Casimiro-Soriguer, Inés; Aguilar-Benitez, David; Gutierrez, Natalia; Torres, Ana M.
Transcriptome Analysis of Stigmas of Vicia faba L. Flowers Artículo de revista
En: Plants, vol. 13, no 11, 2024, ISSN: 2223-7747.
@article{Casimiro-Soriguer2024,
title = {Transcriptome Analysis of Stigmas of Vicia faba L. Flowers},
author = {Inés Casimiro-Soriguer and David Aguilar-Benitez and Natalia Gutierrez and Ana M. Torres},
doi = {10.3390/plants13111443},
issn = {2223-7747},
year = {2024},
date = {2024-06-00},
journal = {Plants},
volume = {13},
number = {11},
publisher = {MDPI AG},
abstract = {Pollination in angiosperms depends on complex communication between pollen grains and stigmas, classified as wet or dry, depending on the presence or absence of secretions at the stigma surface, respectively. In species with wet stigma, the cuticle is disrupted and the presence of exudates is indicative of their receptivity. Most stigma studies are focused on a few species and families, many of them with self-incompatibility systems. However, there is scarce knowledge about the stigma composition in Fabaceae, the third angiosperm family, whose stigmas have been classified as semidry. Here we report the first transcriptome profiling and DEGs of Vicia faba L. styles and stigmas from autofertile (flowers able to self-fertilize in the absence of manipulation, whose exudate is released spontaneously) and autosterile (flowers that need to be manipulated to break the cuticle and release the exudates to be receptive) inbred lines. From the 76,269 contigs obtained from the de novo assembly, only 45.1% of the sequences were annotated with at least one GO term. A total of 115,920, 75,489, and 70,801 annotations were assigned to Biological Process (BP), Cellular Component (CC), and Molecular Function (MF) categories, respectively, and 5918 differentially expressed genes (DEGs) were identified between the autofertile and the autosterile lines. Among the most enriched metabolic pathways in the DEGs subset were those related with amino acid biosynthesis, terpenoid metabolism, or signal transduction. Some DEGs have been related with previous QTLs identified for autofertility traits, and their putative functions are discussed. The results derived from this work provide an important transcriptomic reference for style-stigma processes to aid our understanding of the molecular mechanisms involved in faba bean fertilization. },
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Espinosa, Elena; Bautista, Rocio; Larrosa, Rafael; Plata, Oscar
Advancements in long-read genome sequencing technologies and algorithms Artículo de revista
En: Genomics, vol. 116, no 3, pp. 110842, 2024, ISSN: 0888-7543.
@article{Espinosa_2024,
title = {Advancements in long-read genome sequencing technologies and algorithms},
author = {Elena Espinosa and Rocio Bautista and Rafael Larrosa and Oscar Plata},
url = {http://dx.doi.org/10.1016/j.ygeno.2024.110842},
doi = {10.1016/j.ygeno.2024.110842},
issn = {0888-7543},
year = {2024},
date = {2024-05-01},
journal = {Genomics},
volume = {116},
number = {3},
pages = {110842},
publisher = {Elsevier BV},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Cordoba-Caballero, Jose; Perkins, James R; García-Criado, Federico; Gallego, Diana; Navarro-Sánchez, Alicia; Moreno-Estellés, Mireia; Garcés, Concepción; Bonet, Fernando; Romá-Mateo, Carlos; Toro, Rocio; Perez, Belén; Sanz, Pascual; Kohl, Matthias; Rojano, Elena; Seoane, Pedro; Ranea, Juan A G
Exploring miRNA–target gene pair detection in disease with coRmiT Artículo de revista
En: vol. 25, no 2, 2024, ISSN: 1477-4054.
@article{Cordoba-Caballero2024,
title = {Exploring miRNA–target gene pair detection in disease with coRmiT},
author = {Jose Cordoba-Caballero and James R Perkins and Federico García-Criado and Diana Gallego and Alicia Navarro-Sánchez and Mireia Moreno-Estellés and Concepción Garcés and Fernando Bonet and Carlos Romá-Mateo and Rocio Toro and Belén Perez and Pascual Sanz and Matthias Kohl and Elena Rojano and Pedro Seoane and Juan A G Ranea},
doi = {10.1093/bib/bbae060},
issn = {1477-4054},
year = {2024},
date = {2024-01-22},
volume = {25},
number = {2},
publisher = {Oxford University Press (OUP)},
abstract = {Abstract
A wide range of approaches can be used to detect micro RNA (miRNA)–target gene pairs (mTPs) from expression data, differing in the ways the gene and miRNA expression profiles are calculated, combined and correlated. However, there is no clear consensus on which is the best approach across all datasets. Here, we have implemented multiple strategies and applied them to three distinct rare disease datasets that comprise smallRNA-Seq and RNA-Seq data obtained from the same samples, obtaining mTPs related to the disease pathology. All datasets were preprocessed using a standardized, freely available computational workflow, DEG_workflow. This workflow includes coRmiT, a method to compare multiple strategies for mTP detection. We used it to investigate the overlap of the detected mTPs with predicted and validated mTPs from 11 different databases. Results show that there is no clear best strategy for mTP detection applicable to all situations. We therefore propose the integration of the results of the different strategies by selecting the one with the highest odds ratio for each miRNA, as the optimal way to integrate the results. We applied this selection-integration method to the datasets and showed it to be robust to changes in the predicted and validated mTP databases. Our findings have important implications for miRNA analysis. coRmiT is implemented as part of the ExpHunterSuite Bioconductor package available from https://bioconductor.org/packages/ExpHunterSuite. },
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Pedroza-Perez, Diego Daniel; Toutouh, Jamal; Luque, Gabriel
Optimizing Urban Infrastructure for E-Scooter Mobility Proceedings Article
En: Smith, Stephen; Correia, João; Cintrano, Christian (Ed.): Applications of Evolutionary Computation, pp. 341–357, Springer Nature Switzerland, Cham, 2024, ISBN: 978-3-031-56852-7.
