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1. On commutators of unipotent matrices of index 2

Author

Rosa, Kennett L. Dela and Santos, Juan Paolo C.

Subjects
Mathematics - Rings and Algebras, 15A21, 15A23, 15B33, 15B99, 20H20
Abstract

A commutator of unipotent matrices of index 2 is a matrix of the form $XYX^{-1}Y^{-1}$, where $X$ and $Y$ are unipotent matrices of index 2, that is, $X\ne I_n$, $Y\ne I_n$, and $(X-I_n)^2=(Y-I_n)^2=0_n$. If $n>2$ and $\mathbb F$ is a field with $|\mathbb F|\geq 4$, then it is shown that every $n\times n$ matrix over $\mathbb F$ with determinant 1 is a product of at most four commutators of unipotent matrices of index 2. Consequently, every $n\times n$ matrix over $\mathbb F$ with determinant 1 is a product of at most eight unipotent matrices of index 2. Conditions on $\mathbb F$ are given that improve the upper bound on the commutator factors from four to three or two. The situation for $n=2$ is also considered. This study reveals a connection between factorability into commutators of unipotent matrices and properties of $\mathbb F$ such as its characteristic or its set of perfect squares., Comment: 23 pages

Published
2024

2. Black box meta-learning intrinsic rewards for sparse-reward environments

Author

Pappalardo, Octavio, Ramele, Rodrigo, and Santos, Juan Miguel

Subjects
Computer Science - Machine Learning
Abstract

Despite the successes and progress of deep reinforcement learning over the last decade, several challenges remain that hinder its broader application. Some fundamental aspects to improve include data efficiency, generalization capability, and ability to learn in sparse-reward environments, which often require human-designed dense rewards. Meta-learning has emerged as a promising approach to address these issues by optimizing components of the learning algorithm to meet desired characteristics. Additionally, a different line of work has extensively studied the use of intrinsic rewards to enhance the exploration capabilities of algorithms. This work investigates how meta-learning can improve the training signal received by RL agents. The focus is on meta-learning intrinsic rewards under a framework that doesn't rely on the use of meta-gradients. We analyze and compare this approach to the use of extrinsic rewards and a meta-learned advantage function. The developed algorithms are evaluated on distributions of continuous control tasks with both parametric and non-parametric variations, and with only sparse rewards accessible for the evaluation tasks.

Published
2024

4. Selection on Visual Opsin Genes in Diurnal Neotropical Frogs and Loss of the SWS2 Opsin in Poison Frogs.

Author

Wan, Yin, Navarrete Méndez, María, OConnell, Lauren, Uricchio, Lawrence, Roland, Alexandre-Benoit, Maan, Martine, Ron, Santiago, Betancourth-Cundar, Mileidy, Pie, Marcio, Howell, Kimberly, Richards-Zawacki, Corinne, Cummings, Molly, Cannatella, David, Santos, Juan, and Tarvin, Rebecca

Subjects
Atelopus, Brachycephalus, Dendrobatidae, blue-sensitive opsin, gene loss, spectral tuning, Animals, Opsins, Poisons, Phylogeny, Rod Opsins
Abstract

Amphibians are ideal for studying visual system evolution because their biphasic (aquatic and terrestrial) life history and ecological diversity expose them to a broad range of visual conditions. Here, we evaluate signatures of selection on visual opsin genes across Neotropical anurans and focus on three diurnal clades that are well-known for the concurrence of conspicuous colors and chemical defense (i.e., aposematism): poison frogs (Dendrobatidae), Harlequin toads (Bufonidae: Atelopus), and pumpkin toadlets (Brachycephalidae: Brachycephalus). We found evidence of positive selection on 44 amino acid sites in LWS, SWS1, SWS2, and RH1 opsin genes, of which one in LWS and two in RH1 have been previously identified as spectral tuning sites in other vertebrates. Given that anurans have mostly nocturnal habits, the patterns of selection revealed new sites that might be important in spectral tuning for frogs, potentially for adaptation to diurnal habits and for color-based intraspecific communication. Furthermore, we provide evidence that SWS2, normally expressed in rod cells in frogs and some salamanders, has likely been lost in the ancestor of Dendrobatidae, suggesting that under low-light levels, dendrobatids have inferior wavelength discrimination compared to other frogs. This loss might follow the origin of diurnal activity in dendrobatids and could have implications for their behavior. Our analyses show that assessments of opsin diversification in across taxa could expand our understanding of the role of sensory system evolution in ecological adaptation.

