Detection and enumeration of sulphate-reducing bacteria in estuarine sediments by competitive PCR

The distribution of sulphate-reducing bacteria (SRB) in the sediments of the Colne River estuary, Essex, UK covering different saline concentrations of sediment porewater was investigated by the use of quantitative competitive PCR. Here, we show that a new PCR primer set and a new quantitative method using PCR are useful tools for the detection and the enumeration of SRB in natural environments. A PCR primer set selective for the dissimilatory sulphite reductase gene (dsr) of SRB was designed. PCR amplification using the single set of dsr-specific primers resulted in PCR products of the expected size from all 27 SRB strains tested, including Gram-negative and positive species. Sixty clones derived from sediment DNA using the primers were sequenced and all were closely related with the predicted dsr of SRB. These results indicate that PCR using the newly designed primer set are useful for the selective detection of SRB from a natural sample. This primer set was used to estimate cell numbers by dsr selective competitive PCR using a competitor, which was about 20% shorter than the targeted region of dsr. This procedure was applied to sediment samples from the River Colne estuary, Essex, UK together with simultaneous measurement of in situ rates of sulphate reduction. High densities of SRB ranging from 0.2 - 5.7 × 108 cells ml-1 wet sediment were estimated by the competitive PCR assuming that all SRB have a single copy of dsr. Using these estimates cell specific sulphate reduction rates of 10-17 to 10-15 mol of SO42- cell-1 day-1 were calculated, which is within the range of, or lower than, those previously reported for pure cultures of SRB. Our results show that the newly developed competitive PCR technique targeted to dsr is a powerful tool for rapid and reproducible estimation of SRB numbers in situ and is superior to the use of culture-dependent techniques.

Performance of GPRS coding scheme detection under severe multipath and co-channel interference as a function of soft-bit width

The General Packet Radio Service (GPRS) has been developed for the mobile radio environment to allow the migration from the traditional circuit switched connection to a more efficient packet based communication link particularly for data transfer. GPRS requires the addition of not only the GPRS software protocol stack, but also more baseband functionality for the mobile as new coding schemes have be en defined, uplink status flag detection, multislot operation and dynamic coding scheme detect. This paper concentrates on evaluating the performance of the GPRS coding scheme detection methods in the presence of a multipath fading channel with a single co-channel interferer as a function of various soft-bit data widths. It has been found that compressing the soft-bit data widths from the output of the equalizer to save memory can influence the likelihood decision of the coding scheme detect function and hence contribute to the overall performance loss of the system. Coding scheme detection errors can therefore force the channel decoder to either select the incorrect decoding scheme or have no clear decision which coding scheme to use resulting in the decoded radio block failing the block check sequence and contribute to the block error rate. For correct performance simulation, the performance of the full coding scheme detection must be taken into account.

Detection of somaclonal variation during cocoa somatic embryogenesis characterised using cleaved amplified polymorphic sequence and the new freeware Artbio

The scarcity and stochastic nature of genetic mutations presents a significant challenge for scientists seeking to characterise de novo mutation frequency at specific loci. Such mutations can be particularly numerous during regeneration of plants from in vitro culture and can undermine the value of germplasm conservation efforts. We used cleaved amplified polymorphic sequence (CAPS) analysis to characterise new mutations amongst a clonal population of cocoa plants regenerated via a somatic embryogenesis protocol used previously for cocoa cryopreservation. Efficacy of the CAPS system for mutation detection was greatly improved after an ‘a priori’ in silico screen of reference target sequences for actual and potential restriction enzyme recognition sites using a new freely available software called Artbio. Artbio surveys known sequences for existing restriction enzyme recognition sites but also identifies all single nucleotide polymorphism (SNP) deviations from such motifs. Using this software, we performed an in silico screen of seven loci for restriction sites and their potential mutant SNP variants that were possible from 21 restriction enzymes. The four most informative locus-enzyme combinations were then used to survey the regenerant populations for de novo mutants. We characterised the pattern of point mutations and, using the outputs of Artbio, calculated the ratio of base substitution in 114 somatic embryo-derived cocoa regenerants originating from two explant genotypes. We found 49 polymorphisms, comprising 26.3% of the samples screened, with an inferred rate of 2.8 × 10−3 substitutions/screened base. This elevated rate is of a similar order of magnitude to previous reports of de novo microsatellite length mutations arising in the crop and suggests caution should be exercised when applying somatic embryogenesis for the conservation of plant germplasm.

