A Linked Data Mosaic for Policy-Relevant Research on Science and Innovation: Value, Transparency, Rigor, and Community.

This article presents a new framework for realizing the value of linked data understood as a strategic asset and increasingly necessary form of infrastructure for policy-making and research in many domains. We outline a framework, the 'data mosaic' approach, which combines socio-organizational and technical aspects. After demonstrating the value of linked data, we highlight key concepts and dangers for community-developed data infrastructures.

Publications as predictors of racial and ethnic differences in NIH research awards.

This research expands efforts to understand differences in NIH funding associated with the self-identified race and ethnicity of applicants. We collected data from 2,397 NIH Biographical Sketches submitted between FY 2003 and 2006 as part of new NIH R01 Type 1 applications to obtain detailed information on the applicants' training and scholarly activities, including publications. Using these data, we examined the association between an NIH R01 applicant's race or ethnicity and the probability of receiving an R01 award.

Measuring the evolution and output of cross-disciplinary collaborations within the NCI Physical Sciences-Oncology Centers Network.

Development of effective quantitative indicators and methodologies to assess the outcomes of cross-disciplinary collaborative initiatives has the potential to improve scientific program management and scientific output. This article highlights an example of a prospective evaluation that has been developed to monitor and improve progress of the National Cancer Institute Physical Sciences-Oncology Centers (PS-OC) program. Study data, including collaboration information, was captured through progress reports and compiled using the web-based analytic database: Interdisciplinary Team Reporting, Analysis, and Query Resource.

Detecting internally symmetric protein structures.

Background: Many functional proteins have a symmetric structure. Most of these are multimeric complexes, which are made of non-symmetric monomers arranged in a symmetric manner. However, there are also a large number of proteins that have a symmetric structure in the monomeric state.

Binless estimation of the potential of mean force.

For a system in thermal equilibrium, described by classical statistical mechanics, we derive an unbiased estimator for the marginal probability distribution of a coordinate of interest, rho( x). This result provides a "binless" method for estimating the potential of mean force, Phi = -beta (-1) ln rho, eliminating the need to construct histograms or perform numerical thermodynamic integration. In our method, the distribution that we seek to compute is expressed as the sum of a reference distribution, rho 0(x)essentially an initial guess or estimate of rho( x)and a correction term.

How enzyme dynamics helps catalyze a reaction in atomic detail: a transition path sampling study.

We have applied the Transition Path Sampling algorithm to the reaction catalyzed by the enzyme Lactate Dehydrogenase. This study demonstrates the ease of scaling Transition Path Sampling for applications on many degree of freedom systems, whose energy surface is a complex terrain of valleys and saddle points. As a Monte Carlo importance sampling method, transition path sampling is capable of surmounting barriers in path phase space and focuses simulation on the rare event of enzyme catalyzed atom transfers.