Machine learning and structural analysis of Mycobacterium tuberculosis pan-genome identifies genetic signatures of antibiotic resistance.

Mycobacterium tuberculosis is a serious human pathogen threat exhibiting complex evolution of antimicrobial resistance (AMR). Accordingly, the many publicly available datasets describing its AMR characteristics demand disparate data-type analyses. Here, we develop a reference strain-agnostic computational platform that uses machine learning approaches, complemented by both genetic interaction analysis and 3D structural mutation-mapping, to identify signatures of AMR evolution to 13 antibiotics. This platform is applied to 1595 sequenced strains to yield four key results. First, a pan-genome analysis shows that M. tuberculosis is highly conserved with sequenced variation concentrated in PE/PPE/PGRS genes. Second, the platform corroborates 33 genes known to confer resistance and identifies 24 new genetic signatures of AMR. Third, 97 epistatic interactions across 10 resistance classes are revealed. Fourth, detailed structural analysis of these genes yields mechanistic bases for their selection. The platform can be used to study other human pathogens

Forecasting Particulate Matter Concentrations: Use of Unorganized Machines

Air pollution is an environmental issue studied worldwide, as it has serious impacts on human health. Therefore, forecasting its concentration is of great importance. Then, this study presents an analysis comprising the appliance of Unorganized Machines – Extreme Learning Machines (ELM) and Echo State Networks (ESN) aiming to predict particulate matter with aerodynamic diameter less than 2.5 m (PM2.5) and less than 10 m (PM10). The databases were from Kallio and Vallilla stations in Helsinki, Finland. The computational results showed that the ELM presented best results to PM2.5, while the ESN achieved the best performance to PM10

Adhesion of Epiphany and AH Plus sealers to human root dentin treated with different solutions

This study evaluated comparatively the adhesion of Epiphany and AH Plus endodontic sealers to human root dentin treated with 1% NaOCl and 1% NaOCl+17% EDTA, using the push-out test. Sixty root cylinders obtained from maxillary canines had the canals prepared and were randomly assigned to 3 groups (n=20), according to root dentin treatment: GI - distilled water (control), GII - 1% NaOCl and GIII - 1% NaOCl+17% EDTA. Each group was divided into 2 subgroups (n=10) filled with either Epiphany or AH Plus. Bond strength push-out test data (kN) were obtained and analyzed statistically by ANOVA and Tukey&#39;s post-hoc test. There was statistically significant difference between sealers (AH Plus: 0.78 ± 0.13; Epiphany: 0.61 ± 0.19; p<0.01) and among root dentin treatments (distilled water: 0.58 ± 0.19; 1% NaOCl: 0.71 ± 0.12; 1% NaOCl+17% EDTA: 0.80 ± 0.17; p<0.05). In conclusion, AH Plus sealer presented greater adhesion to dentin than Epiphany, regardless of the treatment of root canal walls.O objetivo do presente estudo foi avaliar a adesividade do cimento Epiphany à dentina radicular previamente tratada com hipoclorito de sódio a 1% e EDTA a 17%, em comparação ao cimento AH Plus, pelo método do "push-out". Foram preparados sessenta cilindros de raízes de caninos superiores humanos que foram distribuídos em 3 grupos (n=20) de acordo com o tratamento da dentina: GI água destilada (controle), GII hipoclorito de sódio 1% e GIII EDTA 17 %. Esses grupos de corpos-de-prova foram distribuídos em 2 subgrupos para receber os cimentos obturadores a serem testados: Ephiphany e AH Plus. Foi realizado o teste do "push-out" e os resultados (em kN) foram analisados estatisticamente por ANOVA e o teste "post-hoc" de Tukey. A análise demonstrou diferença estatisticamente significativa entre os cimentos (AH Plus: 0,78 ± 0,13; Epiphany: 0,61 ± 0,19; p < 0,01) e entre as soluções testadas (água destilada: 0,58 ± 0,19; NaOCl: 0,71 ± 0,12; EDTA: 0,80 ± 0,17; p<0,05). Conclui-se que o cimento AH Plus apresentou valores de adesividade superiores aos obtidos pelo cimento Epiphany, independente do tratamento realizado nas paredes dos canais radiculares

