A gene signature in histologically normal surgical margins is predictive of oral carcinoma recurrence

Background: Oral Squamous Cell Carcinoma (OSCC) is a major cause of cancer death worldwide, which is mainly due to recurrence leading to treatment failure and patient death. Histological status of surgical margins is a currently available assessment for recurrence risk in OSCC; however histological status does not predict recurrence, even in patients with histologically negative margins. Therefore, molecular analysis of histologically normal resection margins and the corresponding OSCC may aid in identifying a gene signature predictive of recurrence.Methods: We used a meta-analysis of 199 samples (OSCCs and normal oral tissues) from five public microarray datasets, in addition to our microarray analysis of 96 OSCCs and histologically normal margins from 24 patients, to train a gene signature for recurrence. Validation was performed by quantitative real-time PCR using 136 samples from an independent cohort of 30 patients.Results: We identified 138 significantly over-expressed genes (> 2-fold, false discovery rate of 0.01) in OSCC. By penalized likelihood Cox regression, we identified a 4-gene signature with prognostic value for recurrence in our training set. This signature comprised the invasion-related genes MMP1, COL4A1, P4HA2, and THBS2. Overexpression of this 4-gene signature in histologically normal margins was associated with recurrence in our training cohort (p = 0.0003, logrank test) and in our independent validation cohort (p = 0.04, HR = 6.8, logrank test).Conclusion: Gene expression alterations occur in histologically normal margins in OSCC. Over-expression of the 4-gene signature in histologically normal surgical margins was validated and highly predictive of recurrence in an independent patient cohort. Our findings may be applied to develop a molecular test, which would be clinically useful to help predict which patients are at a higher risk of local recurrence.

Factors predictive of inappropriateness in requests for parenteral antimicrobials for therapeutic purposes: A study in a small teaching hospital in Brazil

Background: The identification of patterns of inappropriate antimicrobial prescriptions in hospitals contributes to the improvement of antimicrobial stewardship programs (ASP). Methods: We conducted a cross-sectional study to identify predictors of inappropriateness in requests for parenteral antimicrobials (RPAs) in a teaching hospital with 285 beds. We reviewed 25% of RPAs for therapeutic purposes from y 2005. Appropriateness was evaluated according to current guidelines for antimicrobial therapy. We assessed predictors of inappropriateness through univariate and multivariate models. RPAs classified as 'appropriate' or 'probably appropriate' were selected as controls. Case groups comprised inappropriate RPAs, either in general or for specific errors. Results: Nine hundred and sixty-three RPAs were evaluated, 34.6% of which were considered inappropriate. In the multivariate analysis, general predictors of inappropriateness were: prescription on week-ends/holidays (odds ratio (OR) 1.67, 95% confidence interval (CI) 1.20-2.28, p = 0.002), patient in the intensive care unit (OR 1.57, 95% CI 1.11-2.23, p = 0.01), peritoneal infection (OR 2.15, 95% CI 1.27-3.65, p = 0.004), urinary tract infection (OR 1.89, 95% CI 1.25 -2.87, p = 0.01), combination therapy with 2 or more antimicrobials (OR 1.72, 95% CI 1.15-2.57, p = 0.008) and prescriptions including penicillins (OR 2.12, 95% CI 1.39-3.25, p = 0.001) or 1(st) generation cephalosporins (OR 1.74, 95% CI 1.01-3.00, p = 0.048). Previous consultation with an infectious diseases (ID) specialist had a protective effect against inappropriate prescription (OR 0.34, 95% CI 0.24-0.50, p < 0.001). Factors independently associated with specific prescription errors varied. However, consultation with an ID specialist was protective against both unnecessary antimicrobial use (OR 0.04, 95% CI 0.01-0.26, p = 0.001) and requests for agents with an insufficient antimicrobial spectrum (OR 0.14, 95% CI 0.03-0.30, p = 0.01). Conclusions: Our results demonstrate the importance of previous consultation with an ID specialist in assuring the quality of prescriptions. Also, they highlight prescription patterns that should be approached by ASP policies.

