Comparison of bottom-up protein identification methods

With the rapid development of proteomics, a number of different methods appeared for the basic task of protein identification. We made a simple comparison between a common liquid chromatography-tandem mass spectrometry (LC-MS/MS) workflow using an ion trap mass spectrometer and a combined LC-MS and LC-MS/MS method using Fourier transform ion cyclotron resonance (FTICR) mass spectrometry and accurate peptide masses. To compare the two methods for protein identification, we grew and extracted proteins from E. coli using established protocols. Cystines were reduced and alkylated, and proteins digested by trypsin. The resulting peptide mixtures were separated by reversed-phase liquid chromatography using a 4 h gradient from 0 to 50% acetonitrile over a C18 reversed-phase column. The LC separation was coupled on-line to either a Bruker Esquire HCT ion trap or a Bruker 7 tesla APEX-Qe Qh-FTICR hybrid mass spectrometer. Data-dependent Qh-FTICR-MS/MS spectra were acquired using the quadrupole mass filter and collisionally induced dissociation into the external hexapole trap. Proteins were in both schemes identified by Mascot MS/MS ion searches and the peptides identified from these proteins in the FTICR MS/MS data were used for automatic internal calibration of the FTICR-MS data, together with ambient polydimethylcyclosiloxane ions.

Application of a hybrid tracking algorithm to motion analysis

An algorithm for tracking multiple feature positions in a dynamic image sequence is presented. This is achieved using a combination of two trajectory-based methods, with the resulting hybrid algorithm exhibiting the advantages of both. An optimizing exchange algorithm is described which enables short feature paths to be tracked without prior knowledge of the motion being studied. The resulting partial trajectories are then used to initialize a fast predictor algorithm which is capable of rapidly tracking multiple feature paths. As this predictor algorithm becomes tuned to the feature positions being tracked, it is shown how the location of occluded or poorly detected features can be predicted. The results of applying this tracking algorithm to data obtained from real-world scenes are then presented.

J-measure based hybrid pruning for complexity reduction in classification rules

Prism is a modular classification rule generation method based on the ‘separate and conquer’ approach that is alternative to the rule induction approach using decision trees also known as ‘divide and conquer’. Prism often achieves a similar level of classification accuracy compared with decision trees, but tends to produce a more compact noise tolerant set of classification rules. As with other classification rule generation methods, a principle problem arising with Prism is that of overfitting due to over-specialised rules. In addition, over-specialised rules increase the associated computational complexity. These problems can be solved by pruning methods. For the Prism method, two pruning algorithms have been introduced recently for reducing overfitting of classification rules - J-pruning and Jmax-pruning. Both algorithms are based on the J-measure, an information theoretic means for quantifying the theoretical information content of a rule. Jmax-pruning attempts to exploit the J-measure to its full potential because J-pruning does not actually achieve this and may even lead to underfitting. A series of experiments have proved that Jmax-pruning may outperform J-pruning in reducing overfitting. However, Jmax-pruning is computationally relatively expensive and may also lead to underfitting. This paper reviews the Prism method and the two existing pruning algorithms above. It also proposes a novel pruning algorithm called Jmid-pruning. The latter is based on the J-measure and it reduces overfitting to a similar level as the other two algorithms but is better in avoiding underfitting and unnecessary computational effort. The authors conduct an experimental study on the performance of the Jmid-pruning algorithm in terms of classification accuracy and computational efficiency. The algorithm is also evaluated comparatively with the J-pruning and Jmax-pruning algorithms.

Acoustic scattering : high frequency boundary element methods and unified transform methods

We describe some recent advances in the numerical solution of acoustic scattering problems. A major focus of the paper is the efficient solution of high frequency scattering problems via hybrid numerical-asymptotic boundary element methods. We also make connections to the unified transform method due to A. S. Fokas and co-authors, analysing particular instances of this method, proposed by J. A. De-Santo and co-authors, for problems of acoustic scattering by diffraction gratings.

