PDNAsite:identification of DNA-binding site from protein sequence by incorporating spatial and sequence context

Protein-DNA interactions are involved in many fundamental biological processes essential for cellular function. Most of the existing computational approaches employed only the sequence context of the target residue for its prediction. In the present study, for each target residue, we applied both the spatial context and the sequence context to construct the feature space. Subsequently, Latent Semantic Analysis (LSA) was applied to remove the redundancies in the feature space. Finally, a predictor (PDNAsite) was developed through the integration of the support vector machines (SVM) classifier and ensemble learning. Results on the PDNA-62 and the PDNA-224 datasets demonstrate that features extracted from spatial context provide more information than those from sequence context and the combination of them gives more performance gain. An analysis of the number of binding sites in the spatial context of the target site indicates that the interactions between binding sites next to each other are important for protein-DNA recognition and their binding ability. The comparison between our proposed PDNAsite method and the existing methods indicate that PDNAsite outperforms most of the existing methods and is a useful tool for DNA-binding site identification. A web-server of our predictor (http://hlt.hitsz.edu.cn:8080/PDNAsite/) is made available for free public accessible to the biological research community.

Retail restructuring and consumer choice 1:long term local changes in consumer behaviour : Portsmouth 1980-2002

Over the last two decades fundamental changes have taken place in the global supply and local structure of provision of British food retailing. Consumer lifestyles have also changed markedly. Despite some important studies of local interactions between new retail developments and consumers, we argue in this paper that there is a critical need to gauge the cumulative effects of these changes on consumer behaviour over longer periods. In this, the first of two papers, we present the main findings of a study of the effects of long-term retail change on consumers at the local level. We provide in this paper an overview of the changing geography of retail provision and patterns of consumption at the local level. We contextualise the Portsmouth study area as a locality that typifies national changes in retail provision and consumer lifestyles; outline the main findings of two large-scale surveys of food shopping behaviour carried out in 1980 and 2002; and reveal the impacts of retail restructuring on consumer behaviour. We focus in particular on choice between stores at the local level and end by problematising our understanding of how consumers experience choice, emphasising the need for qualitative research. This issue is then dealt with in our complementary second paper, which explores choice within stores and how this relates to the broader spatial context.

Le prix de l'individualité. Maine de Brian, Samuel Taylor Coleridge et la volonté: Deux postétités distinctes

