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F R Pinto

Publications and source records attributed to F R Pinto.

6 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

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↗
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↗
PubMed2000

[Cervical perforating foreign body: case report].

BACKGROUND: Neck perforations by foreign bodies are uncommon. The surgical approach depends on the extension of visceral wounds and the development of cervical or mediastinal infection. PURPOSE: The objective of this paper is to report a neck perforation trauma by a piece of wire, with associated laryngeal and hypopharyngeal wounds and extensive cervico-mediastinal emphysema. Anatomic and clinical correlations are discussed, as well as the management of the case. MATERIAL AND METHODS: A 28-year-old male patient suffered a perforating trauma in his neck by a piece of wire. This foreign body was laid in the retropharyngeal space, at the level of the sixth cervical vertebra, after perforating the larynx and hypopharynx. There are no similar cases previously reported. The imaging tests are presented. Despite the potential severity of the lesions, the patient had a favorable outcome, and no surgical approach was necessary. CONCLUSIONS: This case illustrates, by the imaging tests, the complex anatomy of the cervical fasciae and deep neck spaces, and confirms the possibility of conservative management in a great number of laryngeal and hypopharyngeal traumatic lesions.

Adult↗
PubMedDate not supplied

[Deep neck spaces and their significance in cervical infections].

BACKGROUND: Although rare, deep neck space infections are associated with high morbidity and mortality rates. The surgical approach is necessary in the majority of the cases, and the surgeon must know the complex anatomy of the cervical fasciae and deep neck spaces. PURPOSE: The anatomy of the cervical fasciae and deep neck spaces in reviewed. As an illustration, a series of deep neck space infections is presented. MATERIAL AND METHOD: Four clinical cases are reported: 1) a case of Ludwig's angina with several complications (mediastinitis, pericarditis, pneumonia, pleural effusion and empyema, esophageal fistula and septic shock), 2) a case of cervical abscess that appeared without apparent cause, in a young diabetic patient, 3) a case of abscess of the submandibular triangle, and 4) a case of parapharyngeal abscess that came forth after a dental treatment. Data from history taking, physical examination, X-rays, echography, CT scan and treatment and the follow-up are presented. The image tests were valuable and, in two of the cases, they demonstrated that more than one deep neck space were affected. CONCLUSIONS: The literature reinforces the high mortality and morbidity rates, the diversified etiology (dental infection, intravenous drug abuse, infections of the upper aerodigestive tract and others), and the tracheostomy indication made in about half of the cases. It stresses also the need for combined therapy (antibiotics and surgery). Evaluation with CT scan and other radiologic methods is indispensable to determine the site and extent of the process and to plan properly the treatment.

Abscess↗