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Benchmarking genome assemblers for four bacterial models based on contiguity, correctness, and completeness
(2025) Rojas Miranda, Hanzel Jesús; Madrigal Ly, Vanessa; Molina Mora, José Arturo
De novo genome assembly allows for the genome reconstruction of an organism without using a reference sequence. Assembly results depend on various sequencing technologies that generate data with differing fidelity, read lengths, and coverage levels, as well as on performance of a wide variety of algorithms. These attributes generate a diversity of assemblies for each single genome, which collectively defines the pan-assembly. In this study, we aimed to benchmark pan-assemblies of the prokaryotic models Brucella henselae, Escherichia coli, Pseudomonas aeruginosa, and Xylella fastidiosa, using different attributes and their impact on metrics of the 3C (contiguity, correctness, and completeness) criterion for selecting the best conditions for de novo genome assembly. Results showed that short-read assembly strategies presented higher accuracy with fewer errors (high correctness) and a high degree of completeness but lower contiguity due to fragmented assemblies. In contrast, long-read-based strategies showed high contiguity but lower completeness and accuracy. The hybrid strategy yielded the best overall results across all parameters by leveraging the strengths of both types of technology. Regarding assembly algorithms, Unicycler was the top assembler in 3C metrics, using any of the short-read (compared to Megahit), long-read (compared to Canu), or hybrid strategies (compared to Wengan). Overall, the hybrid approach with Unicycler proved to be the best general approach for genome assembly of the four bacterial models. Finally, regarding coverage depth, increasing depth did not significantly affect assembly quality results if a minimum data level was maintained, indicating that high-quality assemblies can be achieved using moderate coverage levels. Jointly, the results of the pan-assembly provide working conditions for de novo genome assembly that can be applied to bacterial models of interest, guiding the selection of optimized experimental and bioinformatics conditions while reducing sequencing costs for generating high-quality sequences.
The effect of an energy drink on cycling performance in male athletes
(2005-05) Umaña Alvarado, Mónica; Moncada Jiménez, José
Purpose: The study was designed to determine if the intake of a commerciallyavailable energy drink (ED) improves intermittent cycling performance in male athletes when compared to a placebo beverage (PL). Methods: In a double-blind, crossover randomized design, 7 young trained cyclists (Mean age = 17.14 ± 1.68 yrs. old), participated in three-50 km intermittent cycling trials. A modified version of the test designed by Schabort et al. (1998) was used, and consisted of three 1-km time trials in the 10, 32 and 48 km, as well as two 4-km time trials in the 20 and 40 km. Athletes became familiarized with the test during the first visit to the laboratory. During the second and third occasions, athletes drank 200 ml of either ED or PL every 20 min of the trial. Tests were performed one-week apart. Dependent variables were total time, 1-km time trials, 4-km time trials, ratings of perceived exertion (RPE), and gastrointestinal (GI) symptoms. Statistical analysis using SPSS 8.0 included descriptive statistics, repeated measures analysis of variance, repeated measures t-test, and McNemar X2 tests. Results: Four (36%) out of the eleven initial participants dropped out after the first test due to GI problems (n = 3) and an injury unrelated to the study protocol (n = 1). Therefore, the statistical analysis was performed on the 7 subjects who finished both experimental conditions. There was no significant mean performance time difference between ED (M= 75.29 ± 14.15 min) and PL (M= 74.00 ± 11.39 min) (p = 0.498). A significant mean difference was found in the first 4-km time trial (ED = 5.38 ± 1.00 min vs PL = 5.13 ± 0.83 min, p = 0.030). No significant mean difference in RPE was found at the end of the test (ED = 8.00 ± 2.52 vs PL = 8.00 ± 1.83). No significant associations were found between the type of drink and GI symptoms during the tests (p >.05). During the experimental tests, 5 participants (71. 4%) reported gastrointestinal problems when drinking either ED or PD. Conclusions: Compared to PL the ED did not improve intermittent cycling performance in a 50-km test. Perceived exertion was the same when drinking ED or PL. No associations were found between the type of drink and GI symptoms during the tests.
