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3. Gut bacterial nutrient preferences quantified in vivo.

Author

Zeng, Xianfeng, Xing, Xi, Gupta, Meera, Keber, Felix, Lopez, Jaime, Lee, Ying-Chiang, Roichman, Asael, Wang, Lin, Neinast, Michael, Donia, Mohamed, Wühr, Martin, Rabinowitz, Joshua, and Jang, Cholsoon

Subjects
diet, host-microbiome interactions, isotope tracing, metabolism, metabolomics, methodology, mice, microbiome, nutrient, proteomics, Animals, Bacteria, Diet, Dietary Fiber, Dietary Proteins, Gastrointestinal Microbiome, Lactates, Mice, Nutrients
Abstract

Great progress has been made in understanding gut microbiomes products and their effects on health and disease. Less attention, however, has been given to the inputs that gut bacteria consume. Here, we quantitatively examine inputs and outputs of the mouse gut microbiome, using isotope tracing. The main input to microbial carbohydrate fermentation is dietary fiber and to branched-chain fatty acids and aromatic metabolites is dietary protein. In addition, circulating host lactate, 3-hydroxybutyrate, and urea (but not glucose or amino acids) feed the gut microbiome. To determine the nutrient preferences across bacteria, we traced into genus-specific bacterial protein sequences. We found systematic differences in nutrient use: most genera in the phylum Firmicutes prefer dietary protein, Bacteroides dietary fiber, and Akkermansia circulating host lactate. Such preferences correlate with microbiome composition changes in response to dietary modifications. Thus, diet shapes the microbiome by promoting the growth of bacteria that preferentially use the ingested nutrients.

Published
2022

4. International consensus on sleep problems in pediatric palliative care: Paving the way

Author

Li, Albert, Wolfson, Amy R., Marinetto, Anna, Santini, Anna, Zanin, Anna, Kuhn, Brett R., Angelhoff, Charlotte, Santos, Cristiane Fumo dos, Goh, Daniel Y.T., Verrillo, Elisabetta, Zhou, Eric S., Ferreira, Esther Angélica Luiz, Bergstraesser, Eva, Pizza, Fabio, Nilsson, Frans, Plazzi, Giuseppe, Wang, Guanghai, Traslaviña, Guillermo Andrey Ariza, Moreira, Gustavo Antonio, Siden, Hal, Hauch, Holger, Huijer, Huda Abu-Saad, Catalano, Igor, Narang, Indra, Avagnina, Irene, Lopez, Jaime Gutierrez Del Alamo, Wille, Joakim, Mindell, Jodi, Bogetz, Jori, Downing, Julia, Hauer, Julie, Streuli, Jürg, Baker, Justin, Spruyt, Karen, Chan, Kate Ching Ching, Soster, Leticia Azevedo, Oliveira, Lia, Ragsdale, Lindsay, Nobili, Lino, Matlen, Lisa, Nosetti, Luana, De Zen, Lucia, Strambi, Luigi Ferini, Stenmarker, Margaretha, Lopes, Maria Cecilia, Blankenburg, Markus, Rios, Marta, Bernadá, Mercedes, Farquhar, Michael, Frühwald, Michael, Gradisar, Michael, Simakajornboon, Narong, Lazzarin, Pierina, Chong, Poh-Heng, Ferri, Raffaele, Martino-Alba, Ricardo, Findling, Robert L., Ferreira, Rosário, Bin-Hasan, Saadoun, Kudchadkar, Sapna R., Mercadante, Sebastiano, Amarri, Sergio, Keenan, Sharon, Noce, Silvia, de Oliveira Iglesias, Simone Brasil, Fagondes, Simone, Suh, Sooyeon, Sheldon, Stephen H., Sejersen, Thomas, Ceranoglu, Tolga Atilla, Crabtree, Valerie, Castronovo, Vincenza, Mercante, Anna, Owens, Judith, Bruni, Oliviero, Nunes, Magda L., Gringras, Paul, Li, Shirley Xin, Papa, Simonetta, Kreicbergs, Ulrika, Wolfe, Joanne, Zernikow, Boris, Lacerda, Ana, and Benini, Franca

Published
2024
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5. Enzyme regulation and mutation in a model serial dilution ecosystem

Author

Erez, Amir, Lopez, Jaime G., Meir, Yigal, and Wingreen, Ned S.