This thesis is concerned with Maine de Biran’s and Samuel Taylor Coleridge’s conceptions of will, and the way in which both thinkers’ posterities have been affected by the central role of these very conceptions in their respective bodies of thought. The research question that animates this work can therefore be divided into two main parts, one of which deals with will, while the other deals with its effects on posterity. In the first pages of the Introduction, I make the case for a comparison between two philosophers, and show how this comparison can bring one closer to truth, understood not in objective, but in subjective terms. I then justify my choice by underlining that, in spite of their many differences, Maine de Biran and Samuel Taylor Coleridge followed comparable paths, intellectually and spiritually, and came to similar conclusions concerning the essential activity of the human mind. Finally, I ask whether it is possible that this very focus on the human will may have contributed to the state of both thinkers’ works and of the reception of those works. This prologue is followed by five parts. In the first part, the similarities and differences between the two thinkers are explored further. In the second part, the connections between philosophy and singularity are examined, in order to show the ambivalence of the will as a foundation for truth. The third part is dedicated to the traditional division between subject and object in psychology, and its relevance in history and in moral philosophy. The fourth part tackles the complexity of the question of influence, with respect to both Maine de Biran’s and Coleridge’s cases, both thinkers being indebted to many philosophers of all times and places, and having to rely heavily on others for the publication, or the interpretation of their own works. The fifth part is concerned with the different aspects of the faculty of will, and primarily its relationship with interiority, as incommensurability, and actual, conditioned existence in a certain historical and spatial context. It ends with a return to the question of will and posterity and an announcement of what will be covered in the main body of the thesis. The main body is divided into three parts:‘L’émancipation’, ‘L’affirmation, and ‘La projection’. The first part is devoted to the way Maine de Biran and Samuel Taylor Coleridge extricated themselves from one epistemological paradigm to contribute to the foundation of another. It is divided in four chapters. The first chapter deals with the aforementioned change of paradigm, as corresponding to the emergence of two separate but associated movements, Romanticism and what the French philosopher refers to as ‘The Age of History’. The second chapter concerns the movement that preceded them, i.e. the Enlightenment, its main features according to both of our thinkers, and the two epistemological models that prevailed under it and influenced them heavily in their early years: Sensationism (Maine de Biran) and Associationism (Coleridge). The third chapter is about the probable influence of Immanuel Kant and his followers on Maine de Biran and Coleridge, and the various facts that allow us to claim originality for both thinkers’ works. In the fourth chapter, I contrast Maine de Biran and Coleridge with other movements and thinkers of their time, showing that, contrary to their respective thoughts, Maine de Biran and Coleridge could not but break free from the then prevailing systematic approach to truth. The second part of the thesis is concerned with the first part of its research question, namely, Maine de Biran’s and Coleridge’s conceptions of the will. It is divided into four chapters. The first chapter is a reflection on the will as a paradox: on the one hand, the will cannot be caused by any other phenomenon, or it is no longer a will; but it cannot be left purely undetermined, as if it is, it is then not different from chance. It thus needs, in order to be, to be contradictorily already moral. The second chapter is a comparison between Maine de Biran’s and Coleridge’s accounts of the origin of the will, where it is found that the French philosopher only observes that he has a will, whereas the English philosopher postulates the existence of this will. The comparison between Maine de Biran’s and Coleridge’s conceptions of the will is pursued in the third chapter, which tackles the question of the coincidence between the will and the self, in both thinkers’ works. It ends with the fourth chapter, which deals with the question of the relationship between the will and what is other to it, i.e. bodily sensations, passions and desires. The third part of the thesis focuses on the second part of its research question, namely the posterity of Maine de Biran’s and Coleridge’s works. It is divided into four chapters. The first chapter constitutes a continuation of the last chapter of the preceding part, in that that it deals with Maine de Biran’s and Coleridge’s relations to the ‘other’, and particularly their potential and actual audience, and with the way these relations may have affected their writing and publishing practices. The second chapter is a survey of both thinkers’ general reception, where it is found that, while Maine de Biran has been claimed by two important movements of thoughts as their initiator, Coleridge has been neglected by the only real movement he could have, or may indeed have pioneered. The third chapter is more directly concerned with the posterities of Maine de Biran’s and Coleridge’s conceptions of will, and attempts to show that the approach to, and the meaning of the will have evolved throughout the nineteenth century, and in the French Spiritualist and the British Idealist movements, from an essentially personal one to a more impersonal one. The fourth chapter is a partial conclusion, whose aim is to give a precise idea of where Maine de Biran and Coleridge stand, in relation to their century and to the philosophical movements and matters we are concerned with. The conclusion is a recapitulation of what has been found, with a particular emphasis on the dialogue initiated between Maine de Biran and Coleridge on the will, and the relation between will and posterity. It suggests that both thinkers have to pay the price of a problematic reception for the individuality that pervades their respective works, and goes further in suggesting that s/he who chooses to found his individuality on the will is bound to feel this incompleteness in his/her own personal life more acutely than s/he who does not. It ends with a reflection on fixedness and movement, as the two antagonistic states that the theoretician of the will paradoxically aspires to.

Higher-order co-occurrences for exploratory point pattern analysis and decision tree clustering on spatial data

Analyzing geographical patterns by collocating events, objects or their attributes has a long history in surveillance and monitoring, and is particularly applied in environmental contexts, such as ecology or epidemiology. The identification of patterns or structures at some scales can be addressed using spatial statistics, particularly marked point processes methodologies. Classification and regression trees are also related to this goal of finding "patterns" by deducing the hierarchy of influence of variables on a dependent outcome. Such variable selection methods have been applied to spatial data, but, often without explicitly acknowledging the spatial dependence. Many methods routinely used in exploratory point pattern analysis are2nd-order statistics, used in a univariate context, though there is also a wide literature on modelling methods for multivariate point pattern processes. This paper proposes an exploratory approach for multivariate spatial data using higher-order statistics built from co-occurrences of events or marks given by the point processes. A spatial entropy measure, derived from these multinomial distributions of co-occurrences at a given order, constitutes the basis of the proposed exploratory methods. © 2010 Elsevier Ltd.

