Rapid detection of multidrug-resistant Mycobacterium tuberculosis by multiplex allele-specific polymerase chain reaction

OBJECTIVE: To evaluate a multiplex allele-specifi c polymerase chain reaction (MAS-PCR) to detect multidrugresistant tuberculosis (MDR-TB) clinical isolates and to describe the main mutations conferring resistance to isoniazid (INH) and rifampicin (RMP). DESIGN: Drug-resistant Mycobacterium tuberculosis clinical isolates were tested to detect mutations using MAS-PCR. The genes involved were katG, inhA promoter and rpoB. RESULTS: Among 193 clinical isolates included in the study, 52.6% of the INH-resistant isolates presented a mutation in the katG (315) gene, 28.1% in the inhAP (−15) and 3.0% in both. For the rpoB gene, 60% of the RMP-resistant isolates showed a mutation in codon 531, 17.5% in 526 and 2.5% in 516. Results were compared with those obtained by sequencing, and 100% concordance was obtained for the detection of the mutation in katG (315), 94.1% for inhAP (−15), and 97.8% for rpoB. The global concordance between both methods was 98%. CONCLUSIONS: The MAS-PCR system allowed the simultaneous and rapid detection of approximately 80.0% of the drug-resistant clinical isolates. This method could be used as a rapid and simple screening tool to detect drug-resistant TB in clinical practice.Fil: Imperiale, Belén Rocío. Provincia de Buenos Aires. Ministerio de Salud. Hospital ; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Cataldi, Ángel Adrián. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Morcillo, N. S.. Provincia de Buenos Aires. Ministerio de Salud. Hospital ; Argentin

Incorporación de n-gramas discriminativos para mejorar un reconocedor de idioma fonotáctico basado en i-vectores

Este artículo describe una nueva técnica que permite combinar la información de dos sistemas fonotácticos distintos con el objetivo de mejorar los resultados de un sistema de reconocimiento automático de idioma. El primer sistema se basa en la creación de cuentas de posteriorgramas utilizadas para la generación de i-vectores, y el segundo es una variante del primero que tiene en cuenta los n-gramas más discriminativos en función de su ocurrencia en un idioma frente a todos los demás. La técnica propuesta permite obtener una mejora relativa de 8.63% en Cavg sobre los datos de evaluación utilizados para la competición ALBAYZIN 2012 LRE

Low-resource language recognition using a fusion of phoneme posteriorgram counts, acoustic and glottal-based i-vectors

This paper presents a description of our system for the Albayzin 2012 LRE competition. One of the main characteristics of this evaluation was the reduced number of available files for training the system, especially for the empty condition where no training data set was provided but only a development set. In addition, the whole database was created from online videos and around one third of the training data was labeled as noisy files. Our primary system was the fusion of three different i-vector based systems: one acoustic system based on MFCCs, a phonotactic system using trigrams of phone-posteriorgram counts, and another acoustic system based on RPLPs that improved robustness against noise. A contrastive system that included new features based on the glottal source was also presented. Official and postevaluation results for all the conditions using the proposed metrics for the evaluation and the Cavg metric are presented in the paper

Protein Fold Recognition from Sequences using Convolutional and Recurrent Neural Networks

The identification of a protein fold type from its amino acid sequence provides important insights about the protein 3D structure. In this paper, we propose a deep learning architecture that can process protein residue-level features to address the protein fold recognition task. Our neural network model combines 1D-convolutional layers with gated recurrent unit (GRU) layers. The GRU cells, as recurrent layers, cope with the processing issues associated to the highly variable protein sequence lengths and so extract a fold-related embedding of fixed size for each protein domain. These embeddings are then used to perform the pairwise fold recognition task, which is based on transferring the fold type of the most similar template structure. We compare our model with several template-based and deep learning-based methods from the state-of-the-art. The evaluation results over the well-known LINDAHL and SCOP_TEST sets,along with a proposed LINDAHL test set updated to SCOP 1.75, show that our embeddings perform significantly better than these methods, specially at the fold level. Supplementary material, source code and trained models are available at http://sigmat.ugr.es/~amelia/CNN-GRU-RF+/

Fast computation of shielding effectiveness of metallic enclosures with apertures and inner elements

In this study, radiated immunity and emission of a metallic box with apertures have been evaluated through a fast approach. The influence of printed circuit boards inside the enclosure has been studied and also the effect of placing conductive polymer sheets in the housing in order to characterize the behaviour of these materials used nowadays for shielding cabinets. Measurements have been carried out in anechoic chamber in order to evaluate the approximated technique showing its limitations and advantages. Since good agreement has been found between simulations and measurements, this approach can be used for design or optimization purposes with the main advantage of reduced time calculations.This work has been funded by Fundación Séneca, Agencia Regional de Ciencia y Tecnología through the project 00700/PPC/04

