Parallel Implementations of Cellular Automata for Traffic Models

The Biham-Middleton-Levine (BML) traffic model is a simple two-dimensional, discrete Cellular Automaton (CA) that has been used to study self-organization and phase transitions arising in traffic flows. From the computational point of view, the BML model exhibits the usual features of discrete CA, where the state of the automaton are updated according to simple rules that depend on the state of each cell and its neighbors. In this paper we study the impact of various optimizations for speeding up CA computations by using the BML model as a case study. In particular, we describe and analyze the impact of several parallel implementations that rely on CPU features, such as multiple cores or SIMD instructions, and on GPUs. Experimental evaluation provides quantitative measures of the payoff of each technique in terms of speedup with respect to a plain serial implementation. Our findings show that the performance gap between CPU and GPU implementations of the BML traffic model can be reduced by clever exploitation of all CPU features

Impact of Single Links in Competitive Percolation -- How complex networks grow under competition

How a complex network is connected crucially impacts its dynamics and function. Percolation, the transition to extensive connectedness upon gradual addition of links, was long believed to be continuous but recent numerical evidence on "explosive percolation" suggests that it might as well be discontinuous if links compete for addition. Here we analyze the microscopic mechanisms underlying discontinuous percolation processes and reveal a strong impact of single link additions. We show that in generic competitive percolation processes, including those displaying explosive percolation, single links do not induce a discontinuous gap in the largest cluster size in the thermodynamic limit. Nevertheless, our results highlight that for large finite systems single links may still induce observable gaps because gap sizes scale weakly algebraically with system size. Several essentially macroscopic clusters coexist immediately before the transition, thus announcing discontinuous percolation. These results explain how single links may drastically change macroscopic connectivity in networks where links add competitively.Comment: non-final version, for final see Nature Physics homepag

Seasonality in Human Zoonotic Enteric Diseases: A Systematic Review

BACKGROUND: Although seasonality is a defining characteristic of many infectious diseases, few studies have described and compared seasonal patterns across diseases globally, impeding our understanding of putative mechanisms. Here, we review seasonal patterns across five enteric zoonotic diseases: campylobacteriosis, salmonellosis, vero-cytotoxigenic Escherichia coli (VTEC), cryptosporidiosis and giardiasis in the context of two primary drivers of seasonality: (i) environmental effects on pathogen occurrence and pathogen-host associations and (ii) population characteristics/behaviour. METHODOLOGY/PRINCIPAL FINDINGS: We systematically reviewed published literature from 1960-2010, resulting in the review of 86 studies across the five diseases. The Gini coefficient compared temporal variations in incidence across diseases and the monthly seasonality index characterised timing of seasonal peaks. Consistent seasonal patterns across transnational boundaries, albeit with regional variations was observed. The bacterial diseases all had a distinct summer peak, with identical Gini values for campylobacteriosis and salmonellosis (0.22) and a higher index for VTEC (Gini  0.36). Cryptosporidiosis displayed a bi-modal peak with spring and summer highs and the most marked temporal variation (Gini = 0.39). Giardiasis showed a relatively small summer increase and was the least variable (Gini = 0.18). CONCLUSIONS/SIGNIFICANCE: Seasonal variation in enteric zoonotic diseases is ubiquitous, with regional variations highlighting complex environment-pathogen-host interactions. Results suggest that proximal environmental influences and host population dynamics, together with distal, longer-term climatic variability could have important direct and indirect consequences for future enteric disease risk. Additional understanding of the concerted influence of these factors on disease patterns may improve assessment and prediction of enteric disease burden in temperate, developed countries

Elevated surface chlorophyll associated with natural oil seeps in the Gulf of Mexico

