Intra-genomic internal transcribed spacer region sequence heterogeneity and molecular diagnosis in clinical microbiology

Internal transcribed spacer region (ITS) sequencing is the most extensively used technology for accurate molecular identification of fungal pathogens in clinical microbiology laboratories. Intra-genomic ITS sequence heterogeneity, which makes fungal identification based on direct sequencing of PCR products difficult, has rarely been reported in pathogenic fungi. During the process of performing ITS sequencing on 71 yeast strains isolated from various clinical specimens, direct sequencing of the PCR products showed ambiguous sequences in six of them. After cloning the PCR products into plasmids for sequencing, interpretable sequencing electropherograms could be obtained. For each of the six isolates, 10–49 clones were selected for sequencing and two to seven intra-genomic ITS copies were detected. The identities of these six isolates were confirmed to be Candida glabrata (n = 2), Pichia (Candida) norvegensis (n = 2), Candida tropicalis (n = 1) and Saccharomyces cerevisiae (n = 1). Multiple sequence alignment revealed that one to four intra-genomic ITS polymorphic sites were present in the six isolates, and all these polymorphic sites were located in the ITS1 and/or ITS2 regions. We report and describe the first evidence of intra-genomic ITS sequence heterogeneity in four different pathogenic yeasts, which occurred exclusively in the ITS1 and ITS2 spacer regions for the six isolates in this study.published_or_final_versio

A domain decomposition non-intrusive reduced order model for turbulent flows

In this paper, a new Domain Decomposition Non-Intrusive Reduced Order Model (DDNIROM) is developed for turbulent flows. The method works by partitioning the computational domain into a number of subdomains in such a way that the summation of weights associated with the finite element nodes within each subdomain is approximately equal, and the communication between subdomains is minimised. With suitably chosen weights, it is expected that there will be approximately equal accuracy associated with each subdomain. This accuracy is maximised by allowing the partitioning to occur through areas of the domain that have relatively little flow activity, which, in this case, is characterised by the pointwise maximum Reynolds stresses.A Gaussian Process Regression (GPR) machine learning method is used to construct a set of local approximation functions (hypersurfaces) for each subdomain. Each local hypersurface represents not only the fluid dynamics over the subdomain it belongs to, but also the interactions of the flow dynamics with the surrounding subdomains. Thus, in this way, the surrounding subdomains may be viewed as providing boundary conditions for the current subdomain.We consider a specific example of turbulent air flow within an urban neighbourhood at a test site in London and demonstrate the effectiveness of the proposed DDNIROM

Non-intrusive reduced order modelling of the Navier–Stokes equations

This article presents two new non-intrusive reduced order models based upon proper orthogonal decomposition (POD) for solving the Navier–Stokes equations. The novelty of these methods resides in how the reduced order models are formed, that is, how the coefficients of the POD expansions are calculated. Rather than taking a standard approach of projecting the underlying equations onto the reduced space through a Galerkin projection, here two different techniques are employed. The first method applies a second order Taylor series to calculate the POD coefficients at each time step from the POD coefficients at earlier time steps. The second method uses a Smolyak sparse grid collocation method to calculate the POD coefficients, where again the coefficients at earlier time steps are used as the inputs. The advantage of both approaches are that they are non-intrusive and so do not require modifications to a system code; they are therefore very easy to implement. They also provide accurate solutions for modelling flow problems, and this has been demonstrated by the simulation of flows past a cylinder and within a gyre. It is demonstrated that accuracy relative to the high fidelity model is maintained whilst CPU times are reduced by several orders of magnitude in comparison to high fidelity models

From regional pulse vaccination to global disease eradication: insights from a mathematical model of Poliomyelitis

Mass-vaccination campaigns are an important strategy in the global fight against poliomyelitis and measles. The large-scale logistics required for these mass immunisation campaigns magnifies the need for research into the effectiveness and optimal deployment of pulse vaccination. In order to better understand this control strategy, we propose a mathematical model accounting for the disease dynamics in connected regions, incorporating seasonality, environmental reservoirs and independent periodic pulse vaccination schedules in each region. The effective reproduction number, $R_e$, is defined and proved to be a global threshold for persistence of the disease. Analytical and numerical calculations show the importance of synchronising the pulse vaccinations in connected regions and the timing of the pulses with respect to the pathogen circulation seasonality. Our results indicate that it may be crucial for mass-vaccination programs, such as national immunisation days, to be synchronised across different regions. In addition, simulations show that a migration imbalance can increase $R_e$ and alter how pulse vaccination should be optimally distributed among the patches, similar to results found with constant-rate vaccination. Furthermore, contrary to the case of constant-rate vaccination, the fraction of environmental transmission affects the value of $R_e$ when pulse vaccination is present.Comment: Added section 6.1, made other revisions, changed titl

Microbial fuel cells: a green and alternative source for bioenergy production

Microbial fuel cell (MFC) represents one of the green technologies for the production of bioenergy. MFCs using microalgae produce bioenergy by converting solar energy into electrical energy as a function of metabolic and anabolic pathways of the cells. In the MFCs with bacteria, bioenergy is generated as a result of the organic substrate oxidation. MFCs have received high attention from researchers in the last years due to the simplicity of the process, the absence in toxic by-products, and low requirements for the algae growth. Many studies have been conducted on MFC and investigated the factors affecting the MFC performance. In the current chapter, the performance of MFC in producing bioenergy as well as the factors which influence the efficacy of MFCs is discussed. It appears that the main factors affecting MFC’s performance include bacterial and algae species, pH, temperature, salinity, substrate, mechanism of electron transfer in an anodic chamber, electrodes materials, surface area, and electron acceptor in a cathodic chamber. These factors are becoming more influential and might lead to overproduction of bioenergy when they are optimized using response surface methodology (RSM)

