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272 results on '"A. Cardenas"'

8. Unraveling Amazon tree community assembly using Maximum Information Entropy: a quantitative analysis of tropical forest ecology

Author

Pos, Edwin, de Souza Coelho, Luiz, de Andrade Lima Filho, Diogenes, Salomão, Rafael P., Amaral, Iêda Leão, de Almeida Matos, Francisca Dionízia, Castilho, Carolina V., Phillips, Oliver L., Guevara, Juan Ernesto, de Jesus Veiga Carim, Marcelo, López, Dairon Cárdenas, Magnusson, William E., Wittmann, Florian, Irume, Mariana Victória, Martins, Maria Pires, Sabatier, Daniel, da Silva Guimarães, José Renan, Molino, Jean-François, Bánki, Olaf S., Piedade, Maria Teresa Fernandez, Pitman, Nigel C. A., Mendoza, Abel Monteagudo, Ramos, José Ferreira, Hawes, Joseph E., Almeida, Everton José, Barbosa, Luciane Ferreira, Cavalheiro, Larissa, dos Santos, Márcia Cléia Vilela, Luize, Bruno Garcia, de Leão Novo, Evlyn Márcia Moraes, Vargas, Percy Núñez, Silva, Thiago Sanna Freire, Venticinque, Eduardo Martins, Manzatto, Angelo Gilberto, Reis, Neidiane Farias Costa, Terborgh, John, Casula, Katia Regina, Coronado, Euridice N. Honorio, Montero, Juan Carlos, Marimon, Beatriz S., Marimon-Junior, Ben Hur, Feldpausch, Ted R., Duque, Alvaro, Baraloto, Chris, Arboleda, Nicolás Castaño, Engel, Julien, Petronelli, Pascal, Zartman, Charles Eugene, Killeen, Timothy J., Vasquez, Rodolfo, Mostacedo, Bonifacio, Assis, Rafael L., Schöngart, Jochen, Castellanos, Hernán, de Medeiros, Marcelo Brilhante, Simon, Marcelo Fragomeni, Andrade, Ana, Camargo, José Luís, Demarchi, Layon O., Laurance, William F., Laurance, Susan G. W., de Sousa Farias, Emanuelle, Lopes, Maria Aparecida, Magalhães, José Leonardo Lima, Nascimento, Henrique Eduardo Mendonça, de Queiroz, Helder Lima, Aymard, Gerardo A. C., Brienen, Roel, Revilla, Juan David Cardenas, Costa, Flávia R. C., Quaresma, Adriano, Vieira, Ima Célia Guimarães, Cintra, Bruno Barçante Ladvocat, Stevenson, Pablo R., Feitosa, Yuri Oliveira, Duivenvoorden, Joost F., Mogollón, Hugo F., Ferreira, Leandro Valle, Comiskey, James A., Draper, Freddie, de Toledo, José Julio, Damasco, Gabriel, Dávila, Nállarett, García-Villacorta, Roosevelt, Lopes, Aline, Vicentini, Alberto, Noronha, Janaína Costa, Barbosa, Flávia Rodrigues, de Sá Carpanedo, Rainiellen, Emilio, Thaise, Levis, Carolina, de Jesus Rodrigues, Domingos, Schietti, Juliana, Souza, Priscila, Alonso, Alfonso, Dallmeier, Francisco, Gomes, Vitor H. F., Lloyd, Jon, Neill, David, de Aguiar, Daniel Praia Portela, Araujo-Murakami, Alejandro, Arroyo, Luzmila, Carvalho, Fernanda Antunes, de Souza, Fernanda Coelho, do Amaral, Dário Dantas, Feeley, Kenneth J., Gribel, Rogerio, Pansonato, Marcelo Petratti, Barlow, Jos, Berenguer, Erika, Ferreira, Joice, Fine, Paul V. A., Guedes, Marcelino Carneiro, Jimenez, Eliana M., Licona, Juan Carlos, Mora, Maria Cristina Peñuela, Peres, Carlos A., Zegarra, Boris Eduardo Villa, Cerón, Carlos, Henkel, Terry W., Maas, Paul, Silveira, Marcos, Stropp, Juliana, Thomas-Caesar, Raquel, Baker, Tim R., Daly, Doug, Dexter, Kyle G., Householder, John Ethan, Huamantupa-Chuquimaco, Isau, Pennington, Toby, Paredes, Marcos Ríos, Fuentes, Alfredo, Pena, José Luis Marcelo, Silman, Miles R., Tello, J. Sebastián, Chave, Jerome, Valverde, Fernando Cornejo, Di Fiore, Anthony, Hilário, Renato Richard, Phillips, Juan Fernando, Rivas-Torres, Gonzalo, van Andel, Tinde R., von Hildebrand, Patricio, Barbosa, Edelcilio Marques, de Matos Bonates, Luiz Carlos, Doza, Hilda Paulette Dávila, Fonty, Émile, Gómez, Ricardo Zárate, Gonzales, Therany, Gonzales, George Pepe Gallardo, Guillaumet, Jean-Louis, Hoffman, Bruce, Junqueira, André Braga, Malhi, Yadvinder, de Andrade Miranda, Ires Paula, Pinto, Linder Felipe Mozombite, Prieto, Adriana, Rudas, Agustín, Ruschel, Ademir R., Silva, Natalino, Vela, César I. A., Vos, Vincent Antoine, Zent, Egleé L., Zent, Stanford, Albuquerque, Bianca Weiss, Cano, Angela, Correa, Diego F., Costa, Janaina Barbosa Pedrosa, Flores, Bernardo Monteiro, Holmgren, Milena, Nascimento, Marcelo Trindade, Oliveira, Alexandre A., Ramirez-Angulo, Hirma, Rocha, Maira, Scudeller, Veridiana Vizoni, Sierra, Rodrigo, Tirado, Milton, Umaña, Maria Natalia, van der Heijden, Geertje, Torre, Emilio Vilanova, Vriesendorp, Corine, Wang, Ophelia, Young, Kenneth R., Reategui, Manuel Augusto Ahuite, Baider, Cláudia, Balslev, Henrik, Cárdenas, Sasha, Casas, Luisa Fernanda, Farfan-Rios, William, Ferreira, Cid, Linares-Palomino, Reynaldo, Mendoza, Casimiro, Mesones, Italo, Torres-Lezama, Armando, Giraldo, Ligia Estela Urrego, Villarroel, Daniel, Zagt, Roderick, Alexiades, Miguel N., Garcia-Cabrera, Karina, Hernandez, Lionel, Milliken, William, Cuenca, Walter Palacios, Pansini, Susamar, Pauletto, Daniela, Arevalo, Freddy Ramirez, Sampaio, Adeilza Felipe, Sandoval, Elvis H. Valderrama, Gamarra, Luis Valenzuela, Boenisch, Gerhard, Kattge, Jens, Kraft, Nathan, Levesley, Aurora, Melgaço, Karina, Pickavance, Georgia, Poorter, Lourens, and ter Steege, Hans

