A Second-Order Finite Volume Method that Reduces Numerical Shockwave Anomalies in One Dimension

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/106462/1/AIAA2013-2699.pd

Raman signatures of classical and quantum phases in coupled dots: A theoretical prediction

We study electron molecules in realistic vertically coupled quantum dots in a strong magnetic field. Computing the energy spectrum, pair correlation functions, and dynamical form factor as a function of inter-dot coupling via diagonalization of the many-body Hamiltonian, we identify structural transitions between different phases, some of which do not have a classical counterpart. The calculated Raman cross section shows how such phases can be experimentally singled out.Comment: 9 pages, 2 postscript figures, 1 colour postscript figure, Latex 2e, Europhysics Letters style and epsfig macros. Submitted to Europhysics Letter

Removing the bottleneck : introducing cMatch - a lightweight tool for construct-matching in synthetic biology

We present a software tool, called cMatch, to reconstruct and identify synthetic genetic constructs from their sequences, or a set of sub-sequences - based on two practical pieces of information: their modular structure, and libraries of components. Although developed for combinatorial pathway engineering problems and addressing their quality control (QC) bottleneck, cMatch is not restricted to these applications. QC takes place post assembly, transformation and growth. It has a simple goal, to verify that the genetic material contained in a cell matches what was intended to be built - and when it is not the case, to locate the discrepancies and estimate their severity. In terms ofreproducibility/reliability, the QC step is crucial. Failure at this step requires repetition of the construction and/or sequencing steps. When performed manually or semi-manually QC is an extremely time-consuming, error prone process, which scales very poorly with the number of constructs and their complexity. To make QC frictionless and more reliable, cMatch performs an operation we have called ‘construct-matching’ and automates it. Construct-matching is more thorough than simple sequence-matching, as it matches at the functional level-and quantifies the matching at the individual component level and across thewhole construct

PASIV - A pooled approach-based workflow to overcome toxicity-induced Design of Experiments failures and inefficiencies

We present here a newly developed workflow - which we have called PASIV - designed to provide a solution to a practical problem with Design of Experiments methodology (DoE): i.e. what can be done if the scoping phase of the DoE cycle is severely hampered by burden and toxicity issues (either caused by the metabolite or an intermediary) making it unreliable or impossible to proceed to the screening phase? PASIV - standing for Pooled Approach, Screening, Identification and Visualization - was designed so the (viable) region of interest can be made to appear through an interplay between biology and software. This was achieved by combining multiplex construction in a pooled approach (one pot reaction) with a viability assay, and with a range of bioinformatic tools (including a novel construct matching tool). PASIV was tested on the exemplar of the lycopene pathway - under stressful constitutive expression yielding a region of interest with comparatively stronger producers

Toward the first data acquisition standard in synthetic biology

This paper describes the development of a new data acquisition standard for synthetic biology. This comprises the creation of a methodology that is designed to capture all the data, metadata, and protocol information associated with biopart characterization experiments. The new standard, called DICOM-SB, is based on the highly successful Digital Imaging and Communications in Medicine (DICOM) standard in medicine. A data model is described which has been specifically developed for synthetic biology. The model is a modular, extensible data model for the experimental process, which can optimize data storage for large amounts of data. DICOM-SB also includes services orientated toward the automatic exchange of data and information between modalities and repositories. DICOM-SB has been developed in the context of systematic design in synthetic biology, which is based on the engineering principles of modularity, standardization, and characterization. The systematic design approach utilizes the design, build, test, and learn design cycle paradigm. DICOM-SB has been designed to be compatible with and complementary to other standards in synthetic biology, including SBOL. In this regard, the software provides effective interoperability. The new standard has been tested by experiments and data exchange between Nanyang Technological University in Singapore and Imperial College London