Subjects
Physics - Biological Physics, Quantitative Biology - Populations and Evolution
Abstract

Microbial communities are ubiquitous in nature and come in a multitude of forms, ranging from communities dominated by a handful of species to communities containing a wide variety of metabolically distinct organisms. This huge range in diversity is not a curiosity - microbial diversity has been linked to outcomes of substantial ecological and medical importance. However, the mechanisms underlying microbial diversity are still under debate, as simple mathematical models only permit as many species to coexist as there are resources. A plethora of mechanisms have been proposed to explain the origins of microbial diversity, but many of these analyses omit a key property of real microbial ecosystems: the propensity of the microbes themselves to change their growth properties within and across generations. In order to explore the impact of this key property on microbial diversity, we expand upon a recently developed model of microbial diversity in fluctuating environments. We implement changes in growth strategy in two distinct ways. First, we consider the regulation of a cell's enzyme levels within short, ecological times, and second we consider evolutionary changes driven by mutations across generations. Interestingly, we find that these two types of microbial responses to the environment can have drastically different outcomes. Enzyme regulation may collapse diversity over long enough times while, conversely, strategy-randomizing mutations can produce a "rich-get-poorer" effect that promotes diversity. This work makes explicit, using a simple serial-dilutions framework, the conflicting ways that microbial adaptation and evolution can affect community diversity., Comment: This work extends the modeling framework from "Nutrient levels and trade-offs control diversity in a serial dilution ecosystem" at https://elifesciences.org/articles/57790 ; Main text: 8 pages, 3 figures. Appendix: 4 pages, 5 figures

Published
2021
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8. Visual Simplified Characters' Emotion Emulator Implementing OCC Model

Author

Laureano-Cruces, Ana Lilia, Hernández-Domínguez, Laura, Mora-Torres, Martha, Torres-Moreno, Juan-Manuel, and Cabrera-López, Jaime Enrique

Subjects
Computer Science - Artificial Intelligence
Abstract

In this paper, we present a visual emulator of the emotions seen in characters in stories. This system is based on a simplified view of the cognitive structure of emotions proposed by Ortony, Clore and Collins (OCC Model). The goal of this paper is to provide a visual platform that allows us to observe changes in the characters' different emotions, and the intricate interrelationships between: 1) each character's emotions, 2) their affective relationships and actions, 3) The events that take place in the development of a plot, and 4) the objects of desire that make up the emotional map of any story. This tool was tested on stories with a contrasting variety of emotional and affective environments: Othello, Twilight, and Harry Potter, behaving sensibly and in keeping with the atmosphere in which the characters were immersed., Comment: 7 pages, 14 figures, 2 tables

Published
2020

9. Spanish Intragastric Balloon Consensus Statement (SIBC): practical guidelines based on experience of over 20 000 cases

Author

Coll, Eduardo Espinet, Garcia, Andres J. del Pozo, Arau, Roman Turro, Duran, Javier Nebreda, Rizo, Xavier Cortes, Jimenez, Andres Serrano, Uso, Miguel Angel Escarti, Tornero, Maria Munoz, Martinez, David Carral, Lopez, Jaime Bernabeu, Bernal, Cristian Sierra, Ares, David Martinez, Diez, Jesus Espinel, Valenciano, Carlos Marra-Lopez, Vera, Javier Sola, Artero, Laura Sanchis, Jimenez, Jose Luis Dominguez, Macian, Ramiro Carreno, Fernandez, Jose Francisco Juanmartinena, Zulueta, Arnulfo Fernandez, Alvarado, Claudia Consiglieri, Grecco, Eduardo, Silva, Lyz Bezerra, and Neto, Manoel Galvao

Published
2023
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11. Nutrient levels and trade-offs control diversity in a serial dilution ecosystem

Author

Erez, Amir, Lopez, Jaime G., Weiner, Benjamin, Meir, Yigal, and Wingreen, Ned S.

