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J S Almeida

Publications and source records attributed to J S Almeida.

At least 19 recordsLinked to original sources
PubMed2006

Illustration of a common framework for relating multiple typing methods by application to macrolide-resistant Streptococcus pyogenes.

The studies that correlate the results obtained by different typing methodologies rely solely on qualitative comparisons of the groups defined by each methodology. We propose a framework of measures for the quantitative assessment of correspondences between different typing methods as a first step to the global mapping of type equivalences. A collection of 325 macrolide-resistant Streptococcus pyogenes isolates associated with pharyngitis cases in Portugal was used to benchmark the proposed measures. All isolates were characterized by macrolide resistance phenotyping, T serotyping, emm sequence typing, and pulsed-field gel electrophoresis (PFGE), using SmaI or Cfr9I and SfiI. A subset of 41 isolates, representing each PFGE cluster, was also characterized by multilocus sequence typing (MLST). The application of Adjusted Rand and Wallace indices allowed the evaluation of the strength and the directionality of the correspondences between the various typing methods and showed that if PFGE or MLST data are available one can confidently predict the emm type (Wallace coefficients of 0.952 for both methods). In contrast, emm typing was a poor predictor of PFGE cluster or MLST sequence type (Wallace coefficients of 0.803 and 0.655, respectively). This was confirmed by the analysis of the larger data set available from http://spyogenes.mlst.net and underscores the necessity of performing PFGE or MLST to unambiguously define clones in S. pyogenes.

Anti-Bacterial Agents↗
PubMed2005

Natural history of drug-resistant clones of Streptococcus pneumoniae colonizing healthy children in Portugal.

A total of 3,539 Streptococcus pneumoniae (Pn) were recovered from 4,969 nasopharyngeal samples of children attending 13 day-care centers (DCCs) located in Lisbon, Portugal, during a surveillance study from January, 2001, through March, 2003, integrated in the European intervention project (EURIS, European Resistance Intervention Study). All Pn isolates were tested for anti-biotyping and drug-resistant pneumococci (DRPn) were further tested by serotyping and pulsed-field gel electrophoresis (PFGE). Overall carriage of Pn was very high (71.2%) and 39.9% of the isolates were resistant to antimicrobials (22.5% with decreased susceptibility to penicillin and 17.4% susceptible to penicillin and resistant to other antimicrobials). Serotypes 6B, 14, 23 F, 19F, and 19 A were prevalent among the 1,287 DRPn and 5.8% of the isolates were non-typeable. Eighty PFGE patterns were identified among 1,285 DRPn, and 93.1% of the DRPn belonged to 26 major clonal types that comprised: Pneumococcal Molecular Epidemiology Network (PMEN) clones (76.3%), Portuguese (PT)-DCC clones, previously detected in 1996-1999 (14.3%), and EURIS PT-DCC new clones, identified for the first time in the EURIS study, during 2001-2003 (9.4%). Comparing with previous Portuguese surveillance studies carried out since 1996, we observed that carriage increased from 47% to 71%, but no major changes were detected on the prevalence of pneumococcal serotypes. Moreover, although PMEN clones were predominant in all DCCs, in the present study the majority of them were gradually decreasing in time whereas several PT-DCC and new clones seemed to be increasing.

Anti-Bacterial Agents↗
PubMed2005

Assessment of band-based similarity coefficients for automatic type and subtype classification of microbial isolates analyzed by pulsed-field gel electrophoresis.

Pulsed-field gel electrophoresis (PFGE) has been the typing method of choice for strain identification in epidemiological studies of several bacterial species of medical importance. The usual procedure for the comparison of strains and assignment of strain type and subtype relies on visual assessment of band difference number, followed by an incremental assignment to the group hosting the most similar type previously seen. Band-based similarity coefficients, such as the Dice or the Jaccard coefficient, are then used for dendrogram construction, which provides a quantitative assessment of strain similarity. PFGE type assignment is based on the definition of a threshold linkage value, below which strains are assigned to the same group. This is typically performed empirically by inspecting the hierarchical cluster analysis dendrogram containing the strains of interest. This approach has the problem that the threshold value selected is dependent on the linkage method used for dendrogram construction. Furthermore, the use of a linkage method skews the original similarity values between strains. In this paper we assess the goodness of classification of several band-based similarity coefficients by comparing it with the band difference number for PFGE type and subtype classification using receiver operating characteristic curves. The procedure described was applied to a collection of PFGE results for 1,798 isolates of Streptococcus pneumoniae, which documented 96 types and 396 subtypes. The band-based similarity coefficients were found to perform equally well for type classification, but with different proportions of false-positive and false-negative classifications in their minimal false discovery rate when they were used for subtype classification.

