Communication and re-use of chemical information in bioscience.

The current methods of publishing chemical information in bioscience articles are analysed. Using 3 papers as use-cases, it is shown that conventional methods using human procedures, including cut-and-paste are time-consuming and introduce errors. The meaning of chemical terms and the identity of compounds is often ambiguous. valuable experimental data such as spectra and computational results are almost always omitted. We describe an Open XML architecture at proof-of-concept which addresses these concerns. Compounds are identified through explicit connection tables or links to persistent Open resources such as PubChem. It is argued that if publishers adopt these tools and protocols, then the quality and quantity of chemical information available to bioscientists will increase and the authors, publishers and readers will find the process cost-effective.An article submitted to BiomedCentral Bioinformatics, created on request with their Publicon system. The transformed manuscript is archived as PDF. Although it has been through the publishers system this is purely automatic and the contents are those of a pre-refereed preprint. The formatting is provided by the system and tables and figures appear at the end. An accommpanying submission, http://www.dspace.cam.ac.uk/handle/1810/34580, describes the rationale and cultural aspects of publishing , abstracting and aggregating chemical information. BMC is an Open Access publisher and we emphasize that all content is re-usable under Creative Commons Licens

Biosecurity: A 21st Century Challenge

Based on a review of key reports and experts' opinions, summarizes the debate over "dual-use" technologies and the various approaches to controlling biosecurity risk. Outlines proposed preventive measures and steps to build response capacity

Skills and Knowledge for Data-Intensive Environmental Research.

The scale and magnitude of complex and pressing environmental issues lend urgency to the need for integrative and reproducible analysis and synthesis, facilitated by data-intensive research approaches. However, the recent pace of technological change has been such that appropriate skills to accomplish data-intensive research are lacking among environmental scientists, who more than ever need greater access to training and mentorship in computational skills. Here, we provide a roadmap for raising data competencies of current and next-generation environmental researchers by describing the concepts and skills needed for effectively engaging with the heterogeneous, distributed, and rapidly growing volumes of available data. We articulate five key skills: (1) data management and processing, (2) analysis, (3) software skills for science, (4) visualization, and (5) communication methods for collaboration and dissemination. We provide an overview of the current suite of training initiatives available to environmental scientists and models for closing the skill-transfer gap

A Scientist's Guide to Achieving Broader Impacts through K-12 STEM Collaboration.

The National Science Foundation and other funding agencies are increasingly requiring broader impacts in grant applications to encourage US scientists to contribute to science education and society. Concurrently, national science education standards are using more inquiry-based learning (IBL) to increase students' capacity for abstract, conceptual thinking applicable to real-world problems. Scientists are particularly well suited to engage in broader impacts via science inquiry outreach, because scientific research is inherently an inquiry-based process. We provide a practical guide to help scientists overcome obstacles that inhibit their engagement in K-12 IBL outreach and to attain the accrued benefits. Strategies to overcome these challenges include scaling outreach projects to the time available, building collaborations in which scientists' research overlaps with curriculum, employing backward planning to target specific learning objectives, encouraging scientists to share their passion, as well as their expertise with students, and transforming institutional incentives to support scientists engaging in educational outreach

A Vertical Channel Model of Molecular Communication based on Alcohol Molecules

The study of Molecular Communication(MC) is more and more prevalence, and channel model of MC plays an important role in the MC System. Since different propagation environment and modulation techniques produce different channel model, most of the research about MC are in horizontal direction,but in nature the communications between nano machines are in short range and some of the information transportation are in the vertical direction, such as transpiration of plants, biological pump in ocean, and blood transportation from heart to brain. Therefore, this paper we propose a vertical channel model which nano-machines communicate with each other in the vertical direction based on pure diffusion. We first propose a vertical molecular communication model, we mainly considered the gravity as the factor, though the channel model is also affected by other main factors, such as the flow of the medium, the distance between the transmitter and the receiver, the delay or sensitivity of the transmitter and the receiver. Secondly, we set up a test-bed for this vertical channel model, in order to verify the difference between the theory result and the experiment data. At last, we use the data we get from the experiment and the non-linear least squares method to get the parameters to make our channel model more accurate.Comment: 5 pages,7 figures, Accepted for presentation at BICT 2015 Special Track on Molecular Communication and Networking (MCN). arXiv admin note: text overlap with arXiv:1311.6208 by other author

Distributed Control of Microscopic Robots in Biomedical Applications

Current developments in molecular electronics, motors and chemical sensors could enable constructing large numbers of devices able to sense, compute and act in micron-scale environments. Such microscopic machines, of sizes comparable to bacteria, could simultaneously monitor entire populations of cells individually in vivo. This paper reviews plausible capabilities for microscopic robots and the physical constraints due to operation in fluids at low Reynolds number, diffusion-limited sensing and thermal noise from Brownian motion. Simple distributed controls are then presented in the context of prototypical biomedical tasks, which require control decisions on millisecond time scales. The resulting behaviors illustrate trade-offs among speed, accuracy and resource use. A specific example is monitoring for patterns of chemicals in a flowing fluid released at chemically distinctive sites. Information collected from a large number of such devices allows estimating properties of cell-sized chemical sources in a macroscopic volume. The microscopic devices moving with the fluid flow in small blood vessels can detect chemicals released by tissues in response to localized injury or infection. We find the devices can readily discriminate a single cell-sized chemical source from the background chemical concentration, providing high-resolution sensing in both time and space. By contrast, such a source would be difficult to distinguish from background when diluted throughout the blood volume as obtained with a blood sample