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DeWAFF: A novel image abstraction approach to improve the performance of a cell tracking system
(IEEE, 2015-06-16) Calderón Ramírez, Saúl; Sáenz, Aránzazu; Mora Rodríguez, Rodrigo Antonio; Siles Canales, Francisco; Orozco, I.; Buemi, M. E.
This paper presents a new image abstraction approach, aiming to improve typical image related pattern recognition tasks such as segmentation, tracking, and classification. The proposed image abstraction framework performs image denoising and homogeneous region simplification, along with border and region enhancement. The proposed framework consists in a novel generalized approach of common weighted averaging denoising algorithms mixed with Unsharp Masking (USM) border enhancement techniques, to avoid typical USM artifacts as ringing. Results of the different configurations within the image abstraction framework for a cell tracking application are presented.
miR-124-2, miR-92-A1 and miR-372 regulate differential gene expression in a mathematical model of the progression of ductal carcinoma in situ (DCIS) to microinvasive breast cancer (MIBC)
(2022-02-02) Chinchilla Monge, Ricardo; Chaves Chaves, Noé; Mora Rodríguez, Rodrigo Antonio
Breast cancer is a widely studied genetic disease that has a clear division between an initial stage, starting with the atypical ductal hyperplasia progressing to ductal carcinoma in situ and ending, although not necessarily, with invasive breast cancer. Nonetheless, if the invasive breast cancer has only colonized less than 1mm of healthy estroma it is classified as microinvasive breast carcinoma. We hypothesized that differentially expressed genes in tumoral cells of early carcinoma are regulated by specific miRNAs and TF that stimulate the progression to an invasive stage. Our main goal was to reach a minimal model that can explain this behavior and identify promising miRNA targets with therapeutic potential. Using BioNetUCR and COPASI for a systems biology approach, we identified miRNAs miR-372, miR-124-2 and miR-92-A1 that modify the differential gene expression in MIBC stage. These miRNAs have potential as therapeutic targets for future treatment strategies by suppressing the transition from DCIS to IBC. There are few studies about DCIS to MIBC transition, but with this computational approach we present one of the first in silico models for this type of cell transition.
mi-RNA129-1 and mi-RNA24-2 as regulators of over-expressed genes in lung typical carcinoid tumors: Potential targets for molecular therapy
(2023-02-02) Abbas Chakhtoura, Jad; Mora RodrÍguez, Rodrigo Antonio; Chinchilla Monge, Ricardo
Lung carcinoid tumors are malignant neuroendocrine neoplasms that account for less than 2% of all lung malignancies and include two histological types: typical and atypical carcinoid tumors. Typical carcinoid tumors do not include areas of necrosis and show less than 2 mitotic figures within 10 high grade fields. On the molecular level, carcinoid tumors present alterations in gene MEN1 as well as a high expression of genes ASCL1 and EIF1AX. We report a systems biology approach using BioNetUCR and Copasi in addition to Cytoscape to identify mi-RNA regulators of the most important altered genes in typical pulmonary carcinoid tumors. The final adjusted and reduced interaction network of our genes of interest included: 3 genes 12 transcription factors and 7 mi-RNAs, leading to a total of 22 nodes and 53 edges. Analysis with Copasi showed that MIR24-2 regulates the expression of MEN1 and MIR129-1 regulates the expression of AIF1AX. Those mi-RNAs could be potential targets for molecular therapy in patients with typical carcinoid tumor of lung.
Analysis of large scale gene expression data sets from TCGA identifies potential candidate genes under dosage compensation in breast cancer
(2018) Oviedo Blanco, Guillermo; Acon Chan, Man Sai; Guevara Coto, José Andrés; Mora Rodríguez, Rodrigo Antonio
In a previous effort, we developed a model to study the hypothesis of gene dosage compensation in the limited data set of NCI60 cancer cell lines. Currently, we have developed a pipeline to extract data from TCGA in order to expand our analysis into larger data sets. To validate our approaches we focused on breast cancer as a test case. Using GMM we identified a cluster of candidate genes, which were subjected to a linear fit to determine potential dosage compensation. This adds support to our hypothesis with about dosage compensation in the NCI60 panel. These genes have multiple structural and functional annotations. These include their over-representation in chromosomes 8,11 and 17. Molecular functions such as protein complex interactions were identified. We found that the candidates are interconnected by a large-scale network of miRNA-TF interactions. These results contribute to the understanding of the phenomenon of gene dosage compensation in cancer and its possible application in developing novel therapies against aneuploid cancer.
Revisión bibliográfica y propuesta de protocolo para la valoración pre-trasplante del riesgo de infecciones de los pacientes candidatos a trasplante renal y hepático pediátrico en el Hospital Nacional de Niños “Dr. Carlos Sáenz Herrera”
(2026) Vílchez León, Mariana; Soriano Fallas, Alejandra
Las infecciones son complicaciones frecuentes en los pacientes trasplantados que confieren alta morbilidad y mortalidad. Además, el tratamiento inmunosupresor recibido por estos pacientes incrementa su vulnerabilidad a infecciones, cuyo riesgo y agentes causales dependen de factores como la edad, comorbilidades, el grado de inmunosupresión y el tiempo en relación con el trasplante. Una evaluación infectológica integral pre-trasplante que incluya factores socio-epidemiológicos, factores de riesgo de exposición, patrón de infecciones previas y el estado vacunal de los pacientes candidatos a ser sometidos a trasplante permite la identificación de infecciones activas que requieren tratamiento o infecciones latentes con potencial de reactivación durante la inmunosupresión, asesorar y optimizar la protección contra infecciones inmunoprevenibles mediante la vacunación y predecir los potenciales agentes infecciosos que podrían afectar a estos pacientes en las diferentes etapas post- trasplante.
Esta evaluación además facilita el establecimiento de un plan de abordaje diagnóstico y tratamiento profiláctico o empírico, según corresponda, en caso de sospecha de infección en el periodo post- trasplante.
Este estudio enumera la evidencia científica disponible y actualizada referente a las mejores prácticas para evaluar y estratificar el riesgo de infecciones en el periodo pre-trasplante en pacientes pediátricos candidatos a trasplante de riñón o hígado y basada en esta evidencia, se propone un protocolo de abordaje para el servicio de Infectología del Hospital Nacional de Niños “Dr. Carlos Sáenz Herrera”, para la identificación de infecciones y estratificación de riesgo de infecciones de los pacientes candidatos a trasplante pediátrico de hígado y de riñón en el periodo pre-trasplante.