access: v.22, no.01, Spring 2009

published or submitted for publicatio

access: v.10, no.02, Summer 1996

published or submitted for publicatio

On the Communication of Scientific Results: The Full-Metadata Format

In this paper, we introduce a scientific format for text-based data files, which facilitates storing and communicating tabular data sets. The so-called Full-Metadata Format builds on the widely used INI-standard and is based on four principles: readable self-documentation, flexible structure, fail-safe compatibility, and searchability. As a consequence, all metadata required to interpret the tabular data are stored in the same file, allowing for the automated generation of publication-ready tables and graphs and the semantic searchability of data file collections. The Full-Metadata Format is introduced on the basis of three comprehensive examples. The complete format and syntax is given in the appendix

Towards a Stable Numerical Evolution of Strongly Gravitating Systems in General Relativity: The Conformal Treatments

We study the stability of three-dimensional numerical evolutions of the Einstein equations, comparing the standard ADM formulation to variations on a family of formulations that separate out the conformal and traceless parts of the system. We develop an implementation of the conformal-traceless (CT) approach that has improved stability properties in evolving weak and strong gravitational fields, and for both vacuum and spacetimes with active coupling to matter sources. Cases studied include weak and strong gravitational wave packets, black holes, boson stars and neutron stars. We show under what conditions the CT approach gives better results in 3D numerical evolutions compared to the ADM formulation. In particular, we show that our implementation of the CT approach gives more long term stable evolutions than ADM in all the cases studied, but is less accurate in the short term for the range of resolutions used in our 3D simulations.Comment: 17 pages, 15 figures. Small changes in the text, and a change in the list of authors. One new reference adde

Global mapping of highly pathogenic avian influenza H5N1 and H5Nx clade 2.3.4.4 viruses with spatial cross-validation.

Global disease suitability models are essential tools to inform surveillance systems and enable early detection. We present the first global suitability model of highly pathogenic avian influenza (HPAI) H5N1 and demonstrate that reliable predictions can be obtained at global scale. Best predictions are obtained using spatial predictor variables describing host distributions, rather than land use or eco-climatic spatial predictor variables, with a strong association with domestic duck and extensively raised chicken densities. Our results also support a more systematic use of spatial cross-validation in large-scale disease suitability modelling compared to standard random cross-validation that can lead to unreliable measure of extrapolation accuracy. A global suitability model of the H5 clade 2.3.4.4 viruses, a group of viruses that recently spread extensively in Asia and the US, shows in comparison a lower spatial extrapolation capacity than the HPAI H5N1 models, with a stronger association with intensively raised chicken densities and anthropogenic factors

Statistical Emulation of Winter Ambient Fine Particulate Matter Concentrations From Emission Changes in China

Air pollution exposure remains a leading public health problem in China. The use of chemical transport models to quantify the impacts of various emission changes on air quality is limited by their large computational demands. Machine learning models can emulate chemical transport models to provide computationally efficient predictions of outputs based on statistical associations with inputs. We developed novel emulators relating emission changes in five key anthropogenic sectors (residential, industry, land transport, agriculture, and power generation) to winter ambient fine particulate matter (PM2.5) concentrations across China. The emulators were optimized based on Gaussian process regressors with Matern kernels. The emulators predicted 99.9% of the variance in PM2.5 concentrations for a given input configuration of emission changes. PM2.5 concentrations are primarily sensitive to residential (51%–94% of first‐order sensitivity index), industrial (7%–31%), and agricultural emissions (0%–24%). Sensitivities of PM2.5 concentrations to land transport and power generation emissions are all under 5%, except in South West China where land transport emissions contributed 13%. The largest reduction in winter PM2.5 exposure for changes in the five emission sectors is by 68%–81%, down to 15.3–25.9 μg m−3, remaining above the World Health Organization annual guideline of 10 μg m−3. The greatest reductions in PM2.5 exposure are driven by reducing residential and industrial emissions, emphasizing the importance of emission reductions in these key sectors. We show that the annual National Air Quality Target of 35 μg m−3 is unlikely to be achieved during winter without strong emission reductions from the residential and industrial sectors

Cancer Pharmacogenomics and Pharmacoepidemiology: Setting a Research Agenda to Accelerate Translation

Recent advances in genomic research have demonstrated a substantial role for genomic factors in predicting response to cancer therapies. Researchers in the fields of cancer pharmacogenomics and pharmacoepidemiology seek to understand why individuals respond differently to drug therapy, in terms of both adverse effects and treatment efficacy. To identify research priorities as well as the resources and infrastructure needed to advance these fields, the National Cancer Institute (NCI) sponsored a workshop titled “Cancer Pharmacogenomics: Setting a Research Agenda to Accelerate Translation” on July 21, 2009, in Bethesda, MD. In this commentary, we summarize and discuss five science-based recommendations and four infrastructure-based recommendations that were identified as a result of discussions held during this workshop. Key recommendations include 1) supporting the routine collection of germline and tumor biospecimens in NCI-sponsored clinical trials and in some observational and population-based studies; 2) incorporating pharmacogenomic markers into clinical trials; 3) addressing the ethical, legal, social, and biospecimen- and data-sharing implications of pharmacogenomic and pharmacoepidemiologic research; and 4) establishing partnerships across NCI, with other federal agencies, and with industry. Together, these recommendations will facilitate the discovery and validation of clinical, sociodemographic, lifestyle, and genomic markers related to cancer treatment response and adverse events, and they will improve both the speed and efficiency by which new pharmacogenomic and pharmacoepidemiologic information is translated into clinical practice

access: v.13, no.02, Summer 2000

published or submitted for publicatio