Primera evaluación en Argentina de GenoType® MTBDRplus para la detección de Mycobacterium tuberculosis multidrogo-resistente desde aislamientos y especímenes clínicos

Tuberculosis (tB) and multidrug and extensively drug-resistant (dR) tB are important public health problems that are spreading worldwide. The aims of this study were to determine the sensitivity and specificity of the genotype® mtBdRplus assay from smear-positive clinical specimens and isolates and to explore its possible application in routine work. Clinical samples were previously decontaminated using naoH-n-acetyl-l-cystein or naoH-Clna hypertonic solution for Ziehl-neelsen staining and cultures. The leftover sediments of smear-positive samples were stored at -20 °C, 70 of which were selected to be included in this study according to their dR profile. thirty dR Mycobacterium tuberculosis isolates were also assessed. Sequencing was used as gold standard to detect mutations conferring isoniazid (InH) and rifampicin (RIF) resistance. Valid results were obtained in 94.0 % of the samples and 85.5 % (53/62) of the InH-R samples were properly identified. mutations in the katGS315t gene and inhA C-15t gene promoter region were present in 59.7 % (37/62) and 25.8 % (16/62) of the InH-R samples, respectively. the system could also identify 97.7 % (41/42) of the RIF-R samples; the mutations found were rpoBS531l (66.7 %, 28/42), d516V (19.0 %, 8/42), H526Y and S531p/W (4.8 %, 2/42 each one), and S522l/Q (2.4 %, 1/42). a 98.8 % concordance between the genotype assay and sequencing was obtained. genotype® mtBdRplus has demonstrated to be easy to implement and to perform in clinical laboratories and useful for a rapid detection of dR M. tuberculosis from decontaminated sputa and clinical isolates. Therefore, this assay could be applied as a rapid tool to predict InH-R and/or RIF-R in dR risk cases.La tuberculosis (TBC), y la TBC multi y extensivamente drogo-resistentes (DR) son importantes problemas de salud pública mundial. El objetivo de este estudio fue determinar la sensibilidad y especificidad del sistema GenoType® MTBDRplus a partir de esputos (baciloscopía positiva) y aislamientos clínicos de Mycobacterium tuberculosis, explorando su aplicación clínica. Previo a la tinción de Ziehl-Neelsen y al cultivo, las muestras fueron descontaminadas mediante NaOH-N-acetyl-L-cisteina o la solución hipertónica NaOH-NaCl. Los sedimentos remanentes se conservaron a –20 ºC, y 70 de ellos fueron incluidos en este estudio según su perfil de DR. Treinta cepas de M. tuberculosis DR fueron también evaluadas. La secuenciación fue utilizada como método de referencia para la detección de mutaciones que confieren resistencia a isoniacida (INH) y rifampicina (RIF). Se obtuvieron resultados válidos en el 94,0 % de las muestras, identificándose al 85,5 % (53/62) de las INH-R. La mutación katG S315T estuvo presente en 59,7 % (37/62), y la mutación C-15T del promotor del gen inhA en 25,8 % (16/62) de las mismas. El sistema identificó el 97,7 % (41/42) de las muestras RIF-R. Las mutaciones encontradas fueron rpoB S531L (66,7 %, 28/42), D516V (19,0 %, 8/42), H526Y y S531P/W (4,8 %, 2/42 cada una de ellas) y S522L/Q (2,4 %, 1/42). La concordancia entre el GenoType y la secuenciación fue del 98,8 %. El sistema GenoType® MTBDRplus resultó ser útil, fácil de realizar e implementar para la detección rápida de M. tuberculosis DR. Por lo tanto, este ensayo podría ser aplicado como una herramienta rápida para el diagnostico de TBC DR, principalmente en aquellos casos asociados a factores de riesgo.Fil: Imperiale, Belén Rocío. Provincia de Buenos Aires. Ministerio de Salud. Hospital ; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Zumárraga, Martín José. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Weltman, Gabriela. Provincia de Buenos Aires. Ministerio de Salud. Hospital ; ArgentinaFil: Zudiker, Roxana. Provincia de Buenos Aires. Ministerio de Salud. Hospital ; ArgentinaFil: Cataldi, Ángel Adrián. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Morcillo, Nora Susana. Provincia de Buenos Aires. Ministerio de Salud. Hospital ; Argentin

