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Fast adaptive stacking of ensembles
No full textThis paper presents a new ensemble method for learning from non-stationary data streams. In these situations, massive data are constantly generated at high speed and their target function can change over time. The proposed method, named Fast Adaptive Stacking of Ensembles (FASE), uses a meta-classifier to combine the predictions from the base classifiers in the ensemble. FASE maintains a set of adaptive learners, in order to deal with concept drifting data. The new algorithm is able to process the input data in constant time and space computational complexity. It only receives as parameters the confidence level for the change detection mechanism and the number of base classifiers. These characteristics make FASE very suitable for learning from non-stationary data streams. We empirically compare the new algorithm with various state-of-the-art ensemble methods for learning in non-stationary data streams. We use a Naïve Bayes classifier and a Perceptron to evaluate the performance of the algorithms over real-world datasets. The experiment results show that FASE presents higher predictive accuracy in the investigated tasks, being also able to bound its computational cost.FAPESP (Fundação de Amparo à Pesquisa do Estado de São Paulo) (grant number 2015/03355-0
A multiplex nested PCR for the detection and identification of Candida species in blood samples of critically ill paediatric patients
No full textAbstract
Background
Nosocomial candidaemia is associated with high mortality rates in critically ill paediatric patients; thus, the early detection and identification of the infectious agent is crucial for successful medical intervention. The PCR-based techniques have significantly increased the detection of Candida species in bloodstream infections. In this study, a multiplex nested PCR approach was developed for candidaemia detection in neonatal and paediatric intensive care patients.
Methods
DNA samples from the blood of 54 neonates and children hospitalised in intensive care units with suspected candidaemia were evaluated by multiplex nested PCR with specific primers designed to identify seven Candida species, and the results were compared with those obtained from blood cultures.
Results
The multiplex nested PCR had a detection limit of four Candida genomes/mL of blood for all Candida species. Blood cultures were positive in 14.8% of patients, whereas the multiplex nested PCR was positive in 24.0% of patients, including all culture-positive patients. The results obtained with the molecular technique were available within 24 hours, and the assay was able to identify Candida species with 100% of concordance with blood cultures. Additionally, the multiplex nested PCR detected dual candidaemia in three patients.
Conclusions
Our proposed PCR method may represent an effective tool for the detection and identification of Candida species in the context of candidaemia diagnosis in children, showing highly sensitive detection and the ability to identify the major species involved in this infection
Genome-wide CNV analysis reveals variants associated with growth traits in Bos indicus
No full textAbstract\ud
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Background\ud
Apart from single nucleotide polymorphism (SNP), copy number variation (CNV) is another important type of genetic variation, which may affect growth traits and play key roles for the production of beef cattle. To date, no genome-wide association study (GWAS) for CNV and body traits in beef cattle has been reported, so the present study aimed to investigate this type of association in one of the most important cattle subspecies: Bos indicus (Nellore breed).\ud
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Results\ud
We have used intensity data from over 700,000 SNP probes across the bovine genome to detect common CNVs in a sample of 2230 Nellore cattle, and performed GWAS between the detected CNVs and nine growth traits. After filtering for frequency and length, a total of 231 CNVs ranging from 894 bp to 4,855,088 bp were kept and tested as predictors for each growth trait using linear regression analysis with principal components correction. There were 49 significant associations identified among 17 CNVs and seven body traits after false discovery rate correction (P < 0.05). Among the 17 CNVs, three were significant or marginally significant for all the traits. We have compared the locations of associated CNVs with quantitative trait locus and the RefGene database, and found two sets of 9 CNVs overlapping with either known QTLs or genes, respectively. The gene overlapping with CNV100, KCNJ12, is a functional candidate for muscle development and plays critical roles in muscling traits.\ud
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Conclusion\ud
This study presents the first CNV-based GWAS of growth traits using high density SNP microarray data in cattle. We detected 17 CNVs significantly associated with seven growth traits and one of them (CNV100) may be involved in growth traits through KCNJ12.We thank Reuben Anderson, and Alexandre Dimtchev for technical assistance.\ud