Published
2023

7. Equilivest: A Robotic Vest to aid in Post-Stroke Dynamic Balance Rehabilitation

Author

Paviotti, Franco, Buniak, Esteban, Ramele, Rodrigo, Freixes, Orestes, and Santos, Juan Miguel

Subjects
Computer Science - Robotics
Abstract

Stroke is a medical condition that can affect motor function, particularly dynamic balance. Biofeedback can aid in rehabilitation procedures which help patients to regain lost motor activity and recover functionality. In this work, we are presenting a robotic smart-vest device that can analyze Inertial Measurement Unit (IMU) data and assist in rehabilitation procedures by providing timed feedback in the form of vibrotactile stimulation. Information provided by principal caregivers and patients in the form of surveys and interviews, is used to hypothesize potential clinical causes and to derive alternative three alternative clinical modalities: Artificial Vestibular Feedback, Gait Pacemaker and Risk-Predictor., Comment: This extended abstract was presented at the "Workshop on Assistive Robotic Systems for Human Balancing and Walking: Emerging Trends and Perspectives" at IROS2022

Published
2023

8. Enantioselective Adsorption and Desorption Behaviour of Chiral Ofloxacin and Its Main Metabolites in Agricultural Soils

Author

Mejías, Carmen, Santos, Juan Luis, Martín, Julia, Aparicio, Irene, Alonso, Esteban, Ghosh, Arindam, Series Editor, Chua, Daniel, Series Editor, de Souza, Flavio Leandro, Series Editor, Aktas, Oral Cenk, Series Editor, Han, Yafang, Series Editor, Gong, Jianghong, Series Editor, Jawaid, Mohammad, Series Editor, Torres, Yadir, editor, Beltran, Ana M., editor, Felix, Manuel, editor, Peralta, Estela, editor, and Larios, Diego F., editor

Published
2024
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9. 2b or not 2b? 2bRAD is an effective alternative to ddRAD for phylogenomics

Author

Chambers, E Anne, Tarvin, Rebecca D, Santos, Juan C, Ron, Santiago R, Betancourth‐Cundar, Mileidy, Hillis, David M, Matz, Mikhail V, and Cannatella, David C

Subjects
Genetics, Dendrobatidae, missing data, phylogenetic signal, Ranidae, restriction-site-associated DNA sequencing, restriction‐site‐associated DNA sequencing, Ecology, Evolutionary Biology
Abstract

Restriction-site-associated DNA sequencing (RADseq) has become an accessible way to obtain genome-wide data in the form of single-nucleotide polymorphisms (SNPs) for phylogenetic inference. Nonetheless, how differences in RADseq methods influence phylogenetic estimation is poorly understood because most comparisons have largely relied on conceptual predictions rather than empirical tests. We examine how differences in ddRAD and 2bRAD data influence phylogenetic estimation in two non-model frog groups. We compare the impact of method choice on phylogenetic information, missing data, and allelic dropout, considering different sequencing depths. Given that researchers must balance input (funding, time) with output (amount and quality of data), we also provide comparisons of laboratory effort, computational time, monetary costs, and the repeatability of library preparation and sequencing. Both 2bRAD and ddRAD methods estimated well-supported trees, even at low sequencing depths, and had comparable amounts of missing data, patterns of allelic dropout, and phylogenetic signal. Compared to ddRAD, 2bRAD produced more repeatable datasets, had simpler laboratory protocols, and had an overall faster bioinformatics assembly. However, many fewer parsimony-informative sites per SNP were obtained from 2bRAD data when using native pipelines, highlighting a need for further investigation into the effects of each pipeline on resulting datasets. Our study underscores the importance of comparing RADseq methods, such as expected results and theoretical performance using empirical datasets, before undertaking costly experiments.

Published
2023

11. An evaluation of dogs’ exposure to benzophenones through hair sample analysis

Author

Gonkowski Sławomir, Martín Julia, Rychlik Andrzej, Aparicio Irene, Santos Juan Luis, Alonso Esteban, and Makowska Krystyna

Subjects
endocrine disruptors, pets, dogs, benzophenones, exposure, Veterinary medicine, SF600-1100
Abstract

Benzophenones (BPs) are used in various branches of industry as ultraviolet radiation filters, but they pollute the natural environment, penetrate living organisms, and disrupt endocrine balance. Knowledge of the exposure of domestic animals to these substances is extremely scant. The aim of the study was to investigate long-term exposure of companion dogs to BPs and relate this to environmental factors.

