstract
Alternative splicing (AS) is an important regulatory process that leads to the creation of multiple RNA transcripts from a single gene. Alternative transcripts often carry premature termination codons (PTCs), which trigger nonsense-mediated decay (NMD), a cytoplasmic RNA degradation pathway. However, intron retention, the most prevalent AS event in plants, often leads to PTC-carrying splice variants that are insensitive to NMD; this led us to question the fate of these special RNA variants. Here, we present an innovative approach to monitor and characterize endogenous mRNA splice variants within living plant cells. This method combines standard confocal laser scanning microscopy for molecular beacon detection with a robust statistical pipeline for sample comparison. We demonstrate this technique on the localization of NMD-insensitive splice variants of two Arabidopsis thaliana genes, RS2Z33 and the SEF factor. The experiments reveal that these intron-containing splice variants remain within the nucleus, which allows them to escape the NMD machinery. Moreover, fluorescence recovery after photobleaching experiments in the nucleoplasm show a decreased mobility of intron-retained mRNAs compared with fully spliced RNAs. In addition, differences in mobility were observed for an mRNA dependent on its origin from an intron-free or an intron-containing gene.
Stability of source mechanisms inverted from P‐wave amplitude microseismic monitoring data acquired at the surface
Authors: Staněk František , Eisner Leo , Jan Moser Tijmen 
Published: February 2014

ABSTRACTWe study the stability of source mechanisms inverted from data acquired at surface and near‐surface monitoring arrays. The study is focused on P‐wave data acquired on vertical components, as this is the most common type of acquisition. We apply ray modelling on three models: a fully homogeneous isotropic model, a laterally homogeneous isotropic model and a laterally homogeneous anisotropic model to simulate three commonly used models in inversion. We use geometries of real arrays, one consisting in surface receivers and one consisting in ‘buried’ geophones at the near‐surface. Stability was tested for two of the frequently observed source mechanisms: strike‐slip and dip‐slip and was evaluated by comparing the parameters of correct and inverted mechanisms. We assume these double‐couple source mechanisms and use quantitatively the inversion allowing non‐double‐couple components to measure stability of the inversion. To test the robustness we inverted synthetic amplitudes computed for a laterally homogeneous isotropic model and contaminated with noise using a fully homogeneous model in the inversion. Analogously amplitudes computed in a laterally homogeneous anisotropic model were inverted in all three models. We show that a star‐like surface acquisition array provides very stable inversion up to a very high level of noise in data. Furthermore, we reveal that strike‐slip inversion is more stable than dip‐slip inversion for the receiver geometries considered here. We show that noise and an incorrect velocity model may result in narrow bands of source mechanisms in Hudson's plots.
Pyromorphite formation in a fungal biofilm community growing on lead metal
Authors: Rhee Young Joon , Hillier Stephen , Pendlowski Helen , Gadd Geoffrey Michael 
Published: February 2014

SummaryLead is a priority pollutant, and lead metal is widely found in the environment as a waterproofing structural component in roofing, fence post covers, venting and flashing, as well as in industrial and urban waste. However, little is known of microbial interactions with metallic lead. The objective of this research was to investigate fungal roles in transformations of lead in a surface biofilm community growing on lead sheeting. The lead surface was found to support a diverse fungal community with several members, such as Aureobasidum pullulans, Phoma macrostoma, Penicillium sp. and Botryotinia fuckeliana, probably originating from adjacent phylloplane communities. Many fungal isolates showed tolerance to lead compounds in growth inhibition assays and were able to mediate production of lead‐containing secondary minerals in the presence of metallic lead. These exhibited widely differing morphologies to the lead‐containing secondary minerals produced under abiotic conditions. The presence of pyromorphite (Pb5(PO4)3Cl) (approximately 50 wt%) was detected in the lead sheet biofilm, and we speculate that animal (bird) faeces could be a significant source of phosphorus in this location. Pyromorphite formation represents biomineralization of mobile lead species into a very stable form, and this research provides the first demonstration of its occurrence in the natural environment.
Cyclic‐di‐GMP levels affect Pseudomonas aeruginosa fitness in the presence of imipenem
Authors: Nicastro Gianlucca G. , Kaihami Gilberto H. , Pereira Thays O. , Meireles Diogo A. , Groleau Marie‐Christine , Déziel Eric , Baldini Regina L. 
Published: February 2014

