BioPartsDB: a synthetic biology workflow web-application for education and research

Synthetic biology has become a widely used technology, and expanding applications in research, education and industry require progress tracking for team-based DNA synthesis projects. Although some vendors are beginning to supply multi-kilobase sequence-verified constructs, synthesis workflows starting with short oligos remain important for cost savings and pedagogical benefit. We developed BioPartsDB as an open source, extendable workflow management system for synthetic biology projects with entry points for oligos and larger DNA constructs and ending with sequence-verified clones

Kinetic studies of CO<inf>2</inf> methanation over a Ni/γ-Al<inf>2</inf>O<inf>3</inf> catalyst using a batch reactor

The methanation of CO₂ was investigated over a wide range of partial pressures of products and reactants using a gradientless, spinning-basket reactor operated in batch mode. The rate and selectivity of CO₂ methanation, using a 12 wt% Ni/γ-Al₂O₃ catalyst, were explored at temperatures 453 – 483 K and pressures up to 20 bar. The rate was found to increase with increasing partial pressures of H₂ and CO₂ when the partial pressures of these reactants were low; however, the rate of reaction was found to be insensitive to changes in the partial pressures of H₂ and CO₂ when their partial pressures were high. A convenient method of determining the effect of H₂O on the rate of reaction was also developed using the batch reactor and the inhibitory effect of H₂O on CO₂ methanation was quantified. The kinetic measurements were compared with a mathematical model of the reactor, in which different kinetic expressions were explored. The kinetics of the reaction were found to be consistent with a mechanism in which adsorbed CO₂ dissociated to adsorbed CO and O on the surface of the catalyst with the rate-limiting step being the subsequent dissociation of adsorbed CO.JYL was funded by the Cambridge International Scholarship Scheme. The Cambridge Philosophical Society, the Lundgren Research Award and Corpus Christi College are also gratefully thanked for contributing to the support of his PhD studies.This is the author accepted manuscript. The final version is available from Elsevier via http://dx.doi.org/10.1016/j.ces.2015.10.02

Dimerization-Induced Fermi-Surface Reconstruction in IrTe2

We report a de Haas-van Alphen (dHvA) oscillation study on IrTe2 single crystals showing complex dimer formations. By comparing the angle dependence of dHvA oscillations with band structure calculations, we show distinct Fermi surface reconstruction induced by a 1/5-type and a 1/8-type dimerizations. This verifies that an intriguing quasi-two-dimensional conducting plane across the layers is induced by dimerization in both cases. A phase transition to the 1/8 phase with higher dimer density reveals that local instabilities associated with intra-and interdimer couplings are the main driving force for complex dimer formations in IrTe2.X11149sciescopu

Decision support for personalized cloud service selection through multi-attribute trustworthiness evaluation

Facing a customer market with rising demands for cloud service dependability and security, trustworthiness evaluation techniques are becoming essential to cloud service selection. But these methods are out of the reach to most customers as they require considerable expertise. Additionally, since the cloud service evaluation is often a costly and time-consuming process, it is not practical to measure trustworthy attributes of all candidates for each customer. Many existing models cannot easily deal with cloud services which have very few historical records. In this paper, we propose a novel service selection approach in which the missing value prediction and the multi-attribute trustworthiness evaluation are commonly taken into account. By simply collecting limited historical records, the current approach is able to support the personalized trustworthy service selection. The experimental results also show that our approach performs much better than other competing ones with respect to the customer preference and expectation in trustworthiness assessment. © 2014 Ding et al

Sample entropy analysis of EEG signals via artificial neural networks to model patients' consciousness level based on anesthesiologists experience.

Electroencephalogram (EEG) signals, as it can express the human brain's activities and reflect awareness, have been widely used in many research and medical equipment to build a noninvasive monitoring index to the depth of anesthesia (DOA). Bispectral (BIS) index monitor is one of the famous and important indicators for anesthesiologists primarily using EEG signals when assessing the DOA. In this study, an attempt is made to build a new indicator using EEG signals to provide a more valuable reference to the DOA for clinical researchers. The EEG signals are collected from patients under anesthetic surgery which are filtered using multivariate empirical mode decomposition (MEMD) method and analyzed using sample entropy (SampEn) analysis. The calculated signals from SampEn are utilized to train an artificial neural network (ANN) model through using expert assessment of consciousness level (EACL) which is assessed by experienced anesthesiologists as the target to train, validate, and test the ANN. The results that are achieved using the proposed system are compared to BIS index. The proposed system results show that it is not only having similar characteristic to BIS index but also more close to experienced anesthesiologists which illustrates the consciousness level and reflects the DOA successfully.This research is supported by the Center forDynamical Biomarkers and Translational Medicine, National Central University, Taiwan, which is sponsored by Ministry of Science and Technology (Grant no. MOST103-2911-I-008-001). Also, it is supported by National Chung-Shan Institute of Science & Technology in Taiwan (Grant nos. CSIST-095-V301 and CSIST-095-V302)