Published
2023
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10. Multi-organ segmentation of abdominal structures from non-contrast and contrast enhanced CT images

Author

Yu, Cenji, Anakwenze, Chidinma P, Zhao, Yao, Martin, Rachael M, Ludmir, Ethan B, S.Niedzielski, Joshua, Qureshi, Asad, Das, Prajnan, Holliday, Emma B, Raldow, Ann C, Nguyen, Callistus M, Mumme, Raymond P, Netherton, Tucker J, Rhee, Dong Joo, Gay, Skylar S, Yang, Jinzhong, Court, Laurence E, and Cardenas, Carlos E

Subjects
Medical and Biological Physics, Biomedical and Clinical Sciences, Clinical Sciences, Physical Sciences, Oncology and Carcinogenesis, Biomedical Imaging, Rare Diseases, Digestive Diseases, Clinical Research, Humans, Tomography, X-Ray Computed, Organs at Risk, Abdomen, Liver, Patient Care Planning, Image Processing, Computer-Assisted
Abstract

Manually delineating upper abdominal organs at risk (OARs) is a time-consuming task. To develop a deep-learning-based tool for accurate and robust auto-segmentation of these OARs, forty pancreatic cancer patients with contrast-enhanced breath-hold computed tomographic (CT) images were selected. We trained a three-dimensional (3D) U-Net ensemble that automatically segments all organ contours concurrently with the self-configuring nnU-Net framework. Our tool's performance was assessed on a held-out test set of 30 patients quantitatively. Five radiation oncologists from three different institutions assessed the performance of the tool using a 5-point Likert scale on an additional 75 randomly selected test patients. The mean (± std. dev.) Dice similarity coefficient values between the automatic segmentation and the ground truth on contrast-enhanced CT images were 0.80 ± 0.08, 0.89 ± 0.05, 0.90 ± 0.06, 0.92 ± 0.03, 0.96 ± 0.01, 0.97 ± 0.01, 0.96 ± 0.01, and 0.96 ± 0.01 for the duodenum, small bowel, large bowel, stomach, liver, spleen, right kidney, and left kidney, respectively. 89.3% (contrast-enhanced) and 85.3% (non-contrast-enhanced) of duodenum contours were scored as a 3 or above, which required only minor edits. More than 90% of the other organs' contours were scored as a 3 or above. Our tool achieved a high level of clinical acceptability with a small training dataset and provides accurate contours for treatment planning.