Natural hydrocarbon seeps occur on the sea floor along continental margins, and account for up to 47% of the oil released into the oceans. Hydrocarbon seeps are known to support local benthic productivity, but little is known about their impact on photosynthetic organisms in the overlying water column. Here we present observations with high temporal and spatial resolution of chlorophyll concentrations in the northern Gulf of Mexico using in situ and shipboard flow-through fluorescence measurements from May to July 2012, as well as an analysis of ocean-colour satellite images from 1997 to 2007. All three methods reveal elevated chlorophyll concentrations in waters influenced by natural hydrocarbon seeps. Temperature and nutrient profiles above seep sites suggest that nutrient-rich water upwells from depth, which may facilitate phytoplankton growth and thus support the higher chlorophyll concentrations observed. Because upwelling occurs at natural seep locations around the world, we conclude that offshore hydrocarbon seeps, and perhaps other types of deep ocean vents and seeps at depths exceeding 1,000 m, may influence biogeochemistry and productivity of the overlying water column

How a Diverse Research Ecosystem Has Generated New Rehabilitation Technologies: Review of NIDILRR’s Rehabilitation Engineering Research Centers

Over 50 million United States citizens (1 in 6 people in the US) have a developmental, acquired, or degenerative disability. The average US citizen can expect to live 20% of his or her life with a disability. Rehabilitation technologies play a major role in improving the quality of life for people with a disability, yet widespread and highly challenging needs remain. Within the US, a major effort aimed at the creation and evaluation of rehabilitation technology has been the Rehabilitation Engineering Research Centers (RERCs) sponsored by the National Institute on Disability, Independent Living, and Rehabilitation Research. As envisioned at their conception by a panel of the National Academy of Science in 1970, these centers were intended to take a “total approach to rehabilitation”, combining medicine, engineering, and related science, to improve the quality of life of individuals with a disability. Here, we review the scope, achievements, and ongoing projects of an unbiased sample of 19 currently active or recently terminated RERCs. Specifically, for each center, we briefly explain the needs it targets, summarize key historical advances, identify emerging innovations, and consider future directions. Our assessment from this review is that the RERC program indeed involves a multidisciplinary approach, with 36 professional fields involved, although 70% of research and development staff are in engineering fields, 23% in clinical fields, and only 7% in basic science fields; significantly, 11% of the professional staff have a disability related to their research. We observe that the RERC program has substantially diversified the scope of its work since the 1970’s, addressing more types of disabilities using more technologies, and, in particular, often now focusing on information technologies. RERC work also now often views users as integrated into an interdependent society through technologies that both people with and without disabilities co-use (such as the internet, wireless communication, and architecture). In addition, RERC research has evolved to view users as able at improving outcomes through learning, exercise, and plasticity (rather than being static), which can be optimally timed. We provide examples of rehabilitation technology innovation produced by the RERCs that illustrate this increasingly diversifying scope and evolving perspective. We conclude by discussing growth opportunities and possible future directions of the RERC program

The evolution of sex-specific virulence in infectious diseases

Fatality rates of infectious diseases are often higher in men than women. Although this difference is often attributed to a stronger immune response in women, we show that differences in the transmission routes that the sexes provide can result in evolution favouring pathogens with sex-specific virulence. Because women can transmit pathogens during pregnancy, birth or breast-feeding, pathogens adapt, evolving lower virulence in women. This can resolve the long-standing puzzle on progression from Human T-cell Lymphotropic Virus Type 1 (HTLV-1) infection to lethal Adult T-cell Leukaemia (ATL); a progression that is more likely in Japanese men than women, while it is equally likely in Caribbean women and men. We argue that breastfeeding, being more prolonged in Japan than in the Caribbean, may have driven the difference in virulence between the two populations. Our finding signifies the importance of investigating the differences in genetic expression profile of pathogens in males and females

GEP100/Arf6 Is Required for Epidermal Growth Factor-Induced ERK/Rac1 Signaling and Cell Migration in Human Hepatoma HepG2 Cells