Molecular dynamics simulations of oscillatory Couette flows with slip boundary conditions

The effect of interfacial slip on steady-state and time-periodic flows of monatomic liquids is investigated using non-equilibrium molecular dynamics simulations. The fluid phase is confined between atomically smooth rigid walls, and the fluid flows are induced by moving one of the walls. In steady shear flows, the slip length increases almost linearly with shear rate. We found that the velocity profiles in oscillatory flows are well described by the Stokes flow solution with the slip length that depends on the local shear rate. Interestingly, the rate dependence of the slip length obtained in steady shear flows is recovered when the slip length in oscillatory flows is plotted as a function of the local shear rate magnitude. For both types of flows, the friction coefficient at the liquid-solid interface correlates well with the structure of the first fluid layer near the solid wall.Comment: 31 pages, 11 figure

Cell number quantification of USPIO-labeled stem cells by MRI: An in vitro study

MRI plays an expanding role in stem cell therapies. The non-invasive nature and high spatial resolution of MR imaging make MR imaging a powerful tool to investigate biologic processes at the molecular and cellular level in vivo longitudinally. Quantitative detection of stem cells after transplantation may allow assessment of stem cell localization and migration, and monitoring of the therapeutic effectiveness of stem cell therapy. In this study, we present a technique for MR quantification of magnetically labeled mouse embryonic stem cells distributed or injected in agarose gel phantoms. Apparent transverse relaxation rate enhancements (ΔR2*) were measured by gradient echo sequences. The linear relationship between ΔR2* and the concentration of USPIO-labeled mouse embryonic stem cells was observed and used for quantifying cell density and cell number after injection or transplantation. The MRI acquisition and analysis protocol were validated by good agreement between actual cell numbers and MRI-estimated cell numbers over a wide range of cell numbers. This MR technique for cell number and cell density quantification is applicable to future in vivo studies. © 2006 IEEE.published_or_final_versio

Improving hydrogen yields, and hydrogen: Steam ratio in the chemical looping production of hydrogen using Ca<inf>2</inf>Fe<inf>2</inf>O<inf>5</inf>

A thermodynamic property of Ca2Fe2O5 was exploited to improve the efficiency of the steam-iron process to produce hydrogen. The ability of reduced Ca2Fe2O5 to convert a higher fraction of steam to hydrogen than chemically unmodified Fe was demonstrated in a packed bed. At 1123 K, the use of Ca2Fe2O5 achieved an equilibrium conversion of steam to hydrogen of 75%, in agreement with predicted thermodynamics and substantially higher than that theoretically achievable by iron oxide, viz. 62%. Furthermore, in Ca2Fe2O5, the full oxidation from Fe(0) to Fe(III) can be utilised for hydrogen production – an improvement from the Fe to Fe3O4 transition for unmodified iron. Thermodynamic considerations demonstrated in this study allow for the rational design of oxygen carriers in the future. Modifications of reactors to capitalise on this new material are discussed.Dr Matthew T. Dunstan is acknowledged for help with the XRD analysis. M.S.C.C acknowledges financial support from an EPSRC Doctoral Training Grant. W.L and Y.Y acknowledge funding from the National Research Foundation (NRF), Prime Minister’s Office, Singapore under its Campus for Research Excellence and Technological Enterprise (CREATE) programme.This is the final version of the article. It first appeared from Elsevier via http://dx.doi.org/10.1016/j.cej.2016.03.13

Influenza-associated hospitalisation.

The disease burden associated with influenza includes not only acute respiratory diseases but also cerebrovascular disease, ischaemic heart disease and diabetes mellitus.published_or_final_versio

On the stability of high-speed milling with spindle speed variation

Spindle speed variation is a well-known technique to suppress regenerative machine tool vibrations, but it is usually considered to be effective only for low spindle speeds. In this paper, the effect of spindle speed variation is analyzed in the high-speed domain for spindle speeds corresponding to the first flip (period doubling) and to the first Hopf lobes. The optimal amplitudes and frequencies of the speed modulations are computed using the semidiscre- tization method. It is shown that period doubling chatter can effectively be suppressed by spindle speed variation, although, the technique is not effective for the quasiperiodic chatter above the Hopf lobe. The results are verified by cutting tests. Some special cases are also discussed where the practical behavior of the system differs from the predicted one in some ways. For these cases, it is pointed out that the concept of stability is understood on the scale of the principal period of the system—that is, the speed modulation period for variable spindle speed machining and the tooth passing period for constant spindle speed machining