Published
2022

11. Epigenome-wide association study and epigenetic age acceleration associated with cigarette smoking among Costa Rican adults

Author

Cardenas, Andres, Ecker, Simone, Fadadu, Raj P, Huen, Karen, Orozco, Allan, McEwen, Lisa M, Engelbrecht, Hannah-Ruth, Gladish, Nicole, Kobor, Michael S, Rosero-Bixby, Luis, Dow, William H, and Rehkopf, David H

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Genetics, Tobacco Smoke and Health, Clinical Research, Human Genome, Tobacco, Aging, Cancer, Good Health and Well Being, Acceleration, Adult, Aged, Cigarette Smoking, Costa Rica, DNA, DNA Methylation, Epigenesis, Genetic, Epigenome, Hispanic or Latino, Humans
Abstract

Smoking-associated DNA methylation (DNAm) signatures are reproducible among studies of mostly European descent, with mixed evidence if smoking accelerates epigenetic aging and its relationship to longevity. We evaluated smoking-associated DNAm signatures in the Costa Rican Study on Longevity and Healthy Aging (CRELES), including participants from the high longevity region of Nicoya. We measured genome-wide DNAm in leukocytes, tested Epigenetic Age Acceleration (EAA) from five clocks and estimates of telomere length (DNAmTL), and examined effect modification by the high longevity region. 489 participants had a mean (SD) age of 79.4 (10.8) years, and 18% were from Nicoya. Overall, 7.6% reported currently smoking, 35% were former smokers, and 57.4% never smoked. 46 CpGs and five regions (e.g. AHRR, SCARNA6/SNORD39, SNORA20, and F2RL3) were differentially methylated for current smokers. Former smokers had increased Horvath's EAA (1.69-years; 95% CI 0.72, 2.67), Hannum's EAA (0.77-years; 95% CI 0.01, 1.52), GrimAge (2.34-years; 95% CI1.66, 3.02), extrinsic EAA (1.27-years; 95% CI 0.34, 2.21), intrinsic EAA (1.03-years; 95% CI 0.12, 1.94) and shorter DNAmTL (- 0.04-kb; 95% CI - 0.08, - 0.01) relative to non-smokers. There was no evidence of effect modification among residents of Nicoya. Our findings recapitulate previously reported and novel smoking-associated DNAm changes in a Latino cohort.

Published
2022

12. DNA methylation architecture of the ACE2 gene in nasal cells of children.

Author

Cardenas, Andres, Rifas-Shiman, Sheryl L, Sordillo, Joanne E, DeMeo, Dawn L, Baccarelli, Andrea A, Hivert, Marie-France, Gold, Diane R, and Oken, Emily

Subjects
Nasal Mucosa, Humans, Severity of Illness Index, Risk Factors, DNA Methylation, Adolescent, Child, Female, Male, COVID-19, Angiotensin-Converting Enzyme 2, SARS-CoV-2
Abstract

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has led to the global coronavirus disease 2019 (COVID-19) pandemic. SARS-CoV-2 enters cells via angiotensin-Converting Enzyme 2 (ACE2) receptors, highly expressed in nasal epithelium with parallel high infectivity.1,2 The nasal epigenome is in direct contact with the environment and could explain COVID-19 disparities by reflecting social and environmental influences on ACE2 regulation. We collected nasal swabs from anterior nares of 547 children, measured DNA methylation (DNAm), and tested differences at 15 ACE2 CpGs by sex, age, race/ethnicity and epigenetic age. ACE2 CpGs were differentially methylated by sex with 12 sites having lower DNAm (mean = 12.71%) and 3 sites greater DNAm (mean = 1.45%) among females relative to males. We observed differential DNAm at 5 CpGs for Hispanic females (mean absolute difference = 3.22%) and lower DNAm at 8 CpGs for Black males (mean absolute difference = 1.33%), relative to white participants. Longer DNAm telomere length was associated with greater ACE2 DNAm at 11 and 13 CpGs among males (mean absolute difference = 7.86%) and females (mean absolute difference = 8.21%), respectively. Nasal ACE2 DNAm differences could contribute to our understanding COVID-19 severity and disparities reflecting upstream environmental and social influences. Findings need to be confirmed among adults and patients with risk factors for COVID-19 severity.

Published
2021

13. Heterogeneous ozone effects on the DNA methylome of bronchial cells observed in a crossover study.

Author

Bind, M-AC, Rubin, DB, Cardenas, A, Dhingra, R, Ward-Caviness, C, Liu, Z, Mirowsky, J, Schwartz, JD, Diaz-Sanchez, D, and Devlin, RB

Abstract

We used a randomized crossover experiment to estimate the effects of ozone (vs. clean air) exposure on genome-wide DNA methylation of target bronchial epithelial cells, using 17 volunteers, each randomly exposed on two separated occasions to clean air or 0.3-ppm ozone for two hours. Twenty-four hours after exposure, participants underwent bronchoscopy to collect epithelial cells whose DNA methylation was measured using the Illumina 450 K platform. We performed global and regional tests examining the ozone versus clean air effect on the DNA methylome and calculated Fisher-exact p-values for a series of univariate tests. We found little evidence of an overall effect of ozone on the DNA methylome but some suggestive changes in PLSCR1, HCAR1, and LINC00336 DNA methylation after ozone exposure relative to clean air. We observed some participant-to-participant heterogeneity in ozone responses.