SummaryA large number of genes coding for enzymes predicted to synthesize and degrade 3′–5′‐cyclic diguanylic acid (c‐di‐GMP) is found in most bacterial genomes and this dinucleotide emerged as an intracellular signal‐controlling bacterial behaviour. An association between high levels of c‐di‐GMP and antibiotic resistance may be expected because c‐di‐GMP regulates biofilm formation and this mode of growth leads to enhanced antibiotic resistance. However, a clear understanding of this correlation has not been established. We found that increased levels of c‐di‐GMP in Pseudomonas aeruginosa improve fitness in the presence of imipenem, even when grown as planktonic cells. P. aeruginosa post‐transcriptionally regulates the amounts of five porins in response to c‐di‐GMP, including OprD, responsible for imipenem uptake. Cells with low c‐di‐GMP levels are consequently more sensitive to this antibiotic. Main efflux pumps or β‐lactamase genes did not show altered mRNA levels in P. aeruginosa strains with modified different c‐di‐GMP concentrations. Together, our findings show that c‐di‐GMP levels modulate fitness of planktonic cultures in the presence of imipenem.
Bees under stress: sublethal doses of a neonicotinoid pesticide and pathogens interact to elevate honey bee mortality across the life cycle
Authors: Doublet Vincent , Labarussias Maureen , de Miranda Joachim R. , Moritz Robin F. A. , Paxton Robert J. 
Published: February 2014

SummaryMicrobial pathogens are thought to have a profound impact on insect populations. Honey bees are suffering from elevated colony losses in the northern hemisphere possibly because of a variety of emergent microbial pathogens, with which pesticides may interact to exacerbate their impacts. To reveal such potential interactions, we administered at sublethal and field realistic doses one neonicotinoid pesticide (thiacloprid) and two common microbial pathogens, the invasive microsporidian Nosema ceranae and black queen cell virus (BQCV), individually to larval and adult honey bees in the laboratory. Through fully crossed experiments in which treatments were administered singly or in combination, we found an additive interaction between BQCV and thiacloprid on host larval survival likely because the pesticide significantly elevated viral loads. In adult bees, two synergistic interactions increased individual mortality: between N. ceranae and BQCV, and between N. ceranae and thiacloprid. The combination of two pathogens had a more profound effect on elevating adult mortality than N. ceranae plus thiacloprid. Common microbial pathogens appear to be major threats to honey bees, while sublethal doses of pesticide may enhance their deleterious effects on honey bee larvae and adults. It remains an open question as to whether these interactions can affect colony survival.
Behaviour change and social blinkers? The role of sociology in trials of self‐management behaviour in chronic conditions
Authors: Ong Bie Nio , Rogers Anne , Kennedy Anne , Bower Peter , Sanders Tom , Morden Andrew , Cheraghi‐Sohi Sudeh , Richardson Jane C. , Stevenson Fiona 
Published: February 2014

AbstractIndividual‐focused self‐management interventions are one response to both an ageing society and the purported increase in chronic conditions. They tend to draw on psychological theories in self‐management interventions, but over‐reliance on these theories can reinforce a narrow focus on specified attitudinal and behavioural processes, omitting aspects of living with a chronic condition. While advances have been made in health behaviour change theory and practice, scant attention has been paid to the social, with the question of social context remaining under‐theorised and under‐explored empirically. This is particularly noticeable in trials of behaviour change interventions for self‐management. The common sociological critique is that these ignore context and thus no explanation can be given as to why, for whom and under what circumstances a treatment works. Conversely, sociologists are criticised for offering no positive suggestions as to how context can be taken into account and for over‐emphasising context with the risk of inhibiting innovation. This article provides an overview of these issues and provides examples of how context can be incorporated into the rigid method of trials of self‐management for chronic conditions. We discuss modifications to both trial interventions and design that make constructive use of the concept of context.
Enjoy your food: on losing weight and taking pleasure
Authors: Vogel Else , Mol Annemarie 
Published: February 2014