Higher-order co-occurrences for exploratory point pattern analysis and decision tree clustering on spatial data

Analyzing geographical patterns by collocating events, objects or their attributes has a long history in surveillance and monitoring, and is particularly applied in environmental contexts, such as ecology or epidemiology. The identification of patterns or structures at some scales can be addressed using spatial statistics, particularly marked point processes methodologies. Classification and regression trees are also related to this goal of finding "patterns" by deducing the hierarchy of influence of variables on a dependent outcome. Such variable selection methods have been applied to spatial data, but, often without explicitly acknowledging the spatial dependence. Many methods routinely used in exploratory point pattern analysis are2nd-order statistics, used in a univariate context, though there is also a wide literature on modelling methods for multivariate point pattern processes. This paper proposes an exploratory approach for multivariate spatial data using higher-order statistics built from co-occurrences of events or marks given by the point processes. A spatial entropy measure, derived from these multinomial distributions of co-occurrences at a given order, constitutes the basis of the proposed exploratory methods. © 2010 Elsevier Ltd.

Elevated left and reduced right orbitomedial prefrontal fractional anisotropy in adults with bipolar disorder revealed by tract-based spatial statistics

Context - Diffusion tensor imaging (DTI) studies in adults with bipolar disorder (BD) indicate altered white matter (WM) in the orbitomedial prefrontal cortex (OMPFC), potentially underlying abnormal prefrontal corticolimbic connectivity and mood dysregulation in BD. Objective - To use tract-based spatial statistics (TBSS) to examine WM skeleton (ie, the most compact whole-brain WM) in subjects with BD vs healthy control subjects. Design - Cross-sectional, case-control, whole-brain DTI using TBSS. Setting - University research institute. Participants - Fifty-six individuals, 31 having a DSM-IV diagnosis of BD type I (mean age, 35.9 years [age range, 24-52 years]) and 25 controls (mean age, 29.5 years [age range, 19-52 years]). Main Outcome Measures - Fractional anisotropy (FA) longitudinal and radial diffusivities in subjects with BD vs controls (covarying for age) and their relationships with clinical and demographic variables. Results - Subjects with BD vs controls had significantly greater FA (t > 3.0, P = .05 corrected) in the left uncinate fasciculus (reduced radial diffusivity distally and increased longitudinal diffusivity centrally), left optic radiation (increased longitudinal diffusivity), and right anterothalamic radiation (no significant diffusivity change). Subjects with BD vs controls had significantly reduced FA (t > 3.0, P = .05 corrected) in the right uncinate fasciculus (greater radial diffusivity). Among subjects with BD, significant negative correlations (P < .01) were found between age and FA in bilateral uncinate fasciculi and in the right anterothalamic radiation, as well as between medication load and FA in the left optic radiation. Decreased FA (P < .01) was observed in the left optic radiation and in the right anterothalamic radiation among subjects with BD taking vs those not taking mood stabilizers, as well as in the left optic radiation among depressed vs remitted subjects with BD. Subjects having BD with vs without lifetime alcohol or other drug abuse had significantly decreased FA in the left uncinate fasciculus. Conclusions - To our knowledge, this is the first study to use TBSS to examine WM in subjects with BD. Subjects with BD vs controls showed greater WM FA in the left OMPFC that diminished with age and with alcohol or other drug abuse, as well as reduced WM FA in the right OMPFC. Mood stabilizers and depressed episode reduced WM FA in left-sided sensory visual processing regions among subjects with BD. Abnormal right vs left asymmetry in FA in OMPFC WM among subjects with BD, likely reflecting increased proportions of left-sided longitudinally aligned and right-sided obliquely aligned myelinated fibers, may represent a biologic mechanism for mood dysregulation in BD.

Performance evaluation of adaptive context aware rate selection algorithm (ACARS) for road safety applications in vehicular network

One of the major drawbacks for mobile nodes in wireless networks is power management. Our goal is to evaluate the performance power control scheme to be used to reduce network congestion, improve quality of service and collision avoidance in vehicular network and road safety application. Some of the importance of power control (PC) are improving spatial reuse, and increasing network capacity in mobile wireless communications. In this simulation we have evaluated the performance of existing rate algorithms compared with context Aware Rate selection algorithm (ACARS) and also seen the performance of ACARS and how it can be applied to road safety, improve network control and power management. Result shows that ACARS is able to minimize the total transmit power in the presence of propagation processes and mobility of vehicles, by adapting to the fast varying channels conditions with the Path loss exponent values that was used for that environment which is shown in the network simulation parameter. Our results have shown that ACARS is a very robust algorithm which performs very well with the effect of propagation processes that is prone to every transmitted signal in mobile networks. © 2013 IEEE.