Published
2024
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12. EPOC Emotiv EEG Basics

Author

Ramele, Rodrigo, Villar, Ana Julia, and Santos, Juan Miguel

Subjects
Electrical Engineering and Systems Science - Signal Processing, Quantitative Biology - Neurons and Cognition
Abstract

This document provides some basic guidance to start working with the EPOC Emotiv neuroheadset device and describes how to use it to perform basic Brain-Computer Interface (BCI) research. A brief tutorial on how to set up the device, from its electrophysiological point of view, as well as a description and practical code to perform some basic analysis, is explained. A basic experiment is introduced to detect one of the oldest and, indeed, quite still valuable electrophysiological correlate, visual occipital alpha waves, or Berger Rhythm. An additional experiment is expounded where the power spectrum of alpha waves is reduced when a subject is affected by background cognitive disturbances. This document also briefs about the extraction of information by using the EPOC Emotiv library and also with python Emokit package. This report presents a basic guide on how to use EEGLAB and MATLAB, as well as python stack to perform the neurophysiological analysis. Finally, a basic analysis on different feature extraction and classification methods is provided., Comment: 14 pages, 9 figures

Published
2022

15. Improving prediction of COVID-19 mortality using machine learning in the Spanish SEMI-COVID-19 registry

Author

Casas-Rojo, José-Manuel, Ventura, Paula Sol, Antón Santos, Juan Miguel, de Latierro, Aitor Ortiz, Arévalo-Lorido, José Carlos, Mauri, Marc, Rubio-Rivas, Manuel, González-Vega, Rocío, Giner-Galvañ, Vicente, Otero Perpiñá, Bárbara, Fonseca-Aizpuru, Eva, Muiño, Antonio, Del Corral-Beamonte, Esther, Gómez-Huelgas, Ricardo, Arnalich-Fernández, Francisco, Llorente Barrio, Mónica, Sancha-Lloret, Aresio, Rábago Lorite, Isabel, Loureiro-Amigo, José, Pintos-Martínez, Santiago, García-Sardón, Eva, Montaño-Martínez, Adrián, Rojano-Rivero, María Gloria, Ramos-Rincón, José-Manuel, and López-Escobar, Alejandro

Published
2023
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16. Effectiveness and Safety of Direct-acting Antivirals for Treatment of Adolescents With HCV/HIV Coinfection: Real-world Data From Europe