AbstractDoes healthy eating require people to control themselves and abstain from pleasure? This idea is dominant, but in our studies of dieting in The Netherlands we encountered professionals who work in other ways. They encourage their clients to enjoy their food, as only such joy provides satisfaction and the sense that one has eaten enough. Enjoying one's food is not easy. It depends on being sensitive. This does not come naturally but needs training. And while one kind of hunger may be difficult to distinguish from another, feeling pleasure may open the doors to feeling pain. What is more, sensitivity is not enough: enjoying one's food also depends on the food being enjoyable. A lot of care is required for that. But while engaging in such care is hard work, along the way clients are encouraged to no longer ask ‘Am I being good?’ but to wonder instead ‘Is this good for me?’ Both these questions are normative and focus on the person rather than on her socio‐material context. However, in the situations related here the difference is worth making. For it entails a shift from externally controlling your behaviour to self‐caringly enjoying your food.
From health behaviours to health practices: an introduction
Authors: Cohn Simon 
Published: February 2014

AbstractThe concept of health behaviour has become ubiquitous in health‐related research and intervention studies, as well as among policymakers. Developed from psychology, it is based on a number of key underlying assumptions that enable it to be integrated in an existing health research paradigm. However, by conceiving individual health behaviour as discrete, stable, homogeneous and measurable, many other aspects of health‐related activities, in particular those relating to power and sociality, are excluded. As a consequence, any genuine contribution from medical sociology or related disciplines is, at best, limited. To counter this, it is proposed that reconceptualising what people do in terms of health practices, rather than health behaviour, captures the emergent and contingent properties of people's activities in particular situations. Rather than serving as a direct replacement term, and thus reproducing the same epistemological assumptions, it is argued that its very flexibility and capacity to articulate different theoretical orientations is likely to be its major strength.
Accuracy of diagnosing gastroesophageal reflux disease by GerdQ, esophageal impedance monitoring and histology
Authors: Zhou Li Ya , Wang Ye , Lu Jing Jing , Lin Lin , Cui Rong Li , Zhang He Jun , Xue Yan , Ding Shi Gang , Lin San Ren 
Published: February 2014

ObjectiveTo assess the performance of self‐assessment gastroesophageal reflux disease questionnaire (GerdQ), 24‐h impedance monitoring, proton pump inhibitor (PPI) test and intercellular space of esophageal mucosal epithelial cells in the diagnosis of gastroesophageal reflux disease (GERD).MethodsPatients with symptoms suspected of GERD were administered the GerdQ and underwent endoscopy (measurement of intercellular space in the biopsy specimen sampling at 2 cm above the Z‐line) and 24‐h impedance pH monitoring, together with a 2‐week experimental treatment with esomeprazole.ResultsA total of 636 patients were included for the final analysis, including 352 with GERD. The sensitivity and specificity of GerdQ and 24‐h impedance monitoring for diagnosing GERD were 57.7% and 48.9%, and 66.4% and 43.3%, respectively. The sensitivity of 24‐h impedance pH monitoring increased to 93.7%. The sensitivity and specificity of dilated intercellular spaces (DIS) (≥0.9 μm) for diagnosing GERD were 61.2% and 56.1%, respectively, whereas those for PPI test were 70.5% and 44.4%.ConclusionsGerdQ score or PPI test alone cannot accurately diagnose GERD in a Chinese population suspected of GERD. A definitive diagnosis of GERD still depends on endoscopy or 24‐h pH monitoring. 24‐h impedance pH monitoring may increase the sensitivity for diagnosing GERD by 20%; however, when used alone, it results in poor specificity in patients without acid suppressive therapy.