Describing complex design practices with a cross-domain framework: learning from Synthetic Biology and Swarm Robotics

This paper reports on the development of a cross-domain framework for describing complex design practices. The framework is grounded in studies of two different complex design fields: Synthetic Biology and Swarm Robotics. In the first study, we interviewed practitioners in Synthetic Biology, identifying three essential aspects of complex design problems and practices. The first of these aspects is the characterisation of system complexity, the second is the design objective taken with respect to this complexity, and the third is the design approach applied to realise this objective. In the second study, we interviewed designers in Swarm Robotics, confirming the domain generality of the three aspects identified in the first study and permitting a comparison to be made of how the two fields differ from each other in these aspects. Considered together, the two studies provide the basis for building a cross-domain framework for describing complex design practices. Such a framework is presented here, not to exhaust all possible descriptions of complex design practice but rather to provide a structured yet adaptable way of highlighting the important aspects of these descriptions. Indeed, each aspect of complex design can be can be broken down into different elements depending on the design contexts under consideration. Having such a framework enables designers to identify fundamental similarities and differences both between and within fields.This work was funded by the UK’s Engineering and Physical Sciences Research Council (EP/K008196/1).This is the final version of the article. It first appeared from Springer via http://dx.doi.org/10.1007/s00163-016-0219-

Extending local features with contextual information in graph kernels

Graph kernels are usually defined in terms of simpler kernels over local substructures of the original graphs. Different kernels consider different types of substructures. However, in some cases they have similar predictive performances, probably because the substructures can be interpreted as approximations of the subgraphs they induce. In this paper, we propose to associate to each feature a piece of information about the context in which the feature appears in the graph. A substructure appearing in two different graphs will match only if it appears with the same context in both graphs. We propose a kernel based on this idea that considers trees as substructures, and where the contexts are features too. The kernel is inspired from the framework in [6], even if it is not part of it. We give an efficient algorithm for computing the kernel and show promising results on real-world graph classification datasets.Comment: To appear in ICONIP 201

Monitoring lipid accumulation in the green microalga Botryococcus braunii with frequency-modulated stimulated Raman scattering

© 2015 SPIE.The potential of microalgae as a source of renewable energy has received considerable interest because they can produce lipids (fatty acids and isoprenoids) that can be readily converted into biofuels. However, significant research in this area is required to increase yields to make this a viable renewable source of energy. An analytical tool that could provide quantitative in situ spectroscopic analysis of lipids synthesis in individual microalgae would significantly enhance our capability to understand the synthesis process at the cellular level and lead to the development of strategies for increasing yield. Stimulated Raman scattering (SRS) microscopy has great potential in this area however, the pump-probe signal from two-color two-photon absorption of pigments (chlorophyll and carotenoids) overwhelm the SRS signal and prevent its application. Clearly, the development of a background suppression technique is of significant value for this important research area. To overcome the limitation of SRS in pigmented specimens, we establish a frequency-modulated stimulated Raman scattering (FM-SRS) microscopy that eliminates the non-Raman background by rapidly toggling on-and-off the targeted Raman resonance. Moreover, we perform the background-free imaging and analysis of intracellular lipid droplets and extracellular hydrocarbons in a green microalga with FM-SRS microscopy. We believe that FM-SRS microscopy demonstrates the potential for many applications in pigmented cells and provides the opportunity for improved selective visualization of the chemical composition of algae and plants.We thank Delong Zhang at Purdue University for fruitful discussion. This research was supported by grants (BB/K013602/1) from the Biotechnology and Biological Sciences Research Council (BBSRC) and Syngenta

Photoluminescence upconversion at GaAs/InGaP2 interfaces driven by a sequential two-photon absorption mechanism

This paper reports on the results of an investigation into the nature of photoluminescence upconversion at GaAs/InGaP2 interfaces. Using a dual-beam excitation experiment, we demonstrate that the upconversion in our sample proceeds via a sequential two-photon optical absorption mechanism. Measurements of photoluminescence and upconversion photoluminescence revealed evidence of the spatial localization of carriers in the InGaP2 material, arising from partial ordering of the InGaP2. We also observed the excitation of a two-dimensional electron gas at the GaAs/InGaP2 heterojunction that manifests as a high-energy shoulder in the GaAs photoluminescence spectrum. Furthermore, the results of upconversion photoluminescence excitation spectroscopy demonstrate that the photon energy onset of upconversion luminescence coincides with the energy of the two-dimensional electron gas at the GaAs/InGaP2 interface, suggesting that charge accumulation at the interface can play a crucial role in the upconversion process