BACKGROUND: Epidermal growth factor (EGF) signaling is implicated in the invasion and metastasis of hepatoma cells. However, the signaling pathways for EGF-induced motility of hepatoma cells remain undefined. METHODOLOGY/PRINCIPAL FINDINGS: We found that EGF dose-dependently stimulated the migration of human hepatoma cells HepG2, with the maximal effect at 10 ng/mL. Additionally, EGF increased Arf6 activity, and ectopic expression of Arf6 T27N, a dominant negative Arf6 mutant, largely abolish EGF-induced cell migration. Blocking GEP100 with GEP100 siRNA or GEP100-△PH, a pleckstrin homology (PH) domain deletion mutant of GEP100, blocked EGF-induced Arf6 activity and cell migration. EGF also increased ERK and Rac1 activity. Ectopic expression GEP100 siRNA, GEP100-△PH, or Arf6-T27N suppressed EGF-induced ERK and Rac1 activity. Furthermore, blocking ERK signaling with its inhibitor U0126 remarkably inhibited both EGF-induced Rac1 activation as well as cell migration, and ectopic expression of inactive mutant form of Rac1 (Rac1-T17N) also largely abolished EGF-induced cell migration. CONCLUSIONS/SIGNIFICANCE: Taken together, this study highlights the function of the PH domain of GEP100 and its regulated Arf6/ERK/Rac1 signaling cascade in EGF-induced hepatoma cell migration. These findings could provide a rationale for designing new therapy based on inhibition of hepatoma metastasis

Transcriptomic alterations in the heart of non-obese type 2 diabetic Goto-Kakizaki rats

BACKGROUND: There is a spectacular rise in the global prevalence of type 2 diabetes mellitus (T2DM) due to the worldwide obesity epidemic. However, a significant proportion of T2DM patients are non-obese and they also have an increased risk of cardiovascular diseases. As the Goto-Kakizaki (GK) rat is a well-known model of non-obese T2DM, the goal of this study was to investigate the effect of non-obese T2DM on cardiac alterations of the transcriptome in GK rats. METHODS: Fasting blood glucose, serum insulin and cholesterol levels were measured at 7, 11, and 15 weeks of age in male GK and control rats. Oral glucose tolerance test and pancreatic insulin level measurements were performed at 11 weeks of age. At week 15, total RNA was isolated from the myocardium and assayed by rat oligonucleotide microarray for 41,012 genes, and then expression of selected genes was confirmed by qRT-PCR. Gene ontology and protein-protein network analyses were performed to demonstrate potentially characteristic gene alterations and key genes in non-obese T2DM. RESULTS: Fasting blood glucose, serum insulin and cholesterol levels were significantly increased, glucose tolerance and insulin sensitivity were significantly impaired in GK rats as compared to controls. In hearts of GK rats, 204 genes showed significant up-regulation and 303 genes showed down-regulation as compared to controls according to microarray analysis. Genes with significantly altered expression in the heart due to non-obese T2DM includes functional clusters of metabolism (e.g. Cyp2e1, Akr1b10), signal transduction (e.g. Dpp4, Stat3), receptors and ion channels (e.g. Sln, Chrng), membrane and structural proteins (e.g. Tnni1, Mylk2, Col8a1, Adam33), cell growth and differentiation (e.g. Gpc3, Jund), immune response (e.g. C3, C4a), and others (e.g. Lrp8, Msln, Klkc1, Epn3). Gene ontology analysis revealed several significantly enriched functional inter-relationships between genes influenced by non-obese T2DM. Protein-protein interaction analysis demonstrated that Stat is a potential key gene influenced by non-obese T2DM. CONCLUSIONS: Non-obese T2DM alters cardiac gene expression profile. The altered genes may be involved in the development of cardiac pathologies and could be potential therapeutic targets in non-obese T2DM

Contemporary contestations over working time: time for health to weigh in

Non-communicable disease (NCD) incidence and prevalence is of central concern to most nations, along with international agencies such as the UN, OECD, IMF and World Bank. As a result, the search has begun for ‘causes of the cause’ behind health risks and behaviours responsible for the major NCDs. As part of this effort, researchers are turning their attention to charting the temporal nature of societal changes that might be associated with the rapid rise in NCDs. From this, the experience of time and its allocation are increasingly understood to be key individual and societal resources for health (7–9). The interdisciplinary study outlined in this paper will produce a systematic analysis of the behavioural health dimensions, or ‘health time economies’ (quantity and quality of time necessary for the practice of health behaviours), that have accompanied labour market transitions of the last 30 years - the period in which so many NCDs have risen sharply