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.

Transmission Potential of Rift Valley Fever virus over the course of the 2010 epidemic in South Africa

A Rift Valley fever (RVF) epidemic affecting animals on domestic livestock farms was reported in South Africa during January-August 2010. The first cases occurred after heavy rainfall, and the virus subsequently spread countrywide. To determine the possible effect of environmental conditions and vaccination on RVF virus transmissibility, we estimated the effective reproduction number (R) for the virus over the course of the epidemic by extending the Wallinga and Teunis algorithm with spatial information. Re reached its highest value in mid-February and fell below unity around mid-March, when vaccination coverage was 7.5%-45.7% and vector-suitable environmental conditions were maintained. The epidemic fade-out likely resulted first from the immunization of animals following natural infection or vaccination. The decline in vector-suitable environmental conditions from April onwards and further vaccination helped maintain R below unity. Increased availability of vaccine use data would enable evaluation of the effect of RVF vaccination campaigns.

The worldwide epidemic of diabetic retinopathy

Diabetic retinopathy (DR), a major microvascular complication of diabetes, has a significant impact on the world′s health systems. Globally, the number of people with DR will grow from 126.6 million in 2010 to 191.0 million by 2030, and we estimate that the number with vision-threatening diabetic retinopathy (VTDR) will increase from 37.3 million to 56.3 million, if prompt action is not taken. Despite growing evidence documenting the effectiveness of routine DR screening and early treatment, DR frequently leads to poor visual functioning and represents the leading cause of blindness in working-age populations. DR has been neglected in health-care research and planning in many low-income countries, where access to trained eye-care professionals and tertiary eye-care services may be inadequate. Demand for, as well as, supply of services may be a problem. Rates of compliance with diabetes medications and annual eye examinations may be low, the reasons for which are multifactorial. Innovative and comprehensive approaches are needed to reduce the risk of vision loss by prompt diagnosis and early treatment of VTDR.

Evidence for an "epidemic" of myopia.

INTRODUCTION:

It has been widely suggested that the prevalence of myopia is growing worldwide, and that the increases observed in East Asia, in particular, are sufficiently severe as to warrant the term "epidemic". Data in favour of a cohort effect in myopia prevalence are reviewed, with attention to significant shortcomings in the quality of available evidence. Additional factors contributing to myopia prevalence, including near work, genetics and socioeconomic status, are detailed.

MATERIALS AND METHODS:

Medline search of articles regarding myopia prevalence, trends and mechanisms.

RESULTS:

Age-related changes in myopia prevalence (increase during childhood, and regression in the fifth and sixth decades) are discussed as an alternative explanation for cross-sectional patterns in myopia prevalence. There have only been a handful of studies that have examined the relative contribution of longitudinal changes in refraction over life and birth cohort differences on age-specific myopia prevalence as measured in cross-sectional studies. Available data suggest that both longitudinal changes and cohort effects may be present, and that their relative contribution may differ in different racial groups.

CONCLUSIONS:

In view of the relatively weak evidence in favour of a large cohort effect for myopia in East Asia, and the even greater lack of evidence for increased prevalence of secondary ocular pathology, there appears to be inadequate support for large-scale interventions to prevent or delay myopia at the present time.

TELL ME Design: Protective Behaviour During an Epidemic

The TELL ME agent based model simulates the connections between health agency communication, personal decisions to adopt protective behaviour during an influenza epidemic, and the effect of those decisions on epidemic progress. The behaviour decisions are modelled with a combination of personal attitude, behaviour adoption by neighbours, and the local recent incidence of influenza. This paper sets out and justifies the model design, including how these decision factors have been operationalised. By exploring the effects of different communication strategies, the model is intended to assist health authorities with their influenza epidemic communication plans. It can both assist users to understand the complex interactions between communication, personal behaviour and epidemic progress, and guide future data collection to improve communication planning.