This work was supported in part by Agriculture and Food Research Initiative\ud
(AFRI) competitive grant No. 2011-67015-30183 from the USDA National Institute\ud
of Food and Agriculture (NIFA) Animal Genome Program. Mention of trade\ud
names or commercial products in this article is solely for the purpose of providing\ud
specific information and does not imply recommendation or endorsement by\ud
the US Department of Agriculture
Impact of weight loss diet associated with flaxseed on inflammatory markers in men with cardiovascular risk factors: a clinical study
No full textAbstract\ud
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Background\ud
Flaxseed has received attention for its anti-inflammatory and antioxidant role. The present study hypothesizes if flaxseed added to a weight loss diet could improve the lipid and metabolic profiles and decrease risk factors related to cardiovascular disease.\ud
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Methods\ud
In a prospective, single blinded 42 days protocol, subjects were allocated into two groups with low carbohydrates intake: GriceLC (35% of carbohydrate and 60g of raw rice powder per day) and GflaxLC (32% of carbohydrate and 60g of flaxseed powder per day). Blood pressure, anthropometric measures and serum levels of isoprostane, C-reactive protein, Tumor Necrosis Factor-alpha, glucose, lipidic profile, uric acid, adiponectin, leptin and insulin were measured at baseline and at the end of interventions. Serum and urinary enterodiol and enterolactione were also measured.\ud
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Results\ud
A total of 27 men with cardiovascular risk factors were evaluated, with mean age of 33 ± 10 years to GriceLC and 40 ± 9 years to GflaxLC. Both groups experienced weight loss and systolic blood pressure reduction. A decrease in inflammatory markers (CRP and TNF-α) was observed after flaxseed intake (mean decrease of 25% and 46% for GflaxLC respectively). All groups also showed improvement in levels of total cholesterol, LDL-c, uric acid and adiponectin. Only GflaxLC group showed a decrease in triglyceride levels.\ud
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Conclusion\ud
This study suggests that flaxseed added to a weight loss diet could be an important nutritional strategy to reduce inflammation markers such as CRP and TNF-α.\ud
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Trial registration\ud
ClinicalTrials.gov \ud
NCT02132728\ud
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.This study was partially financed by CNPq grant (304127/2009-4) intended\ud
to JSM and also by FAEPA – Fundação de Apoio ao Ensino, Pesquisa e\ud
Assistência do Hospital das Clínicas da Faculdade de Medicina de Ribeirão\ud
Preto/University of São Paulo. PGF, JHS and CMML received scholarships\ud
2012/22543-3, 2012/21579-4 and 2012/21626-2, respectively from FAPESP -\ud
Fundação de Amparo à Pesquisa de São Paulo. CNPq, FAEPA and FAPESP\ud
are government agencies that provide financial resources, but generated no\ud
influences in the study
MYLIP p.N342S polymorphism is not associated with lipid profile in the Brazilian population
No full textAbstract
Background
A recent study investigated the MYLIP region in the Mexican population in order to fine-map the actual susceptibility variants of this locus. The p.N342S polymorphism was identified as the underlying functional variant accounting for one of the previous signals of genome-wide association studies and the N342 allele was associated with higher cholesterol concentrations in Mexican dyslipidemic individuals. To date, there is no further evaluation on this genotype-phenotype association in the literature. In this scenario, and because of a possible pharmacotherapeutic target of dyslipidemia, the main aim of this study was to assess the influence of the MYLIP p.N342S polymorphism on lipid profile in Brazilian individuals.
Methods
1295 subjects of the general population and 1425 consecutive patients submitted to coronary angiography were selected. General characteristics, biochemical tests, blood pressures, pulse wave velocity, and coronary artery disease scores were analyzed. Genotypes for the MYLIP rs9370867 (p.N342S, c.G1025A) polymorphism were detected by high resolution melting analysis.
Results
No association of the MYLIP rs9370867 genotypes with lipid profile, hemodynamic data, and coronary angiographic data was found. Analysis stratified by hyperlipidemia, gender, and ethnicity was also performed and the sub-groups presented similar results. In both general population and patient samples, the MYLIP rs9370867 polymorphism was differently distributed according to ethnicity. In the general population, subjects carrying GG genotypes had higher systolic blood pressure (BP), diastolic BP, and mean BP values (129.0 ± 23.3; 84.9 ± 14.6; 99.5 ± 16.8 mmHg) compared with subjects carrying AA genotypes (123.7 ± 19.5; 81.6 ± 11.8; 95.6 ± 13.6 mmHg) (p = 0.01; p = 0.02; p = 0.01, respectively), even after adjustment for covariates. However, in analysis stratified by ethnicity, this finding was not found and there is no evidence that the polymorphism influences BP.
