Methicillin-resistant Staphylococcus aureus in Finland: recent changes in the epidemiology, long-term facility aspects, and phenotypic and molecular detection of isolates

Staphylococcus aureus is one of the most important bacteria that cause disease in humans, and methicillin-resistant S. aureus (MRSA) has become the most commonly identified antibiotic-resistant pathogen in many parts of the world. MRSA rates have been stable for many years in the Nordic countries and the Netherlands with a low MRSA prevalence in Europe, but in the recent decades, MRSA rates have increased in those low-prevalence countries as well. MRSA has been established as a major hospital pathogen, but has also been found increasingly in long-term facilities (LTF) and in communities of persons with no connections to the health-care setting. In Finland, the annual number of MRSA isolates reported to the National Infectious Disease Register (NIDR) has constantly increased, especially outside the Helsinki metropolitan area. Molecular typing has revealed numerous outbreak strains of MRSA, some of which have previously been associated with community acquisition. In this work, data on MRSA cases notified to the NIDR and on MRSA strain types identified with pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), and staphylococcal cassette chromosome mec (SCCmec) typing at the National Reference Laboratory (NRL) in Finland from 1997 to 2004 were analyzed. An increasing trend in MRSA incidence in Finland from 1997 to 2004 was shown. In addition, non-multi-drug resistant (NMDR) MRSA isolates, especially those resistant only to methicillin/oxacillin, showed an emerging trend. The predominant MRSA strains changed over time and place, but two internationally spread epidemic strains of MRSA, FIN-16 and FIN-21, were related to the increase detected most recently. Those strains were also one cause of the strikingly increasing invasive MRSA findings. The rise of MRSA strains with SCCmec types IV or V, possible community-acquired MRSA was also detected. With questionnaires, the diagnostic methods used for MRSA identification in Finnish microbiology laboratories and the number of MRSA screening specimens studied were reviewed. Surveys, which focused on the MRSA situation in long-term facilities in 2001 and on the background information of MRSA-positive persons in 2001-2003, were also carried out. The rates of MRSA and screening practices varied widely across geographic regions. Part of the NMDR MRSA strains could remain undetected in some laboratories because of insufficient diagnostic techniques used. The increasing proportion of elderly population carrying MRSA suggests that MRSA is an emerging problem in Finnish long-term facilities. Among the patients, 50% of the specimens were taken on a clinical basis, 43% on a screening basis after exposure to MRSA, 3% on a screening basis because of hospital contact abroad, and 4% for other reasons. In response to an outbreak of MRSA possessing a new genotype that occurred in a health care ward and in an associated nursing home of a small municipality in Northern Finland in autumn 2003, a point-prevalence survey was performed six months later. In the same study, the molecular epidemiology of MRSA and methicillin-sensitive S. aureus (MSSA) strains were also assessed, the results to the national strain collection compared, and the difficulties of MRSA screening with low-level oxacillin-resistant isolates encountered. The original MRSA outbreak in LTF, which consisted of isolates possessing a nationally new PFGE profile (FIN-22) and internationally rare MLST type (ST-27), was confined. Another previously unrecognized MRSA strain was found with additional screening, possibly indicating that current routine MRSA screening methods may be insufficiently sensitive for strains possessing low-level oxacillin resistance. Most of the MSSA strains found were genotypically related to the epidemic MRSA strains, but only a few of them had received the SCCmec element, and all those strains possessed the new SCCmec type V. In the second largest nursing home in Finland, the colonization of S. aureus and MRSA, and the role of screening sites along with broth enrichment culture on the sensitivity to detect S. aureus were studied. Combining the use of enrichment broth and perineal swabbing, in addition to nostrils and skin lesions swabbing, may be an alternative for throat swabs in the nursing home setting, especially when residents are uncooperative. Finally, in order to evaluate adequate phenotypic and genotypic methods needed for reliable laboratory diagnostics of MRSA, oxacillin disk diffusion and MIC tests to the cefoxitin disk diffusion method at both +35°C and +30°C, both with or without an addition of sodium chloride (NaCl) to the Müller Hinton test medium, and in-house PCR to two commercial molecular methods (the GenoType® MRSA test and the EVIGENETM MRSA Detection test) with different bacterial species in addition to S. aureus were compared. The cefoxitin disk diffusion method was superior to that of oxacillin disk diffusion and to the MIC tests in predicting mecA-mediated resistance in S. aureus when incubating at +35°C with or without the addition of NaCl to the test medium. Both the Geno Type® MRSA and EVIGENETM MRSA Detection tests are usable, accurate, cost-effective, and sufficiently fast methods for rapid MRSA confirmation from a pure culture.