Primera evaluación en Argentina de GenoType® MTBDRplus para la detección de Mycobacterium tuberculosis multidrogo-resistente desde aislamientos y especímenes clínicos

Tuberculosis (tB) and multidrug and extensively drug-resistant (dR) tB are important public health problems that are spreading worldwide. The aims of this study were to determine the sensitivity and specificity of the genotype® mtBdRplus assay from smear-positive clinical specimens and isolates and to explore its possible application in routine work. Clinical samples were previously decontaminated using naoH-n-acetyl-l-cystein or naoH-Clna hypertonic solution for Ziehl-neelsen staining and cultures. The leftover sediments of smear-positive samples were stored at -20 °C, 70 of which were selected to be included in this study according to their dR profile. thirty dR Mycobacterium tuberculosis isolates were also assessed. Sequencing was used as gold standard to detect mutations conferring isoniazid (InH) and rifampicin (RIF) resistance. Valid results were obtained in 94.0 % of the samples and 85.5 % (53/62) of the InH-R samples were properly identified. mutations in the katGS315t gene and inhA C-15t gene promoter region were present in 59.7 % (37/62) and 25.8 % (16/62) of the InH-R samples, respectively. the system could also identify 97.7 % (41/42) of the RIF-R samples; the mutations found were rpoBS531l (66.7 %, 28/42), d516V (19.0 %, 8/42), H526Y and S531p/W (4.8 %, 2/42 each one), and S522l/Q (2.4 %, 1/42). a 98.8 % concordance between the genotype assay and sequencing was obtained. genotype® mtBdRplus has demonstrated to be easy to implement and to perform in clinical laboratories and useful for a rapid detection of dR M. tuberculosis from decontaminated sputa and clinical isolates. Therefore, this assay could be applied as a rapid tool to predict InH-R and/or RIF-R in dR risk cases.La tuberculosis (TBC), y la TBC multi y extensivamente drogo-resistentes (DR) son importantes problemas de salud pública mundial. El objetivo de este estudio fue determinar la sensibilidad y especificidad del sistema GenoType® MTBDRplus a partir de esputos (baciloscopía positiva) y aislamientos clínicos de Mycobacterium tuberculosis, explorando su aplicación clínica. Previo a la tinción de Ziehl-Neelsen y al cultivo, las muestras fueron descontaminadas mediante NaOH-N-acetyl-L-cisteina o la solución hipertónica NaOH-NaCl. Los sedimentos remanentes se conservaron a –20 ºC, y 70 de ellos fueron incluidos en este estudio según su perfil de DR. Treinta cepas de M. tuberculosis DR fueron también evaluadas. La secuenciación fue utilizada como método de referencia para la detección de mutaciones que confieren resistencia a isoniacida (INH) y rifampicina (RIF). Se obtuvieron resultados válidos en el 94,0 % de las muestras, identificándose al 85,5 % (53/62) de las INH-R. La mutación katG S315T estuvo presente en 59,7 % (37/62), y la mutación C-15T del promotor del gen inhA en 25,8 % (16/62) de las mismas. El sistema identificó el 97,7 % (41/42) de las muestras RIF-R. Las mutaciones encontradas fueron rpoB S531L (66,7 %, 28/42), D516V (19,0 %, 8/42), H526Y y S531P/W (4,8 %, 2/42 cada una de ellas) y S522L/Q (2,4 %, 1/42). La concordancia entre el GenoType y la secuenciación fue del 98,8 %. El sistema GenoType® MTBDRplus resultó ser útil, fácil de realizar e implementar para la detección rápida de M. tuberculosis DR. Por lo tanto, este ensayo podría ser aplicado como una herramienta rápida para el diagnostico de TBC DR, principalmente en aquellos casos asociados a factores de riesgo.Fil: Imperiale, Belén Rocío. Provincia de Buenos Aires. Ministerio de Salud. Hospital ; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Zumárraga, Martín José. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Weltman, Gabriela. Provincia de Buenos Aires. Ministerio de Salud. Hospital ; ArgentinaFil: Zudiker, Roxana. Provincia de Buenos Aires. Ministerio de Salud. Hospital ; ArgentinaFil: Cataldi, Ángel Adrián. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Morcillo, Nora Susana. Provincia de Buenos Aires. Ministerio de Salud. Hospital ; Argentin

Un proyecto audiovisual sobre el equilibrio químico para el máster en formación del profesorado de educación secundaria

