'Datafication': Making sense of (big) data in a complex world

This is a pre-print of an article published in European Journal of Information Systems. The definitive publisher-authenticated version is available at the link below. Copyright @ 2013 Operational Research Society Ltd.No abstract available (Editorial

Genome-wide analyses of cassava Pathogenesis-related (PR) gene families reveal core transcriptome responses to whitefly infestation, salicylic acid and jasmonic acid.

BACKGROUND:Whiteflies are a threat to cassava (Manihot esculenta), an important staple food in many tropical/subtropical regions. Understanding the molecular mechanisms regulating cassava's responses against this pest is crucial for developing control strategies. Pathogenesis-related (PR) protein families are an integral part of plant immunity. With the availability of whole genome sequences, the annotation and expression programs of the full complement of PR genes in an organism can now be achieved. An understanding of the responses of the entire complement of PR genes during biotic stress and to the defense hormones, salicylic acid (SA) and jasmonic acid (JA), is lacking. Here, we analyze the responses of cassava PR genes to whiteflies, SA, JA, and other biotic aggressors. RESULTS:The cassava genome possesses 14 of the 17 plant PR families, with a total of 447 PR genes. A cassava PR gene nomenclature is proposed. Phylogenetic relatedness of cassava PR proteins to each other and to homologs in poplar, rice and Arabidopsis identified cassava-specific PR gene family expansions. The temporal programs of PR gene expression in response to the whitefly (Aleurotrachelus socialis) in four whitefly-susceptible cassava genotypes showed that 167 of the 447 PR genes were regulated after whitefly infestation. While the timing of PR gene expression varied, over 37% of whitefly-regulated PR genes were downregulated in all four genotypes. Notably, whitefly-responsive PR genes were largely coordinately regulated by SA and JA. The analysis of cassava PR gene expression in response to five other biotic stresses revealed a strong positive correlation between whitefly and Xanthomonas axonopodis and Cassava Brown Streak Virus responses and negative correlations between whitefly and Cassava Mosaic Virus responses. Finally, certain associations between PR genes in cassava expansions and response to biotic stresses were observed among PR families. CONCLUSIONS:This study represents the first genome-wide characterization of PR genes in cassava. PR gene responses to six biotic stresses and to SA and JA are demonstrably different to other angiosperms. We propose that our approach could be applied in other species to fully understand PR gene regulation by pathogens, pests and the canonical defense hormones SA and JA

Human Arm simulation for interactive constrained environment design

During the conceptual and prototype design stage of an industrial product, it is crucial to take assembly/disassembly and maintenance operations in advance. A well-designed system should enable relatively easy access of operating manipulators in the constrained environment and reduce musculoskeletal disorder risks for those manual handling operations. Trajectory planning comes up as an important issue for those assembly and maintenance operations under a constrained environment, since it determines the accessibility and the other ergonomics issues, such as muscle effort and its related fatigue. In this paper, a customer-oriented interactive approach is proposed to partially solve ergonomic related issues encountered during the design stage under a constrained system for the operator's convenience. Based on a single objective optimization method, trajectory planning for different operators could be generated automatically. Meanwhile, a motion capture based method assists the operator to guide the trajectory planning interactively when either a local minimum is encountered within the single objective optimization or the operator prefers guiding the virtual human manually. Besides that, a physical engine is integrated into this approach to provide physically realistic simulation in real time manner, so that collision free path and related dynamic information could be computed to determine further muscle fatigue and accessibility of a product designComment: International Journal on Interactive Design and Manufacturing (IJIDeM) (2012) 1-12. arXiv admin note: substantial text overlap with arXiv:1012.432

Scalar Multiplet Dark Matter

We perform a systematic study of the phenomenology associated to models where the dark matter consists in the neutral component of a scalar SU(2)_L n-uplet, up to n=7. If one includes only the pure gauge induced annihilation cross-sections it is known that such particles provide good dark matter candidates, leading to the observed dark matter relic abundance for a particular value of their mass around the TeV scale. We show that these values actually become ranges of values -which we determine- if one takes into account the annihilations induced by the various scalar couplings appearing in these models. This leads to predictions for both direct and indirect detection signatures as a function of the dark matter mass within these ranges. Both can be largely enhanced by the quartic coupling contributions. We also explain how, if one adds right-handed neutrinos to the scalar doublet case, the results of this analysis allow to have altogether a viable dark matter candidate, successful generation of neutrino masses, and leptogenesis in a particularly minimal way with all new physics at the TeV scale.Comment: 43 pages, 20 figure

Data, ideology, and the developing critical program of social informatics

The rapidly shifting ideological terrain of computing has a profound impact on Social Informatics's critical and empirical analysis of computerization movements. As these movements incorporate many of the past critiques concerning social fit and situational context leveled against them by Social Informatics research, more subtle and more deeply ingrained modes of ideological practice have risen to support movements of computerization. Among these, the current emphasis on the promises of data and data analytics presents the most obvious ideological challenge. In order to reorient Social Informatics in relation to these new ideological challenges, Louis Althusser's theory of ideology is discussed, with its implications for Social Informatics considered. Among these implications, a changed relationship between Social Informatics's critical stance and its reliance on empirical methods is advanced. Addressed at a fundamental level, the practice of Social Informatics comes to be reoriented in a more distinctly reflective and ethical direction