Thermoresistance sperm tests are not predictive of potential fertility for cryopreserved bull semen

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

Predictive factors of outcome following staphylococcal peritonitis in continuous ambulatory peritoneal dialysis

Background and aims: Staphylococcus epidermidis and other coagulase-negative staphylococci (CoNS) are the most common agents of continuous ambulatory peritoneal dialysis (CAPD) peritonitis. Episodes caused by Staphylococcus aureus evolve with a high method failure rate while CoNS peritonitis is generally benign. The purpose of this study was to compare episodes of peritonitis caused by CoNS species and S. aureus to evaluate the microbiological and host factors that affect outcome. Material and methods: Microbiological and clinical data were retrospectively studied from 86 new episodes of peritonitis caused by staphylococci species between January 1996 and December 2000 in a university dialysis center. The influence of microbiological and host factors (age, sex, diabetes, use of vancomycin, exchange system and treatment time on CAPD) was analyzed by logistic regression model. The clinical outcome was classified into two results (resolution and non-resolution). Results: the odds of peritonitis resolution were not influenced by host factors. Oxacillin susceptibility was present in 30 of 35 S. aureus lineages and 22 of 51 CoNS (p = 0.001). There were 32 of 52 (61.5%) episodes caused by oxacillin-susceptible and 20 of 34 (58.8%) by oxacillin-resistant lineages resolved (p = 0.9713). of the 35 cases caused by S. aureus, 17 (48.6%) resolved and among 51 CoNS episodes 40 (78.4%) resolved. Resolution odds were 7.1 times higher for S. epidermidis than S. aureus (p = 0.0278), while other CoNS had 7.6 times higher odds resolution than S. epidermidis cases (p = 0.052). Episodes caused by S. haemolyticus had similar resolution odds to S. epidermidis (p = 0.859). Conclusions: S. aureus etiology is an independent factor associated with peritonitis non-resolution in CAPD, while S. epidermidis and S. haemolyticus have a lower resolution rate than other CoNS. Possibly the aggressive nature of these agents, particularly S. aureus, can be explained by their recognized pathogenic factors, more than antibiotic resistance.

Cloning and Identification of a Complete cDNA Coding for a Bactericidal and Antitumoral Acidic Phospholipase A(2) from Bothrops jararacussu Venom

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

14-3-3: Defense and regulatory proteins coding by Eucalyptus genome

The data mining of Eucalyptus ESTs genome finds four clusters (EGCEST2257E11.g, EGBGRT3213F11.g, and EGCCFB1223H11.g) from highly conservative 14-3-3 protein family which modulates a wide variety of cellular processes. Multiple alignments were built from twenty four sequences of 14-3-3 proteins searched into the GenBank databases and into the four pools of Eucalyptus genome programs. The alignment has shown two regions highly conservative on the sequences corresponding to the motifs of protein phosphorylation and nine highly conservative regions on the sequence corresponding to the linkage regions of alpha helices structure based on three dimensional of dimer functional structure. The differences of amino acid into the structural and functional domains of 14-3-3 plant protein were identified and can explain the functional diversity of different isoforms. The phylogenic protein trees were built by the maximum parsimony and neighborjoining procedures of Clustal X alignments and PAUP software for phylogenic analysis.

Sequence characterization of coding regions of the myostatin gene (GDF8) from Brazilian Murrah buffaloes (Bubalus bubalis) and comparison with the Bos taurus sequence

Within about 30 years the Brazilian buffalo (Bubalus bubalis) herd will reach approximately 50 million head as a result of the great adaptive capacity of these animals to tropical climates, together with the good productive and reproductive potential which make these animals an important animal protein source for poor and developing countries. The myostatin gene (GDF8) is important in the physiology of stock animals because its product produces a direct effect on muscle development and consequently also on meat production. The myostatin sequence is known in several mammalian species and shows a high degree of amino acid sequence conservation, although the presence of non-silent and silent changes in the coding sequences and several alterations in the introns and untranslated regions have been identified. The objective of our work was to characterize the myostatin coding regions of B. bubalis (Murrah breed) and to compare them with the Bos taurus regions looking for variations in nucleotide and protein sequences. In this way, we were able to identify 12 variations at DNA level and five alterations on the presumed myostatin protein sequence as compared to non double-muscled bovine sequences.