Subjects
Physics - Biological Physics, Quantitative Biology - Populations and Evolution
Abstract

Microbial communities feature an immense diversity of species and this diversity is linked with outcomes ranging from ecosystem stability to medical prognoses. Yet the mechanisms underlying microbial diversity are under debate. While simple resource-competition models don't allow for coexistence of a large number of species, it was recently shown that metabolic trade-offs can allow unlimited diversity. Does this diversity persist with more realistic, intermittent nutrient supply? Here, we demonstrate theoretically that in serial dilution culture, metabolic trade-offs allow for high diversity. When a small amount of nutrient is supplied to each batch, the serial dilution dynamics mimic a chemostat-like steady state. If more nutrient is supplied, diversity depends on the amount of nutrient supplied due to an "early-bird" effect. The interplay of this effect with different environmental factors and diversity-supporting mechanisms leads to a variety of relationships between nutrient supply and diversity, suggesting that real ecosystems may not obey a universal nutrient-diversity relationship., Comment: Appendix follows main text

Published
2019
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14. How to perform the one-step conservative surgery for placenta accreta spectrum move by move

Author

Nieto-Calvache, Albaro José, Palacios-Jaraquemada, José Miguel, Aryananda, Rozi, Basanta, Nicolas, Aguilera, Rudy, Benavides, Juan Pablo, López, Jaime, Campos, Clara, Valencia, Luisa, Arboleda, Kevin, Cabrera, Valentina, Cabrera, Jesús, Tavera-Martinez, Geraldine Minachi, Sinisterra, Stiven, Maya, Juliana, Peña, Tatiana, Burgos-Luna, Juan Manuel, and Messa, Adriana

Published
2023
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17. Pharmacokinetic and clinical improvements after PK-guided switch from standard half-life to extended half-life factor VIII products

Author

Megías-Vericat, J.E., Bonanad Boix, S., Berrueco Moreno, R., Mingot-Castellano, M.E., Rodríguez López, M., Canaro Hirnyk, M., Mateo Arranz, J., Calvo Villas, J.M., Haya Guaita, S., Mesegué Medà, M., López Jaime, F., Albo-López, C., Palomero-Massanet, A., Vilalta Seto, N., Leciñena, I. Larrodé, Haro, A.R. Cid, and Poveda Andrés, J.L.

Published
2022
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18. Immunomodulatory activity of Trypanosoma cruzi recombinant antigen combination TSA-1-C4 and Tc24-C4 induce activation of macrophages and CD8+ T cells.

Author

Dzul-Huchim, Victor Manuel, Rosado-Vallado, Miguel, Euan-Canto, Antonio, Torres-Romero, Julio, Ortega-Lopez, Jaime, Cruz-Chan, Julio Vladimir, Villanueva-Lizama, Liliana Estefania, and Arana-Argáez, Victor

Abstract

Chagas disease is a chronic infection caused by the protozoan parasite, Trypanosoma cruzi, with limited benefits of the currently available anti-parasitic chemotherapeutic approaches to halt the progression of heart disease. Recombinant TSA-1-C4 and Tc24-C4 proteins have been developed as promising antigen candidates for therapeutic vaccines, leading to propose them in combination as a bivalent recombinant protein strategy. In this study, we evaluated the immunomodulatory effect of the combined TSA-1-C4 and Tc24-C4 recombinant proteins by in vitro assays using murine macrophages. Macrophages from naïve Balb/c mice were isolated and stimulated with TSA-1-C4 plus Tc24-C4 recombinant proteins, hence, supernatants were recovered to measure host NO, H2O2, as well as, TNF-α, IL-1β, IL-6 and IL-10 cytokine responses. Later, stimulated macrophages were co-cultured with CD8+ T cells from naïve mice, and inflammatory cytokine-profiles were measured from supernatants. We observed that combining both antigens promotes the activation of host macrophages by NO and H2O2 release; moreover, these macrophages also induced considerable pro-inflammatory immune-responses mediated by TNF-, IL-1β and IL-6 cytokines compared to either TSA-1-C4 or Tc24-C4 stimulated macrophages. In addition, naïve CD8+ T cells in presence of TSA-1-C4 plus Tc24-C4 stimulated-macrophages similarly boosted the pro-inflammatory immune profile by significant production of IFN-γ and TNF-α cytokines. These results support immunological advantages for the use of TSA-1-C4 and Tc24-C4 combination as vaccine candidates against T. cruzi. [ABSTRACT FROM AUTHOR]

Published
2025
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19. Investing in Public School Kitchens and Equipment as a Pathway to Healthy Eating and Equitable Access to Healthy Food