@inproceedings{10.1007/978-3-031-56852-7_22,
title = {Optimizing Urban Infrastructure for E-Scooter Mobility},
author = {Diego Daniel Pedroza-Perez and Jamal Toutouh and Gabriel Luque},
editor = {Stephen Smith and João Correia and Christian Cintrano},
isbn = {978-3-031-56852-7},
year = {2024},
date = {2024-01-01},
booktitle = {Applications of Evolutionary Computation},
pages = {341–357},
publisher = {Springer Nature Switzerland},
address = {Cham},
abstract = {This paper addresses the optimization of urban infrastructure for e-scooter mobility through a multi-criteria approach. The proposed problem considers redesigning road infrastructure to integrate e-scooters into a city's multimodal transportation system. The objectives involve improving cycle lane coverage for e-scooters while minimizing installation costs. A parallel multi-objective evolutionary algorithm is introduced to solve this problem, applied to a real-world instance based on Málaga city data. The results showcase the algorithm's effectiveness in exploring the Pareto front, offering diverse trade-off solutions. Key solutions are analyzed, highlighting different zones with varying trade-offs between travel time improvement and installation costs. Visualization of proposed infrastructure changes illustrates significant reductions in travel time and enhanced multimodality. Computational efficiency analysis indicates successful parallelization, achieving substantial speedup and high efficiency with up to 32 processing elements.},
keywords = {},
pubstate = {published},
tppubtype = {inproceedings}
}
This paper addresses the optimization of urban infrastructure for e-scooter mobility through a multi-criteria approach. The proposed problem considers redesigning road infrastructure to integrate e-scooters into a city's multimodal transportation system. The objectives involve improving cycle lane coverage for e-scooters while minimizing installation costs. A parallel multi-objective evolutionary algorithm is introduced to solve this problem, applied to a real-world instance based on Málaga city data. The results showcase the algorithm's effectiveness in exploring the Pareto front, offering diverse trade-off solutions. Key solutions are analyzed, highlighting different zones with varying trade-offs between travel time improvement and installation costs. Visualization of proposed infrastructure changes illustrates significant reductions in travel time and enhanced multimodality. Computational efficiency analysis indicates successful parallelization, achieving substantial speedup and high efficiency with up to 32 processing elements.
Morell, José Ángel; Dahi, Zakaria Abdelmoiz; Chicano, Francisco; Luque, Gabriel; Alba, Enrique
A multi-objective approach for communication reduction in federated learning under devices heterogeneity constraints Artículo de revista
En: Future Generation Computer Systems, vol. 155, pp. 367-383, 2024, ISSN: 0167-739X.