A new hybrid BCI paradigm based on P300 and SSVEP

Background: P300 and steady-state visual evoked potential(SSVEP) approaches have been widely used for brain–computer interface (BCI) systems. However, neither of these approaches can work for all subjects. Some groups have reported that a hybrid BCI that combines two or more approaches might provide BCI functionality to more users. Hybrid P300/SSVEP BCIs have only recently been developed and validated, and very few avenues to improve performance have been explored. New method: The present study compares an established hybrid P300/SSVEP BCIs paradigm to a new paradigm in which shape changing, instead of color changing, is adopted for P300 evocation to decrease the degradation on SSVEP strength. Result: The result shows that the new hybrid paradigm presented in this paper yields much better performance than the normal hybrid paradigm. Comparison with existing method: A performance increase of nearly 20% in SSVEP classification is achieved using the new hybrid paradigm in comparison with the normal hybrid paradigm.Allthe paradigms except the normal hybrid paradigm used in this paper obtain 100% accuracy in P300 classification. Conclusions: The new hybrid P300/SSVEP BCIs paradigm in which shape changing, instead of color changing, could obtain as high classification accuracy of SSVEP as the traditional SSVEP paradigm and could obtain as high classification accuracy of P300 as the traditional P300 paradigm. P300 did not interfere with the SSVEP response using the new hybrid paradigm presented in this paper, which was superior to the normal hybrid P300/SSVEP paradigm.

Methods to assess the effectiveness of naturally ventilated classrooms in Gauteng, South Africa

There is a tendency to reduce ventilation rates and natural or hybrid ventilation systems to ensure the conservation of energy in school buildings. However, high indoor pollutant concentration, due to natural or hybrid ventilation systems may have a significant adverse impact on the health and academic performance of pupils and students. Reviewed evidence shows that this can be detrimental to health and wellbeing in schools because of the learner density within a small area, eventually indicating that CO2 concentrations can rise to very high levels (about 4000 ppm) in classrooms during occupancy periods. In South Africa’s naturally ventilated classrooms, it is not clear whether the environmental conditions are conducive for learning. In addition, natural ventilation will be minimized given the fact that in cold, wet or windy weather, doors and windows will commonly remain closed. Evidence from literature based studies indicates that the significance of ventilation techniques is not understood satisfactorily and additional information concerning naturally ventilated schools has to be provided for better design and policy formulation. To develop a thorough understanding of the environments in classrooms, many other parameters have to be considered as well, such as outdoor air quality, CO2 concentrations, temperature and relative humidity and safety issues that may be important drawbacks for naturally ventilated schools. The aim of this paper is to develop a conceptual understanding of methods that can be implemented to assess the effectiveness of naturally ventilated classrooms in Gauteng, South Africa. A theoretical concept with an embedded practical methodology have been proposed for the research programme to investigate the relationship between ventilation rates and learning in schools in Gauteng , a province in South Africa. It is important that existing and future school buildings must include adequate outdoor ventilation, control of moisture, and avoidance of indoor exposures to microbiologic and chemical substances considered likely to have adverse effects in South Africa. Adequate ventilation in classrooms is necessary to reduce and/or eradicate the transmission of indoor pollutants.

A hybrid approach to learn with imbalanced classes using evolutionary algorithms

There is an increasing interest in the application of Evolutionary Algorithms (EAs) to induce classification rules. This hybrid approach can benefit areas where classical methods for rule induction have not been very successful. One example is the induction of classification rules in imbalanced domains. Imbalanced data occur when one or more classes heavily outnumber other classes. Frequently, classical machine learning (ML) classifiers are not able to learn in the presence of imbalanced data sets, inducing classification models that always predict the most numerous classes. In this work, we propose a novel hybrid approach to deal with this problem. We create several balanced data sets with all minority class cases and a random sample of majority class cases. These balanced data sets are fed to classical ML systems that produce rule sets. The rule sets are combined creating a pool of rules and an EA is used to build a classifier from this pool of rules. This hybrid approach has some advantages over undersampling, since it reduces the amount of discarded information, and some advantages over oversampling, since it avoids overfitting. The proposed approach was experimentally analysed and the experimental results show an improvement in the classification performance measured as the area under the receiver operating characteristics (ROC) curve.

