Alignment, persuasiveness and the putative reader in opinion writing

This paper explores a new line of analysis for comparing opinion writing by reference to differences in the relationships being indicated between author and addressee. It draws on recent work within the appraisal framework literature to offer proposals for linguistics-based analyses of what has variously been termed the ‘intended’, ‘imagined’, ‘ideal’, ‘virtual’, ‘model’, ‘implied’ and ‘putative’ reader (the ‘reader written into the text’). A discussion is provided of those means by which beliefs, attitudes and expectations are projected onto this ‘reader in the text’, formulations which signal anticipations that the reader either shares the attitude or belief currently being advanced by the author, potentially finds it novel or otherwise problematic, or may reject it outright. The discussion is conducted with respect to written, persuasive texts, and specifically with respect to news journalism’s commentary pieces. It is proposed that such texts can usefully be characterised and compared by reference to tendencies in such ‘construals’ or ‘positionings’ of the putative reader – tendencies in terms of whether the signalled anticipation is of the reader being aligned or, conversely, potentially unaligned or dis-aligned with the author. The terms ‘flag waving’ and ‘advocacy’ are proposed as characterisations which can be applied to texts, with ‘flag waving’ applicable to texts which construe the reader as largely sharing the author’s beliefs and attitudes, while ‘advocacy’ is applicable to texts where the reader is construed as actually or potentially not sharing the author’s beliefs and attitudes and thereby needing to be won over. This line of analysis is demonstrated through a comparison of two journalistic opinion pieces written in response to visits by Japanese politicians to the Yasukuni Shrine in Tokyo, one published in the English-language version of the mainland China newspaper,China Dailyand one in the English-language version of the JapaneseAsahi Shimbun. It is shown that one piece can usefully be characterised as oriented towards ‘flag waving’ and the other towards ‘advocacy’

Modelling endoplasmic reticulum network maintenance in a plant cell

This is the author accepted manuscript. The final version is available from Elsevier via the DOI in this record.The endoplasmic reticulum (ER) in plant cells forms a highly dynamic network of complex geometry. ER network morphology and dynamics are influenced by a number of biophysical processes, including filament/tubule tension, viscous forces, Brownian diffusion and interactions with many other organelles and cytoskeletal elements. Previous studies have indicated that ER networks can be thought of as constrained minimal-length networks acted on by a variety of forces that perturb and/or remodel the network. Here, we study two specific biophysical processes involved in remodelling. One is the dynamic relaxation process involving a combination of tubule tension and viscous forces. The other is the rapid creation of cross-connection tubules by direct or indirect interactions with cytoskeletal elements. These processes are able to remodel the ER network: the first reduces network length and complexity while the second increases both. Using live cell imaging of ER network dynamics in tobacco leaf epidermal cells, we examine these processes on ER network dynamics. Away from regions of cytoplasmic streaming, we suggest that the dynamic network structure is a balance between the two processes, and we build an integrative model of the two processes for network remodelling. This model produces quantitatively similar ER networks to those observed in experiments. We use the model to explore the effect of parameter variation on statistical properties of the ER network.This work was funded by a Leverhulme Trust grant (RPG-2015-106)

Plant ER geometry and dynamics: biophysical and cytoskeletal control during growth and biotic response.

This is the author accepted manuscript. The final version is available from Springer via the DOI in this record.The endoplasmic reticulum (ER) is an intricate and dynamic network of membrane tubules and cisternae. In plant cells, the ER 'web' pervades the cortex and endoplasm and is continuous with adjacent cells as it passes through plasmodesmata. It is therefore the largest membranous organelle in plant cells. It performs essential functions including protein and lipid synthesis, and its morphology and movement are linked to cellular function. An emerging trend is that organelles can no longer be seen as discrete membrane-bound compartments, since they can physically interact and 'communicate' with one another. The ER may form a connecting central role in this process. This review tackles our current understanding and quantification of ER dynamics and how these change under a variety of biotic and developmental cues.IS, RW and CL are funded by a Leverhulme Trust grant (RPG-2015-106) and CP by a Sainsbury studentship. LG is funded by the Gordon and Betty Moore Foundation for the lattice light sheet microscopy and by the Biology Department, Texas A&M University. L. Griffing would like to thank John Heddleston and Teng-Leong Chew at the Advanced Imaging Center in Janelia-HHMI Research Campus, Ashburn VA, for images taken with the light sheet microscope

Large-scale proteomic analysis of T. spiralis muscle-stage ESPs identifies a novel upstream motif for in silico prediction of secreted products

The Trichinella genus contains parasitic nematodes capable of infecting a wide range of hosts including mammals, birds and reptiles. Like other helminths, T. spiralis secretes a complex mixture of bioactive molecules capable of modulating its immediate surroundings and creating a hospitable environment for growth, survival and ultimately transmission. The constitution of these excretory-secretory products (ESPs) changes depending on the tissue niche and the specific stage of parasite development. Unique to T. spiralis is a true intracellular stage wherein larvae develop inside striated myotubes. Remarkably, the parasite larvae do not destroy the host cell but rather reprogram it to support their presence and growth. This transformation is largely mediated through stage-specific secretions released into the host cell cytoplasm. In this study, we apply state of the art proteomics and computational approaches to elucidate the composition and functions of muscle-stage T. spiralis ESPs. Moreover, we define a recurring, upstream motif associated with the stichosome, the main secretory organ of this worm, and can be used to predict secreted proteins across experimentally less tractable T. spiralis life cycle stages

Alcohol, tobacco and breast cancer: should alcohol be condemned and tobacco acquitted?