Nutrient regulation of pancreatic beta-cell function in diabetes: problems and potential solutions

increasing prevalence of obesity combined with longevity will produce an epidemic of Type 2 (non-insulin-dependent) diabetes in the next 20 years. This. disease is associated with defects in insulin secretion, specifically abnormalities of insulin secretory kinetics and pancreatic beta-cell glucose responsiveness. Mechanisms underlying beta-cell dysfunction include glucose toxicity, lipotoxicity and beta-cell hyperactivity. Defects at various sites in beta-cell signal transduction pathways contribute, but no single lesion can account for the common form of Type 2 diabetes. Recent studies highlight diverse beta-cell actions of GLP-1 (glucagon-like peptide-1) and GIP (glucose-dependent insulinotropic polypeptide). These intestinal hormones target the beta-cell to stimulate glucose-dependent insulin secretion through activation of protein kinase A and associated pathways. Both increase gene expression and proinsulin biosynthesis, protect against apoptosis and stimulate replication/neogenesis of beta-cells. Incretin hormones therefore represent an exciting future multi-action solution to correct beta-cell defect in Type 2 diabetes.

BELFAST centenarians: A Case of Optimal Cardiovascular Risk?

Introduction: Centenarians are reservoirs of genetic and environmental information to successful ageing and local centenarian groups may help us to understand some of the factors that contribute to longevity. The current centenarian cohort in Belfast survived the 1970s epidemic of death from coronary heart disease in Northern Ireland, where cardiovascular mortality was almost highest in the world. These centenarians provided an opportunity to assess biological and genetic factors important in cardiovascular risk and ageing. Methods: Thirty-five (27 female, 8 male) centenarians, participants of the Belfast Elderly Longitudinal Free-living Ageing STudy (BELFAST), were community-living and of good cognition at enrolment. Results: Centenarians showed median Body Mass Index (BMI) at 25.7, systolic blood pressure 140mmHg and diastolic blood pressure 90mmHg, and fasting glucose of 5.54 mmol/l with no sex-related difference. Lipoproteins showed median cholesterol 5.3, High Density Lipoprotein (HDL) 1.10 and Low Density Lipoprotein (LDL) 3.47umol/l respectively. Centenarian smokers showed no different blood pressure or lipid measurements compared with non-smokers. Malondialdehyde, a measure of lipid peroxidation, was low at 1.19 umol/l, and measures of antioxidant status were varied. Male centenarians did not carry any of the vascular risk genotypes studied-ApoE4 for Apolipoprotein E (ApoE), DD for Angiotensinogen Converting Enzyme (ACE) and tt for 5,10-methylenetetrahydrofolate reductase (MTFHR), though this was not true for female centenarians.. Conclusions: This small local study shows that Belfast centenarians carry a reasonably favourable risk profile, except for age, with respect to cardiovascular disease. There is also some evidence that vascular risk factors and genotypes may be tolerated differently between the male and female centenarians. Maintaining a favourable cardiovascular risk profile seems likely to improve the chance of becoming a centenarian, especially for males.

Avandia (TM) - From molecule to market for type 2 diabetes.

Type 2 diabetes is a disease fast approaching epidemic proportions throughout the world. From insulin sensitizers to PPARg agonists, the lecture will outline the successful medicinal chem. and biol. strategy underpinning the discovery and selection of Avandia, an innovative new medicine for this disease.

Emergence of CTX-M Group 1-ESBL producing Klebsiella pneumonia from a tertiary care centre in Karachi, Pakistan.

http://www.jidc.org/index.php/journal/article/view/20818098/422 Background: Extended-spectrum beta-lactamase (ESBL)-producing Klebsiella pneumoniae have been reported previously from Pakistan but the genotypic characteristics of these enzymes is not known. Hence the aim of the study was first to characterise the genotypic content of these beta-lactamases and secondly to assess the clonal relationship of these isolates. Methodology: We analysed 65 non-duplicate ESBL positive, K. pneumoniae isolates prospectively collected based on phenotype as detected using the two-disc method. Isolates were collected from different sources: blood cultures (46.15%; n = 30); tracheal aspirates (24.6%; n = 16); urine (10.7%; n = 7); wound swabs, pus and tissue (18.4%; n = 12). ESBL production was confirmed by the ESBL E-test method and the presence of the blaCTX-M encoding genes was confirmed by polymerase chain reaction. The clonal relationship of clinical isolates was studied by Pulsed Field Gel Electrophoresis. Results: The results showed that 93.84% (n = 61) isolates of K. pneumoniae were positive for the blaCTX-M-1 group. One isolate showed PCR signals for blaCTX-M-25 group. None of our isolates were positive for CTX-M groups 2, 8 and 9. The majority of blaCTX-M positive isolates were genetically unrelated and no epidemic clones were identified. Conclusion: This study reports the emergence of CTX-M groups 1 and 25 producing isolates of K. pneumoniae with genetic diversity in Karachi, Pakistan.