地震波场模拟及叠前深度偏移的李群方法

The processes of seismic wave propagation in phase space and one way wave extrapolation in frequency-space domain, if without dissipation, are essentially transformation under the action of one parameter Lie groups. Consequently, the numerical calculation methods of the propagation ought to be Lie group transformation too, which is known as Lie group method. After a fruitful study on the fast methods in matrix inversion, some of the Lie group methods in seismic numerical modeling and depth migration are presented here. Firstly the Lie group description and method of seismic wave propagation in phase space is proposed, which is, in other words, symplectic group description and method for seismic wave propagation, since symplectic group is a Lie subgroup and symplectic method is a special Lie group method. Under the frame of Hamiltonian, the propagation of seismic wave is a symplectic group transformation with one parameter and consequently, the numerical calculation methods of the propagation ought to be symplectic method. After discrete the wave field in time and phase space, many explicit, implicit and leap-frog symplectic schemes are deduced for numerical modeling. Compared to symplectic schemes, Finite difference (FD) method is an approximate of symplectic method. Consequently, explicit, implicit and leap-frog symplectic schemes and FD method are applied in the same conditions to get a wave field in constant velocity model, a synthetic model and Marmousi model. The result illustrates the potential power of the symplectic methods. As an application, symplectic method is employed to give synthetic seismic record of Qinghai foothills model. Another application is the development of Ray+symplectic reverse-time migration method. To make a reasonable balance between the computational efficiency and accuracy, we combine the multi-valued wave field & Green function algorithm with symplectic reverse time migration and thus develop a new ray+wave equation prestack depth migration method. Marmousi model data and Qinghai foothills model data are processed here. The result shows that our method is a better alternative to ray migration for complex structure imaging. Similarly, the extrapolation of one way wave in frequency-space domain is a Lie group transformation with one parameter Z and consequently, the numerical calculation methods of the extrapolation ought to be Lie group methods. After discrete the wave field in depth and space, the Lie group transformation has the form of matrix exponential and each approximation of it gives a Lie group algorithm. Though Pade symmetrical series approximation of matrix exponential gives a extrapolation method which is traditionally regarded as implicit FD migration, it benefits the theoretic and applying study of seismic imaging for it represent the depth extrapolation and migration method in a entirely different way. While, the technique of coordinates of second kind for the approximation of the matrix exponential begins a new way to develop migration operator. The inversion of matrix plays a vital role in the numerical migration method given by Pade symmetrical series approximation. The matrix has a Toepelitz structure with a helical boundary condition and is easy to inverse with LU decomposition. A efficient LU decomposition method is spectral factorization. That is, after the minimum phase correlative function of each array of matrix had be given by a spectral factorization method, all of the functions are arranged in a position according to its former location to get a lower triangular matrix. The major merit of LU decomposition with spectral factorization (SF Decomposition) is its efficiency in dealing with a large number of matrixes. After the setup of a table of the spectral factorization results of each array of matrix, the SF decomposition can give the lower triangular matrix by reading the table. However, the relationship among arrays is ignored in this method, which brings errors in decomposition method. Especially for numerical calculation in complex model, the errors is fatal. Direct elimination method can give the exact LU decomposition But even it is simplified in our case, the large number of decomposition cost unendurable computer time. A hybrid method is proposed here, which combines spectral factorization with direct elimination. Its decomposition errors is 10 times little than that of spectral factorization, and its decomposition speed is quite faster than that of direct elimination, especially in dealing with a large number of matrix. With the hybrid method, the 3D implicit migration can be expected to apply on real seismic data. Finally, the impulse response of 3D implicit migration operator is presented.