Author

Malik, Farihah, Crichton, Siobhan, Plotnikova, Yulia, Latysheva, Inga, Samarina, Anna, Pokorska-Śpiewak, Maria, Gomez, Marisa Navarro, Bailey, Heather, Thorne, Claire, Judd, Ali, Turkova, Anna, Collins, Intira Jeannie, Marczyńska, Magdalena, Popielska, Jolanta, Ołdakowska, Agnieszka, Zawadka, Konrad, Pluta, Magdalena, Doroba, Małgorzata, Okhonskaya, Liubov, Rozenberg, Vladimir, Voronin, Evgeny, Plynsky, Alexksey A., José Mellado, María, Escosa, Luis, García Hortelano, Milagros, Sainz, Talía, Grasa, Carlos, Rodríguez, Paula, Rojo, Pablo, Prieto-Tato, Luis, Epalza, Cristina, Tagarro, Alfredo, Domínguez, Sara, Ballesteros, Álvaro, Tomás Ramos, José, Illán, Marta, Berzosa, Arantxa, Guillén, Sara, Soto, Beatriz, Luisa Navarro, María, Saavedra, Jesús, Santos, Mar, Aguilera, David, Santiago, Begoña, Jimenez de Ory, Santiago, Bermejo, Amanda, Penín, María, Martínez, Jorge, Badillo, Katie, Belén Jiménez, Ana, Navas, Adriana, Oñate, Eider, Pocheville, Itziar, Garrote, Elisa, Colino, Elena, Afonso, Olga, Gómez Sirvent, Jorge, Garzón, Mónica, Román, Vicente, Angulo, Raquel, Neth, Olaf, Falcón, Lola, Terol, Pedro, Luis Santos, Juan, Vázquez, Álvaro, Carazo, Begoña, Medina, Antonio, Lendínez, Francisco, Ibáñez, Mercedes, Peromingo, Estrella, Isabel Sánchez, María, Ruiz, Beatriz, Grande, Ana, José Romero, Francisco, Pérez, Carlos, Calle, Laura, Pareja, Marta, Losada, Begoña, Herranz, Mercedes, Bustillo, Matilde, Collado, Pilar, Antonio Couceiro, José, Vila, Leticia, Calviño, Consuelo, Isabel Piqueras, Ana, Oltra, Manuel, Gavilán, César, Montesinos, Elena, Dapena, Marta, Jiménez, Beatriz, Gloria Andrés, Ana, Marugán, Víctor, Ochoa, Carlos, Isabel Menasalvas, Ana, Cervantes, Eloísa, Álvarez, Beatriz, Díez, Cristina, Bernardino, Ignacio, Luisa Montes, María, Valencia, Eulalia, Delgado, Ana, Rubio, Rafael, Pulido, Federico, Bisbal, Otilia, Monereo Alonso, Alfonso, Berenguer, Juan, Díez, Cristina, Aldamiz, Teresa, Tejerina, Francisco, Carlos Bernaldo de Quirós, Juan, Padilla, Belén, Carrillo, Raquel, Montilla, Pedro, Bermúdez, Elena, Valerio, Maricela, Sanz, Jose, Gimeno, Alejandra, Cervero, Miguel, Torres, Rafael, Moreno, Santiago, Jesús Perez, María, del Campo, Santos, Ryan, Pablo, Troya, Jesus, Sanz, Jesus, Losa, Juan, Gomez, Rafael, Górgolas, Miguel, Díaz, Alberto, de la Fuente, Sara, Antonio Iribarren, Jose, Jose Aramburu, Maria, Martinez, Lourdes, Josune Goikoetxea, Ane, Ibarra, Sofia, de la Peña, Mireia, Asensi, Víctor, Hernandez, Michele, Remedios Alemán, María, Pelazas, Ricardo, del Mar Alonso, María, María López, Ana, García, Dácil, Rodriguez, Jehovana, Angel Cardenes, Miguel, Castaño, Manuel A., Orihuela, Francisco, Pérez, Inés, Isabel Mayorga, Mª, Fernando Lopez-Cortes, Luis, Roca, Cristina, Llaves, Silvia, Jose Rios, Maria, Rodriguez, Jesus, Palomo, Virginia, Pasquau, Juan, Garcia, Coral, Hernandez, Jose, Martinez, Clara, Rivero, Antonio, Camacho, Angela, Merino, Dolores, Raffo, Miguel, Corpa, Laura, Martinez, Elisa, Mateos, Fernando, Javier Blanch, Jose, Torralba, Miguel, Arazo, Piedad, Samperiz, Gloria, Miralles, Celia, Ocampo, Antonio, Pousada, Guille, Mena, Alvaro, Montero, Marta, Salavert, Miguel, Jose Galindo, Maria, Pretel, Natalia, Portilla, Joaquín, Portilla, Irene, Gutierrez, Felix, Masia, Mar, Robledano, Cati, Adsuar, Araceli, Hinojosa, Carmen, Monteagudo, Begoña, Bachiller, Pablo, Abadía, Jesica, Galera, Carlos, Albendin, Helena, Fernandez, Marian, and Ramon Blanco, Jose

Published
2024
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20. Nomenclature in Palliative and Kidney Supportive Care: Not Just at the End-of-Life

Author

Nitola-Mendoza, Lina, Sánchez-Cárdenas, Miguel, Rodriguez-Chitiva, Néstor, Mora Gutiérrez, José María, Rodriguez-Pena, Rosely, Romero-González, Gregorio, Bleda Pérez, Monserrat, Cuenca Casbas, Paula, Calsina-Berna, Agnès, Álvaro-Pardo, Margarita, Granados Casas, Virginia, Garrido Ballart, Paula, Beroiz Groh, Patricia, Bover, Jordi, Miralles Basseda, Ramón, Leiva-Santos, Juan Pablo, Alonso-Babarro, Alberto, and Julià-Torras, Joaquim

Published
2024
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21. Nomenclatura en cuidados paliativos y de soporte renal: no solo al final de la vida