Data model for biopart datasheets

This study introduces a new data model, based on the DICOM-SB (see glossary of terms for definition of acronyms) standard for synthetic biology, that is capable of describing/incorporating the data, metadata and ancillary information from detailed characterisation experiments - to present DNA components (bioparts) in datasheets. The data model offers a standardised mechanism to associate bioparts with data and information about component performance - in a particular biological context (or a range of contexts, e.g. chassis). The data model includes the raw, experimental data for each characterisation run, and the protocol details needed to reliably reproduce the experiment. In addition, it provides metrics (e.g. relative promoter units, synthesis/growth rates etc.) that constitute the main content of a biopart datasheet. The data model has been developed to directly link to DICOM-SB, but also to be compatible with existing data standards, e.g. SBOL and SBML. It has been implemented within the latest version of the API that enables access to the SynBIS information system. The work should contribute significantly to the current standardisation effort in synthetic biology. The standard data model for datasheets is seen as a necessary step towards effective interoperability between part repositories, and between repositories and BioCAD applications

Multimodal evaluation for medical image segmentation

This paper is a joint effort between five institutionsthat introduces several novel similarity measures andcombines them to carry out a multimodal segmentationevaluation. The new similarity measures proposed arebased on the location and the intensity values of themisclassified voxels as well as on the connectivity andthe boundaries of the segmented data. We showexperimentally that the combination of these measuresimprove the quality of the evaluation. The study that weshow here has been carried out using four differentsegmentation methods from four different labs applied toa MRI simulated dataset of the brain. We claim that ournew measures improve the robustness of the evaluation andprovides better understanding about the differencebetween segmentation methods

Motility of adherent hemocytes as a potential marker of immunocompetence and immunotoxic effects in bivalves

International audienc

Bioturbation and soil resistance to wind erosion in Southern Tunisia

International audienceWind erosion is a major threat to the sustainability of arid and semi-arid ecosystems. In these environments, biological soil crusts positively impact soil resistance to erosion. Less is known, however, on the impact of soil bioturbation by animals. In Southern Tunisia, bioturbation is mainly carried out by termites, ants and rodents which deposit mineral and organic components on the soil surface in the form of soil sheetings for termites or as soil heaps for ants and rodents. We here question the properties of these soils and measure their resistance to wind erosion. We showed that soil sheetings are made of sand grains linked together by bridges of organic matter, clay particles and other small size minerals such as carbonates and gypsum. The stability of these aggregates is comparable to that of biological soil crusts, despite their very different organizations. Conversely, the soil excavated by ants and rodents mainly consists in individual sand grains, which are impoverished in organic carbon and prone to wind erosion. In conclusion, this study highlights the importance of termites, as key soil bioturbator, on the dynamics of soil aggregates in Southern Tunisia. It also shows that they have an opposite effect than that of ants and rodents on the resistance of soil to erosion

Constructing synthetic biology workflows in the cloud

The synthetic biology design process has traditionally been heavily dependent upon manual searching, acquisition and integration of existing biological data. A large amount of such data is already available from Internet-based resources, but data exchange between these resources is often undertaken manually. Automating the communication between different resources can be done by the generation of computational workflows to achieve complex tasks that cannot be carried out easily or efficiently by a single resource. Computational workflows involve the passage of data from one resource, or process, to another in a distributed computing environment. In a typical bioinformatics workflow, the predefined order in which processes are invoked in a synchronous fashion and are described in a workflow definition document. However, in synthetic biology the diversity of resources and manufacturing tasks required favour a more flexible model for process execution. Here, the authors present the Protocol for Linking External Nodes (POLEN), a Cloud-based system that facilitates synthetic biology design workflows that operate asynchronously. Messages are used to notify POLEN resources of events in real time, and to log historical events such as the availability of new data, enabling networks of cooperation. POLEN can be used to coordinate the integration of different synthetic biology resources, to ensure consistency of information across distributed repositories through added support for data standards, and ultimately to facilitate the synthetic biology life cycle for designing and implementing biological systems