Vascular calcification progression modulates the risk associated with vascular calcification burden in incident to dialysis patients

Background: It is estimated that chronic kidney disease (CKD) accounts globally for 5 to 10 million deaths annually, mainly due to cardiovascular (CV) diseases. Traditional as well as non-traditional CV risk factors such as vascular calcification are believed to drive this disproportionate risk burden. We aimed to investigate the association of coronary artery calcification (CAC) progression with all-cause mortality in patients new to hemodialysis (HD). Methods: Post hoc analysis of the Independent study (NCT00710788). At study inception and after 12 months of follow-up, 414 patients underwent computed tomography imaging for quantification of CAC via the Agatston methods. The square root method was used to assess CAC progression (CACP), and survival analyses were used to test its association with mortality. Results: Over a median follow-up of 36 months, 106 patients died from all causes. Expired patients were older, more likely to be diabetic or to have experienced an atherosclerotic CV event, and exhibited a significantly greater CAC burden (p = 0.002). Survival analyses confirmed an independent association of CAC burden (hazard ratio: 1.29; 95% confidence interval: 1.17–1.44) and CACP (HR: 5.16; 2.61–10.21) with all-cause mortality. CACP mitigated the risk associated with CAC burden (p = 0.002), and adjustment for calcium-free phosphate binder attenuated the strength of the link between CACP and mortality. Conclusions: CAC burden and CACP predict mortality in incident to dialysis patients. However, CACP reduced the risk associated with baseline CAC, and calcium-free phosphate binders attenuated the association of CACP and outcomes, suggesting that CACP modulation may improve survival in this population. Future endeavors are needed to confirm whether drugs or kidney transplantation may attenuate CACP and improve survival in HD patients

Ischemic heart disease and heart failure. role of coronary ion channels

Heart failure is a complex syndrome responsible for high rates of death and hospitalization. Ischemic heart disease is one of the most frequent causes of heart failure and it is normally attributed to coronary artery disease, defined by the presence of one or more obstructive plaques, which determine a reduced coronary blood flow, causing myocardial ischemia and consequent heart failure. However, coronary obstruction is only an element of a complex pathophysiological process that leads to myocardial ischemia. In the literature, attention paid to the role of microcirculation, in the pathophysiology of ischemic heart disease and heart failure, is growing. Coronary microvascular dysfunction determines an inability of coronary circulation to satisfy myocardial metabolic demands, due to the imbalance of coronary blood flow regulatory mechanisms, including ion channels, leading to the development of hypoxia, fibrosis and tissue death, which may determine a loss of myocardial function, even beyond the presence of atherosclerotic epicardial plaques. For this reason, ion channels may represent the link among coronary microvascular dysfunction, ischemic heart disease and consequent heart failure

A metabolomics characterisation of natural variation in the resistance of cassava to whitefly

Background: Cassava whitefly outbreaks were initially reported in East and Central Africa cassava (Manihot esculenta Crantz) growing regions in the 1990's and have now spread to other geographical locations, becoming a global pest severely affecting farmers and smallholder income. Whiteflies impact plant yield via feeding and vectoring cassava mosaic and brown streak viruses, making roots unsuitable for food or trading. Deployment of virus resistant varieties has had little impact on whitefly populations and therefore development of whitefly resistant varieties is also necessary as part of integrated pest management strategies. Suitable sources of whitefly resistance exist in germplasm collections that require further characterization to facilitate and assist breeding programs. Results: In the present work, a hierarchical metabolomics approach has been employed to investigate the underlying biochemical mechanisms associated with whitefly resistance by comparing two naturally occurring accessions of cassava, one susceptible and one resistant to whitefly. Quantitative differences between genotypes detected at pre-infestation stages were consistently observed at each time point throughout the course of the whitefly infestation. This prevalent differential feature suggests that inherent genotypic differences override the response induced by the presence of whitefly and that they are directly linked with the phenotype observed. The most significant quantitative changes relating to whitefly susceptibility were linked to the phenylpropanoid super-pathway and its linked sub-pathways: monolignol, flavonoid and lignan biosynthesis. These findings suggest that the lignification process in the susceptible variety is less active, as the susceptible accession deposits less lignin and accumulates monolignol intermediates and derivatives thereof, differences that are maintained during the time-course of the infestation. Conclusions: Resistance mechanism associated to the cassava whitefly-resistant accession ECU72 is an antixenosis strategy based on reinforcement of cell walls. Both resistant and susceptible accessions respond differently to whitefly attack at biochemical level, but the inherent metabolic differences are directly linked to the resistance phenotype rather than an induced response in the plant

Supersymmetry in models with strong on-site Coulomb repulsion - application to t-J model

A supersymmetric way of imposing the constraint of no double occupancy in models with strong on-site Coulomb repulsion is presented in this paper. In this formulation the physical operators in the constrainted Hilbert space are invariant under local unitary transformations mixing boson and fermion representations. As an illustration the formulation is applied to the $t-J$ model. The model is studied in the mean-field level in the J=0 limit where we show how both the slave-boson and slave-fermion formulations are included naturally in the present approach and how further results beyond both approaches are obtained.Comment: 12 pages, Latex file, 1 figur