Overcoming the Scalability Challenges of Epidemic Simulations on Blue Waters

Modeling dynamical systems represents an important application class covering a wide range of disciplines including but not limited to biology, chemistry, finance, national security, and health care. Such applications typically involve large-scale, irregular graph processing, which makes them difficult to scale due to the evolutionary nature of their workload, irregular communication and load imbalance. EpiSimdemics is such an application simulating epidemic diffusion in extremely large and realistic social contact networks. It implements a graph-based system that captures dynamics among co-evolving entities. This paper presents an implementation of EpiSimdemics in Charm++ that enables future research by social, biological and computational scientists at unprecedented data and system scales. We present new methods for application-specific processing of graph data and demonstrate the effectiveness of these methods on a Cray XE6, specifically NCSA's Blue Waters system.

Borders, Asylum and Global Non-Citizenship: The Other Side of the Fence

The experience of border crossing for refugees and irregular migrants challenges global border and migration controls in multiple contexts. Using qualitative field research in Tanzania, Spain, Morocco and Australia, Heather Johnson asks how a global regime of migration management and control can be perceived through the dynamics of particular border spaces: refugee camps, border zones and detention centres. She explores how irregular migrants are impacted by the increasingly security-oriented practices of border control, and how they confront these practices. Johnson rejects the characterization of border spaces as exceptional, abject and exclusionary, arguing instead for an understanding of politics as everyday contestation that reveals a radical political agency, re-imagining the global non-citizen as a transgressive and powerful figure. Building on recent scholarship that rethinks irregularity and non-citizenship, her conclusions have broad implications for how we understand irregular migration from a position of dialogue and solidarity.

Use of the γ-H2AX Assay to Investigate DNA Repair Dynamics Following Multiple Radiation Exposures

Radiation therapy is one of the most common and effective strategies used to treat cancer. The irradiation is usually performed with a fractionated scheme, where the dose required to kill tumour cells is given in several sessions, spaced by specific time intervals, to allow healthy tissue recovery. In this work, we examined the DNA repair dynamics of cells exposed to radiation delivered in fractions, by assessing the response of histone-2AX (H2AX) phosphorylation (γ-H2AX), a marker of DNA double strand breaks. γ-H2AX foci induction and disappearance were monitored following split dose irradiation experiments in which time interval between exposure and dose were varied. Experimental data have been coupled to an analytical theoretical model, in order to quantify key parameters involved in the foci induction process. Induction of γ-H2AX foci was found to be affected by the initial radiation exposure with a smaller number of foci induced by subsequent exposures. This was compared to chromatin relaxation and cell survival. The time needed for full recovery of γ-H2AX foci induction was quantified (12 hours) and the 1:1 relationship between radiation induced DNA double strand breaks and foci numbers was critically assessed in the multiple irradiation scenarios.

Attempting to rewrite History:Challenges with the analysis of histidine-phosphorylated peptides

A significant number of proteins in both eukaryotes and prokaryotes are known to be post-translationally modified by the addition of phosphate, serving as a means of rapidly regulating protein function. Phosphorylation of the amino acids serine, threonine and tyrosine are the focus of the vast majority of studies aimed at elucidating the extent and roles of such modification, yet other amino acids, including histidine and aspartate, are also phosphorylated. Although histidine phosphorylation is known to play extensive roles in signalling in eukaryotes, plants and fungi, roles for phosphohistidine are poorly defined in higher eukaryotes. Characterization of histidine phosphorylation aimed at elucidating such information is problematic due to the acid-labile nature of the phosphoramidate bond, essential for many of its biological functions. Although MSbased strategies have proven extremely useful in the analysis of other types of phosphorylated peptides, the chromatographic procedures essential for such approaches promote rapid hydrolysis of phosphohistidinecontaining peptides. Phosphate transfer to non-biologically relevant aspartate residues during MS analysis further complicates the scenario. © 2013 Biochemical Society.

Uncovering the challenges of managing cachexia in advanced cancer: Preliminary results from semi-structured interviews with healthcare professionals in a regional cancer centre

Background: Cancer cachexia is a complex metabolic syndrome characterised by severe and progressive weight loss which is predominantly muscle mass. It is a devastating and distressing complication of advanced cancer with profound bio-psycho-social implications for patients and their families. At present there is no curative treatment for cachexiain advanced cancer therefore the most important healthcare response entails the minimisation of the psycho-social distress associated with it. However the literature suggests healthcare professionals’are missing opportunities to intervene and respond to the multi-dimensional needs of this population.

Objective:The objective of this study was to explore healthcare professionals’ response to cachexia in advanced cancer.

Methods: An interpretative qualitative approach was adopted in this study. A purposive sample of doctors, nurses, specialist nurses and dieticians were recruited from a regional cancer centre between November 2009 and November 2010. Data was collection was twofold: two multi-professional focus groups were conducted first to uncover the main themes and issues in cachexia management. This data then informed the interview schedule for the following 25 individual semi-structured interviews.

Results: Preliminary data analysis of the semi-structured interviews revealed distinct differences between disciplines in their perceptions of cancer cachexia which influenced their response to it in clinical practice. The commonality between disciplines, with the exception of palliative care, was a reliance on the biomedical approach to cancer cachexia management.

Discussion and Conclusions: Cancer cachexia is a complex and challenging syndrome which needs to be addressed from a holistic model of care to reflect the multi-dimensional needs of this patient group. The perspectives of those involved in care delivery is required in order to inform the development of interventions aimed at minimising the distress associated with this devastating syndrome.

Challenges of a Developmental Idea towards Sustainability

This paper attempts to situate and deconstruct the meanings associated with the term development in the context of the developing world. The arguments made highlights the deeply contested and fragmented terrain of development. The paper provides a historical overview of the changing nature of discourses on development, how the imageries of development have shifted since the postwar period. It deploys diverse meanings associated with development as a concept and as a theory. Thus development without dignity means little for those living in the margins of the society. At the same time the language of development has undergone revolutions and convulsions and the role of buzzwords and catch phrases have only helped to prolong misery in a neoliberal world. Development has become a 'one size fits all' concept shorn of cultural and regional specificities. It has been decontextualised and dehumanised to relate to targets
resulting in greater dissonance than resolution of aim and outcomes. The way forward is a better appreciation of the cultural capacity of the social groups for whom development is critical for survival. The conclusion highlights the endemic contradictions inherent in the meaning and delivery of development as a goal, especially when we seek to achieve resilient and sustainable development.

Keywords: Development, Neoliberalism, growth, participation, empowerment,
efficiency, market, state, societies, entitlements and capabilities, stakeholder, rights, structural adjustments, globalisation, self-help, doing development, freedom and
unfreedom.