Conclusion
Our findings indicate that association studies involving this MYLIP variant can present distinct results according to the studied population. In this moment, further studies are needed to reaffirm if the MYLIP p.N342S polymorphism is functional or not, and to identify other functional markers within this gene
LPA rs10455872 polymorphism is associated with coronary lesions in Brazilian patients submitted to coronary angiography
No full textAbstract
Background
Polymorphisms in the LPA gene were associated with coronary artery disease (CAD). However, there are differences in the allelic frequencies, Lp(a) levels, and significant association with CAD according to ethnic groups. In this scenario, the main aim of this study was to assess the influence of the LPA polymorphisms on coronary lesions in Brazilian patients.
Methods
1,394 consecutive patients submitted to coronary angiography to study suggestive CAD and twenty coronary segments were scored. Genotyping for the LPA rs10455872 and rs3798220 polymorphisms were performed by high resolution melting analysis.
Results
The frequencies of the rs10455872 G and rs3798220 C variant alleles were 6.4% and 6.2%, respectively. LPA rs10455872 G variant allele was associated with higher odds ratio of having coronary lesions in an adjusted model (OR = 2.02, 95% CI = 1.10-3.72, p = 0.02). Scores of coronary lesions (extension, severity, and Gensini scores) were significantly different among rs10455872 genotype groups. Coronary lesions was not associated with LPA rs3798220 (OR = 1.09, 95% CI = 0.67-1.76, p = 0.73) and scores of coronary lesions were not different among rs3798220 genotypes.
Conclusions
We confirmed the association of the LPA rs10455872 with CAD in a large sample of Brazilian patients. For the LPA rs3798220, our finding is consistent with studies which showed the lack of this genetic association
Effects of nateglinide and rosiglitazone on pancreatic alpha- and beta-cells, GLP-1 secretion and inflammatory markers in patients with type 2 diabetes: randomized crossover clinical study
No full textAbstract\ud
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Background\ud
To compare the effects of nateglinide and rosiglitazone on inflammatory markers, GLP-1 levels and metabolic profile in patients with type 2 diabetes (DM2).\ud
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Methods\ud
A prospective study was performed in 20 patients with DM2, mean age 51.82 ± 8.05 years, previously treated with dietary intervention. Participants were randomized into rosiglitazone (4–8 mg/day) or nateglinide (120 mg 3 times a day) therapy. After 4 months, the patients were crossed-over with 8 weeks washout period to the alternative treatment for an additional 4-month period on similar dosage schedule. The following variables were assessed before and after 4 months of each treatment period: (1) a test with a standardized 500 calories meal for 5 h including frequent measurements of glucose, insulin, glucagon, proinsulin, GLP-1, free fat acids (FFA), and triglycerides levels was obtained. The lipid profile and HbA1 levels were measured at fasting. (2) Haemostatic and inflammatory markers: platelet aggregation, fibrinogen, PAI-1 activity, C reactive protein (CRP), IL-6, TNF-α, leptin, sICAM and TGFβ levels.\ud
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Results\ud
Both therapy decreased blood glucose levels under the postprandial curve but neither affected glucagon and GLP-1 levels. Nateglinide was associated with higher insulin and pro-insulin secretion, but similar pro-insulin/insulin ratio when compared with rosiglitazone. Only rosiglitazone decreased Homa β, PAI-1 activity, CRP, fibrinogen, TGFβ, FFA and triglyceride levels.\ud
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Conclusions\ud
Nateglinide and rosiglitazone were effective in improving glucose and lipid profile and β cell function, but rosiglitazone afforded a better anti-inflammatory effect. No drug restored alpha cell sensitivity or changed GLP-1 levels. Maintenance of haemostatic factors, inflammatory factors and glucagon levels can be related to the continuously worsening of cardiovascular function and glucose control observed in DM2.To Greci de Paula Souza for procedures assistance. This study was supported\ud
by State of São Paulo Research Foundation (Fundação de Amparo à Pesquisa\ud
do Estado de São Paulo-FAPESP)
In situ remineralisation response of different artificial caries-like enamel lesions to home-care and professional fluoride treatments
No full textAbstract\ud
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Background\ud
Artificial lesions produced by different protocols might directly influence the response to different remineralising treatments. This study compared the response of different artificial caries-like enamel lesions to home-care and professional fluoride based-remineralising treatments in situ.\ud
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Methods\ud
The tested demineralising protocols were methylcellulose- MC gel, polyacrylic acid - PA gel, tetraethyl methylene diphosphanate - TEMDP solution, and acetate- Buffer solution. The lesions were remineralised using an in situ model, following a crossover and double blind design. Twelve subjects wore intra-oral appliances during 3 phases (3 d each): control (C) (saliva); home-care F− treatment (FD) (1,100 ppm F− dentifrice, 2x1 min/day); and professional (FVD) (22,600 ppm F− varnish) plus FD. The de-remineralisation was measured by transverse microradiography-TMR and hardness (surface hardness/cross-sectional hardness, SH/CSH, respectively).\ud