@article{MORELL2024367,
title = {A multi-objective approach for communication reduction in federated learning under devices heterogeneity constraints},
author = {José Ángel Morell and Zakaria Abdelmoiz Dahi and Francisco Chicano and Gabriel Luque and Enrique Alba},
url = {https://www.sciencedirect.com/science/article/pii/S0167739X24000682},
doi = {https://doi.org/10.1016/j.future.2024.02.022},
issn = {0167-739X},
year = {2024},
date = {2024-01-01},
journal = {Future Generation Computer Systems},
volume = {155},
pages = {367-383},
abstract = {Federated learning is a paradigm that proposes protecting data privacy by sharing local models instead of raw data during each iteration of model training. However, these models can be large, with many parameters, provoking a substantial communication cost and having a notable environmental impact. Reducing communication overhead is paramount but conflictual to maintaining the model’s accuracy. Most research has dealt with the different factors influencing communication reduction separately without addressing their correlations. Moreover, most of them do not consider the heterogeneity of clients’ hardware. Finding the optimal configuration to fulfil all these training aspects can become intractable for classical techniques. This work explores the add-in that multi-objective evolutionary algorithms can provide for solving the communication overhead problem while achieving high accuracy. We do this by 1) realistically modelling and formulating this task as a multi-objective problem by considering the devices’ heterogeneity, 2) including all the communication-triggering aspects, and 3) applying a multi-objective evolutionary algorithm with an intensification operator to solve the problem. A simulated client–server architecture of four devices with four different processing speeds is studied. Both fully connected and convolutional neural network models are investigated with 33,400 and 887,530 weights, respectively. The experiments are performed using the MNIST and Fashion-MNIST datasets. A comparison is made between three approaches using an extensive set of metrics. Results prove that our approach obtains solutions with better accuracy than the full-communication setting and other methods while getting reductions in communications by around 1,000 times in most cases and up to 10,000 times in some cases compared to the maximum communication setting.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Federated learning is a paradigm that proposes protecting data privacy by sharing local models instead of raw data during each iteration of model training. However, these models can be large, with many parameters, provoking a substantial communication cost and having a notable environmental impact. Reducing communication overhead is paramount but conflictual to maintaining the model’s accuracy. Most research has dealt with the different factors influencing communication reduction separately without addressing their correlations. Moreover, most of them do not consider the heterogeneity of clients’ hardware. Finding the optimal configuration to fulfil all these training aspects can become intractable for classical techniques. This work explores the add-in that multi-objective evolutionary algorithms can provide for solving the communication overhead problem while achieving high accuracy. We do this by 1) realistically modelling and formulating this task as a multi-objective problem by considering the devices’ heterogeneity, 2) including all the communication-triggering aspects, and 3) applying a multi-objective evolutionary algorithm with an intensification operator to solve the problem. A simulated client–server architecture of four devices with four different processing speeds is studied. Both fully connected and convolutional neural network models are investigated with 33,400 and 887,530 weights, respectively. The experiments are performed using the MNIST and Fashion-MNIST datasets. A comparison is made between three approaches using an extensive set of metrics. Results prove that our approach obtains solutions with better accuracy than the full-communication setting and other methods while getting reductions in communications by around 1,000 times in most cases and up to 10,000 times in some cases compared to the maximum communication setting.
Naranjo, Ángela; Álvarez-Soria, M. Josefa; Aranda-Villalobos, Pilar; Martínez-Rodríguez, Ana M.; Martínez-Lara, Esther; Siles, Eva
Hydroxytyrosol, a Promising Supplement in the Management of Human Stroke: An Exploratory Study Artículo de revista
En: International Journal of Molecular Sciences, vol. 25, no 9, 2024, ISSN: 1422-0067.
@article{ijms25094799,
title = {Hydroxytyrosol, a Promising Supplement in the Management of Human Stroke: An Exploratory Study},
author = {Ángela Naranjo and M. Josefa Álvarez-Soria and Pilar Aranda-Villalobos and Ana M. Martínez-Rodríguez and Esther Martínez-Lara and Eva Siles},
url = {https://www.mdpi.com/1422-0067/25/9/4799},
doi = {10.3390/ijms25094799},
issn = {1422-0067},
year = {2024},
date = {2024-01-01},
journal = {International Journal of Molecular Sciences},
volume = {25},
number = {9},
abstract = {Hydroxytyrosol (HT) is a bioactive olive oil phenol with beneficial effects in a number of pathological situations. We have previously demonstrated that an HT-enriched diet could serve as a beneficial therapeutic approach to attenuate ischemic-stroke-associated damage in mice. Our exploratory pilot study examined this effect in humans. Particularly, a nutritional supplement containing 15 mg of HT/day was administered to patients 24 h after the onset of stroke, for 45 days. Biochemical and oxidative-stress-related parameters, blood pressure levels, serum proteome, and neurological and functional outcomes were evaluated at 45 and 90 days and compared to a control group. The main findings were that the daily administration of HT after stroke could: (i) favor the decrease in the percentage of glycated hemoglobin and diastolic blood pressure, (ii) control the increase in nitric oxide and exert a plausible protective effect in oxidative stress, (iii) modulate the evolution of the serum proteome and, particularly, the expression of apolipoproteins, and (iv) be beneficial for certain neurological and functional outcomes. Although a larger trial is necessary, this study suggests that HT could be a beneficial nutritional complement in the management of human stroke.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Hydroxytyrosol (HT) is a bioactive olive oil phenol with beneficial effects in a number of pathological situations. We have previously demonstrated that an HT-enriched diet could serve as a beneficial therapeutic approach to attenuate ischemic-stroke-associated damage in mice. Our exploratory pilot study examined this effect in humans. Particularly, a nutritional supplement containing 15 mg of HT/day was administered to patients 24 h after the onset of stroke, for 45 days. Biochemical and oxidative-stress-related parameters, blood pressure levels, serum proteome, and neurological and functional outcomes were evaluated at 45 and 90 days and compared to a control group. The main findings were that the daily administration of HT after stroke could: (i) favor the decrease in the percentage of glycated hemoglobin and diastolic blood pressure, (ii) control the increase in nitric oxide and exert a plausible protective effect in oxidative stress, (iii) modulate the evolution of the serum proteome and, particularly, the expression of apolipoproteins, and (iv) be beneficial for certain neurological and functional outcomes. Although a larger trial is necessary, this study suggests that HT could be a beneficial nutritional complement in the management of human stroke.
