The correctness of large scale analysis of genomic data

Implementing a large genomic project is a demanding task, also from the computer science point of view. Besides collecting many genome samples and sequencing them, there is processing of a huge amount of data at every stage of their production and analysis. Efficient transfer and storage of the data is also an important issue. During the execution of such a project, there is a need to maintain work standards and control quality of the results, which can be difficult if a part of the work is carried out externally. Here, we describe our experience with such data quality analysis on a number of levels - from an obvious check of the quality of the results obtained, to examining consistency of the data at various stages of their processing, to verifying, as far as possible, their compatibility with the data describing the sample.

A graph-based data quality analysis in distributed telemedicine systems

Telemedicine is one of the most rapidly developing areas of healthcare and it plays an increasing role in modern medicine. As the amount of data and demand for features increase, the data paths are becoming ever-more complex. Owing to this, it is vital in telemedicine to find a proper balance between consistency and availability under any given circumstances. However, making a trade-off can significantly influence the quality of the data. This study seeks to get an in-depth view of the problem by considering a real-world telemedicine use-case and elaborating the formal system specification of the scenario. After evaluating the specification, the constructed state graph is examined using graph coloring and other graph algorithms.

Influencia del juego interior de la selección española de baloncesto en el rendimiento: análisis de coordenadas polares.

En los últimos años se ha incrementado el interés por conocer las acciones más efectivas durante la competición ya que este hecho se ha mostrado esencial para mejorar el rendimiento de los jugadores en el deporte de élite; particularmente en los deportes colectivos el análisis táctico ha crecido de forma exponencial. El objetivo de este estudio fue detectar las relaciones que se establecen entre las conductas de finalización de los jugadores interiores de un equipo de baloncesto y su repercusión en el rendimiento del equipo. Para ello, y utilizando un diseño nomotético, de seguimiento y multidimensional, se realizó un análisis de coordenadas polares con las observaciones del juego de la Selección Española de Baloncesto Senior Masculina durante su participación en el Campeonato de Europa de 2015. La herramienta de observación creada ha superado el análisis de calidad del dato exigible en Metodología Observacional y está compuesta por 5 criterios y 29 categorías exhaustivas y mutuamente excluyentes. Se registraron un total de 316 acciones ofensivas, que pusieron de manifiesto la influencia de los jugadores que ocupan las posiciones interiores en el ataque estático. Los resultados muestran una alta efectividad cuando los ataques son acabados por ellos y la alta producción ofensiva de estos jugadores en acciones individuales, siendo capaces de conseguir canastas o provocar faltas a sus defensores. El análisis de coordenadas polares se ha mostrado como una técnica útil para el análisis táctico de las conductas que suceden en el deporte de competición. In recent years, there has been an increased interest in knowing the most effective actions during competition, as this fact has proven essential to improve the performance of players in elite sport; particularly in team sports, tactical analysis has grown exponentially. The objective of this study was to detect the relationships that were obtained between the finishing behaviors of the inside players of a basketball team and it is impact on team performance. To do so, and using nomothetic, follow-up and multidimensional observational design, polar coordinates analysis was performed from the observations of the game of the Spanish men basketball team during European Championships in 2015. The observational tool, formed by 5 criteria and 29 exhaustive and mutually exclusive categories, was created and passed the data quality analysis required in Observational Methodology. A total of 316 offensive actions were registered and revealed the influence of the inside players in the static attack. The results showed a high effectiveness when the attacks are finished by inside players, and the high offensive production of these players in individual actions, being able to get baskets or cause fouls to their defenders. Polar coordinates analysis has been shown as a useful technique to tactical analysis of the behaviors that occur in competitive sport. Nos últimos anos tem havido um interesse crescente em conhecer as acções mais eficazes durante a competição, uma vez que este facto se revelou essencial para melhorar o desempenho dos jogadores no desporto de elite; particularmente nos desportos colectivos, a análise táctica tem crescido exponencialmente. O objectivo deste estudo era detectar as relações estabelecidas entre os comportamentos finais dos jogadores internos de uma equipa de basquetebol e o seu impacto no desempenho da equipa. Para o fazer, e utilizando um design nomotético, de seguimento e multidimensional, foi realizada uma análise de coordenadas polares com as observações do jogo da Selecção Espanhola de Basquetebol Masculino Sénior durante a sua participação no Campeonato Europeu de 2015. O instrumento de observação criado passou a análise da qualidade dos dados exigida na Metodologia de Observação e é composto por 5 critérios e 29 categorias exaustivas e mutuamente excludentes. Foi registado um total de 316 acções ofensivas, que mostraram a influência de jogadores que ocupavam posições internas no ataque estático. Os resultados mostram uma elevada eficácia quando os ataques são finalizados por eles e a elevada produção ofensiva destes jogadores em acções individuais, podendo obter cestos ou causar faltas aos seus defensores. A análise das coordenadas polares demonstrou ser uma técnica útil para a análise táctica dos comportamentos que ocorrem no desporto de competição.

Detection of genes responsible for cetuximab sensitization in colorectal cancer cells using CRISPR-Cas9

Colorectal cancer (CRC) is a common malignant tumor in digestive tract with highly invasive and metastatic capacity. Drug sensitivity remains a significant obstacle to successful chemotherapy in CRC patients. The present study aimed to explore genes related to cetuximab (CTX) sensitivity in CRC by clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9. Celigo image cytometer was used to detect suitable cells and optimal dosage of CTX. Inhibition rate of CTX on Caco-2 cells was evaluated by cell counting kit-8 (CCK-8) method before and after transfection. 3-(4,5-dimethylthiazol-2-yl)2,5-diphenyl tetrazolium bromide (MTT) was performed to explore suitable concentration of puromycin and multiplicity of infection (MOI). CRISPR-Cas9, sequencing data quality analysis and cell viability test were used for the selection of genes related to CTX sensitivity in CRC cells. Finally, the selected genes associated with CTX sensitivity in CRC cells were further validated by colony formation and CCK-8 assays. In the present study, Caco-2 cells had a better prolificacy, and CTX 100 μg/ml exhibited a good inhibition trend on the 7th and 14th days of infection. MTT assay indicated that the minimum lethal concentration of puromycin was 2.5 μg/ml. Forty-six candidate genes were preliminarily screened via sequencing data quality analysis. Subsequently, we found that knockout of any of the four genes (MMP15, MRPL48, CALN1 and HADHB) could enhance CTX sensitivity in Caco-2 cells, which was further confirmed by colony formation assay. In summary, MMP15, MRPL48, CALN1 and HADHB genes are related to the mediation of CTX sensitivity in CRC.