Unravelling transmission trees of infectious diseases by combining genetic and epidemiological data

Knowledge on the transmission tree of an epidemic can provide valuable insights into disease dynamics. The transmission tree can be reconstructed by analysing either detailed epidemiological data (e.g. contact tracing) or, if sufficient genetic diversity accumulates over the course of the epidemic, genetic data of the pathogen. We present a likelihood-based framework to integrate these two data types, estimating probabilities of infection by taking weighted averages over the set of possible transmission trees. We test the approach by applying it to temporal, geographical and genetic data on the 241 poultry farms infected in an epidemic of avian influenza A (H7N7) in The Netherlands in 2003. We show that the combined approach estimates the transmission tree with higher correctness and resolution than analyses based on genetic or epidemiological data alone. Furthermore, the estimated tree reveals the relative infectiousness of farms of different types and sizes. (Résumé d'auteur

The association between naevi and melanoma in populations with different levels of sun exposure: a joint case-control study of melanoma in the UK and Australia.

Two case-control studies were set up to investigate the relationship between melanocytic naevi and risk of melanoma and to compare the naevus phenotype in two countries exposed to greatly different levels of sun exposure and different melanoma rates. In England 117 melanoma cases and 163 controls were recruited from the North-East Thames Region and 183 melanoma cases and 162 controls from New South Wales, Australia. Each subject underwent a whole-body naevus count performed by the same examiner in each country. Relative risks associated with melanocytic naevi in each country were calculated with comparison of naevus data in controls between Australia and England. Atypical naevi were strong risk factors for melanoma in both countries: the odds ratio (OR) for three or more atypical naevi was 4.6 (95% CI 2.0-10.7) in Australia compared with 51.7 (95% CI 6.5-408.4) in England. Common naevi were also significant risk factors in Australia and England with similar odds ratios in the two countries. Prevalence of atypical naevi was greater in Australian controls than in English controls: OR 9.7 (95% CI 1.2-81.7) for three or more atypical naevi in Australia compared with England. For young age groups, the median number of common naevi was greater in Australia than in the UK, whereas for older individuals this difference in naevi number between the two countries disappeared. The prevalence of naevi on non-sun-exposed sites in controls was not significantly different between the two countries. The atypical mole syndrome (AMS) phenotype was more prevalent in Australian controls (6%) than in English controls (2%). The results of this study support the role of sun exposure in the induction of atypical naevi in adults. There was a trend towards stronger risk factors associated with atypical naevi in England compared with Australia. The atypical mole syndrome, usually associated with a genetic susceptibility to melanoma, was more common in Australia than in England, suggesting genetic environmental interactions with the possibility of phenocopies induced by sunlight

Status of QCD

I have been asked to discuss the status of QCD. It seems to me that there are three main points to be made about the present status of QCD: $\bullet$ QCD is right, and we can do many beautiful things with it. $\bullet$ There are several important concrete problems that lie just beyond the edge of our current understanding. $\bullet$ There are some foundational issues in QCD, and some recent developments, that may point toward entirely new directions. These points will, I believe, emerge quite clearly from the following more detailed discussion. The discussion will be in three parts. I'll first discuss elementary processes, then more complicated processes, and then finally foundational issues.Comment: 28 pages, use Phyzzx, figures available by FAX or mail on request, IASSNS-HEP-93/6

Datocracy

Datocracy is a compound neologism that embraces transhistorical liberations and reconfigurations of data, in its multiple perceptual-linguistic forms, into new value relations and systems of governance, democratic or otherwise. Datocracy evolves from the often-violent separation of data from its habitual matrices, by virtue of dispositifs, or apparatuses, as defined by Michel Foucault and elaborated by Gilles Deleuze. This paper examines material examples of the functioning of such dispositifs through Georges Bataille, Walter Benjamin, François Rabelais (through Mikhail Bakhtin), and William Burroughs. These examples demonstrate how emancipated data is readily recuperated into new relations of governance, as liberatory socio-political tools (or apparatuses), or vehicles of tyranny. In its passage between liberation and recuperation, in its state of utterance, perhaps, data experiences a protosemantic moment, a pre-definitional state, which offers the promise of a momentary escape from, or rather within, value relations

Care in the time of catastrophe: citizenship, community and the ecological imagination

Published without an abstract

The Saffman-Taylor problem on a sphere

The Saffman-Taylor problem addresses the morphological instability of an interface separating two immiscible, viscous fluids when they move in a narrow gap between two flat parallel plates (Hele-Shaw cell). In this work, we extend the classic Saffman-Taylor situation, by considering the flow between two curved, closely spaced, concentric spheres (spherical Hele-Shaw cell). We derive the mode-coupling differential equation for the interface perturbation amplitudes and study both linear and nonlinear flow regimes. The effect of the spherical cell (positive) spatial curvature on the shape of the interfacial patterns is investigated. We show that stability properties of the fluid-fluid interface are sensitive to the curvature of the surface. In particular, it is found that positive spatial curvature inhibits finger tip-splitting. Hele-Shaw flow on weakly negative, curved surfaces is briefly discussed.Comment: 26 pages, 4 figures, RevTex, accepted for publication in Phys. Rev.

A framework to develop semiautomated surveillance of surgical site infections: An international multicenter study

Objective: Automated surveillance of healthcare-associated infections reduces workload and improves standardization, but it has not yet been adopted widely. In this study, we assessed the performance and feasibility of an easy implementable framework to develop algorithms for semiautomated surveillance of deep incisional and organ-space surgical site infections (SSIs) after orthopedic, cardiac, and colon surgeries. Design: Retrospective cohort study in multiple countries. Methods: European hospitals were recruited and selected based on the availability of manual SSI surveillance data from 2012 onward (reference standard) and on the ability to extract relevant data from electronic health records. A questionnaire on local manual surveillance and clinical practices was administered to participating hospitals, and the information collected was used to pre-emptively design semiautomated surveillance algorithms standardized for multiple hospitals and for center-specific application. Algorithm sensitivity, positive predictive value, and reduction of manual charts requiring review were calculated. Reasons for misclassification were explored using discrepancy analyses. Results: The study included 3 hospitals, in the Netherlands, France, and Spain. Classification algorithms were developed to indicate procedures with a high probability of SSI. Components concerned microbiology, prolonged length of stay or readmission, and reinterventions. Antibiotics and radiology ordering were optional. In total, 4,770 orthopedic procedures, 5,047 cardiac procedures, and 3,906 colon procedures were analyzed. Across hospitals, standardized algorithm sensitivity ranged between 82% and 100% for orthopedic surgery, between 67% and 100% for cardiac surgery, and between 84% and 100% for colon surgery, with 72%-98% workload reduction. Center-specific algorithms had lower sensitivity. Conclusions: Using this framework, algorithms for semiautomated surveillance of SSI can be successfully developed. The high performance of standardized algorithms holds promise for large-scale standardization