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Results\ud
For SH, lesions produced by PA gel were the only one showing significant differences among the remineralising treatments (C x FD x FVD); while the TEMDP lesion were not responsive to any fluoride treatment (for both SH/CSH). For TMR, there were no differences among the remineralising treatments, regardless of the type of lesion. Generally, the most responsive lesions to fluoride were the less demineralised lesions (considering hardness: PA gel and Buffer).\ud
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Conclusions\ud
The type of lesion has influence on the surface remineralisation degree induced by home-care and professional fluoride treatments using this in situ model.We would like to thank the subjects who took part of the in situ research\ud
and FAPESP by the financial support (scholarship for the first author, Process number: 2011/03907-1)
Functional and evolutionary analyses of the miR156 and miR529 families in land plants
No full textAbstract\ud
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Background\ud
MicroRNAs (miRNAs) are important regulatory elements of gene expression. Similarly to coding genes, miRNA genes follow a birth and death pattern of evolution likely reflecting functional relevance and divergence. For instance, miRNA529 is evolutionarily related to miRNA156 (a highly conserved miRNA in land plants), but it is lost in Arabidopsis thaliana. Interestingly, both miRNAs target sequences overlap in some members of the SQUAMOSA promoter-binding protein like (SPL) family, raising important questions regarding the diversification of the miR156/miR529-associated regulatory network in land plants.\ud
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Results\ud
In this study, through phylogenic reconstruction of miR156/529 target sequences from several taxonomic groups, we have found that specific eudicot SPLs, despite miRNA529 loss, retained the corresponding target site. Detailed molecular evolutionary analyses of miR156/miR529-target sequence showed that loss of miR529 in core eudicots, such as Arabidopsis, is correlated with a more relaxed selection of the miRNA529 specific target element, while miRNA156-specific target sequence is under stronger selection, indicating that these two target sites might be under distinct evolutionary constraints. Importantly, over-expression in Arabidopsis of MIR529 precursor from a monocot, but not from a basal eudicot, demonstrates specific miR529 regulation of AtSPL9 and AtSPL15 genes, which contain conserved responsive elements for both miR156 and miR529.\ud
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Conclusions\ud
Our results suggest loss of functionality of MIR529 genes in the evolutionary history of eudicots and show that the miR529-responsive element present in some eudicot SPLs is still functional. Our data support the notion that particular miRNA156 family members might have compensated for the loss of miR529 regulation in eudicot species, which concomitantly may have favored diversification of eudicot SPLs.We thank Dr. Scott Poethig for 35S::AtMIR156a seeds; Dr. Peter Huijser for\ud
spl9;spl15 seeds; Dr. Renato Vicentini for initial bioinformatic analyses and\ud
helpful discussions; and Dr. Luiz Del Bem for initial phylogenetic analyses.\ud
This work was supported by the State of Sao Paulo Research Foundation,\ud
FAPESP, Brazil (grants no. 07/58289-5 and 12/51146-2). EGOM was a recipient\ud
of a fellowship from Coordination for the Improvement of Higher Education\ud
Personnel (CAPES, Brazil). GFFS (from Centro de Energia Nuclear na\ud
Agricultura –CENA/USP) and EMS were recipients of a fellowship from the\ud
State of Sao Paulo Research Foundation, FAPESP, Brazil
Near-drowning-associated pneumonia with bacteremia caused by coinfection with methicillin-susceptible Staphylococcus aureus and Edwardsiella tarda in a healthy white man: a case report
No full textAbstract\ud
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Background\ud
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Edwardsiella tarda is an Enterobacteriaceae found in aquatic environments. Extraintestinal infections caused by Edwardsiella tarda in humans are rare and occur in the presence of some risk factors. As far as we know, this is the first case of near-drowning-associated pneumonia with bacteremia caused by coinfection with methicillin-susceptible Staphylococcus aureus and Edwardsiella tarda in a healthy patient.\ud
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Case presentation\ud
A 27-year-old previously healthy white man had an episode of fresh water drowning after acute alcohol consumption. Edwardsiella tarda and methicillin-sensitive Staphylococcus aureus were isolated in both tracheal aspirate cultures and blood cultures.\ud
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Conclusion\ud
This case shows that Edwardsiella tarda is an important pathogen in near drowning even in healthy individuals, and not only in the presence of risk factors, as previously known