Author

O'Neill, Moira, Mujahid, Mahasin, Hutson, Malo, Fukutome, Amanda, Robichaud, Raine, and Lopez, Jaime

Abstract

Background: We gathered baseline data about student need of healthy, free school food, and if current school meal programming serves students in need of healthy free school food, in anticipation of the completion of a district-wide kitchen infrastructure and educational farm project in a high-poverty urban school district. Methods: We used mixed methods to assess student hunger, whether the school meal program met student needs, and to determine associations between presence of a cooking kitchen and perceptions of healthy food. Participants included 72 staff, 143 parents, and 6437 K-5 students in the qualitative component, and 9078 parents and 1693 staff in the quantitative component. Results: Staff participants stated packaging and reheating food influenced student consumption. During observations, students at seven of nine high poverty sites with packaged reheated food did not eat school meals, but this was not true at four out of four high-poverty sites with unpackaged fresh food. Parents (OR = 1.17, 95% CI 1.00-1.39) and staff (OR = 1.58, 95% CI 1.15-2.17) from schools with a cooking kitchen were more likely to perceive school lunch as healthy in adjusted models. Conclusions: Food preparation and presentation appears to influence student consumption of school food and adult perception of school meal quality.

Published
2020
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21. How to identify patients who require aortic vascular control in placenta accreta spectrum disorders?

Author

Nieto-Calvache, Albaro José, Palacios-Jaraquemada, José Miguel, Aryananda, Rozi Aditya, Rodriguez, Fernando, Ordoñez, Carlos A., Messa Bryon, Adriana, Calvache, Juan Pablo Benavides, Lopez, Jaime, Campos, Clara Ivette, Mejia, Mauricio, Rengifo, Martin, Galliadi, Lina Maria Vergara, Maya, Juliana, Zambrano, Maria Andrea, Aguayo, Isabella Prado, Carabalí, Isabella Gutierrez, and Burgos, Juan Manuel

Published
2022
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27. Evaluation of specialized training in hospital pharmacy

Author

Gimeno-Jordá, María José, Giménez-Poderos, Teresa, Negro-Vega, Eva, Gamarra, Edurne Fernández-de, Sanmartín-Fenollera, Patricia, Lozano-Blázquez, Ana, González-López, Jaime, Talens-Bolós, Amparo, Arrieta-Navarro, Raquel, and Soria-Soto, Manuel

Published
2020
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33. International consensus on sleep problems in pediatric palliative care: paving the way

Author

MERCANTE, Anna, primary, OWENS, Judith, additional, BRUNI, Oliviero, additional, NUNES, Magda L., additional, GRINGRAS, Paul, additional, LI, Shirley Xin, additional, PAPA, Simonetta, additional, KREICBERGS, Ulrika, additional, WOLFE, Joanne, additional, ZERNIKOW, Boris, additional, LACERDA, Ana, additional, BENINI, Franca, additional, Li, Albert, additional, Wolfson, Amy R., additional, Marinetto, Anna, additional, Santini, Anna, additional, Zanin, Anna, additional, Kuhn, Brett R., additional, Angelhoff, Charlotte, additional, Santos, Cristiane Fumo dos, additional, Goh, Daniel YT., additional, Verrillo, Elisabetta, additional, Zhou, Eric S., additional, Ferreira, Esther Angélica Luiz, additional, Bergstraesser, Eva, additional, Pizza, Fabio, additional, Nilsson, Frans, additional, Plazzi, Giuseppe, additional, Wang, Guanghai, additional, Traslaviña, Guillermo Andrey Ariza, additional, Moreira, Gustavo Antonio, additional, Siden, Hal, additional, Hauch, Holger, additional, Huijer, Huda Abu-Saad, additional, Catalano, Igor, additional, Narang, Indra, additional, Avagnina, Irene, additional, Lopez, Jaime Gutierrez Del Alamo, additional, Wille, Joakim, additional, Mindell, Jodi, additional, Bogetz, Jori, additional, Downing, Julia, additional, Hauer, Julie, additional, Streuli, Jürg, additional, Baker, Justin, additional, Spruyt, Karen, additional, Chan, Kate Ching Ching, additional, Soster, Leticia Azevedo, additional, Oliveira, Lia, additional, Ragsdale, Lindsay, additional, Nobili, Lino, additional, Matlen, Lisa, additional, Nosetti, Luana, additional, De Zen, Lucia, additional, Strambi, Luigi Ferini, additional, Stenmarker, Margaretha, additional, Lopes, Maria Cecilia, additional, Blankenburg, Markus, additional, Rios, Marta, additional, Bernadá, Mercedes, additional, Farquhar, Michael, additional, Frühwald, Michael, additional, Gradisar, Michael, additional, Simakajornboon, Narong, additional, Lazzarin, Pierina, additional, Chong, Poh-Heng, additional, Ferri, Raffaele, additional, Martino-Alba, Ricardo, additional, Findling, Robert L., additional, Ferreira, Rosário, additional, Bin-Hasan, Saadoun, additional, Kudchadka, Sapna, additional, Mercadante, Sebastiano, additional, Amarri, Sergio, additional, Keenan, Sharon, additional, Noce, Silvia, additional, de Oliveira Iglesias, Simone Brasil, additional, Fagondes, Simone, additional, Suh, Sooyeon, additional, Sheldon, Stephen H., additional, Sejersen, Thomas, additional, Ceranoglu, Tolga Atilla, additional, Crabtree, Valerie, additional, and Castronovo, Vincenza, additional