Early crime writing and the state: Jonathan Wild, Daniel Defoe and Bernard Mandeville in 1720s London

This article argues that the early development of crime writing needs to be understood in relation to the consolidation of the modern state. It demonstrates that London in the 1720s constitutes a significant moment in this early development for three main reasons. First, the period witnessed a crime epidemic which reached its climax in the 1720s and which precipitated a set of particularly aggressive counter-measures by the state; second, it saw the rise and eventual fall of the infamous Jonathan Wild who acted as both thief and surrogate policeman; and third, it was also marked by a surge in interests on the part of writers like Daniel Defoe and Bernard Mandeville in the related matters of crime and punishment. This article explores the ways in which accounts of crime and punishment in this period deployed and in some instances interrogated the rhetoric of social contract theory and writings on statecraft, particularly by Thomas Hobbes and Mandeville. But while the criminal biographies and gallows sermons produced by the Newgate prison’s ‘ordinaries’ provided crude and reductive accounts of the efficacy of the state, the article shows how two accounts of the life of Jonathan Wild (by Defoe and H.D) responded in highly complex ways to the issues of crime and policing and provided a consistently and self-consciously ambivalent reading of the state and state power. To conclude, I suggest that this ambivalence can be read as a critique of the impartial or neutral state and that it constitutes one of the key features of what we would later understand to be crime writing as a dedicated literary genre.

TheShifting Sands of Uncertainty: Risk Construction and BSE/vCJD

It is more than a decade since scientists in the UK put forward evidence of a link between the emergence of a new variant of Creutzfeldt-Jakob Disease (vCJD) in humans, and a diminishing epidemic of Bovine Spongiform Encephalopathy, or BSE, in cattle. In the wake of this anniversary, the paper revisits two scientific narratives of risk, forged at different points along the developmental pathway of BSE science, including a series of advisory reports provided to the UK government between 1989 and 1994, and a symposium held in 2001 to assess the impact of the Phillips Inquiry. While the primary pathology of BSE became apparent relatively early on, uncertainties remain about the origins of BSE and its human variant, vCJD. The paper examines the handling of this sensitivity, and its communication, within these key documents, noting changes in patterns of uncertainty construction over time.

Genomic insights into the origin of parasitism in the emerging plant pathogen Bursaphelenchus xylophilus.

Bursaphelenchus xylophilus is the nematode responsible for a devastating epidemic of pine wilt disease in Asia and Europe, and represents a recent, independent origin of plant parasitism in nematodes, ecologically and taxonomically distinct from other nematodes for which genomic data is available. As well as being an important pathogen, the B. xylophilus genome thus provides a unique opportunity to study the evolution and mechanism of plant parasitism. Here, we present a high-quality draft genome sequence from an inbred line of B. xylophilus, and use this to investigate the biological basis of its complex ecology which combines fungal feeding, plant parasitic and insect-associated stages. We focus particularly on putative parasitism genes as well as those linked to other key biological processes and demonstrate that B. xylophilus is well endowed with RNA interference effectors, peptidergic neurotransmitters (including the first description of ins genes in a parasite) stress response and developmental genes and has a contracted set of chemosensory receptors. B. xylophilus has the largest number of digestive proteases known for any nematode and displays expanded families of lysosome pathway genes, ABC transporters and cytochrome P450 pathway genes. This expansion in digestive and detoxification proteins may reflect the unusual diversity in foods it exploits and environments it encounters during its life cycle. In addition, B. xylophilus possesses a unique complement of plant cell wall modifying proteins acquired by horizontal gene transfer, underscoring the impact of this process on the evolution of plant parasitism by nematodes. Together with the lack of proteins homologous to effectors from other plant parasitic nematodes, this confirms the distinctive molecular basis of plant parasitism in the Bursaphelenchus lineage. The genome sequence of B. xylophilus adds to the diversity of genomic data for nematodes, and will be an important resource in understanding the biology of this unusual parasite.