Summary
1. Here, I present a new, multifunctional phylogenetics package, phytools, for the R statistical computing environment.

2. The focus of the package is on methods for phylogenetic comparative biology; however, it also includes tools for tree inference, phylogeny input/output, plotting, manipulation and several other tasks.

3. I describe and tabulate the major methods implemented in phytools, and in addition provide some demonstration of its use in the form of two illustrative examples.

4. Finally, I conclude by briefly describing an active web-log that I use to document present and future developments for phytools. I also note other web resources for phylogenetics in the R computational environment.

/pdf/phytools-an-r-package-for-phylogenetic-comparative-biology-yli0omoidd.pdf

phytools: an R package for phylogenetic comparative biology (and other things)

Associations between modifiable exposures and disease seen in observational epidemiology are sometimes confounded and thus misleading, despite our best efforts to improve the design and analysis of studies. Mendelian randomization-the random assortment of genes from parents to offspring that occurs during gamete formation and conception-provides one method for assessing the causal nature of some environmental exposures. The association between a disease and a polymorphism that mimics the biological link between a proposed exposure and disease is not generally susceptible to the reverse causation or confounding that may distort interpretations of conventional observational studies. Several examples where the phenotypic effects of polymorphisms are well documented provide encouraging evidence of the explanatory power of Mendelian randomization and are described. The limitations of the approach include confounding by polymorphisms in linkage disequilibrium with the polymorphism under study, that polymorphisms may have several phenotypic effects associated with disease, the lack of suitable polymorphisms for studying modifiable exposures of interest, and canalization-the buffering of the effects of genetic variation during development. Nevertheless, Mendelian randomization provides new opportunities to test causality and demonstrates how investment in the human genome project may contribute to understanding and preventing the adverse effects on human health of modifiable exposures.

/pdf/mendelian-randomization-can-genetic-epidemiology-contribute-vb0zjyrtxf.pdf

‘Mendelian randomization’: can genetic epidemiology contribute to understanding environmental determinants of disease?

In recent months there has been an explosion of interest in using the Web to create, assemble, and disseminate geographic information provided voluntarily by individuals. Sites such as Wikimapia and OpenStreetMap are empowering citizens to create a global patchwork of geographic information, while Google Earth and other virtual globes are encouraging volunteers to develop inter- esting applications using their own data. I review this phenomenon, and examine associated issues: what drives people to do this, how accurate are the results, will they threaten individual privacy, and how can they augment more conventional sources? I compare this new phenomenon to more traditional citizen science and the role of the amateur in geographic observation.

/pdf/citizens-as-sensors-the-world-of-volunteered-geography-phibl484h3.pdf

Citizens as sensors: the world of volunteered geography

We review the recent rapid progress in the statistical physics of evolving networks. Interest has focused mainly on the structural properties of complex networks in communications, biology, social sciences and economics. A number of giant artificial networks of this kind have recently been created, which opens a wide field for the study of their topology, evolution, and the complex processes which occur in them. Such networks possess a rich set of scaling properties. A number of them are scale-free and show striking resilience against random breakdowns. In spite of the large sizes of these networks, the distances between most of their vertices are short - a feature known as the 'small-world' effect. We discuss how growing networks self-organize into scale-free structures, and investigate the role of the mechanism of preferential linking. We consider the topological and structural properties of evolving networks, and percolation and disease spread on these networks. We present a number of models demonstrat...

/pdf/evolution-of-networks-27h4ny8xbi.pdf

Evolution of networks

Yuelong Shu1, John McCauley2 1. WHO Collaborating Center for Reference and Research on Influenza, Chinese National Influenza Center, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China 2. WHO Collaborating Centre for Reference and Research on Influenza, Crick Worldwide Influenza Centre, the Francis Crick Institute, London, United Kingdom

GISAID: Global initiative on sharing all influenza data - from vision to reality.

A partial rescue plan has been agreed for the first large-scale study of whether passengers on long-haul flights are at increased risk of developing life-threatening blood clots. Scientists have obtained only around a quarter of the 12 million euros (US$11 million) needed for the project, but they nonetheless aim to launch it this week, while continuing to search for the remaining funds. The past month has seen a spate of lawsuits against airlines by victims of deep-vein thrombosis (DVT) — ‘economy-class syndrome’ — and their relatives. Proper scientific data are needed to improve our understanding of the risks involved so that we can offer sound safety advice for air travel, says William Toff, a cardiologist at the University of Leicester and a member of the project team. The proposed project is far larger than previous studies of the problem. Its scientific protocol — called the WHO Research Initiative on Global Hazards of Travel (WRIGHT) — was approved by the World Health Organisation (WHO) last August. The International Air Transport Association, which represents the airlines, has welcomed the study — at least in public — and has agreed to help the WHO and the International Civil Aviation Organization with the logistics involved. Fund-raising is being done by the WHO, but only 2.8 million euros has been raised so far, all from within the European Union. Frits Rosendaal, a researcher at Leiden University in the Netherlands, resigned from the project last month, citing a “lack of confidence in the complete commitment from the WHO”. Shanthi Mendis, a Geneva-based WHO official involved in project planning, says the WHO is “disappointed” that funding has not materialized. “We expected a more enthusiastic response from governments,” she says. But several DVT researchers blame bureaucracy at the WHO for the lack of uptake. At a meeting in Geneva last week of the project’s scientific committee and its European funders, DVT researchers said that they would try to bypass the WHO and solicit funding directly from governments and other sources. To safeguard the study’s independence, airlines will not be asked for money. The meeting agreed that the first two phases of the study will begin this month. One will examine the role of passenger risk factors, such as alcohol consumption, seating conditions and predisposition to the disease. The second will involve the use of experimental pressurized cabins to determine whether low air pressure during flights contributes to the risks of sitting in cramped conditions for long periods. In the final, most expensive phase, the study would track the health of passengers on some 200,000 flights. But this phase will begin only when full funding has been obtained. And the prospects for that have worsened following the decision by Australia — the nation that arguably depends most on long-haul flights — to snub the WHO effort and pursue its own study. “We are all impatiently waiting for the funds, with our troops ready to go,” says Bo Eklof, chief of the Straub Foundation’s Vascular Center at the University of Hawaii. ■ news

/pdf/air-travel-study-struggles-to-get-airborne-3zc96b09k8.pdf

Air-travel study struggles to get airborne.

/pdf/infrared-images-map-invisible-matter-5a0mxgervt.pdf

Infrared images map Invisible' matter

/pdf/us-plays-hard-to-get-as-unesco-continues-to-woo-support-2ehm3g0xb3.pdf

US plays hard to get as Unesco continues to woo support

/pdf/blood-scandal-raises-spectre-of-dreyfus-case-rqtm25w5ta.pdf

Blood scandal raises spectre of Dreyfus case.

/pdf/esa-avoids-split-over-space-station-plans-uylirn12hr.pdf

Declan Butler

Papers

Air-travel study struggles to get airborne.

Infrared images map Invisible' matter

US plays hard to get as Unesco continues to woo support

Blood scandal raises spectre of Dreyfus case.

ESA avoids split over space station plans ...