A Robust, Fully Adaptive Hybrid Level-Set/Front-Tracking Method for Two-Phase Flows with an Accurate Surface Tension Computation

We present a variable time step, fully adaptive in space, hybrid method for the accurate simulation of incompressible two-phase flows in the presence of surface tension in two dimensions. The method is based on the hybrid level set/front-tracking approach proposed in [H. D. Ceniceros and A. M. Roma, J. Comput. Phys., 205, 391400, 2005]. Geometric, interfacial quantities are computed from front-tracking via the immersed-boundary setting while the signed distance (level set) function, which is evaluated fast and to machine precision, is used as a fluid indicator. The surface tension force is obtained by employing the mixed Eulerian/Lagrangian representation introduced in [S. Shin, S. I. Abdel-Khalik, V. Daru and D. Juric, J. Comput. Phys., 203, 493-516, 2005] whose success for greatly reducing parasitic currents has been demonstrated. The use of our accurate fluid indicator together with effective Lagrangian marker control enhance this parasitic current reduction by several orders of magnitude. To resolve accurately and efficiently sharp gradients and salient flow features we employ dynamic, adaptive mesh refinements. This spatial adaption is used in concert with a dynamic control of the distribution of the Lagrangian nodes along the fluid interface and a variable time step, linearly implicit time integration scheme. We present numerical examples designed to test the capabilities and performance of the proposed approach as well as three applications: the long-time evolution of a fluid interface undergoing Rayleigh-Taylor instability, an example of bubble ascending dynamics, and a drop impacting on a free interface whose dynamics we compare with both existing numerical and experimental data.

An effortless hybrid method to solve economic load dispatch problem in power systems

This paper proposes a new approach and coding scheme for solving economic dispatch problems (ED) in power systems through an effortless hybrid method (EHM). This novel coding scheme can effectively prevent futile searching and also prevents obtaining infeasible solutions through the application of stochastic search methods, consequently dramatically improves search efficiency and solution quality. The dominant constraint of an economic dispatch problem is power balance. The operational constraints, such as generation limitations, ramp rate limits, prohibited operating zones (POZ), network loss are considered for practical operation. Firstly, in the EHM procedure, the output of generator is obtained with a lambda iteration method and without considering POZ and later in a genetic based algorithm this constraint is satisfied. To demonstrate its efficiency, feasibility and fastness, the EHM algorithm was applied to solve constrained ED problems of power systems with 6 and 15 units. The simulation results obtained from the EHM were compared to those achieved from previous literature in terms of solution quality and computational efficiency. Results reveal that the superiority of this method in both aspects of financial and CPU time. (C) 2011 Elsevier Ltd. All rights reserved.

Modular hybrid total hip arthroplasty. Experimental study in dogs

Background: This prospective experimental study evaluated the surgical procedure and results of modular hybrid total hip arthroplasty in dogs.Methods: Ten skeletally mature healthy mongrel dogs with weights varying between 19 and 27 kg were used. Cemented modular femoral stems and uncemented porous-coated acetabular cups were employed. Clinical and radiographic evaluations were performed before surgery and at 30, 60, 90, 120, 180 and 360 days post-operation.Results: Excellent weight bearing was noticed in the operated limb in seven dogs. Dislocation followed by loosening of the prosthesis was noticed in two dogs, which were therefore properly treated with a femoral head osteotomy. Femoral fracture occurred in one dog, which was promptly treated with full implant removal and femoral osteosynthesis.Conclusions: The canine modular hybrid total hip arthroplasty provided excellent functionality of the operated limb.

Hybrid layer thickness and resin tag length of a self-etching adhesive bonded to sound dentin

Objectives: the purpose of this study is to employ optical microscopy to measure the thickness of the hybrid layer and the penetration (tags) of an aggressive self-etching adhesive system into sound dentin.Methods: occtusat cavities were prepared in 40 extracted human posterior teeth. The prepared teeth were randomly assigned to four experimental groups with 10 specimens each. The self-etching adhesive system Adper Prompt L-Pop was applied to the dentin surface as follows: Group 1: cavosurface enamel was etched for 60 s and dentin for 20 s with 35% phosphoric acid get, immediately followed by application of the self -etching adhesive with a brush to the entire cavity for 15 s; Groups 2, 3, and 4: no pre-etching was performed, and the self -etching adhesive was applied to both enamel and dentin for 15, 30 and 45 s, respectively. After curing, the cavities were fitted with composite resin Fittek Z250. Afterwards, the teeth were decalcified and the restorations were carefully removed for later embedding in paraffin. The specimens were serially sectioned at 6 mu m of thickness and sequentially mounted in glass slides. These sections were stained with Brown and Brenn staining for posterior analysis and measurement of the hybrid layer and resin tags on a tight microscope with a micrometric ocular 40/075. The results were submitted to analysis of variance at the 5% level.Results: whenever there was significance, the Tukey test was applied at the 5% level. The specimens receiving application of acid etching before the selfetching. adhesive displayed a larger thickness of the hybrid layer; on the other hand, specimens receiving only application of the self -etching adhesive on dentin for 15, 30 and 45 s exhibited similar thickness of the hybrid layer. As regards the resin tags, no statistically significant differences could be found between the study groups.Conclusions: it could be concluded that the increase in the time of application of the self-etching adhesive Adper Prompt L-Pop did not significantly influence the formation and thickness of hybrid layer, as well as its penetration into the sound dentin surface. (c) 2005 Elsevier Ltd. All rights reserved.