Published
2020

14. Rarity of monodominance in hyperdiverse Amazonian forests.

Author

Ter Steege, Hans, Henkel, Terry W, Helal, Nora, Marimon, Beatriz S, Marimon-Junior, Ben Hur, Huth, Andreas, Groeneveld, Jürgen, Sabatier, Daniel, Coelho, Luiz de Souza, Filho, Diogenes de Andrade Lima, Salomão, Rafael P, Amaral, Iêda Leão, Matos, Francisca Dionízia de Almeida, Castilho, Carolina V, Phillips, Oliver L, Guevara, Juan Ernesto, Carim, Marcelo de Jesus Veiga, Cárdenas López, Dairon, Magnusson, William E, Wittmann, Florian, Irume, Mariana Victória, Martins, Maria Pires, Guimarães, José Renan da Silva, Molino, Jean-François, Bánki, Olaf S, Piedade, Maria Teresa Fernandez, Pitman, Nigel CA, Mendoza, Abel Monteagudo, Ramos, José Ferreira, Luize, Bruno Garcia, Moraes de Leão Novo, Evlyn Márcia, Núñez Vargas, Percy, Silva, Thiago Sanna Freire, Venticinque, Eduardo Martins, Manzatto, Angelo Gilberto, Reis, Neidiane Farias Costa, Terborgh, John, Casula, Katia Regina, Honorio Coronado, Euridice N, Montero, Juan Carlos, Feldpausch, Ted R, Duque, Alvaro, Costa, Flávia RC, Arboleda, Nicolás Castaño, Schöngart, Jochen, Killeen, Timothy J, Vasquez, Rodolfo, Mostacedo, Bonifacio, Demarchi, Layon O, Assis, Rafael L, Baraloto, Chris, Engel, Julien, Petronelli, Pascal, Castellanos, Hernán, de Medeiros, Marcelo Brilhante, Quaresma, Adriano, Simon, Marcelo Fragomeni, Andrade, Ana, Camargo, José Luís, Laurance, Susan GW, Laurance, William F, Rincón, Lorena M, Schietti, Juliana, Sousa, Thaiane R, de Sousa Farias, Emanuelle, Lopes, Maria Aparecida, Magalhães, José Leonardo Lima, Mendonça Nascimento, Henrique Eduardo, Lima de Queiroz, Helder, Aymard C, Gerardo A, Brienen, Roel, Revilla, Juan David Cardenas, Vieira, Ima Célia Guimarães, Cintra, Bruno Barçante Ladvocat, Stevenson, Pablo R, Feitosa, Yuri Oliveira, Duivenvoorden, Joost F, Mogollón, Hugo F, Araujo-Murakami, Alejandro, Ferreira, Leandro Valle, Lozada, José Rafael, Comiskey, James A, de Toledo, José Julio, Damasco, Gabriel, Dávila, Nállarett, Draper, Freddie, García-Villacorta, Roosevelt, Lopes, Aline, Vicentini, Alberto, Alonso, Alfonso, Dallmeier, Francisco, Gomes, Vitor HF, Lloyd, Jon, Neill, David, de Aguiar, Daniel Praia Portela, Arroyo, Luzmila, Carvalho, Fernanda Antunes, de Souza, Fernanda Coelho, do Amaral, Dário Dantas, and Feeley, Kenneth J

Abstract

Tropical forests are known for their high diversity. Yet, forest patches do occur in the tropics where a single tree species is dominant. Such "monodominant" forests are known from all of the main tropical regions. For Amazonia, we sampled the occurrence of monodominance in a massive, basin-wide database of forest-inventory plots from the Amazon Tree Diversity Network (ATDN). Utilizing a simple defining metric of at least half of the trees ≥ 10 cm diameter belonging to one species, we found only a few occurrences of monodominance in Amazonia, and the phenomenon was not significantly linked to previously hypothesized life history traits such wood density, seed mass, ectomycorrhizal associations, or Rhizobium nodulation. In our analysis, coppicing (the formation of sprouts at the base of the tree or on roots) was the only trait significantly linked to monodominance. While at specific locales coppicing or ectomycorrhizal associations may confer a considerable advantage to a tree species and lead to its monodominance, very few species have these traits. Mining of the ATDN dataset suggests that monodominance is quite rare in Amazonia, and may be linked primarily to edaphic factors.