Bacterial Typing Techniques↗
PubMed2005

Trends in drug resistance, serotypes, and molecular types of Streptococcus pneumoniae colonizing preschool-age children attending day care centers in Lisbon, Portugal: a summary of 4 years of annual surveillance.

Of the nasopharyngeal cultures recovered from 942 day care center (DCC) attendees in Lisbon, Portugal, 591 (62%) yielded Streptococcus pneumoniae during a surveillance performed in February and March of 1999. Forty percent of the isolates were resistant to one or more antimicrobial agents. In particular, 2% were penicillin resistant and 20% had intermediate penicillin resistance. Multidrug resistance to macrolides, lincosamides, and tetracycline was the most frequent antibiotype (17% of all isolates). Serotyping and molecular typing by pulsed-field gel electrophoresis were performed for 202 out of 237 drug-resistant pneumococci (DRPn). The most frequent serotypes were 6B (26%), 14 (22%), 19F (16%), 23F (10%), and nontypeable (12%). The majority (67%) of the DRPn strains were representatives of nine international clones included in the Pneumococcal Molecular Epidemiology Network; eight of them had been detected in previous studies. Fourteen novel clones were identified, corresponding to 26% of the DRPn strains. The remaining 7% of the strains were local clones detected in our previous studies. Comparison with studies conducted since 1996 in Portuguese DCCs identified several trends: (i) the rate of DRPn frequency has fluctuated between 40 and 50%; (ii) the serotypes most frequently recovered have remained the same; (iii) nontypeable strains appear to be increasing in frequency; and (iv) a clone of serotype 33F emerged in 1999. Together, our observations highlight that the nasopharynxes of children in DCCs are a melting pot of successful DRPn clones that are important to study and monitor if we aim to gain a better understanding on the epidemiology of this pathogen.

Bacterial Typing Techniques↗
PubMed2005

Modelling of the extractive membrane bioreactor process based on natural fluorescence fingerprints and process operation history.

A method for non-mechanistic and non-linear modelling of complex biological processes is presented, using the example of the extractive membrane bioreactor (EMB). The model is based on artificial neural networks (ANN), which are able to predict the state of the process from a combination of reactor operational parameters and natural fluorescence fingerprints. Current as well as historic process operation is included in the ANN input vector, in order to account for lag-times within the reactor system and for biofilm dynamics that are dependent on process history. The model is especially relevant for practitioners, as it does not require assumptions on underlying process mechanisms, and it relies on routinely available operational data and on an easy-to-install, non-invasive, in-situ, on-line monitoring method. Moreover, it focuses on the prediction of overall process performance parameters, which are of immediate relevance in practice. The developed model was able to predict the process state very well. Sensitivity analysis revealed that the main impact on process performance stems from process operation rather than the physiological state of the biological culture, and that in the EMB configuration employed process operation history decisively impacts on the process outcome.

Biofilms↗
PubMed2004

Local correlation of expression profiles with gene annotations--proof of concept for a general conciliatory method.

MOTIVATION: Integrated analysis of expression data and gene ontology annotations is a prime example of biological data that need co-explanatory interpretation. This particular application is used to validate a new method for integrated analysis of varied biological information. RESULTS: The proposed method consists of determining local correlation coefficients and the corresponding P-values calculated per biological entity. This measure considers the combined intensity and significance of the agreement or disagreement, between two data sources about the same biological entity. The method is applied to the integrated analysis of gene expression and annotation of two gene sets, one from yeast and other from mouse. The potential of the method to generate accurate mechanistic hypothesis is also demonstrated. Specially, negative correlation results pose a new kind of biological hypothesis. Method performance was compared with annotation enrichment methods, and optimal conditions for the superiority of local correlation results are discussed.