Molecular diagnostic methods for identifying Serrasalmid fish (Pacu, Pirapitinga, and Tambaqui) and their hybrids in the Brazilian aquaculture industry

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

In vitro evaluation of dental bleaching effectiveness using hybrid lights activation

OBJETIVO: Avaliar se fontes de luz aumentam a eficácia do peróxido de hidrogênio na técnica de clareamento profissional. METODOLOGIA: Foram empregados 60 dentes incisivos bovinos, com dimensões coronárias e radiculares padronizadas a partir do limite amelo-cementário, sendo descartada a porção lingual. Os corpos-de-prova (cp) foram limpos em ultra-som por 20 min e a dentina condicionada com H3PO4 a 38% por 15 s, sendo os (cp) imersos em solução de café solúvel a 25% por duas semanas. A dentina foi impermeabilizada com esmalte e os (cp) divididos em 5 grupos, sendo a cor inicial mensurada através do espectofotômetro-EasyShade (VITA). Todos os (cp) receberam três aplicações por 10 min do gel clareador Opalescence Xtra-Boost (Ultradent) conforme segue: Grupo 1 - controle, não recebeu fotoativação, Grupo 2 - ativado com luz halôgena, Grupo 3 - ativado com LED azul/LASER, Grupo 4 - ativado com LED verde/LASER e Grupo 5 - ativado com LED vermelho. Após o clareamento foi mensurada a variação de cor E, a*, b*e L* e as referentes à escala de cor Vita Clássico. Os dados foram submetidos à análise de variância, teste de Tukey e de Dunn (α=5%). RESULTADOS: A diferença geral da cor foi reduzida quando se empregou LED Azul e Luz Halógena, sendo que o desempenho do peróxido de hidrogênio a 38% foi intensificado dependendo da fonte de luz utilizada. A avaliação quantitativa de cor, obtida por espectrofotômetro e pela escala de cor Vita Clássico, foram coincidentes. CONCLUSÃO: O tipo de fonte de luz empregada interfere na eficácia do agente clareador.

Assessment of the effectiveness of light-emitting diode and diode laser hybrid light sources to intensify dental bleaching treatment

Objective. To evaluate the effectiveness of the color change of hybrid light-emitting diode (LED) and low-intensity infrared diode laser devices for activating dental bleaching and to verify the occurrence of a color regression with time. Material and methods. A total of 180 specimens obtained from human premolars were immersed in a coffee solution for 15 days for darkening and then divided into eight experimental groups (n = 20 in each) as follows: G1, bleaching without light; G2, bleaching with halogen light; G3, bleaching with a blue LED (1000 mW/470 nm) and a laser device (120 mW/795 nm) simultaneously; G4, bleaching with an LED emitting blue light (1000 mW/470 nm); G5, bleaching with a blue LED (800 mW/470 nm) and a laser device (500 mW/830 nm) simultaneously; G6, bleaching with a blue LED device (800 mW); G7, bleaching with a green LED (600 mW/530 nm) and a laser device (120 mW/795 nm) simultaneously; and G8, bleaching with a green LED (600 mW). Three measurements were performed (at baseline and 14 days and 12 months after bleaching) using a Vita Easyshade spectrophotometer. The data were submitted to two-way ANOVA and a Tukey test. Results. All groups showed significantly higher Delta E values than Group G1, with the exception of Group G8. Variations in the Delta E values at 14 days were significant when compared with those obtained at baseline and after 12 months. Conclusions. Light activation of the bleaching gel provided faster and more intense bleaching than use of the bleaching gel without light activation. Combinations of low-intensity diode lasers are ineffective as a bleaching gel activator. Color regression was observed after 12 months of storage.