Correlação genótipo-fenótipo em pacientes brasileiras com síndrome de Rett

BACKGROUND: Rett syndrome (RS) is a severe neurodevelopmental X-linked dominant disorder caused by mutations in the MECP2 gene. PURPOSE: To search for point mutations on the MECP2 gene and to establish a correlation between the main point mutations found and the phenotype. METHOD: Clinical evaluation of 105 patients, following a standard protocol. Detection of point mutations on the MECP2 gene was performed on peripheral blood DNA by sequencing the coding region of the gene. RESULTS: Classical RS was seen in 68% of the patients. Pathogenic point mutations were found in 64.1% of all patients and in 70.42% of those with the classical phenotype. Four new sequence variations were found, and their nature suggests patogenicity. Genotype-phenotype correlations were performed. CONCLUSION: Detailed clinical descriptions and identification of the underlying genetic alterations of this Brazilian RS population add to our knowledge of genotype/phenotype correlations, guiding the implementation of mutation searching programs.INTRODUÇÃO: A síndrome de Rett é uma grave doença do neurodesenvolvimento ligada ao X dominante, causada por mutações no gene MECP2. OBJETIVOS: Identificar mutações de ponto no gene MECP2 e estabelecer uma correlação entre as principais mutações encontradas e o fenótipo. MÉTODO: Avaliação clínica de 105 pacientes, seguindo um protocolo estabelecido. A identificação de mutações de ponto foi realizada em DNA de sangue periférico por sequenciamento da região codificante do gene amplificada por PCR. RESULTADOS: Em 68% dos pacientes observou-se o quadro clássico da síndrome. Mutações de ponto patogênicas foram encontradas em 64,1% dos pacientes e em 70,42% das pacientes com o quadro clássico. Quatro novas variações de seqüência foram identificadas e sua natureza sugere patogenicidade. Correlações genótipo-fenótipo foram estabelecidas. CONCLUSÃO: Descrições clínicas detalhadas desta população brasileira de pacientes acrescenta conhecimento às correlações genótipo-fenótipo nesta grave condição, que podem auxiliar na implantação de programas de triagem de mutações

Relação genética entre cepas de Neisseria meningitidis sorogrupo B sorotipo 4

We compared the results obtained by serotyping of PorB epitopes using an expanded panel of monoclonal antibodies (mAb) including mAb 7 and mAb 10, with results obtained by RFLP of rRNA genes (ribotyping). The purpose of this study was to assess the correlation between phenotypic- and genotypic- methods for typing N. meningitidis. The ribotypes obtained using ClaI or EcoRV endonucleases grouped the strains in seven and two different patterns, respectively. This additional characterization of PorB epitopes improved the correlation between these two methods of typing N. meningitidis.Nós comparamos os resultados obtidos pela sorotipagem usando um painel de anticorpos monoclonais (mAb) ao qual se incluíam os mAbs 7 e 10, com os resultados obtidos pelo RFLP do gene rRNA (ribotipagem). O propósito deste estudo foi avaliar a correlação entre os métodos fenotípico e genotípico de tipagem de N. meningitidis. Os ribotipos obtidos usando as endonucleases de restrição ClaI e EcoRV foram hábeis em dividir as cepas em sete e dois diferentes perfis de restrição, respectivamente. A caracterização adicional de epítopos na proteína PorB melhorou a correlação entre os dois métodos de tipagem de N. meningitidis

Arousal, Sleep and Cardiovascular Responses to Intermittent Hypercapnic Hypoxia in Piglets

Clinical studies have demonstrated an arousal deficit in infants suffering Obstructive Sleep Apnoea (OSA), and that treatment to alleviate the symptoms of OSA appears to reverse the deficit in arousability. Some sudden infant deaths are thought to be contingent upon such an arousal deficit. This research utilised young piglets during early postnatal development, and exposed them to intermittent hypercapnic hypoxia (IHH) as a model of clinical respiratory diseases. Arousal responses of control animals were compared to the animals exposed to IHH. Comparisons were also made between successive exposures on the first and the fourth consecutive days of IHH. Time to arouse after the onset of the respiratory stimulus, and frequency of arousals during recovery, demonstrated that arousal deficits arose after successive exposures and that these were further exacerbated on the fourth study day. After an overnight recovery period, the arousal deficit was apparently dormant, and only triggered by HH exposure. These studies confirm that both acute and chronic deficits can be induced on a background of otherwise normal postnatal development, suggesting that deficits observed in the clinical setting may be a secondary phenomenon

Adhesion of an endodontic sealer to dentin and gutta-percha: shear and push-out bond strength measurements and SEM analysis

The use of an adequate method for evaluation of the adhesion of root canal filling materials provides more reliable results to allow comparison of the materials and substantiate their clinical choice. The aims of this study were to compare the shear bond strength (SBS) test and push-out test for evaluation of the adhesion of an epoxy-based endodontic sealer (AH Plus) to dentin and gutta-percha, and to assess the failure modes on the debonded surfaces by means of scanning electron microscopy (SEM). Three groups were established (n=7): in group 1, root cylinders obtained from human canines were embedded in acrylic resin and had their canals prepared and filled with sealer; in group 2, longitudinal sections of dentin cylinders were embedded in resin with the canal surface smoothed and turned upwards; in group 3, gutta-percha cylinders were embedded in resin. Polyethylene tubes filled with sealer were positioned on the polished surface of the specimens (groups 2 and 3). The push-out test (group 1) and the SBS test (groups 2 and 3) were performed in an Instron universal testing machine running at crosshead speed of 1 mm/min. Means (±SD) in MPa were: G1 (8.8±1.13), G2 (5.9±1.05) and G3 (3.8±0.55). Statistical analysis by ANOVA and Student's t-test (a=0.05) revealed statistically significant differences (p<0.01) among the groups. SEM analysis showed a predominance of adhesive and mixed failures of AH Plus sealer. The tested surface affected significantly the results with the sealer reaching higher bond strength to dentin than to gutta-percha with the SBS test. The comparison of the employed methodologies showed that the SBS test produced significantly lower bond strength values than the push-out test, was skilful in determining the adhesion of AH Plus sealer to dentin and gutta-percha, and required specimens that could be easily prepared for SEM, presenting as a viable alternative for further experiments