Published
2019

15. Sub-cycle dynamics in relativistic nanoplasma acceleration.

Author

Cardenas, DE, Ostermayr, TM, Di Lucchio, L, Hofmann, L, Kling, MF, Gibbon, P, Schreiber, J, and Veisz, L

Abstract

The interaction of light with nanometer-sized solids provides the means of focusing optical radiation to sub-wavelength spatial scales with associated electric field enhancements offering new opportunities for multifaceted applications. We utilize collective effects in nanoplasmas with sub-two-cycle light pulses of extreme intensity to extend the waveform-dependent electron acceleration regime into the relativistic realm, by using 106 times higher intensity than previous works to date. Through irradiation of nanometric tungsten needles, we obtain multi-MeV energy electron bunches, whose energy and direction can be steered by the combined effect of the induced near-field and the laser field. We identified a two-step mechanism for the electron acceleration: (i) ejection within a sub-half-optical-cycle into the near-field from the target at >TVm-1 acceleration fields, and (ii) subsequent acceleration in vacuum by the intense laser field. Our observations raise the prospect of isolating and controlling relativistic attosecond electron bunches, and pave the way for next generation electron and photon sources.

Published
2019

17. Diel activity patterns of two distinct populations of Aedes aegypti in Miami, FL and Brownsville, TX

Author

Mutebi, John-Paul, Wilke, André Barretto Bruno, Ostrum, Erik, Vasquez, Chalmers, Cardenas, Gabriel, Carvajal, Augusto, Moreno, Maday, Petrie, William D., Rodriguez, Arturo, Presas, Henry, Rodriguez, Jesus, Barnes, Fred, Hamer, Gabriel L., Juarez, Jose G., Carbajal, Ester, Vitek, Christopher J., Estrada, Xochitl, Rios, Thalia, Marshall, Jeremy, and Beier, John C.

Published
2022
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21. Persistent DNA methylation changes associated with prenatal mercury exposure and cognitive performance during childhood.

Author

Cardenas, Andres, Rifas-Shiman, Sheryl, Agha, Golareh, Hivert, Marie-France, Litonjua, Augusto, DeMeo, Dawn, Lin, Xihong, Amarasiriwardena, Chitra, Oken, Emily, Gillman, Matthew, and Baccarelli, Andrea

Subjects
Aryldialkylphosphatase, Cognition, DNA Methylation, Epigenesis, Genetic, Female, Fetal Blood, Humans, Maternal Exposure, Maternal-Fetal Exchange, Mercury, Pregnancy, Prenatal Exposure Delayed Effects
Abstract

Prenatal exposure to mercury, a known neurotoxic metal, is associated with lower cognitive performance during childhood. Disruption of fetal epigenetic programming could explain mercurys neurodevelopmental effects. We screened for epigenome-wide methylation differences associated with maternal prenatal blood mercury levels in 321 cord blood DNA samples and examined the persistence of these alterations during early (n = 75; 2.9-4.9 years) and mid-childhood (n = 291; 6.7-10.5 years). Among males, prenatal mercury levels were associated with lower regional cord blood DNA methylation at the Paraoxonase 1 gene (PON1) that persisted in early childhood and was attenuated in mid-childhood blood. Cord blood methylation at the PON1 locus predicted lower cognitive test scores measured during early childhood. Methylation at the PON1 locus was associated with PON1 expression in an independent set of cord blood samples. The observed persistent epigenetic disruption of the PON1 gene may modulate mercury toxicity in humans and might serve as a biomarker of exposure and disease susceptibility.

Published
2017

34. Serum angiopoietin-like 3 levels are elevated in obese non diabetic men but are unaffected during an oral glucose tolerance test

Author

Garcés, Maria Fernanda, Buell-Acosta, Julieth Daniela, Rodríguez-Navarro, Haiver Antonio, Pulido-Sánchez, Estefania, Rincon-Ramírez, Juan José, Moreno-Ordóñez, Diana Carolina, Franco-Vega, Roberto, Roncancio-Muñoz, Jhoan Sebastian, Burgos-Cardenas, Alvaro Javier, Lacunza, Ezequiel, Castaño, Justo P., Diéguez, Carlos, Nogueiras, Rubén, Sanchez, Elizabeth, and Caminos, Jorge Eduardo

Published
2020
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37. Transcriptome and methylome analysis reveals three cellular origins of pituitary tumors

Author

Taniguchi-Ponciano, Keiko, Andonegui-Elguera, Sergio, Peña-Martínez, Eduardo, Silva-Román, Gloria, Vela-Patiño, Sandra, Gomez-Apo, Erick, Chavez-Macias, Laura, Vargas-Ortega, Guadalupe, Espinosa-de-los-Monteros, Laura, Gonzalez-Virla, Baldomero, Perez, Carolina, Ferreira-Hermosillo, Aldo, Espinosa-Cardenas, Etual, Ramirez-Renteria, Claudia, Sosa, Ernesto, Lopez-Felix, Blas, Guinto, Gerardo, Marrero-Rodríguez, Daniel, and Mercado, Moises