Rubira, Rafael J. G.; Correia, Rafael R.; Batista, Victor R. G.; Pazin, Wallance M.; González, Francisco G.; Otero, Juan C.; Teixeira, Giovana R.; Job, Aldo E.
Assessing the negative impact of chlorantraniliprole, isoxaflutole, and simazine pesticides on phospholipid membrane models and tilapia gill tissues Artículo de revista
En: Environmental Pollution, vol. 349, pp. 123904, 2024, ISSN: 0269-7491.
@article{RUBIRA2024123904,
title = {Assessing the negative impact of chlorantraniliprole, isoxaflutole, and simazine pesticides on phospholipid membrane models and tilapia gill tissues},
author = {Rafael J. G. Rubira and Rafael R. Correia and Victor R. G. Batista and Wallance M. Pazin and Francisco G. González and Juan C. Otero and Giovana R. Teixeira and Aldo E. Job},
url = {https://www.sciencedirect.com/science/article/pii/S0269749124006183},
doi = {https://doi.org/10.1016/j.envpol.2024.123904},
issn = {0269-7491},
year = {2024},
date = {2024-01-01},
journal = {Environmental Pollution},
volume = {349},
pages = {123904},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Valdivia, Samuel; Aranda, Daniel; Otero, Juan Carlos; López-Tocón, Isabel
Voltage tuning of photoinduced charge transfer resonances between 2, 2'-bipyridine and a nanostructured silver electrode Artículo de revista
En: Applied Surface Science, vol. 646, pp. 158871, 2024, ISSN: 0169-4332.
@article{VALDIVIA2024158871,
title = {Voltage tuning of photoinduced charge transfer resonances between 2, 2'-bipyridine and a nanostructured silver electrode},
author = {Samuel Valdivia and Daniel Aranda and Juan Carlos Otero and Isabel López-Tocón},
url = {https://www.sciencedirect.com/science/article/pii/S0169433223025515},
doi = {https://doi.org/10.1016/j.apsusc.2023.158871},
issn = {0169-4332},
year = {2024},
date = {2024-01-01},
journal = {Applied Surface Science},
volume = {646},
pages = {158871},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Alvarez, M Angeles; García, M Esther; García-Vivó, Daniel; Guerra, Ana M; Ruiz, Miguel A
C$equiv$ N and N$equiv$ O Bond Cleavages of Acetonitrile and Nitrosyl Ligands at a Dimolybdenum Center to Render Ethylidyne and Acetamidinate Ligands Artículo de revista
En: Inorganic Chemistry, 2024.
@article{alvarez2024c,
title = {C$equiv$ N and N$equiv$ O Bond Cleavages of Acetonitrile and Nitrosyl Ligands at a Dimolybdenum Center to Render Ethylidyne and Acetamidinate Ligands},
author = {M Angeles Alvarez and M Esther García and Daniel García-Vivó and Ana M Guerra and Miguel A Ruiz},
doi = {https://doi.org/10.1021/acs.inorgchem.3c03697},
year = {2024},
date = {2024-01-01},
journal = {Inorganic Chemistry},
publisher = {ACS Publications},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Rodrigo-Faus, Maria; Vincelle-Nieto, Africa; Vidal, Natalia; Puente, Javier; Saiz-Pardo, Melchor; Lopez-Garcia, Alejandra; Mendiburu-Eliçabe, Marina; Palao, Nerea; Baquero, Cristina; Linzoain-Agos, Paula; Cuesta, Angel M.; Qu, Hui-Qi; Hakonarson, Hakon; Musteanu, Monica; Reyes-Palomares, Armando; Porras, Almudena; Bragado, Paloma; Gutierrez-Uzquiza, Alvaro
CRISPR/Cas9 screenings unearth protein arginine methyltransferase 7 as a novel essential gene in prostate cancer metastasis Artículo de revista
En: Cancer Letters, vol. 588, pp. 216776, 2024, ISSN: 0304-3835.