Universal scaling relation in high-temperature superconductors

Scaling laws express a systematic and universal simplicity among complex systems in nature. For example, such laws are of enormous significance in biology. Scaling relations are also important in the physical sciences. The seminal 1986 discovery of high transition-temperature (high-T_c) superconductivity in cuprate materials has sparked an intensive investigation of these and related complex oxides, yet the mechanism for superconductivity is still not agreed upon. In addition, no universal scaling law involving such fundamental properties as T_c and the superfluid density \rho_s, a quantity indicative of the number of charge carriers in the superconducting state, has been discovered. Here we demonstrate that the scaling relation \rho_s \propto \sigma_{dc} T_c, where the conductivity \sigma_{dc} characterizes the unidirectional, constant flow of electric charge carriers just above T_c, universally holds for a wide variety of materials and doping levels. This surprising unifying observation is likely to have important consequences for theories of high-T_c superconductivity.Comment: 11 pages, 2 figures, 2 table

Impaired vowel discrimination in Mandarin-speaking congenital amusics

2015-2016 > Academic research: refereed > Refereed conference paperVersion of RecordPublishe

The orthogonally aligned dark halo of an edge-on lensing galaxy in the Hubble Frontier Fields: a challenge for modified gravity

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Switching off malignant mesothelioma : exploiting the hypoxic microenvironment

Malignant mesotheliomas are aggressive, asbestos-related cancers with poor patient prognosis, typically arising in the mesothelial surfaces of tissues in pleural and peritoneal cavity. The relative unspecific symptoms of mesotheliomas, misdiagnoses, and lack of precise targeted therapies call for a more critical assessment of this disease. In the present review, we categorize commonly identified genomic aberrations of mesotheliomas into their canonical pathways and discuss targeting these pathways in the context of tumor hypoxia, a hallmark of cancer known to render solid tumors more resistant to radiation and most chemo-therapy. We then explore the concept that the intrinsic hypoxic microenvironment of mesotheliomas can be Achilles’ heel for targeted, multimodal therapeutic intervention

A simple and robust method for connecting small-molecule drugs using gene-expression signatures

Interaction of a drug or chemical with a biological system can result in a gene-expression profile or signature characteristic of the event. Using a suitably robust algorithm these signatures can potentially be used to connect molecules with similar pharmacological or toxicological properties. The Connectivity Map was a novel concept and innovative tool first introduced by Lamb et al to connect small molecules, genes, and diseases using genomic signatures [Lamb et al (2006), Science 313, 1929-1935]. However, the Connectivity Map had some limitations, particularly there was no effective safeguard against false connections if the observed connections were considered on an individual-by-individual basis. Further when several connections to the same small-molecule compound were viewed as a set, the implicit null hypothesis tested was not the most relevant one for the discovery of real connections. Here we propose a simple and robust method for constructing the reference gene-expression profiles and a new connection scoring scheme, which importantly allows the valuation of statistical significance of all the connections observed. We tested the new method with the two example gene-signatures (HDAC inhibitors and Estrogens) used by Lamb et al and also a new gene signature of immunosuppressive drugs. Our testing with this new method shows that it achieves a higher level of specificity and sensitivity than the original method. For example, our method successfully identified raloxifene and tamoxifen as having significant anti-estrogen effects, while Lamb et al's Connectivity Map failed to identify these. With these properties our new method has potential use in drug development for the recognition of pharmacological and toxicological properties in new drug candidates.Comment: 8 pages, 2 figures, and 2 tables; supplementary data supplied as a ZIP fil

Fat area and lipid droplet morphology of porcine oocytes during in vitro maturation with trans-10, cis-12 conjugated linoleic acid and forskolin

Lipid droplets (LD) in porcine oocytes form a dark mass reaching almost all cytoplasm. Herein we investigated changes in fat areas, cytoplasmic tone and LD morphology during in vitro maturation (IVM) of porcine oocytes cultured with 100mM trans-10, cis-12 conjugated linoleic acid (t10,c12 CLA) or 10mM forskolin at different time periods. Four groups were constituted: control, excipient, t10,c12 CLA and forskolin, with drugs being supplemented during 44 to 48h and the initial 22 to 24h in Experiments 1 and 2, respectively. In Experiment 3, forskolin was supplemented for the first 2 h. Matured oocytes were inseminated with frozen-thawed boar semen and cleavage rate recorded. Before and during IVM, samples of oocytes were evaluated for LD, total and fat areas and fat gray value or for meiotic progression. Results showed that forskolin supplementation during 44 to 48 h or 22 to 24 h inhibits oocyte maturation (exp. 1: forskolin = 5.1±8.0%, control = 72.6±5.0%; exp. 2: forskolin =24.3±7.4%, control =71.6±5.6%) and cleavage (exp. 1: forskolin=0.0±0.0%, control=55.4±4.1%; exp. 2: forskolin=8.3±3.3%, control=54.5±3.0%). Forskolin also reduced oocyte and fat areas. In Experiment 3, forskolin negative effect on oocyte maturation and cleavage disappeared, although minor (P<0.03) LD and oocyte fat areas were identified at 22 to 24 h of IVM. Oocytes supplemented with t10,c12 CLA during 44 to 48h presented a lighter (P<0.04) colour tone cytoplasm than those of control and forskolin. In conclusion, t10,c12 CLA and forskolin were capable of modifying the distribution and morphology of cytoplasmic LD during porcine oocyte maturation, thus reducing its lipid content in a time-dependent manner