Published
2020
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39. Biased-corrected richness estimates for the Amazonian tree flora

Author

ter Steege, Hans, Prado, Paulo I., Lima, Renato A. F. de, Pos, Edwin, de Souza Coelho, Luiz, de Andrade Lima Filho, Diogenes, Salomão, Rafael P., Amaral, Iêda Leão, de Almeida Matos, Francisca Dionízia, Castilho, Carolina V., Phillips, Oliver L., Guevara, Juan Ernesto, de Jesus Veiga Carim, Marcelo, Cárdenas López, Dairon, Magnusson, William E., Wittmann, Florian, Martins, Maria Pires, Sabatier, Daniel, Irume, Mariana Victória, da Silva Guimarães, José Renan, Molino, Jean-François, Bánki, Olaf S., Piedade, Maria Teresa Fernandez, Pitman, Nigel C. A., Ramos, José Ferreira, Monteagudo Mendoza, Abel, Venticinque, Eduardo Martins, Luize, Bruno Garcia, Núñez Vargas, Percy, Silva, Thiago Sanna Freire, de Leão Novo, Evlyn Márcia Moraes, Reis, Neidiane Farias Costa, Terborgh, John, Manzatto, Angelo Gilberto, Casula, Katia Regina, Honorio Coronado, Euridice N., Montero, Juan Carlos, Duque, Alvaro, Costa, Flávia R. C., Castaño Arboleda, Nicolás, Schöngart, Jochen, Zartman, Charles Eugene, Killeen, Timothy J., Marimon, Beatriz S., Marimon-Junior, Ben Hur, Vasquez, Rodolfo, Mostacedo, Bonifacio, Demarchi, Layon O., Feldpausch, Ted R., Engel, Julien, Petronelli, Pascal, Baraloto, Chris, Assis, Rafael L., Castellanos, Hernán, Simon, Marcelo Fragomeni, de Medeiros, Marcelo Brilhante, Quaresma, Adriano, Laurance, Susan G. W., Rincón, Lorena M., Andrade, Ana, Sousa, Thaiane R., Camargo, José Luís, Schietti, Juliana, Laurance, William F., de Queiroz, Helder Lima, Nascimento, Henrique Eduardo Mendonça, Lopes, Maria Aparecida, de Sousa Farias, Emanuelle, Magalhães, José Leonardo Lima, Brienen, Roel, Aymard C., Gerardo A., Revilla, Juan David Cardenas, Vieira, Ima Célia Guimarães, Cintra, Bruno Barçante Ladvocat, Stevenson, Pablo R., Feitosa, Yuri Oliveira, Duivenvoorden, Joost F., Mogollón, Hugo F., Araujo-Murakami, Alejandro, Ferreira, Leandro Valle, Lozada, José Rafael, Comiskey, James A., de Toledo, José Julio, Damasco, Gabriel, Dávila, Nállarett, Lopes, Aline, García-Villacorta, Roosevelt, Draper, Freddie, Vicentini, Alberto, Cornejo Valverde, Fernando, Lloyd, Jon, Gomes, Vitor H. F., Neill, David, Alonso, Alfonso, Dallmeier, Francisco, de Souza, Fernanda Coelho, Gribel, Rogerio, Arroyo, Luzmila, Carvalho, Fernanda Antunes, de Aguiar, Daniel Praia Portela, do Amaral, Dário Dantas, Pansonato, Marcelo Petratti, Feeley, Kenneth J., Berenguer, Erika, Fine, Paul V. A., Guedes, Marcelino Carneiro, Barlow, Jos, Ferreira, Joice, Villa, Boris, Peñuela Mora, Maria Cristina, Jimenez, Eliana M., Licona, Juan Carlos, Cerón, Carlos, Thomas, Raquel, Maas, Paul, Silveira, Marcos, Henkel, Terry W., Stropp, Juliana, Paredes, Marcos Ríos, Dexter, Kyle G., Daly, Doug, Baker, Tim R., Huamantupa-Chuquimaco, Isau, Milliken, William, Pennington, Toby, Tello, J. Sebastián, Pena, José Luis Marcelo, Peres, Carlos A., Klitgaard, Bente, Fuentes, Alfredo, Silman, Miles R., Di Fiore, Anthony, von Hildebrand, Patricio, Chave, Jerome, van Andel, Tinde R., Hilário, Renato Richard, Phillips, Juan Fernando, Rivas-Torres, Gonzalo, Noronha, Janaína Costa, Prieto, Adriana, Gonzales, Therany, de Sá Carpanedo, Rainiellene, Gonzales, George Pepe Gallardo, Gómez, Ricardo Zárate, de Jesus Rodrigues, Domingos, Zent, Egleé L., Ruschel, Ademir R., Vos, Vincent Antoine, Fonty, Émile, Junqueira, André Braga, Doza, Hilda Paulette Dávila, Hoffman, Bruce, Zent, Stanford, Barbosa, Edelcilio Marques, Malhi, Yadvinder, de Matos Bonates, Luiz Carlos, de Andrade Miranda, Ires Paula, Silva, Natalino, Barbosa, Flávia Rodrigues, Vela, César I. A., Pinto, Linder Felipe Mozombite, Rudas, Agustín, Albuquerque, Bianca Weiss, Umaña, Maria Natalia, Carrero Márquez, Yrma Andreina, van der Heijden, Geertje, Young, Kenneth R., Tirado, Milton, Correa, Diego F., Sierra, Rodrigo, Costa, Janaina Barbosa Pedrosa, Rocha, Maira, Vilanova Torre, Emilio, Wang, Ophelia, Oliveira, Alexandre A., Kalamandeen, Michelle, Vriesendorp, Corine, Ramirez-Angulo, Hirma, Holmgren, Milena, Nascimento, Marcelo Trindade, Galbraith, David, Flores, Bernardo Monteiro, Scudeller, Veridiana Vizoni, Cano, Angela, Ahuite Reategui, Manuel Augusto, Mesones, Italo, Baider, Cláudia, Mendoza, Casimiro, Zagt, Roderick, Urrego Giraldo, Ligia Estela, Ferreira, Cid, Villarroel, Daniel, Linares-Palomino, Reynaldo, Farfan-Rios, William, Farfan-Rios, William, Casas, Luisa Fernanda, Cárdenas, Sasha, Balslev, Henrik, Torres-Lezama, Armando, Alexiades, Miguel N., Garcia-Cabrera, Karina, Valenzuela Gamarra, Luis, Valderrama Sandoval, Elvis H., Ramirez Arevalo, Freddy, Hernandez, Lionel, Sampaio, Adeilza Felipe, Pansini, Susamar, Palacios Cuenca, Walter, de Oliveira, Edmar Almeida, Pauletto, Daniela, Levesley, Aurora, Melgaço, Karina, and Pickavance, Georgia