Published
2024
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37. Experimental and numerical study on hydrodynamics of coupled FPSO and mooring/riser systems in deepwater GOM

Author

Torres Lopez, Jaime Jose

Subjects
627
Abstract

Floating production storage and offloading (FPSO) systems have been proposed for the development of recent oil discoveries in the southern region of the Gulf of Mexico (GOM) in water depths ranging from 1000 to 2000 metres. It is increasingly challenging to predict the environmental forces and the global responses of FPSO systems and the associated dynamic behaviour of their mooring lines and risers at these depths. The combination of an appropriate FPSO scale model with a suitable level of equivalent effect reduced depth for the mooring lines and risers using a hybrid passive truncated experimental methodology is a feasible approach. This thesis provides an effective technique to study the equivalent hydrodynamic behaviour of floating systems to validate numerical models and to predict full water depth behaviour, based on a hybrid passive truncated experimental method and a non-linear time domain coupled numerical analysis. The extreme motion response of an FPSO and the dynamics of the mooring lines and risers in the context of prevailing environmental conditions are investigated. Several important findings are obtained based on the present experimental and the numerical study: The linear motion transfer functions are sensitive to the direction of the incident waves, and the differences between the Full and the Ballast load conditions were found to be insignificant, except for the roll motion, which showed slight differences in resonant frequency responses and the maximum peak motion amplitudes. Further, the spectra analysis revealed that the risers have a great influence on low-frequency damping, particularly in the surge direction, whereas the damping mainly contributes to roll in the wave frequency motion response. The main horizontal motion response of the FPSO (surge) under the non-collinear environmental loading condition was found to be slightly higher than that obtained for the collinear loading condition and the numerical simulation identified that the Newman’s approximation is reliable to predict the extreme motion response. The dynamic tension responses of the risers are sensitive to the environment force directions and the mooring lines/risers dynamics do not affect significantly the wave frequency motion responses in heave and pitch. Additionally, the mean motion of the FPSO and the mean tensions in the mooring lines are dominant in deep-water and ultra-deepwater installations and conversely the dynamic components of the tension responses of the mooring lines decreases as the water depth increases. The findings are not only improve the understanding of the complex hydrodynamics, the extensive experimental and numerical results will also provide welcome benchmarks for ii future study of the FPSO with its mooring lines and risers under both collinear and non-collinear environment loading conditions.

Published
2016

39. Grow now, pay later: When should a bacterium go into debt?

Author

Lopez, Jaime G., Hein, Yaïr, Erez, Amir, Lopez, Jaime G., Hein, Yaïr, and Erez, Amir

Abstract

Microbes grow in a wide variety of environments and must balance growth and stress resistance. Despite the prevalence of such trade-offs, understanding of their role in nonsteady environments is limited. In this study, we introduce a mathematical model of "growth debt," where microbes grow rapidly initially, paying later with slower growth or heightened mortality. We first compare our model to a classical chemostat experiment, validating our proposed dynamics and quantifying Escherichia coli's stress resistance dynamics. Extending the chemostat theory to include serial-dilution cultures, we derive phase diagrams for the persistence of "debtor" microbes. We find that debtors cannot coexist with nondebtors if "payment" is increased mortality but can coexist if it lowers enzyme affinity. Surprisingly, weak noise considerably extends the persistence of resistance elements, pertinent for antibiotic resistance management. Our microbial debt theory, broadly applicable across many environments, bridges the gap between chemostat and serial dilution systems.