Algorithms↗
PubMed2003

Automated biofilm morphology quantification from confocal laser scanning microscopy imaging.

In spite of the immediate visual appeal of confocal laser scanning microscopy images, the extraction of accurate reconstitutions of biofilm morphology requires a lengthy and computational intensive succession of processing steps. However, once performed, it provides ample reward by enabling the quantitative study of biofilm structure. A software suite of image processing tools for full automation of biofilm morphology quantification was developed by integrating preprocessing, segmentation and morphology quantification operations. This software toolbox was implemented in a web server and a user friendly interface was developed to facilitate image submission, storage and sharing, its access being unrestricted for scientific applications. The image bioinformatics tool which results from the integration of the processing operations can be accessed at http://www.itqb.unl.pt:111/clsmip/. Its use is described in this paper and is illustrated with an example of processing of experimental data describing the growth of a mixed species dentrifying biofilm.

Automation↗
PubMed2003

Monitoring of biofilm reactors using natural fluorescence fingerprints.

Natural fluorescence as a method to monitor biofilm processes was studied, using the example of an extractive membrane bioreactor for the degradation of 3-chloro-4 methylaniline and 1,2-dichloroethane. Non-invasive, on-line, in-situ 2D fluorometry monitoring was employed to elicit biofilm process status. The fluorescence fingerprints were deconvoluted in a pattern recognition approach using artificial neural networks (ANN) through association with key process performance parameters.

Biofilms↗
PubMed2003

Nutrient removal in a sequencing batch reactor operated with short anaerobic/aerobic cycles.

A single sequencing batch reactor operated with short intermittent aeration cycles was used to simultaneously remove carbon, nitrogen and phosphorus. The complete cycle, comprising feeding, anaerobiosis, aerobiosis, settling and decanting, was only 36 minutes long. The system has shown high and stable nutrient removal at 30 degrees C with acetate as carbon source and it has proved to be rather robust and dynamic, efficiently adapting to most of the changes in operating parameters tested: presence of nitrate in the feeding medium, different substrates (propionate and butyrate), temperature and nutrient shock loads. For the optimum conditions used, a removal efficiency of over 90% was obtained for each nutrient. Description of the population kinetics was obtained for each operating condition, by performing batch tests. Kinetic and stoichiometric parameters were used to infer the relative contribution of each group of microorganisms on SBR performance. Compared to the traditional SBR operated with cycles of 6 hours, the use of short intermittent aeration cycles of 36 minutes corresponds to a 40% reduction on aeration time.

Aerobiosis↗
PubMed2001

Two-dimensional fluorometry coupled with artificial neural networks: a novel method for on-line monitoring of complex biological processes.

The use of two-dimensional scanning fluorometry as an on-line, noninvasive, in situ bioreactor monitoring technique is extended to complex bioprocesses using mixed cultures, with particular attention to biofilm systems. Using the example of spectra subtraction, it is demonstrated that established methods for fluorescence data analysis have a limited capability of utilizing overall fluorometric information. Artificial neural networks (ANNs) are introduced as a novel nonlinear and nonmechanistic technique for interpreting the highly complex fluorescence maps. It is shown that ANNs are able to infer process performance parameters in a pattern recognition approach, based on the entire fluorescence "fingerprint" of the biological system. The studies were carried out using an extractive membrane bioreactor (EMB) for the degradation of chlorinated organic compounds, operating with mixed cultures. Model pollutants em- ployed were 1,2-dichloroethane, 3-chloro-4-methylaniline, and p-toluidine.

Biodegradation, Environmental↗
PubMed2001

Objective threshold selection procedure (OTS) for segmentation of scanning laser confocal microscope images.