Detection and identification of species-specific bacteria associated with synanthropic mites

Internal bacterial communities of synanthropic mites Acarus siro, Dermatophagoides farinae, Lepidoglyphus destructor, and Tyrophagus putrescentiae (Acari: Astigmata) were analyzed by culturing and culture-independent approaches from specimens obtained from laboratory colonies. Homogenates of surface-sterilized mites were used for cultivation on non-selective agar and DNA extraction. Isolated bacteria were identified by sequencing of the 16S rRNA gene. PCR amplified 16S rRNA genes were analyzed by terminal restriction fragment length polymorphism analysis (T-RFLP) and cloning sequencing. Fluorescence in situ hybridization using universal bacterial probes was used for direct bacterial localization. T-RFLP analysis of 16S rRNA gene revealed distinct species-specific bacterial communities. The results were further confirmed by cloning and sequencing (284 clones). L. destructor and D. farinae showed more diverse communities then A. siro and T. putrescentiae. In the cultivated part of the community, the mean CFUs from four mite species ranged from 5.2 × 102 to 1.4 × 103 per mite. D. farinae had significantly higher CFUs than the other species. Bacteria were located in the digestive and reproductive tract, parenchymatical tissue, and in bacteriocytes. Among the clones, Bartonella-like bacteria occurring in A. siro and T. putresecentiae represented a distinct group related to Bartonellaceae and to Bartonella-like symbionts of ants. The clones of high similarity to Xenorhabdus cabanillasii were found in L. destructor and D. farinae, and one clone related to Photorhabdus temperata in A. siro. Members of Sphingobacteriales cloned from D. farinae and A. siro clustered with the sequences of “Candidatus Cardinium hertigii” and as a separate novel cluster.

Use of the checkerboard DNA-DNA hybridisation technique for in vivo detection of cariogenic microorganisms on metallic brackets, with or without use of an antimicrobial agent

Objective: Using checkerboard DNA-DNA hybridisation (CDDH) assay, this randomised clinical study evaluated the contamination of metallic brackets by four cariogenic bacterial strains (Streptococcus mutans, Streptococcus sobrinus, Lactobacillus casei and Lactobacillus acidophilus) and the efficacy of 0.12% chlorhexidine gluconate (CHX) mouthwashes in reducing bacterial contamination. Methods: Thirty-nine 11-33-year-old patients under treatment with fixed orthodontic appliances were enrolled in the study and had 2 new metallic brackets bonded to premolars. Nineteen patients used a 0.12% CHX mouthwash (Periogard (R)) and 20 patients used a placebo mouthwash (control) twice a week. After 30 days, the brackets were removed and samples were obtained for analysis by CDDH. Data were analysed statistically by the Kruskal-Wallis test (alpha = 0.05) using the SAS software. Results: S. mutans, S. sobrinus, L. casei and L. acidophilus were detected in 100% of the samples from both groups. However, brackets of the control group were more heavily contaminated by S. mutans and S. sobrinus (P < 0.01). In the experimental group, although all counts decreased after rinsing with the chlorhexidine solution, there was significant difference only for S. mutans (P = 0.03). Conclusions: The use of 0.12% chlorhexidine gluconate mouthwashes can be useful in clinical practice to reduce the levels of cariogenic microorganisms in patients under treatment with fixed orthodontic appliances. (C) 2011 Elsevier Ltd. All rights reserved.

Topological triangle characterization with application to object detection from images

A novel mathematical framework inspired on Morse Theory for topological triangle characterization in 2D meshes is introduced that is useful for applications involving the creation of mesh models of objects whose geometry is not known a priori. The framework guarantees a precise control of topological changes introduced as a result of triangle insertion/removal operations and enables the definition of intuitive high-level operators for managing the mesh while keeping its topological integrity. An application is described in the implementation of an innovative approach for the detection of 2D objects from images that integrates the topological control enabled by geometric modeling with traditional image processing techniques. (C) 2008 Published by Elsevier B.V.

Advanced functionality for radio analysis in the Offline software framework of the Pierre Auger Observatory

The advent of the Auger Engineering Radio Array (AERA) necessitates the development of a powerful framework for the analysis of radio measurements of cosmic ray air showers. As AERA performs ""radio-hybrid"" measurements of air shower radio emission in coincidence with the surface particle detectors and fluorescence telescopes of the Pierre Auger Observatory, the radio analysis functionality had to be incorporated in the existing hybrid analysis solutions for fluorescence and surface detector data. This goal has been achieved in a natural way by extending the existing Auger Offline software framework with radio functionality. In this article, we lay out the design, highlights and features of the radio extension implemented in the Auger Offline framework. Its functionality has achieved a high degree of sophistication and offers advanced features such as vectorial reconstruction of the electric field, advanced signal processing algorithms, a transparent and efficient handling of FFTs, a very detailed simulation of detector effects, and the read-in of multiple data formats including data from various radio simulation codes. The source code of this radio functionality can be made available to interested parties on request. (C) 2011 Elsevier B.V. All rights reserved.