Author

Nitola-Mendoza, Lina, Sánchez-Cárdenas, Miguel, Rodriguez-Chitiva, Néstor, Mora Gutiérrez, José María, Rodriguez-Pena, Rosely, Romero-González, Gregorio, Bleda Perez, Monserrat, Cuenca Casbas, Paula, Calsina Berna, Agnes, Álvaro Pardo, Margarita, Granados Casas, Virginia, Garrido Ballart, Paula, Beroiz Groh, Patricia, Bover, Jordi, Miralles Basseda, Ramón, Leiva-Santos, Juan Pablo, Alonso-Babarro, Alberto, and Julià-Torras, Joaquim

Published
2024
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27. Mortality reduction in older COVID-19-patients hospitalized in Spain during the second pandemic wave from the SEMI-COVID-19 Registry

Author

Casas-Rojo, José-Manuel, Antón-Santos, Juan-Miguel, Millán-Núñez-Cortés, Jesús, Gómez-Huelgas, Ricardo, Ramos-Rincón, José-Manuel, Rubio-Rivas, Manuel, Corrales-González, Miguel-Ángel, Fernández-Madera-Martínez, Maria-Rosa, Beato-Pérez, José-Luis, Arnalich-Fernández, Francisco, Gállego-Lezaun, Cristina, Pérez-Martínez, Pablo, Molinos-Castro, Sonia, Tung-Chen, Yale, Madrazo, Manuel, Méndez-Bailón, Manuel, Monge-Monge, Daniel, García-García, Gema-María, García-Fenoll, Rosa, Gilabert, Noemí, Fuerte-Martínez, Rebeca, Contreras-Sánchez, Marta, Rhyman, Nicolás, Peris-García, Jorge, and Lumbreras-Bermejo, Carlos

Published
2023
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41. Chronic neuropsychiatric sequelae of SARS‐CoV‐2: Protocol and methods from the Alzheimer's Association Global Consortium

Author

Erausquin, Gabriel A, Snyder, Heather, Brugha, Traolach S, Seshadri, Sudha, Carrillo, Maria, Sagar, Rajesh, Huang, Yueqin, Newton, Charles, Tartaglia, Carmela, Teunissen, Charlotte, Håkanson, Krister, Akinyemi, Rufus, Prasad, Kameshwar, D'Avossa, Giovanni, Gonzalez‐Aleman, Gabriela, Hosseini, Akram, Vavougios, George D, Sachdev, Perminder, Bankart, John, Mors, Niels Peter Ole, Lipton, Richard, Katz, Mindy, Fox, Peter T, Katshu, Mohammad Zia, Iyengar, M Sriram, Weinstein, Galit, Sohrabi, Hamid R, Jenkins, Rachel, Stein, Dan J, Hugon, Jacques, Mavreas, Venetsanos, Blangero, John, Cruchaga, Carlos, Krishna, Murali, Wadoo, Ovais, Becerra, Rodrigo, Zwir, Igor, Longstreth, William T, Kroenenberg, Golo, Edison, Paul, Mukaetova‐Ladinska, Elizabeta, Staufenberg, Ekkehart, Figueredo‐Aguiar, Mariana, Yécora, Agustín, Vaca, Fabiana, Zamponi, Hernan P, Re, Vincenzina Lo, Majid, Abdul, Sundarakumar, Jonas, Gonzalez, Hector M, Geerlings, Mirjam I, Skoog, Ingmar, Salmoiraghi, Alberto, Boneschi, Filippo Martinelli, Patel, Vibuthi N, Santos, Juan M, Arroyo, Guillermo Rivera, Moreno, Antonio Caballero, Felix, Pascal, Gallo, Carla, Arai, Hidenori, Yamada, Masahito, Iwatsubo, Takeshi, Sharma, Malveeka, Chakraborty, Nandini, Ferreccio, Catterina, Akena, Dickens, Brayne, Carol, Maestre, Gladys, Blangero, Sarah Williams, Brusco, Luis I, Siddarth, Prabha, Hughes, Timothy M, Zuñiga, Alfredo Ramírez, Kambeitz, Joseph, Laza, Agustin Ruiz, Allen, Norrina, Panos, Stella, Merrill, David, Ibáñez, Agustín, Tsuang, Debby, Valishvili, Nino, Shrestha, Srishti, Wang, Sophia, Padma, Vasantha, Anstey, Kaarin J, Ravindrdanath, Vijayalakshmi, Blennow, Kaj, Mullins, Paul, Łojek, Emilia, Pria, Anand, Mosley, Thomas H, Gowland, Penny, Girard, Timothy D, Bowtell, Richard, and Vahidy, Farhaan S