@article{RODRIGOFAUS2024216776,
title = {CRISPR/Cas9 screenings unearth protein arginine methyltransferase 7 as a novel essential gene in prostate cancer metastasis},
author = {Maria Rodrigo-Faus and Africa Vincelle-Nieto and Natalia Vidal and Javier Puente and Melchor Saiz-Pardo and Alejandra Lopez-Garcia and Marina Mendiburu-Eliçabe and Nerea Palao and Cristina Baquero and Paula Linzoain-Agos and Angel M. Cuesta and Hui-Qi Qu and Hakon Hakonarson and Monica Musteanu and Armando Reyes-Palomares and Almudena Porras and Paloma Bragado and Alvaro Gutierrez-Uzquiza},
url = {https://www.sciencedirect.com/science/article/pii/S0304383524001691},
doi = {https://doi.org/10.1016/j.canlet.2024.216776},
issn = {0304-3835},
year = {2024},
date = {2024-01-01},
journal = {Cancer Letters},
volume = {588},
pages = {216776},
abstract = {Due to the limited effectiveness of current treatments, the survival rate of patients with metastatic castration-resistant prostate cancer (mCRPC) is significantly reduced. Consequently, it is imperative to identify novel therapeutic targets for managing these patients. Since the invasive ability of cells is crucial for establishing and maintaining metastasis, the aim of this study was to identify the essential regulators of invasive abilities of mCRPC cells by conducting two independent high-throughput CRISPR/Cas9 screenings. Furthermore, some of the top hits were validated using siRNA technology, with protein arginine methyltransferase 7 (PRMT7) emerging as the most promising candidate. We demonstrated that its inhibition or depletion via genetic or pharmacological approaches significantly reduces invasive, migratory and proliferative abilities of mCRPC cells in vitro. Moreover, we confirmed that PRMT7 ablation reduces cell dissemination in chicken chorioallantoic membrane and mouse xenograft assays. Molecularly, PRMT7 reprograms the expression of several adhesion molecules by methylating various transcription factors, such as FoxK1, resulting in the loss of adhesion from the primary tumor and increased motility of mCRPC cells. Furthermore, PRMT7 higher expression correlates with tumor aggressivity and poor overall survival in prostate cancer patients. Thus, this study demonstrates that PRMT7 is a potential therapeutic target and potential biomarker for mPCa.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Due to the limited effectiveness of current treatments, the survival rate of patients with metastatic castration-resistant prostate cancer (mCRPC) is significantly reduced. Consequently, it is imperative to identify novel therapeutic targets for managing these patients. Since the invasive ability of cells is crucial for establishing and maintaining metastasis, the aim of this study was to identify the essential regulators of invasive abilities of mCRPC cells by conducting two independent high-throughput CRISPR/Cas9 screenings. Furthermore, some of the top hits were validated using siRNA technology, with protein arginine methyltransferase 7 (PRMT7) emerging as the most promising candidate. We demonstrated that its inhibition or depletion via genetic or pharmacological approaches significantly reduces invasive, migratory and proliferative abilities of mCRPC cells in vitro. Moreover, we confirmed that PRMT7 ablation reduces cell dissemination in chicken chorioallantoic membrane and mouse xenograft assays. Molecularly, PRMT7 reprograms the expression of several adhesion molecules by methylating various transcription factors, such as FoxK1, resulting in the loss of adhesion from the primary tumor and increased motility of mCRPC cells. Furthermore, PRMT7 higher expression correlates with tumor aggressivity and poor overall survival in prostate cancer patients. Thus, this study demonstrates that PRMT7 is a potential therapeutic target and potential biomarker for mPCa.
Pineda, Salvador; Morales, Juan Miguel; Jiménez-Cordero, Asunción
Learning-assisted optimization for transmission switching Artículo de revista
En: TOP, pp. 1–28, 2024.
@article{pineda2024learning,
title = {Learning-assisted optimization for transmission switching},
author = {Salvador Pineda and Juan Miguel Morales and Asunción Jiménez-Cordero},
doi = {https://doi.org/10.1007/s11750-024-00672-0},
year = {2024},
date = {2024-01-01},
journal = {TOP},
pages = {1–28},
publisher = {Springer},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Cordoba-Caballero, Jose; Perkins, James R; García-Criado, Federico; Gallego, Diana; Navarro-Sánchez, Alicia; Moreno-Estellés, Mireia; Garcés, Concepción; Bonet, Fernando; Romá-Mateo, Carlos; Toro, Rocio; Perez, Belén; Sanz, Pascual; Kohl, Matthias; Rojano, Elena; Seoane, Pedro; Ranea, Juan A G
Exploring miRNA–target gene pair detection in disease with coRmiT Artículo de revista
En: Briefings in Bioinformatics, vol. 25, no 2, pp. bbae060, 2024, ISSN: 1477-4054.
