Characterization of tympanic cavity volume in newborns using computerized tomography scanning / Caracterización del volumen de la cavidad timpánica en recién nacidos usando tomografía computadorizada

This study reports tympanic cavity (TC) volume in newborns, which was missing in the literature. Ex vivo histology and computerized tomography (CT) scans were performed on temporal bone and data were analyzed in part using software developed in house. CT images with a slice thickness of 0.5 mm were obtained from 5 newborn cadavers and analyzed independently by two expert researchers. The border of the TC was delineated manually and measurement of area of interest was calculated on masked images. Then, the area measurements from all sections were added to estimate the total volume. The agreements between the histological and CT findings were then compared for accuracy, repeatability and reliability. The Dice and Jaccard similarity coefficient measures were used as a statistical validation metric to evaluate the assessor's performance in manual volume segmentation. Good assessor agreement was observed with average Dice values above 0.8 indicating that consistent and reliable volume measurements were feasible. The proposed protocol was shown to be accurate in calculating the TC volume, and thus can be used for computer-assisted presurgical planning or for diagnosing structural alterations in TC.

El objetivo fue determinar el volumen de la cavidad timpánica (CT) en recién nacidos, información no encontrada en la literatura. Se realizaron escaners a través de tomografia computadorizada (TC) y estudios histológicos en el hueso temporal; los datos se analizaron utilizando un software desarrollado en nuestra institución. Se obtuvieron imágenes de secciones de TC, de 0,5 mm de grosor, a partir de 5 cadáveres de recién nacidos, los que fueron analizados de forma independiente por dos investigadores expertos. El margen de los cortes de TC fue delineado manualmente y la medición del área de interés se estimó sobre imágenes ocultas. Después, se añadieron las mediciones de área de todas las secciones para estimar el volumen total. Las concordancias entre el estudio histológico y los hallazgos de la TC se compararon en cuanto a precisión, repetibilidad y confiabilidad. Se utilizaron las medidas de coeficiente de similitud de Jaccard y Dice como métrica de validación estadística para evaluar el desempeño del asesor en la medición manual del volumen. Se observó una buena correlación del evaluador con los valores medios de Dice, por encima de 0,8 indicando que es factible obtener mediciones coherentes y confiables de volumen. El protocolo propuesto ha demostrado ser preciso para calcular el volumen de la CT, y por lo tanto se puede utilizar para la planificación prequirúrgica asistida o para el diagnóstico de alteraciones estructurales en la CT.

Exact tandem repeats analyzer (E-TRA): a new program for DNA sequence mining.

Exact Tandem Repeats Analyzer 1.0 (E-TRA) combines sequence motif searches with keywords such as 'organs', 'tissues', 'cell lines' and 'development stages' for finding simple exact tandem repeats as well as non-simple repeats. E-TRA has several advanced repeat search parameters/options compared to other repeat finder programs as it not only accepts GenBank, FASTA and expressed sequence tags (EST) sequence files, but also does analysis of multiple files with multiple sequences. The minimum and maximum tandem repeat motif lengths that E-TRA finds vary from one to one thousand. Advanced user defined parameters/options let the researchers use different minimum motif repeats search criteria for varying motif lengths simultaneously. One of the most interesting features of genomes is the presence of relatively short tandem repeats (TRs). These repeated DNA sequences are found in both prokaryotes and eukaryotes, distributed almost at random throughout the genome. Some of the tandem repeats play important roles in the regulation of gene expression whereas others do not have any known biological function as yet. Nevertheless, they have proven to be very beneficial in DNA profiling and genetic linkage analysis studies. To demonstrate the use of E-TRA, we used 5,465,605 human EST sequences derived from 18,814,550 GenBank EST sequences. Our results indicated that 12.44% (679,800) of the human EST sequences contained simple and non-simple repeat string patterns varying from one to 126 nucleotides in length. The results also revealed that human organs, tissues, cell lines and different developmental stages differed in number of repeats as well as repeat composition, indicating that the distribution of expressed tandem repeats among tissues or organs are not random, thus differing from the un-transcribed repeats found in genomes.