Physically based simulation of heterogeneous deformable models using XFEM

This paper addresses the problem of heterogeneous deformable model accuracy using the finite element methods (FEM). Classic FEM uses predefined shape functions for interpolation and does not account easily for regions of discontinuities. Extended finite element methods (XFEM) use enrichment functions to compensate for the change in an element degrees of freedom (DoFs) in deformable objects. The XFEM is an accurate and fast method as no remeshing is required. In this study we investigate the performance of XFEM and demonstrate how it may be applied to discontinuities of materials that exist in heterogeneous (piece-wise homogeneous) models. The results show realistic stress prediction compared to modeling the same objects with classic FEM.

Efeitos renais e cardiovasculares da infusão de dopamina e da solução de cloreto de sódio a 7,5%: estudo experimental em cães com restrição hídrica

JUSTIFICATIVA E OBJETIVOS: É controvertido o uso da infusão de dopamina na proteção renal. O objetivo desta pesquisa foi estudar o efeito da dopamina, da solução hipertônica e da associação de ambas em cães com restrição hídrica, simulando o jejum pré-operatório. MÉTODO: Foram estudados, em 32 cães anestesiados com tiopental sódico e fentanil, os seguintes parâmetros da função renal: fluxo plasmático efetivo renal (depuração de para-aminohipurato de sódio), ritmo de filtração glomerular (depuração de creatinina) e as depurações de sódio, de potássio e osmolar, excreção fracionária de sódio e potássio, excreção de sódio e potássio e a resistência vascular renal. Os parâmetros cardiovasculares foram: pressão arterial média, freqüência cardíaca, pressão da veia cava inferior, índice cardíaco, hematócrito e índice de resistência vascular periférica. Os animais foram subdivididos, através de sorteio, em 4 grupos experimentais: Grupo 1 - G1 (n = 8) - grupo controle; Grupo 2 - G2 (n = 8) infusão de dopamina (2 µg.kg-1.min-1), Grupo 3 - G3 (n = 8) solução de cloreto de sódio a 7,5% (2 ml.kg-1) e Grupo 4 - G4 (n = 8) - associação de dopamina (2 µg.kg-1.min-1) e cloreto de sódio a 7,5% (2 ml.kg-1). Os grupos tiveram quatro fases experimentais e cada momento com duração de 30 minutos, compreendendo os momentos M1, M2, M3 e M4. RESULTADOS: O grupo da dopamina (G2) apresentou diminuição da pressão arterial média, da resistência vascular renal e da excreção de potássio. O grupo da solução hipertônica de cloreto de sódio (G3) apresentou aumento do índice cardíaco, do volume urinário, da depuração de sódio e de potássio, da excreção urinária de sódio e potássio e da excreção fracionária de sódio. No grupo da solução hipertônica de cloreto de sódio associada à dopamina (G4), ocorreu elevação da freqüência cardíaca, do índice cardíaco, do fluxo plasmático efetivo renal e da excreção urinária de sódio; ocorreu também diminuição do índice de resistência vascular sistêmica e do potássio plasmático. CONCLUSÕES: Deste estudo conclui-se que a solução hipertônica de cloreto de sódio foi capaz de melhorar as condições hemodinâmicas e, conseqüentemente, a função renal de cães sob restrição hídrica de 12 horas. O mesmo não aconteceu com a infusão de 2 µg.kg-1.min-1 de dopamina que, em situação similar, não causou aumento da diurese e da excreção de sódio.

Improving accuracy and speed of optimum-path forest classifier using combination of disjoint training subsets

The Optimum-Path Forest (OPF) classifier is a recent and promising method for pattern recognition, with a fast training algorithm and good accuracy results. Therefore, the investigation of a combining method for this kind of classifier can be important for many applications. In this paper we report a fast method to combine OPF-based classifiers trained with disjoint training subsets. Given a fixed number of subsets, the algorithm chooses random samples, without replacement, from the original training set. Each subset accuracy is improved by a learning procedure. The final decision is given by majority vote. Experiments with simulated and real data sets showed that the proposed combining method is more efficient and effective than naive approach provided some conditions. It was also showed that OPF training step runs faster for a series of small subsets than for the whole training set. The combining scheme was also designed to support parallel or distributed processing, speeding up the procedure even more. © 2011 Springer-Verlag.