British Journal of Cancer (2002) 87, 1195–1196. doi:10.1038/sj.bjc.6600633 www.bjcancer.co

Intravitreal administration of recombinant human opticin protects against hyperoxia-induced pre-retinal neovascularization

Opticin is an extracellular glycoprotein present in the vitreous. Its antiangiogenic properties offer the potential for therapeutic intervention in conditions such as proliferative diabetic retinopathy and retinopathy of prematurity. Here, we investigated the hypothesis that intravitreal administration of recombinant human opticin can safely protect against the development of pathological angiogenesis and promote its regression. We generated and purified recombinant human opticin and investigated its impact on the development and regression of pathological retinal neovascularization following intravitreal administration in murine oxygen-induced retinopathy. We also investigated its effect on normal retinal vascular development and function, following intravitreal injection in neonatal mice, by histological examination and electroretinography. In oxygen-induced retinopathy, intravitreal administration of human recombinant opticin protected against the development of retinal neovascularization to similar extent as aflibercept, which targets VEGF. Opticin also accelerated regression of established retinal neovascularization, though the effect at 18 h was less than that of aflibercept. Intravitreal administration of human recombinant opticin in neonatal mice caused no detectable perturbation of subsequent retinal vascular development or function. In summary we found that intraocular administration of recombinant human opticin protects against the development of pathological angiogenesis in mice and promotes its regression

Prospective modelling of environmental dynamics. A methodological comparison applied to mountain land cover changes

During the last 10 years, scientists performed significant advances in modelling environmental dynamics. A wide range of new methodological approaches in geomatics - such as neural networks, multi-agent systems or fuzzy logics - was developed. Despite these progresses, the modelling softwares available have to be considered as experimental tools rather than as improved procedures able to work for environmental management or decision support. Particularly, the authors consider that a large number of publications suffer from lakes in the validation of the model results. This contribution describes three different modelling approaches applied to prospective land cover prediction. The first one, a combined geomatic method, uses Markov chains for temporal transition prediction while their spatial assignment is supervised manually by the construction of suitability maps. Compared to this directed method, the two others may be considered as semi automatic because both the polychotomous regression and the multilayer perceptron only need to be optimized during a training step - the algorithms detect themselves the spatial-temporal changes in land cover. The authors describe the three methodological approaches and their practical applications to two mountain studied areas: one in French Pyrenees, the second including a large part of Sierra Nevada, Spain. The article focuses on the comparison of results. The main result is that prediction scores are on the more high that land cover is persistent. They also underline that the geomatic model is complementary to the statistical ones which perform higher overall prediction rate but produce worse simulations when land cover changes are numerous

A multivariate hierarchical Bayesian approach to measuring agreement in repeated measurement method comparison studies

Background. Assessing agreement in method comparison studies depends on two fundamentally important components; validity (the between method agreement) and reproducibility (the within method agreement). The Bland-Altman limits of agreement technique is one of the favoured approaches in medical literature for assessing between method validity. However, few researchers have adopted this approach for the assessment of both validity and reproducibility. This may be partly due to a lack of a flexible, easily implemented and readily available statistical machinery to analyse repeated measurement method comparison data. Methods. Adopting the Bland-Altman framework, but using Bayesian methods, we present this statistical machinery. Two multivariate hierarchical Bayesian models are advocated, one which assumes that the underlying values for subjects remain static (exchangeable replicates) and one which assumes that the underlying values can change between repeated measurements (non-exchangeable replicates). Results. We illustrate the salient advantages of these models using two separate datasets that have been previously analysed and presented; (i) assuming static underlying values analysed using both multivariate hierarchical Bayesian models, and (ii) assuming each subject's underlying value is continually changing quantity and analysed using the non-exchangeable replicate multivariate hierarchical Bayesian model. Conclusion. These easily implemented models allow for full parameter uncertainty, simultaneous method comparison, handle unbalanced or missing data, and provide estimates and credible regions for all the parameters of interest. Computer code for the analyses in also presented, provided in the freely available and currently cost free software package WinBUGS

Compensated right ventricular function of the onset of pulmonary hypertension in a rat model depends on chamber remodeling and contractile augmentation.

Right-ventricular function is a good indicator of pulmonary arterial hypertension (PAH) prognosis; however, how the right ventricle (RV) adapts to the pressure overload is not well understood. Here, we aimed at characterizing the time course of RV early remodeling and discriminate the contribution of ventricular geometric remodeling and intrinsic changes in myocardial mechanical properties in a monocrotaline (MCT) animal model. In a longitudinal study of PAH, ventricular morphology and function were assessed weekly during the first four weeks after MCT exposure. Using invasive measurements of RV pressure and volume, heart performance was evaluated at end of systole and diastole to quantify contractility (end-systolic elastance) and chamber stiffness (end-diastolic elastance). To distinguish between morphological and intrinsic mechanisms, a computational model of the RV was developed and used to determine the level of prediction when accounting for wall masses and unloaded volume measurements changes. By four weeks, mean pulmonary arterial pressure and elastance rose significantly. RV pressures rose significantly after the second week accompanied by significant RV hypertrophy, but RV stroke volume and cardiac output were maintained. The model analysis suggested that, after two weeks, this compensation was only possible due to a significant increase in the intrinsic inotropy of RV myocardium. We conclude that this MCT-PAH rat is a model of RV compensation during the first month after treatment, where geometric remodeling on EDPVR and increased myocardial contractility on ESPVR are the major mechanisms by which stroke volume is preserved in the setting of elevated pulmonary arterial pressure. The mediators of this compensation might themselves promote longer-term adverse remodeling and decompensation in this animal model