Published
2024

40. Grow now, pay later: When should a bacterium go into debt?

Author

Sub Cond-Matter Theory, Stat & Comp Phys, Theoretical Physics, Lopez, Jaime G., Hein, Yaïr, Erez, Amir, Sub Cond-Matter Theory, Stat & Comp Phys, Theoretical Physics, Lopez, Jaime G., Hein, Yaïr, and Erez, Amir

Published
2024

45. Ursolic Acid Induces Beneficial Changes in Skeletal Muscle mRNA Expression and Increases Exercise Participation and Performance in Dogs with Age-Related Muscle Atrophy

Author

Ebert, Scott M., primary, Nicolas, Celine S., additional, Schreiber, Paul, additional, Lopez, Jaime G., additional, Taylor, Alan T., additional, Judge, Andrew R., additional, Judge, Sarah M., additional, Rasmussen, Blake B., additional, Talley, John J., additional, Rème, Christophe A., additional, and Adams, Christopher M., additional

Published
2024
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46. Humanistic burden of haemophilia A without inhibitors: A cross‐sectional analysis of the HemoLIFE study.

Author

Álvarez‐Román, María Teresa, Nuñez Vazquez, Ramiro Jose, Benitez Hidalgo, Olga, Quintana Paris, Laura, Entrena Ureña, Laura, Lopez Jaime, Francisco Jose, la De Corte‐Rodríguez, Hortensia, García Dasí, María, Bosch, Pau, Mingot Castellano, María Eva, Guerra Garaeta, Itziar, and Soto‐Ortega, Inmaculada

Subjects
HEMOPHILIA, CROSS-sectional method, HEMOPHILIACS, CHILD patients, LABOR productivity
Abstract

Aim: To evaluate the impact of haemophilia A without inhibitors on humanistic outcomes in patients and caregivers. Herein, we report a cross‐sectional analysis of the baseline data of persons with haemophilia (PWH) participating in the prospective study HEMOLIFE. Methods: These data are part of a prospective, observational, and multicentre study currently being conducted in 20 hospitals in Spain by haematologists. We included subjects 12 years or older diagnosed with haemophilia. The evaluations included the Maladjustment Scale, Haemophilia–Specific Quality of Life Questionnaire for Adults (HaemoQol)/HaemoQol Short Form (Children), haemophilia‐specific version of the Work Productivity and Impairment Questionnaire plus the Classroom Impairment Questionnaire (WPAI+CIQ:HS), Haemophilia Activity List (HAL)/Paediatric Haemophilia Activities List (pedHAL), visual analogue scale (VAS) for evaluating pain, Coping Pain Questionnaire–Reduced (CAD‐R), and Hospital Anxiety and Depression Scale (HADS). Results: A total of 81 PWH were recruited at 18 centres; 66 PWH were ≥18 years (i.e., adults), and PWH 15 were <18 years (i.e., paediatric patients). Out of the 79 evaluable subjects, 16 (20%) showed an impact of haemophilia on daily life, and the areas most affected were "leisure time" (58% showed maladjustment) and "work/studies" (47% showed maladjustment). Patients reported a higher impact of haemophilia on quality of life (mean [SD] of the transformed score) in the dimensions of "sport" (49.4 [28.6]), "physical health" (40.5 [25.8]) and "future" (37.7 [28.9]). In adults, according to HAL scores, greater impairment of function was observed in "lying/sitting/kneeling/standing," "function of legs" and "leisure activities and sports," with mean normalized scores of 64.7, 65.1 and 69.0, respectively. Productivity was mostly impacted by presenteeism. The pain was infrequent and moderate. According to the HADS scores, nine (11.5%) patients had clinical anxiety and depression. Conclusion: PWH without inhibitors exhibited impairments in adjustment, quality of life and functionality, especially related to leisure and sports activities, and exhibit relevant levels of anxiety and depression. [ABSTRACT FROM AUTHOR]

Published
2024
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