Desenvolvimento de biossensores capacitivos constituídos de monocamadas peptídicas nanometricamente estruturadas

Pós-graduação em Biotecnologia - IQ

Optical trapping of a cube

The successful development and optimisation of optically-driven micromachines will be greatly enhanced by the ability to computationally model the optical forces and torques applied to such devices. In principle, this can be done by calculating the light-scattering properties of such devices. However, while fast methods exist for scattering calculations for spheres and axisymmetric particles, optically-driven micromachines will almost always be more geometrically complex. Fortunately, such micromachines will typically possess a high degree of symmetry, typically discrete rotational symmetry. Many current designs for optically-driven micromachines are also mirror-symmetric about a plane. We show how such symmetries can be used to reduce the computational time required by orders of magnitude. Similar improvements are also possible for other highly-symmetric objects such as crystals. We demonstrate the efficacy of such methods by modelling the optical trapping of a cube, and show that even simple shapes can function as optically-driven micromachines.

Otimização e validação de métodos empregando DLLME, SPE, HPLC-DAD e LC-ESI-MS/MS para determinação de agrotóxicos em água subterrânea

A preocupação com a poluição das águas por agrotóxicos tem aumentado, visto que aumentou o número de detecções de agrotóxicos em águas. A falta de avaliação da qualidade da água consumida pela população de áreas rurais onde não existe o abastecimento público de água potável, deve ser considerada, pois essas águas se encontram próximo a áreas de cultivo, onde há intensa aplicação de agrotóxicos. Nessas regiões, o abastecimento de água para as residências e para a irrigação é feito geralmente através das águas de poços. Neste trabalho, um método para determinação dos agrotóxicos carbofurano, clomazona, 2,4-D e tebuconazol em água subterrânea foi desenvolvido e validado. O método utilizou a Extração em Fase Sólida (SPE) e determinação por Cromatografia Líquida de Alta eficiência com Detecção por Arranjo de Diodos (HPLC-DAD) e confirmação por Cromatografia Líquida tandem Espectrometria de Massas (LC-MS/MS). Para a SPE utilizou-se cartuchos C18 de 200 mg, e eluição com 1 mL de metanol. Após a otimização dos parâmetros de extração e separação dos compostos, o método foi validado avaliando-se curva analítica, linearidade, limites de detecção e quantificação, precisão (repetitividade e precisão intermediária) e exatidão (recuperação). Todas as curvas analíticas apresentaram valores de r maiores que 0,99. Os LOQs para o método, considerando a etapa de pré-concentração de 250 vezes, foram de 0,2 µg L -1 para todos os agrotóxicos por HPLC-DAD e, por LC-MS/MS, 4,0 ng L -1 para clomazona, carbofurano e tebuconazol e de 40,0 ng L -1 para 2,4-D. As recuperações foram entre 60,3 e 107,7% para a repetitividade e entre 67,5 e 115,3% para a precisão intermediária, com RSD de 0,8 a 20,7% para todos os compostos por HPLC-DAD. Para o LC-MS/MS a precisão em termos de repetitividade, variou entre 0,97 e 20,7%, e as recuperações entre 67,0 e 108,9%. O método foi aplicado na determinação de agrotóxicos em amostras de águas subterrâneas durante um ano. Nas amostras foram detectados agrotóxicos em níveis de µg L -1 . Dentro do contexto atual da Química Analítica, de desenvolver métodos mais rápidos, que utilizem menor quantidade de solvente, de amostra e com altos fatores de enriquecimento, foi otimizado um método de extração para os agrotóxicos carbofurano, clomazona e tebuconazol utilizando a Microextração Líquido-Líquido Dispersiva (DLLME) e determinação por LC-MS/MS. Foram otimizados alguns parâmetros que influenciam no processo de extração, como: tipo e volume dos solventes dispersores e extratores, tempo de extração, força iônica e velocidade de centrifugação. Nas condições otimizadas, as recuperações para os níveis de concentração entre 0,02 e 2,0 g L -1 variaram entre 62,7 e 120,0%, com valores de RSD entre 1,9 e 9,1%. O LOQ do método foi de 0,02 µg L -1 para todos os compostos. Quando comparado com a SPE se demonstrou rápido, simples, de baixo custo, além de necessitar de menores volumes de amostra para determinação de agrotóxicos em águas. O método mostrou-se adequado à análise dos agrotóxicos em água subterrânea e todos os parâmetros de validação obtidos estão dentro dos limites sugeridos para validação de métodos cromatográficos