Automatic detection of thermal damage in grinding process by artificial neural network

Esse trabalho tem por objetivo o desenvolvimento de um sistema inteligente para detecção da queima no processo de retificação tangencial plana através da utilização de uma rede neural perceptron multi camadas, treinada para generalizar o processo e, conseqüentemente, obter o limiar de queima. em geral, a ocorrência da queima no processo de retificação pode ser detectada pelos parâmetros DPO e FKS. Porém esses parâmetros não são eficientes nas condições de usinagem usadas nesse trabalho. Os sinais de emissão acústica e potência elétrica do motor de acionamento do rebolo são variáveis de entrada e a variável de saída é a ocorrência da queima. No trabalho experimental, foram empregados um tipo de aço (ABNT 1045 temperado) e um tipo de rebolo denominado TARGA, modelo ART 3TG80.3 NVHB.

Detection and classification of voltage disturbances using a Fuzzy-ARTMAP-wavelet network

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

Uma abordagem anotativa para gerência de variabilidade em linhas de processos de software: concepção, implementação e avaliação

Nowadays, the importance of using software processes is already consolidated and is considered fundamental to the success of software development projects. Large and medium software projects demand the definition and continuous improvement of software processes in order to promote the productive development of high-quality software. Customizing and evolving existing software processes to address the variety of scenarios, technologies, culture and scale is a recurrent challenge required by the software industry. It involves the adaptation of software process models for the reality of their projects. Besides, it must also promote the reuse of past experiences in the definition and development of software processes for the new projects. The adequate management and execution of software processes can bring a better quality and productivity to the produced software systems. This work aimed to explore the use and adaptation of consolidated software product lines techniques to promote the management of the variabilities of software process families. In order to achieve this aim: (i) a systematic literature review is conducted to identify and characterize variability management approaches for software processes; (ii) an annotative approach for the variability management of software process lines is proposed and developed; and finally (iii) empirical studies and a controlled experiment assess and compare the proposed annotative approach against a compositional one. One study a comparative qualitative study analyzed the annotative and compositional approaches from different perspectives, such as: modularity, traceability, error detection, granularity, uniformity, adoption, and systematic variability management. Another study a comparative quantitative study has considered internal attributes of the specification of software process lines, such as modularity, size and complexity. Finally, the last study a controlled experiment evaluated the effort to use and the understandability of the investigated approaches when modeling and evolving specifications of software process lines. The studies bring evidences of several benefits of the annotative approach, and the potential of integration with the compositional approach, to assist the variability management of software process lines

Inflammatory cytokine mRNA detection by real time PCR in chorioamniotic membranes from pregnant women with preterm premature rupture of membranes

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

Detection of periapical lesion development by conventional radiography or computed tomography

Objective. The aim of this study was to detect the development of experimentally induced periapical lesions using conventional radiography and computed tomography.Study design. The root canals of dogs' teeth were exposed to the oral environment for 7 days for contamination and then sealed for 7 days (GI), 15 days (GII), 30 days (GIII), and 60 days (GIV). Immediately after each experimental period, radiographs and tomograms were taken in order to detect the occurrence of periapical bone resorption. The periapical radiographs were digitized and areas of bone resorption were measured using the VIXWIN 2000 software. Scores were assigned to the tomograms based on the progression of periapical bone resorption. The specimens were evaluated by calibrated examiners who were blinded to the groups. The radiographic results were analyzed by ANOVA and Tukey's test (P <.05) and the tomographic results were analyzed by Kruskal-Wallis and Dunn's tests (P <.05).Results. The radiographic evaluation did not reveal periapical lesions at the 7-day control. Lesions were radiographically visible at 15 and 30 days (47.4% and 77.8% of the cases, respectively) and presented similar dimensions (P <.05). At 60 days, lesions were detected in all specimens, presenting larger dimensions than those of the earlier evaluation periods (P <.05). The tomographic evaluation detected lesions at 7 and 15 days (32.5% and 83.3% of the cases, respectively). Lesions were detected in all specimens at the 30- and 60-day periods, when the greatest values of bone resorption were observed (P <.05).Conclusions. Tomography was able to detect periapical lesion development in its initial stages, even when the lesions were undetectable radiographically.

Accuracy of Digital Images in the Detection of Marginal Micro leakage: An In Vitro Study

Purpose: To evaluate the accuracy of Image Tool Software 3.0 (ITS 3.0) to detect marginal microleakage using the stereomicroscope as the validation criterion and ITS 3.0 as the tool under study.Materials and Methods: Class V cavities were prepared at the cementoenamel junction of 61 bovine incisors, and 53 halves of them were used. Using the stereomicroscope, microleakage was classified dichotomously: presence or absence. Next, ITS 3.0 was used to obtain measurements of the microleakage, so that 0.75 was taken as the cut-off point, and values equal to or greater than 0.75 indicated its presence, while values between 0.00 and 0.75 indicated its absence. Sensitivity and specificity were calculated by point and given as 95% confidence interval (95% CI).Results: The accuracy of the ITS 3.0 was verified with a sensitivity of 0.95 (95% CI: 0.89 to 1.00) and a specificity of 0.92 (95% CI: 0.84 to 0.99).Conclusion: Digital diagnosis of marginal microleakage using ITS 3.0 was sensitive and specific.