Genetic variability of porcine parvovirus isolates revealed by analysis of partial sequences of the structural coding gene VP2

The 3'-terminal 853 nt (and the putative 283 aa) sequence of the VP2-encoding gene from 29 field strains of porcine parvovirus (PPV) were determined and compared both to each other and with other published sequences. Sequences were examined using maximum-parsimony and statistical analyses for nucleotide diversity and sequence variability. Among the nucleotide sequences of the PPV field strains, 26 polymorphic sites were encountered; 22 polymorphic sites were detected in the putative amino acid sequence. Mapping polymorphic sites of protein data onto the three-dimensional (3D) structure of PPV VP2 revealed that almost all substitutions were located on the external surface of the viral capsid. Mapping amino acid substitutions to the alignment between PPV VP2 sequences and the 3D structure of canine parvovirus (CPV) capsid, many PPV substitutions were observed to map to regions of recognized antigenicity and/or to contain phenotypically important residues for CPV and other parvoviruses. In spite of the high sequence similarity, genetic analysis has shown the existence of at least two virus lineages among the samples. In conclusion, these results highlight the need for close surveillance on PPV genetic drift, with an assessment of its potential ability to modify the antigenic make-up of the virus.

Predictive formulation of the Nambu-Jona-Lasinio model

A novel strategy to handle divergences typical of perturbative calculations is implemented for the Nambu-Jona-Lasinio model and its phenomenological consequences investigated. The central idea of the method is to avoid the critical step involved in the regularization process, namely, the explicit evaluation of divergent integrals. This goal is achieved by assuming a regularization distribution in an implicit way and making use, in intermediary steps, only of very general properties of such regularization. The finite parts are separated from the divergent ones and integrated free from effects of the regularization. The divergent parts are organized in terms of standard objects, which are independent of the ( arbitrary) momenta running in internal lines of loop graphs. Through the analysis of symmetry relations, a set of properties for the divergent objects are identified, which we denominate consistency relations, reducing the number of divergent objects to only a few. The calculational strategy eliminates unphysical dependencies of the arbitrary choices for the routing of internal momenta, leading to ambiguity-free, and symmetry-preserving physical amplitudes. We show that the imposition of scale properties for the basic divergent objects leads to a critical condition for the constituent quark mass such that the remaining arbitrariness is removed. The model becomes predictive in the sense that its phenomenological consequences do not depend on possible choices made in intermediary steps. Numerical results are obtained for physical quantities at the one-loop level for the pion and sigma masses and pion-quark and sigma-quark coupling constants.

Establishing the risk of neonatal mortality using a fuzzy predictive model

O objetivo do artigo foi avaliar o uso da lógica fuzzy para estimar possibilidade de óbito neonatal. Desenvolveu-se um modelo computacional com base na teoria dos conjuntos fuzzy, tendo como variáveis peso ao nascer, idade gestacional, escore de Apgar e relato de natimorto. Empregou-se o método de inferência de Mamdani, e a variável de saída foi o risco de morte neonatal. Criaram-se 24 regras de acordo com as variáveis de entrada, e a validação do modelo utilizou um banco de dados real de uma cidade brasileira. A acurácia foi estimada pela curva ROC; os riscos foram comparados pelo teste t de Student. O programa MATLAB 6.5 foi usado para construir o modelo. Os riscos médios foram menores para os que sobreviveram (p < 0,001). A acurácia do modelo foi 0,90. A maior acurácia foi com possibilidade de risco igual ou menor que 25% (sensibilidade = 0,70, especificidade = 0,98, valor preditivo negativo = 0,99 e valor preditivo positivo = 0,22). O modelo mostrou acurácia e valor preditivo negativo bons, podendo ser utilizado em hospitais gerais.