@article{10.1093/bib/bbae060,
title = {Exploring miRNA–target gene pair detection in disease with coRmiT},
author = {Jose Cordoba-Caballero and James R Perkins and Federico García-Criado and Diana Gallego and Alicia Navarro-Sánchez and Mireia Moreno-Estellés and Concepción Garcés and Fernando Bonet and Carlos Romá-Mateo and Rocio Toro and Belén Perez and Pascual Sanz and Matthias Kohl and Elena Rojano and Pedro Seoane and Juan A G Ranea},
url = {https://doi.org/10.1093/bib/bbae060},
doi = {10.1093/bib/bbae060},
issn = {1477-4054},
year = {2024},
date = {2024-01-01},
journal = {Briefings in Bioinformatics},
volume = {25},
number = {2},
pages = {bbae060},
abstract = {A wide range of approaches can be used to detect micro RNA (miRNA)–target gene pairs (mTPs) from expression data, differing in the ways the gene and miRNA expression profiles are calculated, combined and correlated. However, there is no clear consensus on which is the best approach across all datasets. Here, we have implemented multiple strategies and applied them to three distinct rare disease datasets that comprise smallRNA-Seq and RNA-Seq data obtained from the same samples, obtaining mTPs related to the disease pathology. All datasets were preprocessed using a standardized, freely available computational workflow, DEG_workflow. This workflow includes coRmiT, a method to compare multiple strategies for mTP detection. We used it to investigate the overlap of the detected mTPs with predicted and validated mTPs from 11 different databases. Results show that there is no clear best strategy for mTP detection applicable to all situations. We therefore propose the integration of the results of the different strategies by selecting the one with the highest odds ratio for each miRNA, as the optimal way to integrate the results. We applied this selection-integration method to the datasets and showed it to be robust to changes in the predicted and validated mTP databases. Our findings have important implications for miRNA analysis. coRmiT is implemented as part of the ExpHunterSuite Bioconductor package available from https://bioconductor.org/packages/ExpHunterSuite.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
A wide range of approaches can be used to detect micro RNA (miRNA)–target gene pairs (mTPs) from expression data, differing in the ways the gene and miRNA expression profiles are calculated, combined and correlated. However, there is no clear consensus on which is the best approach across all datasets. Here, we have implemented multiple strategies and applied them to three distinct rare disease datasets that comprise smallRNA-Seq and RNA-Seq data obtained from the same samples, obtaining mTPs related to the disease pathology. All datasets were preprocessed using a standardized, freely available computational workflow, DEG_workflow. This workflow includes coRmiT, a method to compare multiple strategies for mTP detection. We used it to investigate the overlap of the detected mTPs with predicted and validated mTPs from 11 different databases. Results show that there is no clear best strategy for mTP detection applicable to all situations. We therefore propose the integration of the results of the different strategies by selecting the one with the highest odds ratio for each miRNA, as the optimal way to integrate the results. We applied this selection-integration method to the datasets and showed it to be robust to changes in the predicted and validated mTP databases. Our findings have important implications for miRNA analysis. coRmiT is implemented as part of the ExpHunterSuite Bioconductor package available from https://bioconductor.org/packages/ExpHunterSuite.
Paredes, Angel; Aguado, José A
Revenue Stacking of BESSs in Wholesale and aFRR Markets with Delivery Guarantees Proceedings Article
En: 2024.
@inproceedings{paredesrevenue,
title = {Revenue Stacking of BESSs in Wholesale and aFRR Markets with Delivery Guarantees},
author = {Angel Paredes and José A Aguado},
url = {https://www.researchgate.net/profile/Angel-Paredes-Parrilla/publication/379376253_Revenue_Stacking_of_BESSs_in_Wholesale_and_aFRR_Markets_with_Delivery_Guarantees/links/6606e0d4f5a5de0a9fe8dbab/Revenue-Stacking-of-BESSs-in-Wholesale-and-aFRR-Markets-with-Delivery-Guarantees.pdf},
year = {2024},
date = {2024-01-01},
keywords = {},
pubstate = {published},
tppubtype = {inproceedings}
}
García-Alberca, José María; Rojas, Itziar; Sanchez-Mejias, Elisabeth; Garrido-Martín, Diego; Gonzalez-Palma, Laura; Jimenez, Sebastian; Pino-Angeles, Almudena; Cruz-Gamero, Jose Manuel; Mendoza, Silvia; Alarcón-Martín, Emilio; others,
An Insertion Within SIRPβ1 Shows a Dual Effect Over Alzheimer’s Disease Cognitive Decline Altering the Microglial Response Artículo de revista
En: Journal of Alzheimer's Disease, no Preprint, pp. 1–18, 2024.
@article{garcia2024insertion,
title = {An Insertion Within SIRPβ1 Shows a Dual Effect Over Alzheimer’s Disease Cognitive Decline Altering the Microglial Response},
author = {José María García-Alberca and Itziar Rojas and Elisabeth Sanchez-Mejias and Diego Garrido-Martín and Laura Gonzalez-Palma and Sebastian Jimenez and Almudena Pino-Angeles and Jose Manuel Cruz-Gamero and Silvia Mendoza and Emilio Alarcón-Martín and others},
doi = {10.3233/JAD-231150},
year = {2024},
date = {2024-01-01},
journal = {Journal of Alzheimer's Disease},
number = {Preprint},
pages = {1–18},
publisher = {IOS Press},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Cotta, Carlos; Gallardo, José E.