Validez factorial del cuestionario de salud SF-36 en jubilados universitarios costarricenses
(2015) Solano Mora, Luis Carlos; Moncada Jiménez, José; Araya Vargas, Gerardo Alonso; Jiménez Torres, Jairo
El propósito del estudio fue determinar la confiabilidad y la validez del Cuestionario de Salud SF-36 en un grupo de personas jubiladas universitarias costarricenses. Participaron 79 personas (39 mujeres y 40 hombres) jubiladas universitarias entre los 52 y los 75 años, quienes completaron el cuestionario SF-36. Los resultados de la confiabilidad mostraron α de Cronbach altos para tres de las sub escalas de la dimensión de Salud Física (Función Física [FF] = 0.75, Rol Físico [RF] = 0.87, Dolor Corporal [DC] = 0.81) y moderado solo en una (Salud General [SG] = 0.61). En la dimensión de Salud Mental se obtuvieron α de Cronbach altos (Salud Mental [SM] = 0.79, Rol Emocional [RE] = 0.94), uno bajo (Función Social [FS] = 0.44) y un valor negativo (Vitalidad [V] = -0.43). Con respecto a la validez de la estructura factorial, se concluye que el instrumento no mantuvo su estructura original, lo que indica que es necesario realizar un proceso de validación del instrumento SF36 antes de utilizarlo en la población de personas jubiladas en Costa Rica.
The effects of creatine supplementation on biomechanical, body composition, and performance outcomes in humans: A meta-analysis
(2006) Gutiérrez Sancho, Óscar Pablo; Moncada Jiménez, José; Salazar Rojas, Wálter; Robinson, Ellyn
Creatine supplementation has been widely used for athletes and in some studies it has been proved effective; however, there remain some moderator variables that still require meta-analysis. Therefore, the purpose of this study was to conduct such an analysis on the effects of creatine supplementation on biochemical, body composition, and physical performance variables. From a total of 120 experimental studies found in databases, only 55 studies (46 %) were considered appropriate and/or contained the necessary information to obtain effect sizes. Creatine supplementation produced biochemical changes, including increases in excretion parameters. Anthropometric variables, body fat percentage, and lean mass were favorably changed by creatine supplementation. Improved peak power, total work, force power, and a maximal repetition (1RM) were also found following creatine supplementation. There was an evident placebo effect in the variables meta-analyzed; however, there was a clear increase in total work beyond the placebo effect. In summary, creatine supplementation consistently showed positive biochemical, body composition, and power changes in humans.
Translation and cross-cultural validation of the Spanish version of the Mindful Awareness Attention Scale (MAAS): An exploratory analysis and potential applications to exercise psychology, sport and health
(2009-06) Araya Vargas, Gerardo Alonso; Gapper Morrow, Sherry; Moncada Jiménez, José; Buckworth, Jane
The purposes of the study were to (1) translate the Mindful Awareness Attention Scale (MAAS) (Brown & Ryan, 2003) into Spanish and (2) make adjustments for its application to research in exercise psychology, sport and health. For the translation and transcultural validation, the Spanish version (T4) of the MAAS scale was reviewed by 100 advanced students and professors of Physical Education of the Universidad de Costa Rica. Next, T4 and the original English MAAS were completed by 58 students of the Master's program in Translation of the Universidad Nacional (Costa Rica). The scales were randomly applied at the beginning and at the end of a three-hour class. Internal consistency measured by Cronbach's alpha coefficient was adequate (a=0.88 T4 and α=0.84 original). Scores from the two versions were significantly correlated (r=0.94; p<0.01) and were not different (t=0.73; p>0.05). Thus it was found that the Spanish version of the MAAS is sufficiently valid and reliable to be implemented in research in exercise psychology, sports and health. Further studies must test construct validity of the Spanish version of the MAAS.