The determination of volumes and interface areas from confocal laser scanning microscopy (CLSM) images requires the identification of component objects by segmentation. An automated method for the determination of segmentation thresholds for CLSM imaging of biofilms was developed. The procedure, named objective threshold selection (OTS), is a three-dimensional development of the approach introduced by the popular robust automatic threshold selection (RATS) method. OTS is based on the statistical properties of local gray-values and gradients in the image. By characterizing the dependence between a volumetric feature and the intensity threshold used for image segmentation, the former can be determined with an arbitrary confidence level, with no need for user intervention. The identification of an objective segmentation procedure renders the possibility for the full automation of volume and interfacial area measurement. Images from two distinct biofilm systems, acquired using different experimental techniques and instrumental setups were segmented by OTS to determine biofilm volume and interfacial area. The reliability of measurements for each case was analyzed to identify optimal procedure for image acquisition. The automated OTS method was shown to reproduce values obtained manually by an experienced operator.

Automation↗
PubMed2001

Analysis of genomic sequences by Chaos Game Representation.

MOTIVATION: Chaos Game Representation (CGR) is an iterative mapping technique that processes sequences of units, such as nucleotides in a DNA sequence or amino acids in a protein, in order to find the coordinates for their position in a continuous space. This distribution of positions has two properties: it is unique, and the source sequence can be recovered from the coordinates such that distance between positions measures similarity between the corresponding sequences. The possibility of using the latter property to identify succession schemes have been entirely overlooked in previous studies which raises the possibility that CGR may be upgraded from a mere representation technique to a sequence modeling tool. RESULTS: The distribution of positions in the CGR plane were shown to be a generalization of Markov chain probability tables that accommodates non-integer orders. Therefore, Markov models are particular cases of CGR models rather than the reverse, as currently accepted. In addition, the CGR generalization has both practical (computational efficiency) and fundamental (scale independence) advantages. These results are illustrated by using Escherichia coli K-12 as a test data-set, in particular, the genes thrA, thrB and thrC of the threonine operon.

Algorithms↗
PubMed2000

Metabolic characterization of Lactococcus lactis deficient in lactate dehydrogenase using in vivo 13C-NMR.

The metabolism of glucose by nongrowing cells of Lactococcus lactis strain FI7851, constructed from the wild-type L. lactis strain MG1363 by disruption of the lactate dehydrogenase (ldh) gene [Gasson, M.J., Benson, K., Swindel, S. & Griffin, H. (1996) Lait 76, 33-40] was studied in a noninvasive manner by 13C-NMR. The kinetics of the build-up and consumption of the pools of intracellular intermediates mannitol 1-phosphate, fructose 1,6-bisphosphate, 3-phosphoglycerate, and phosphoenolpyruvate as well as the utilization of [1-13C]glucose and formation of products (lactate, acetate, mannitol, ethanol, acetoin, 2,3-butanediol) were monitored in vivo with a time resolution of 30 s. The metabolism of glucose by the parental wild-type strain was also examined for comparison. A clear shift from typical homolactic fermentation (parental strain) to a mixed acid fermentation (lactate dehdydrogenase deficient; LDHd strain) was observed. Furthermore, high levels of mannitol were transiently produced and metabolized once glucose was depleted. Mannitol 1-phosphate accumulated intracellularly up to 76 mM concentration. Mannitol was formed from fructose 6-phosphate by the combined action of mannitol-1-phosphate dehydrogenase and phosphatase. The results show that the formation of mannitol 1-phosphate by the LDHd strain during glucose catabolism is a consequence of impairment in NADH oxidation caused by a highly reduced LDH activity, the transient production of mannitol 1-phosphate serving as a regeneration pathway for NAD+ regeneration. Oxygen availability caused a drastic change in the pattern of intermediates and end-products, reinforcing the key-role of the fulfilment of the redox balance. The flux control coefficients for the step catalysed by mannitol-1-phosphate dehydrogenase were calculated and the implications in the design of metabolic engineering strategies are discussed.

Anaerobiosis↗
PubMed2000

Application of neural computing methods for interpreting phospholipid fatty acid profiles of natural microbial communities.