Evolutionary Algorithms for Optimizing Emergency Exit Placement in Indoor Environments Proceedings Article
En: Smith, Stephen; Correia, João; Cintrano, Christian (Ed.): Applications of Evolutionary Computation, pp. 194–208, Springer Nature Switzerland, Cham, 2024, ISBN: 978-3-031-56852-7.
@inproceedings{10.1007/978-3-031-56852-7_13,
title = {Evolutionary Algorithms for Optimizing Emergency Exit Placement in Indoor Environments},
author = {Carlos Cotta and José E. Gallardo},
editor = {Stephen Smith and João Correia and Christian Cintrano},
isbn = {978-3-031-56852-7},
year = {2024},
date = {2024-01-01},
booktitle = {Applications of Evolutionary Computation},
pages = {194–208},
publisher = {Springer Nature Switzerland},
address = {Cham},
abstract = {The problem of finding the optimal placement of emergency exits in an indoor environment to facilitate the rapid and orderly evacuation of crowds is addressed in this work. A cellular-automaton model is used to simulate the behavior of pedestrians in such scenarios, taking into account factors such as the environment, the pedestrians themselves, and the interactions among them. A metric is proposed to determine how successful or satisfactory an evacuation was. Subsequently, two metaheuristic algorithms, namely an iterated greedy heuristic and an evolutionary algorithm (EA) are proposed to solve the optimization problem. A comparative analysis shows that the proposed EA is able to find effective solutions for different scenarios, and that an island-based version of it outperforms the other two algorithms in terms of solution quality."},
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pubstate = {published},
tppubtype = {inproceedings}
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The problem of finding the optimal placement of emergency exits in an indoor environment to facilitate the rapid and orderly evacuation of crowds is addressed in this work. A cellular-automaton model is used to simulate the behavior of pedestrians in such scenarios, taking into account factors such as the environment, the pedestrians themselves, and the interactions among them. A metric is proposed to determine how successful or satisfactory an evacuation was. Subsequently, two metaheuristic algorithms, namely an iterated greedy heuristic and an evolutionary algorithm (EA) are proposed to solve the optimization problem. A comparative analysis shows that the proposed EA is able to find effective solutions for different scenarios, and that an island-based version of it outperforms the other two algorithms in terms of solution quality."
Gayo, Patricia; Berbel, Concha; Gómez-Maldonado, Josefa; Claros, M. Gonzalo; Manchado, Manuel
Phenotypic features, transcriptomic signatures and genomic regions associated with body ellipticity in the flatfish Senegalese sole Artículo de revista
En: Aquaculture, vol. 583, pp. 740590, 2024, ISSN: 0044-8486.
@article{GAYO2024740590,
title = {Phenotypic features, transcriptomic signatures and genomic regions associated with body ellipticity in the flatfish Senegalese sole},
author = {Patricia Gayo and Concha Berbel and Josefa Gómez-Maldonado and M. Gonzalo Claros and Manuel Manchado},
url = {https://www.sciencedirect.com/science/article/pii/S0044848624000516},
doi = {https://doi.org/10.1016/j.aquaculture.2024.740590},
issn = {0044-8486},
year = {2024},
date = {2024-01-01},
journal = {Aquaculture},
volume = {583},
pages = {740590},
abstract = {Body shape is a complex and plastic trait with a high impact on fish performance and commercialization. Shape is particularly relevant in flatfish with highly asymmetric bodies. In this study we investigated the skeleton features, transcriptomic profiles and genomic regions in two Senegalese sole groups from a full-sib family with positive (named as HE) or negative (LE) breeding values for body ellipticity (ELL). Soles from HE group were heavier and displayed more elongated bodies than LE. A skeleton analysis showed that HE had a higher number of vertebrae, longer vertebral bodies and intervertebral spaces and a lower incidence of skeletal fusions than LE. With respect to the gender effect, females showed a higher height of ventral body and some differences in the ratio urostyle to skeleton length than males for similar ELL values. The PCA analysis using 28 dimensionless morphological traits indicated that PC1 and PC2 explained 51.3% of the total variance and they were mainly associated with ELL and gender variation, respectively. Expression analysis using two factors (ELL and gender) revealed a major effect of gender in muscle, pterygiophores and liver with 6764, 6506 and 7559 differentially expressed transcripts (DETs) between sexes, respectively. In brain, only 16 DETs were identified. When HE and LE were compared controlling by gender, we identified the subset of DETs with conserved responses in both sexes or those regulated in a sex-specific manner in each tissue. A comparison across tissues identified 31 ubiquitous transcripts as differentially expressed in at least two of them. Functional analysis showed that liver and pterygiophores had the highest number of enriched gene ontology categories (24 and 14, respectively). Some of these enriched pathways were related to regulation of cell cycle, cell structure and shape, locomotory behavior, immune system, hormonal responses and homeostasis. A BSR-Seq analysis confirmed five significant genomic windows associated with ELL by using the tricube-smoothed G' and Fst statistics. Windows located in linkage groups (LG) 5 and LG14 included the malt1 and vtg3 genes, respectively, that were also detected within the subset of ubiquitous DETs. Moreover, malt1 appeared located very close to the bmpr1b gene within the significance hotspot of LG5 indicating that mediators of the inflammatory responses and BMP signaling pathway could be responsible for the differences found in the skeleton features and body ellipticity.