NMR methods for fast data acquisition

NMR spectroscopy has witnessed tremendous advancements in recent years with the development of new methodologies for structure determination and availability of high-field strength spectrometers equipped with cryogenic probes. Supported by these advancements, a new dimension in NMR research has emerged which aims to increase the speed with data is collected and analyzed. Several novel methodologies have been proposed in this direction. This review focuses on the principles on which these different approaches are based with an emphasis on G-matrix Fourier transform NMR spectroscopy.

Fast numerical methods for mixed, singular Helmholtz boundary value problems and Laplace eigenvalue problems - with applications to antenna design, sloshing, electromagnetic scattering and spectral geometry

This thesis presents a novel class of algorithms for the solution of scattering and eigenvalue problems on general two-dimensional domains under a variety of boundary conditions, including non-smooth domains and certain "Zaremba" boundary conditions - for which Dirichlet and Neumann conditions are specified on various portions of the domain boundary. The theoretical basis of the methods for the Zaremba problems on smooth domains concern detailed information, which is put forth for the first time in this thesis, about the singularity structure of solutions of the Laplace operator under boundary conditions of Zaremba type. The new methods, which are based on use of Green functions and integral equations, incorporate a number of algorithmic innovations, including a fast and robust eigenvalue-search algorithm, use of the Fourier Continuation method for regularization of all smooth-domain Zaremba singularities, and newly derived quadrature rules which give rise to high-order convergence even around singular points for the Zaremba problem. The resulting algorithms enjoy high-order convergence, and they can tackle a variety of elliptic problems under general boundary conditions, including, for example, eigenvalue problems, scattering problems, and, in particular, eigenfunction expansion for time-domain problems in non-separable physical domains with mixed boundary conditions.

Fast Lattice Green's Function Methods for Viscous Incompressible Flows on Unbounded Domains

In this thesis, a collection of novel numerical techniques culminating in a fast, parallel method for the direct numerical simulation of incompressible viscous flows around surfaces immersed in unbounded fluid domains is presented. At the core of all these techniques is the use of the fundamental solutions, or lattice Green’s functions, of discrete operators to solve inhomogeneous elliptic difference equations arising in the discretization of the three-dimensional incompressible Navier-Stokes equations on unbounded regular grids. In addition to automatically enforcing the natural free-space boundary conditions, these new lattice Green’s function techniques facilitate the implementation of robust staggered-Cartesian-grid flow solvers with efficient nodal distributions and fast multipole methods. The provable conservation and stability properties of the appropriately combined discretization and solution techniques ensure robust numerical solutions. Numerical experiments on thin vortex rings, low-aspect-ratio flat plates, and spheres are used verify the accuracy, physical fidelity, and computational efficiency of the present formulations.

Fast and effective analysis methods for fiber Raman amplifiers

A series of new single-step methods and their corresponding algorithms with automatic step size adjustment for model equations of fiber Raman amplifiers are proposed and compared in this paper. On the basis of the Newton-Raphson method, multiple shooting algorithms for the two-point boundary value problems involved in solving Raman amplifier propagation equations are constructed. A verified example shows that, compared with the traditional Runge-Kutta methods, the proposed methods can increase the accuracy by more than two orders of magnitude under the same conditions. The simulations for Raman amplifier propagation equations demonstrate that our methods can increase the computing speed by more than 5 times, extend the step size significantly, and improve the stability in comparison with the Dormand-Prince method. The numerical results show that the combination of the multiple shooting algorithms and the proposed methods has the capacity to rapidly and effectively solve the model equations of multipump Raman amplifiers under various conditions such as co-, counter- and bi-directionally pumped schemes, as well as dual-order pumped schemes.