Published
2020
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40. The Role of Bone Morphogenetic Protein Signaling in Non-Alcoholic Fatty Liver Disease

Author

Thayer, Timothy E., Lino Cardenas, Christian L., Martyn, Trejeeve, Nicholson, Christopher J., Traeger, Lisa, Wunderer, Florian, Slocum, Charles, Sigurslid, Haakon, Shakartzi, Hannah R., O’Rourke, Caitlin, Shelton, Georgia, Buswell, Mary D., Barnes, Hanna, Neitzel, Leif R., Ledsky, Clara D., Li, Jason Pingcheng, Burke, Megan F., Farber-Eger, Eric, Perrien, Daniel S., Kumar, Ravindra, Corey, Kathleen E., Wells, Quinn S., Bloch, Kenneth D., Hong, Charles C., Bloch, Donald B., and Malhotra, Rajeev

Published
2020
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42. A novel hotspot specific isothermal amplification method for detection of the common PIK3CA p.H1047R breast cancer mutation

Author

Kalofonou, Melpomeni, Malpartida-Cardenas, Kenny, Alexandrou, George, Rodriguez-Manzano, Jesus, Yu, Ling-Shan, Miscourides, Nicholas, Allsopp, Rebecca, Gleason, Kelly L. T., Goddard, Katie, Fernandez-Garcia, Daniel, Page, Karen, Georgiou, Pantelis, Ali, Simak, Coombes, R. Charles, Shaw, Jacqueline, and Toumazou, Christofer

Published
2020
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46. Automated identification of blastocyst regions at different development stages

Author

Adolfo Flores-Saiffe, Farias, Alejandro, Chavez-Badiola, Gerardo, Mendizabal-Ruiz, Roberto, Valencia-Murillo, Andrew, Drakeley, Jacques, Cohen, and Elizabeth, Cardenas-Esparza

Subjects
Blastocyst, Multidisciplinary, Embryo, Mammalian, Zona Pellucida
Abstract

The selection of the best single blastocyst for transfer is typically based on the assessment of the morphological characteristics of the zona pellucida (ZP), trophectoderm (TE), blastocoel (BC), and inner cell-mass (ICM), using subjective and observer-dependent grading protocols. We propose the first automatic method for segmenting all morphological structures during the different developmental stages of the blastocyst (i.e., expansion, hatching, and hatched). Our database contains 592 original raw images that were augmented to 2132 for training and 55 for validation. The mean Dice similarity coefficient (DSC) was 0.87 for all pixels, and for the BC, BG (background), ICM, TE, and ZP was 0.85, 0.96, 0.54, 0.63, and 0.71, respectively. Additionally, we tested our method against a public repository of 249 images resulting in accuracies of 0.96 and 0.93 and DSC of 0.67 and 0.67 for ICM and TE, respectively. A sensitivity analysis demonstrated that our method is robust, especially for the BC, BG, TE, and ZP. It is concluded that our approach can automatically segment blastocysts from different laboratory settings and developmental phases of the blastocysts, all within a single pipeline. This approach could increase the knowledge base for embryo selection.