La implantación del Máster en Formación del Profesorado de Educación Secundaria y Bachillerato, Formación Profesional y Enseñanza de Idiomas (MFPS) está suponiendo la participación de profesorado de diferentes áreas de conocimiento procedentes de distintas facultades. Desde el punto de vista de las didáctica de la química es una gran oportunidad para acercar los resultados de la investigación a otros ámbitos disciplinares de la química y posibilitar su puesta en práctica. Con esta intención, en la UCM, se ha llevado a cabo un proyecto audiovisual, sobre una propuesta didáctica para el equilibrio químico, como estrategia didáctica para la formación inicial de futuros profesores de secundaria de Física y Química

Chiral Distorted Hexa-peri-hexabenzocoronenes Bearing a Nonagon-Embedded Carbohelicene

We acknowledge the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (ERC-2015-STG-677023), the Ministerio de Ciencia, Innovacion y Universidades (MICIU/FEDER/AEI, Spain, PGC2018-101181-B-I00), the Universidad de Granada (UGR) (Plan Propio - Intensificacion de la Investigacion PP2017-PRI.I-02) and the Swiss National Science Foundation (Spark 2019 Grant CRSK-2_190365) for financial support. We thank the CSIRC-Alhambra, the Service and Support for Science IT (S3IT) of the University of Zurich and Prof.Dr. Michal Juriek for supercomputing facilities. Funding for open access charge: Universidad de Granada/CBUA.A new family of chiral saddle-helix hybrid nanographenes is reported. The first hexa-peri-hexabenzocoronene (HBC) analogues bearing a nine-membered carbocycle are presented. Furthermore, for the first time, pi-extended carbo[n]helicenes containing a nine-membered ring as part of the helical moiety have been synthesized. The combination of a [5]helicene moiety and a nonagon ring in a single chiral motif induces a tremendous distortion from planarity into the nanographenic structures compared to other saddle-helix hybrids such as heptagon- and octagon-containing pi-extended carbo[5]helicenes. In fact, the interplanar angle of the two terminal rings reaches the largest angle (134.8 degrees) of a carbohelicene reported to date, thus being by far the most twisted helicene yet prepared. Photophysical properties evaluation showed improved absorption dissymmetry factors (|g(abs)|=4.2x10(-3)) in the new family of nonagon-containing pi-extended carbo[5]helicenes.European Research Council (ERC) ERC-2015-STG-677023Ministerio de Ciencia, Innovacion y Universidades (MICIU/FEDER/AEI, Spain) PGC2018-101181-B-I00Universidad de Granada (UGR) (Plan Propio - Intensificacion de la Investigacion) PP2017-PRI.I-02Swiss National Science Foundation (SNSF) European Commission CRSK-2_190365Universidad de Granada/CBU

IKKβ overexpression together with a lack of tumour suppressor genes causes ameloblastic odontomas in mice

Odontogenic tumours are a heterogeneous group of lesions that develop in the oral cavity region and are characterized by the formation of tumoural structures that differentiate as teeth. Due to the diversity of their histopathological characteristics and clinical behaviour, the classification of these tumours is still under debate. Alterations in morphogenesis pathways such as the Hedgehog, MAPK and WNT/β-catenin pathways are implicated in the formation of odontogenic lesions, but the molecular bases of many of these lesions are still unknown. In this study, we used genetically modified mice to study the role of IKKβ (a fundamental regulator of NF-κB activity and many other proteins) in oral epithelial cells and odontogenic tissues. Transgenic mice overexpressing IKKβ in oral epithelial cells show a significant increase in immune cells in both the oral epithelia and oral submucosa. They also show changes in the expression of several proteins and miRNAs that are important for cancer development. Interestingly, we found that overactivity of IKKβ in oral epithelia and odontogenic tissues, in conjunction with the loss of tumour suppressor proteins (p53, or p16 and p19), leads to the appearance of odontogenic tumours that can be classified as ameloblastic odontomas, sometimes accompanied by foci of secondary ameloblastic carcinomas. These tumours show NF-κB activation and increased β-catenin activity. These findings may help to elucidate the molecular determinants of odontogenic tumourigenesis and the role of IKKβ in the homoeostasis and tumoural transformation of oral and odontogenic epitheliaThis work was funded by project PI17/00578, from the “Instituto de Salud Carlos III” (Ministry of Science, Innovation and Universities) and co-funded by the European Regional Development Fund, and approved by the Ethics Committee of our Institution. It has been founded also by projects CB16/12/00228, PI16/00161, RD16/0011/0011, RD12/0019/0023 and SAF2017–84248-PS