Subjects
Neurosciences, Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD), Brain Disorders, Alzheimer's Disease, Infectious Diseases, Emerging Infectious Diseases, Clinical Research, Dementia, Neurodegenerative, Prevention, Acquired Cognitive Impairment, Aging, Aetiology, 2.1 Biological and endogenous factors, Neurological, Good Health and Well Being, cognitive impairment, dementia, neuropsychiatric sequelae, predictors, SARS-CoV-2, SARS‐CoV‐2
Abstract

IntroductionCoronavirus disease 2019 (COVID-19) has caused >3.5 million deaths worldwide and affected >160 million people. At least twice as many have been infected but remained asymptomatic or minimally symptomatic. COVID-19 includes central nervous system manifestations mediated by inflammation and cerebrovascular, anoxic, and/or viral neurotoxicity mechanisms. More than one third of patients with COVID-19 develop neurologic problems during the acute phase of the illness, including loss of sense of smell or taste, seizures, and stroke. Damage or functional changes to the brain may result in chronic sequelae. The risk of incident cognitive and neuropsychiatric complications appears independent from the severity of the original pulmonary illness. It behooves the scientific and medical community to attempt to understand the molecular and/or systemic factors linking COVID-19 to neurologic illness, both short and long term.MethodsThis article describes what is known so far in terms of links among COVID-19, the brain, neurological symptoms, and Alzheimer's disease (AD) and related dementias. We focus on risk factors and possible molecular, inflammatory, and viral mechanisms underlying neurological injury. We also provide a comprehensive description of the Alzheimer's Association Consortium on Chronic Neuropsychiatric Sequelae of SARS-CoV-2 infection (CNS SC2) harmonized methodology to address these questions using a worldwide network of researchers and institutions.ResultsSuccessful harmonization of designs and methods was achieved through a consensus process initially fragmented by specific interest groups (epidemiology, clinical assessments, cognitive evaluation, biomarkers, and neuroimaging). Conclusions from subcommittees were presented to the whole group and discussed extensively. Presently data collection is ongoing at 19 sites in 12 countries representing Asia, Africa, the Americas, and Europe.DiscussionThe Alzheimer's Association Global Consortium harmonized methodology is proposed as a model to study long-term neurocognitive sequelae of SARS-CoV-2 infection.Key pointsThe following review describes what is known so far in terms of molecular and epidemiological links among COVID-19, the brain, neurological symptoms, and AD and related dementias (ADRD)The primary objective of this large-scale collaboration is to clarify the pathogenesis of ADRD and to advance our understanding of the impact of a neurotropic virus on the long-term risk of cognitive decline and other CNS sequelae. No available evidence supports the notion that cognitive impairment after SARS-CoV-2 infection is a form of dementia (ADRD or otherwise). The longitudinal methodologies espoused by the consortium are intended to provide data to answer this question as clearly as possible controlling for possible confounders. Our specific hypothesis is that SARS-CoV-2 triggers ADRD-like pathology following the extended olfactory cortical network (EOCN) in older individuals with specific genetic susceptibility.The proposed harmonization strategies and flexible study designs offer the possibility to include large samples of under-represented racial and ethnic groups, creating a rich set of harmonized cohorts for future studies of the pathophysiology, determinants, long-term consequences, and trends in cognitive aging, ADRD, and vascular disease.We provide a framework for current and future studies to be carried out within the Consortium. and offers a "green paper" to the research community with a very broad, global base of support, on tools suitable for low- and middle-income countries aimed to compare and combine future longitudinal data on the topic.The Consortium proposes a combination of design and statistical methods as a means of approaching causal inference of the COVID-19 neuropsychiatric sequelae. We expect that deep phenotyping of neuropsychiatric sequelae may provide a series of candidate syndromes with phenomenological and biological characterization that can be further explored. By generating high-quality harmonized data across sites we aim to capture both descriptive and, where possible, causal associations.