Clinical report of cervical arthroplasty in management of spondylotic myelopathy in Chinese

OBJECTIVES: To investigate clinical effects and manual operational point of Bryan cervical disc prosthesis in Chinese, to observe the stability and range of movement (ROM) post-operatively. METHODS AND MATERIALS: From 2003,12 to 2005,12, Bryan disc prosthesis replacement applied in 83 cases (102 levels) of cervical spondylotic myelopathy (CSM) after anterior decompression in our hospital. Clinical (JOA grade and Odom's scale) and radiological (X-ray of flexion, extension; left and right bending position) follow-up was performed. Systemic radiographic study about stability and ROM of replaced level post operationally were measured. CT or MRI scans were applied in all cases to evaluate the signs of the prosthesis deflexion and hetero-ossification in the replaced levels. RESULTS: At least 12 months follow-up were done in 65/83 of these paients. All of 83 patients were improved according to Odsm's scale. JOA score increased from average 8.7 to 15.5. There was no prosthesis subsidence. Replaced segment achieved stability and restored partial of normal ROM 4.73°(3.7°–5.9°) early postoperation and 8.12°(5.8°–13.6°) more than 12 months postoperation in flex and extension position. No obvious loss of lordosis was found. CT or MRI follow-up shows position deflexion of the prosthesis metal endplates (<1.5 mm) in 14/77 levels and (1.5~3 mm) in 4/77. heter-ossification was found in the replaced levels only in 2 cases. CONCLUSION: Byran cervical disc prosthesis restored motion to the level of the intact segment in flexion-extension and lateral bending in post-operative images. At the same time, it can achieve good anterior decompression treatment effect and immediate stability in replaced 1 or 2 levels, and which is a new choice for the treatment of CSM

Temporal and Spatial Dynamics of Carbon Fixation by Moso Bamboo (Phyllostachys pubescens) in Subtropical China

To study the temporal and spatial dynamics of carbon fixation by Moso bamboo (Phyllostachys pubescens) in subtropical China, carbon fixation of leaves within the canopy of P. pubescens was measured with a LI-6400 portable photosynthesis system. The results showed that the capability of carbon fixation of P. pubescens leaves had obvious temporal and spatial dynamic variations. It was revealed that there were two peak periods and two low periods in the season variation of carbon fixation capability. Data also revealed that the capability of carbon fixation by five-year-old P. pubescens was more than that of one-year-old and three-year-old. Daily and seasonal carbon fixation showed a negative correlation with the CO2 concentration. The temporal and spatial dynamics of carbon fixation by P. pubescens described above provided a scientific basis for development of technologies in bamboo timber production

Shaping bursting by electrical coupling and noise

Gap-junctional coupling is an important way of communication between neurons and other excitable cells. Strong electrical coupling synchronizes activity across cell ensembles. Surprisingly, in the presence of noise synchronous oscillations generated by an electrically coupled network may differ qualitatively from the oscillations produced by uncoupled individual cells forming the network. A prominent example of such behavior is the synchronized bursting in islets of Langerhans formed by pancreatic \beta-cells, which in isolation are known to exhibit irregular spiking. At the heart of this intriguing phenomenon lies denoising, a remarkable ability of electrical coupling to diminish the effects of noise acting on individual cells. In this paper, we derive quantitative estimates characterizing denoising in electrically coupled networks of conductance-based models of square wave bursting cells. Our analysis reveals the interplay of the intrinsic properties of the individual cells and network topology and their respective contributions to this important effect. In particular, we show that networks on graphs with large algebraic connectivity or small total effective resistance are better equipped for implementing denoising. As a by-product of the analysis of denoising, we analytically estimate the rate with which trajectories converge to the synchronization subspace and the stability of the latter to random perturbations. These estimates reveal the role of the network topology in synchronization. The analysis is complemented by numerical simulations of electrically coupled conductance-based networks. Taken together, these results explain the mechanisms underlying synchronization and denoising in an important class of biological models

Polypyrrole-Fe2O3 nanohybrid materials for electrochemical storage

We report on the synthesis and electrochemical characterization of nanohybrid polypyrrole (PPy) (PPy/Fe2O3) materials for electrochemical storage applications. We have shown that the incorporation of nanoparticles inside the PPy notably increases the charge storage capability in comparison to the “pure” conducting polymer. Incorporation of large anions, i.e., paratoluenesulfonate, allows a further improvement in the capacity. These charge storage modifications have been attributed to the morphology of the composite in which the particle sizes and the specific surface area are modified with the incorporation of nanoparticles. High capacity and stability have been obtained in PC/NEt4BF4 (at 20 mV/s), i.e., 47 mAh/g, with only a 3% charge loss after one thousand cyles. The kinetics of charge–discharge is also improved by the hybrid nanocomposite morphology modifications, which increase the rate of insertion–expulsion of counter anions in the bulk of the film. A room temperature ionic liquid such as imidazolium trifluoromethanesulfonimide seems to be a promising electrolyte because it further increases the capacity up to 53 mAh/g with a high stability during charge–discharge processes