Published
2023

47. Urbanization favors the proliferation of Aedes aegypti and Culex quinquefasciatus in urban areas of Miami-Dade County, Florida

Author

John C. Beier, Chalmers Vasquez, André Barretto Bruno Wilke, Douglas O. Fuller, Gabriel Cardenas, Maday Moreno, William Petrie, and Augusto Carvajal

Subjects
Ecosystem ecology, Science, Biodiversity, Mosquito Vectors, Aedes aegypti, Evolutionary ecology, Article, Aedes, Abundance (ecology), Urbanization, parasitic diseases, Animals, Population Growth, Relative species abundance, Ecological epidemiology, Multidisciplinary, biology, Ecology, fungi, biology.organism_classification, Culex quinquefasciatus, Culex, Mosquito control, Geography, Florida, Medicine, Species richness
Abstract

Urbanization processes are increasing globally. Anthropogenic alterations in the environment have profound effects on biodiversity. Decreased biodiversity due to biotic homogenization processes as a consequence of urbanization often result in increased levels of mosquito vector species and vector-borne pathogen transmission. Understanding how anthropogenic alterations in the environment will affect the abundance, richness, and composition of vector mosquito species is crucial for the implementation of effective and targeted mosquito control strategies. We hypothesized that anthropogenic alterations in the environment are responsible for increasing the abundance of mosquito species that are adapted to urban environments such as Aedesaegypti and Culexquinquefasciatus. Therefore, our objective was to survey mosquito relative abundance, richness, and community composition in Miami-Dade County, Florida, in areas with different levels of urbanization. We selected 24 areas, 16 remote areas comprised of natural and rural areas, and 8 urban areas comprised of residential and touristic areas in Miami-Dade County, Florida. Mosquitoes were collected weekly in each area for 24 h for 5 consecutive weeks from August to October 2020 using BG-Sentinel traps baited with dry ice. A total of 36,645 mosquitoes were collected, from which 34,048 were collected in the remote areas and 2,597 in the urban areas. Our results show a clear and well-defined pattern of abundance, richness, and community composition according to anthropogenic modifications in land use and land cover. The more urbanized a given area the fewer species were found and those were primary vectors of arboviruses, Ae.aegypti and Cx.quinquefasciatus.

Published
2021

48. Multi-organ segmentation of abdominal structures from non-contrast and contrast enhanced CT images

Author

Cenji Yu, Chidinma P. Anakwenze, Yao Zhao, Rachael M. Martin, Ethan B. Ludmir, Joshua S.Niedzielski, Asad Qureshi, Prajnan Das, Emma B. Holliday, Ann C. Raldow, Callistus M. Nguyen, Raymond P. Mumme, Tucker J. Netherton, Dong Joo Rhee, Skylar S. Gay, Jinzhong Yang, Laurence E. Court, and Carlos E. Cardenas

Subjects
Organs at Risk, Multidisciplinary, Image Processing, Patient Care Planning, X-Ray Computed, Computer-Assisted, Rare Diseases, Liver, Clinical Research, Abdomen, Image Processing, Computer-Assisted, Humans, Biomedical Imaging, Tomography, X-Ray Computed, Digestive Diseases, Tomography
Abstract

Manually delineating upper abdominal organs at risk (OARs) is a time-consuming task. To develop a deep-learning-based tool for accurate and robust auto-segmentation of these OARs, forty pancreatic cancer patients with contrast-enhanced breath-hold computed tomographic (CT) images were selected. We trained a three-dimensional (3D) U-Net ensemble that automatically segments all organ contours concurrently with the self-configuring nnU-Net framework. Our tool’s performance was assessed on a held-out test set of 30 patients quantitatively. Five radiation oncologists from three different institutions assessed the performance of the tool using a 5-point Likert scale on an additional 75 randomly selected test patients. The mean (± std. dev.) Dice similarity coefficient values between the automatic segmentation and the ground truth on contrast-enhanced CT images were 0.80 ± 0.08, 0.89 ± 0.05, 0.90 ± 0.06, 0.92 ± 0.03, 0.96 ± 0.01, 0.97 ± 0.01, 0.96 ± 0.01, and 0.96 ± 0.01 for the duodenum, small bowel, large bowel, stomach, liver, spleen, right kidney, and left kidney, respectively. 89.3% (contrast-enhanced) and 85.3% (non-contrast-enhanced) of duodenum contours were scored as a 3 or above, which required only minor edits. More than 90% of the other organs’ contours were scored as a 3 or above. Our tool achieved a high level of clinical acceptability with a small training dataset and provides accurate contours for treatment planning.

Published
2022

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