Published
2022

42. An SEIR epidemic model of fractional order to analyze the evolution of the COVID-19 epidemic in Argentina

Author

Santos, Juan, Carcione, José, Savioli, Gabriela, and Gauzellino, Patricia

Subjects
Quantitative Biology - Populations and Evolution
Abstract

A pandemic caused by a new coronavirus (COVID-19) has spread worldwide, inducing an epidemic still active in Argentina. In this chapter, we present a case study using an SEIR (Susceptible-Exposed-Infected-Recovered) diffusion model of fractional order in time to analyze the evolution of the epidemic in Buenos Aires and neighboring areas (Regi\'on Metropolitana de Buenos Aires, (RMBA)) comprising about 15 million inhabitants. In the SEIR model, individuals are divided into four classes, namely, susceptible (S), exposed (E), infected (I) and recovered (R). The SEIR model of fractional order allows for the incorporation of memory, with hereditary properties of the system, being a generalization of the classic SEIR first-order system, where such effects are ignored. Furthermore, the fractional model provides one additional parameter to obtain a better fit of the data. The parameters of the model are calibrated by using as data the number of casualties officially reported. Since infinite solutions honour the data, we show a set of cases with different values of the lockdown parameters, fatality rate, and incubation and infectious periods. The different reproduction ratios R0 and infection fatality rates (IFR) so obtained indicate the results may differ from recent reported values, constituting possible alternative solutions. A comparison with results obtained with the classic SEIR model is also included. The analysis allows us to study how isolation and social distancing measures affect the time evolution of the epidemic., Comment: 20 pages, 14 figures. To be published as a Chapter in the book "Analysis of Infectious Disease Problems (Covid-19) and Their Global Impact", edited by Praveen Agarwal, Juan J. Nieto, Michael Ruzhansky, Delfim F. M. Torres, Springer Nature

Published
2021

43. Natural Language Contents Evaluation System for Multi-class News Categorization Using Machine Learning and Transformers

Author

Marrugo, Duván A., Martinez-Santos, Juan Carlos, Puertas, Edwin, Filipe, Joaquim, Editorial Board Member, Ghosh, Ashish, Editorial Board Member, Prates, Raquel Oliveira, Editorial Board Member, Zhou, Lizhu, Editorial Board Member, Figueroa-García, Juan Carlos, editor, Hernández, German, editor, Villa Ramirez, Jose Luis, editor, and Gaona García, Elvis Eduardo, editor

Published
2023
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45. Pharmaceuticals and Their Metabolites in Sewage Sludge and Soils: Distribution and Environmental Risk Assessment

Author

Santos, Juan Luis, Martín, Julia, Mejías, Carmen, Aparicio, Irene, Alonso, Esteban, Barceló, Damià, Series Editor, de Boer, Jacob, Editorial Board Member, Kostianoy, Andrey G., Series Editor, Garrigues, Philippe, Editorial Board Member, Hutzinger, Otto, Founding Editor, Gu, Ji-Dong, Editorial Board Member, Jones, Kevin C., Editorial Board Member, Knepper, Thomas P., Editorial Board Member, Negm, Abdelazim M., Editorial Board Member, Newton, Alice, Editorial Board Member, Nghiem, Duc Long, Editorial Board Member, Garcia-Segura, Sergi, Editorial Board Member, Núñez-Delgado, Avelino, editor, and Arias-Estévez, Manuel, editor

Published
2023
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46. Climate change and collapsing thermal niches of desert reptiles and amphibians: Assisted migration and acclimation rescue from extirpation

Author

Sinervo, Barry, Lara Reséndiz, Rafael A., Miles, Donald B., Lovich, Jeffrey E., Rosen, Philip C., Gadsden, Héctor, Gaytán, Gamaliel Casteñada, Tessaro, Patricia Galina, Luja, Víctor H., Huey, Raymond B., Whipple, Amy, Cordero, Víctor Sánchez, Rohr, Jason B., Caetano, Gabriel, Santos, Juan C., Sites, Jack W., Jr., and Méndez de la Cruz, Fausto R.

Published
2024
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47. A Metabolite Specific 3D Stack-of-Spiral bSSFP Sequence for Improved Lactate Imaging in Hyperpolarized [1-$^{13}$C]Pyruvate Studies on a 3T Clinical Scanner

Author

Tang, Shuyu, Bok, Robert, Qin, Hecong, Reed, Galen, VanCriekinge, Mark, Santos, Romelyn Delos, Overall, William, Santos, Juan, Gordon, Jeremy, Wang, Zhen Jane, Vigneron, Daniel B., and Larson, Peder E. Z.