The microbial community compositions of surface and subsurface marine sediments and sediments lining burrows of marine polychaetes and hemichordates from the North Inlet estuary (near Georgetown, S.C. ) were analyzed by comparing ester-linked phospholipid fatty acid (PLFA) profiles with a back-propagating neural network (NN). The NNs were trained to relate PLFA inputs to sediment type outputs (e.g., surface, subsurface, and burrow lining) and worm species (e.g., Notomastus lobatus, Balanoglossus aurantiacus, and Branchyoasychus americana). Sensitivity analysis was used to determine which of the 60 PLFAs significantly contributed to training the NN. The NN architecture was optimized by changing the number of hidden neurons and calculating the cross-validation error between predicted and actual outputs of training and test data. The optimal NN architecture was found to be four hidden neurons with 60-input neurons representing the 60 PLFAs, and four output neurons coding for both sediment types and worm species. Comparison of cross-validation results using NNs and linear discriminant analysis (LDA) revealed that NNs had significantly fewer incorrect classifications (2.7%) than LDA (8.4%). For the NN cross-validation, both sediment type and worm species had 3 incorrect classifications out of 112. For the LDA cross-validation, sediment type and worm species had 7 and 12 incorrect classifications out of 112, respectively. Sensitivity analysis of the trained NNs revealed that 17 fatty acids explained 50% of variability in the data set. These PLFAs were highly different among sediments and burrow types, indicating significant differences in the microbiota.

Animals↗
PubMed1999

Influence of furfural on anaerobic glycolytic kinetics of Saccharomyces cerevisiae in batch culture.

Furfural was reduced to furfuryl alcohol by Saccaromyces cerevisiae with a yield of 0.97 +/- 0.01 mmol/ mmol causing a lag phase in cell growth. In the presence of 29 mM, furfural the cell-mass yield on glucose decreased from 11.0 +/- 0.1 mg/mmol (0.06 +/- 0.0006 g/g) in a reference fermentation without furfural to 9.7 +/- 0.07 mg/ mmol (0.05 +/- 0.0004 g/g), whereas the ethanol yield on glucose increased from 1.6 +/- 0.03 to 1.7 +/- 0.03 mmol/mmol. No glycerol was excreted during furfural reduction, and the lag phase in acetate production was extended from 1 h in the reference fermentation to 5 h in the presence of furfural. Acetaldehyde and pyruvate were excreted during the furfural reduction phase. Cell growth and cell maintenance were proportional to glucose consumption during the entire fermentation, whereas the cell-mass yield on ATP produced was low during furfural reduction. These observations indicate that furfural addition to a batch culture decreased cell replication without inhibiting cell activity (designated as replicative inactivation). The absence of glycerol production during furfural reduction suggests that furfural acted as an alternative redox sink oxidizing excess NADH formed in biosynthesis. A mechanistic mathematical model was developed that described accurately the fermentation in the absence and presence of furfural. The model was based on the assumptions that: (i) furfural reduction to furfuryl alcohol by NADH-dependent dehydrogenases had a higher priority than reduction of dihydroxyacetone phosphate to glycerol; and (ii) furfural caused inactivation of cell replication. The effect of furfural on cell replication is discussed in relation to acetaldehyde formation. Inactivation of cell replication was modeled by considering two populations within the cell culture, both metabolically active, but only one replicating. The kinetic description was developed as a tool to estimate transient fluxes of carbon, NADH/NAD+ and ATP/ADP.

Anaerobiosis↗
PubMed1999

Registered designation of origin areas of fermented food products defined by microbial phenotypes and artificial neural networks.

Cheese produced from raw ewes' milk and chouriço, a Portuguese dry fermented sausage, are still produced in a traditional way in certain regions of Portugal by relying on colonization by microbial populations associated with the raw materials, equipment, and local environments. For the purpose of describing the product origins and types of these fermented foods, metabolic phenotypes can be used as descriptors of the product as well as to determine the presence of compounds with organoleptic value. The application of artificial neural networks to the metabolic profiles of bacterial isolates was assayed and allowed the separation of products from different regions. This method could then be used for the Registered Designation of Origin certification process of food products. Therefore, besides test panel results for these traditionally produced food products, another tool for validating products for the marketplace is available to the producers. The method can be improved for the detection of counterfeit products.

Animals↗