Report of a chimeric origin of transposable elements in a bovine-coding gene

Despite the wide distribution of transposable elements (TEs) in mammalian genomes, part of their evolutionary significance remains to be discovered. Today there is a substantial amount of evidence showing that TEs are involved in the generation of new exons in different species. In the present study, we searched 22,805 genes and reported the occurrence of TE-cassettes in coding sequences of 542 cow genes using the RepeatMasker program. Despite the significant number (542) of genes with TE insertions in exons only 14 (2.6%) of them were translated into protein, which we characterized as chimeric genes. From these chimeric genes, only the FAST kinase domains 3 (FASTKD3) gene, present on chromosome BTA 20, is a functional gene and showed evidence of the exaptation event. The genome sequence analysis showed that the last exon coding sequence of bovine FASTKD3 is ∼85% similar to the ART2A retrotransposon sequence. In addition, comparison among FASTKD3 proteins shows that the last exon is very divergent from those of Homo sapiens, Pan troglodytes and Canis familiares. We suggest that the gene structure of bovine FASTKD3 gene could have originated by several ectopic recombinations between TE copies. Additionally, the absence of TE sequences in all other species analyzed suggests that the TE insertion is clade-specific, mainly in the ruminant lineage. ©FUNPEC-RP.

Influence of lower cutoff values for 100-g oral glucose tolerance test and glycemic profile for identification of pregnant women at excessive fetal growth risk

Objective: To evaluate data from patients with normal oral glucose tolerance test (OGTT) results and a normal or impaired glycemic profile (GP) to determine whether lower cutoff values for the OGTT and GP (alone or combined) could identify pregnant women at risk for excessive fetal growth. Methods: We classified 701 pregnant women with positive screening for gestational diabetes mellitus (GDM) into 2 categories - (1) normal 100-g OGTT and normal GP and (2) normal 100-g OGTT and impaired GP - to evaluate the influence of lower cutoff points in a 100-g OGTT and GP (alone or in combination) for identification of pregnant women at excessive fetal growth risk. The OGTT is considered impaired if 2 or more values are above the normal range, and the GP is impaired if the fasting glucose level or at least 1 postprandial glucose value is above the normal range. To establish the criteria for the OGTT (for fasting and 1, 2, and 3 hours after an oral glucose load, respectively), we considered the mean (75 mg/dL, 120 mg/dL, 113 mg/dL, and 97 mg/dL), mean plus 1 SD (85 mg/dL, 151 mg/dL, 133 mg/dL, and 118 mg/dL), and mean plus 2 SD (95 mg/dL, 182 mg/dL, 153 mg/dL, and 139 mg/dL); and for the GP, we considered the mean and mean plus 1 SD (78 mg/dL and 92 mg/dL for fasting glucose levels and 90 mg/dL and 130 mg/dL for 1- or 2-hour postprandial glucose levels, respectively). Results: Subsequently, the women were reclassified according to the new cutoff points for both tests (OGTT and GP). Consideration of values, in isolation or combination, yielded 6 new diagnostic criteria. Excessive fetal growth was the response variable for analysis of the new cutoff points. Odds ratios and their respective confidence intervals were estimated, as were the sensitivity and specificity related to diagnosis of excessive fetal growth for each criterion. The new cutoff points for the tests, when used independently rather than collectively, did not help to predict excessive fetal growth in the presence of mild hyperglycemia. Conclusion: Decreasing the cutoff point for the 100-g OGTT (for fasting and 1, 2, and 3 hours) to the mean (75 mg/dL, 120 mg/dL, 113 mg/dL, and 97 mg/dL) in association with the GP (mean or mean plus 1 SD-78 mg/dL and 92 mg/dL for the fasting state and 90 mg/dL and 130 mg/dL for 1- or 2-hour postprandial values-increased the sensitivity and specificity, and both criteria had statistically significant predictive power for detection of excessive fetal growth. © 2008 AACE.