Subjects
Physics - Medical Physics
Abstract

Purpose: The balanced steady-state free precession sequence has been previously explored to improve the efficient use of non-recoverable hyperpolarized $^{13}$C magnetization, but suffers from poor spectral selectivity and long acquisition time. The purpose of this study was to develop a novel metabolite-specific 3D bSSFP ("MS-3DSSFP") sequence with stack-of-spiral readouts for improved lactate imaging in hyperpolarized [1-$^{13}$C]pyruvate studies on a clinical 3T scanner. Methods: Simulations were performed to evaluate the spectral response of the MS-3DSSFP sequence. Thermal $^{13}$C phantom experiments were performed to validate the MS-3DSSFP sequence. In vivo hyperpolarized [1-$^{13}$C]pyruvate studies were performed to compare the MS-3DSSFP sequence with metabolite specific gradient echo ("MS-GRE") sequences for lactate imaging. Results: Simulations, phantom and in vivo studies demonstrate that the MS-3DSSFP sequence achieved spectrally selective excitation on lactate while minimally perturbing other metabolites. Compared with MS-GRE sequences, the MS-3DSSFP sequence showed approximately a 2.5-fold SNR improvement for lactate imaging in rat kidneys, prostate tumors in a mouse model and human kidneys. Conclusions: Improved lactate imaging using the MS-3DSSFP sequence in hyperpolarized [1-$^{13}$C]pyruvate studies was demonstrated in animals and humans. The MS-3DSSFP sequence could be applied for other clinical applications such as in the brain or adapted for imaging other metabolites such as pyruvate and bicarbonate.

Published
2020
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48. A numerical simulation of the COVID-19 epidemic in Argentina using the SEIR model

Author

Santos, Juan E., Carcione, Jose' M., Savioli, Gabriela B., Gauzellino, Patricia M., Ravecca, Alejandro, and Moras, Alfredo

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

A pandemic caused by a new coronavirus has spread worldwide, affecting Argentina. We implement an SEIR model to analyze the disease evolution in Buenos Aires and neighbouring cities. The model parameters are calibrated using the number of casualties officially reported. Since infinite solutions honour the data, we show different cases. In all of them the reproduction ratio $R_0$ decreases after early lockdown, but then raises, probably due to an increase in contagion in highly populated slums. Therefore it is mandatory to reverse this growing trend in $R_0$ by applying control strategies to avoid a high number of infectious and dead individuals. The model provides an effective procedure to estimate epidemic parameters (fatality rate, transmission probability, infection and incubation periods) and monitor control measures during the epidemic evolution., Comment: arXiv admin note: substantial text overlap with arXiv:2004.03575

Published
2020

49. A simulation of a COVID-19 epidemic based on a deterministic SEIR model

Author

Carcione, Jose' M., Santos, Juan E., Bagaini, Claudio, and Ba, Jing

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

An epidemic disease caused by a new coronavirus has spread in Northern Italy with a strong contagion rate. We implement an SEIR model to compute the infected population and number of casualties of this epidemic. The example may ideally regard the situation in the Italian Region of Lombardy, where the epidemic started on February 25. We calibrate the model with the number of dead individuals to date (May 5, 2020) and constraint the parameters on the basis of values reported in the literature. The peak occurs at day 37 (March 31) approximately, when there is a rapid decrease, with a reproduction ratio R0 = 3 initially, 1.36 at day 22 and 0.8 after day 35, indicating different degrees of lockdown. The predicted death toll is approximately 15600 casualties, with 2.7 million infected individuals at the end of the epidemic. The incubation period providing a better fit of the dead individuals is 4.25 days and the infection period is 4 days, with a fatality rate of 0.00144/day [values based on the reported (official) number of casualties]. The infection fatality rate (IFR) is 0.57 %, and 2.36 % if twice the reported number of casualties is assumed. However, these rates depend on the initially exposed individuals. If approximately nine times more individuals are exposed, there are three times more infected people at the end of the epidemic and IFR = 0.47 %. If we relax these constraints and use a wider range of lower and upper bounds for the incubation and infection periods, we observe that a higher incubation period (13 versus 4.25 days) gives the same IFR (0.6 versus 0.57 %), but nine times more exposed individuals in the first case. Therefore, a precise determination of the fatality rate is subject to the knowledge of the characteristics of the epidemic.

Published
2020

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