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Body shape is a complex and plastic trait with a high impact on fish performance and commercialization. Shape is particularly relevant in flatfish with highly asymmetric bodies. In this study we investigated the skeleton features, transcriptomic profiles and genomic regions in two Senegalese sole groups from a full-sib family with positive (named as HE) or negative (LE) breeding values for body ellipticity (ELL). Soles from HE group were heavier and displayed more elongated bodies than LE. A skeleton analysis showed that HE had a higher number of vertebrae, longer vertebral bodies and intervertebral spaces and a lower incidence of skeletal fusions than LE. With respect to the gender effect, females showed a higher height of ventral body and some differences in the ratio urostyle to skeleton length than males for similar ELL values. The PCA analysis using 28 dimensionless morphological traits indicated that PC1 and PC2 explained 51.3% of the total variance and they were mainly associated with ELL and gender variation, respectively. Expression analysis using two factors (ELL and gender) revealed a major effect of gender in muscle, pterygiophores and liver with 6764, 6506 and 7559 differentially expressed transcripts (DETs) between sexes, respectively. In brain, only 16 DETs were identified. When HE and LE were compared controlling by gender, we identified the subset of DETs with conserved responses in both sexes or those regulated in a sex-specific manner in each tissue. A comparison across tissues identified 31 ubiquitous transcripts as differentially expressed in at least two of them. Functional analysis showed that liver and pterygiophores had the highest number of enriched gene ontology categories (24 and 14, respectively). Some of these enriched pathways were related to regulation of cell cycle, cell structure and shape, locomotory behavior, immune system, hormonal responses and homeostasis. A BSR-Seq analysis confirmed five significant genomic windows associated with ELL by using the tricube-smoothed G' and Fst statistics. Windows located in linkage groups (LG) 5 and LG14 included the malt1 and vtg3 genes, respectively, that were also detected within the subset of ubiquitous DETs. Moreover, malt1 appeared located very close to the bmpr1b gene within the significance hotspot of LG5 indicating that mediators of the inflammatory responses and BMP signaling pathway could be responsible for the differences found in the skeleton features and body ellipticity.
Bárcenas-Luque, Antonio José; Moral-Pulido, Francisco; Gutiérrez-Montes, Cándido; Coenen, Wilfried; Martínez-Bazán, Carlos
Oscillating flow around a circular cylindrical post confined between two parallel plates Miscelánea
2024.
@misc{bárcenasluque2024oscillating,
title = {Oscillating flow around a circular cylindrical post confined between two parallel plates},
author = {Antonio José Bárcenas-Luque and Francisco Moral-Pulido and Cándido Gutiérrez-Montes and Wilfried Coenen and Carlos Martínez-Bazán},
year = {2024},
date = {2024-01-01},
keywords = {},
pubstate = {published},
tppubtype = {misc}
}
Hernández-Lao, Tamara; Tienda-Parrilla, Marta; Labella-Ortega, Mónica; Guerrero-Sánchez, Victor M.; Rey, María-Dolores; Jorrín-Novo, Jesús V.; Castillejo-Sánchez, María Angeles
Proteomic and Metabolomic Analysis of the Quercus ilex–Phytophthora cinnamomi Pathosystem Reveals a Population-Specific Response, Independent of Co-Occurrence of Drought Artículo de revista
En: Biomolecules, vol. 14, no 2, 2024, ISSN: 2218-273X.
@article{biom14020160,
title = {Proteomic and Metabolomic Analysis of the Quercus ilex–Phytophthora cinnamomi Pathosystem Reveals a Population-Specific Response, Independent of Co-Occurrence of Drought},
author = {Tamara Hernández-Lao and Marta Tienda-Parrilla and Mónica Labella-Ortega and Victor M. Guerrero-Sánchez and María-Dolores Rey and Jesús V. Jorrín-Novo and María Angeles Castillejo-Sánchez},
url = {https://www.mdpi.com/2218-273X/14/2/160},
doi = {10.3390/biom14020160},
issn = {2218-273X},
year = {2024},
date = {2024-01-01},
journal = {Biomolecules},
volume = {14},
number = {2},
abstract = {Holm oak (Quercus ilex) is considered to be one of the major structural elements of Mediterranean forests and the agrosilvopastoral Spanish “dehesa”, making it an outstanding example of ecological and socioeconomic sustainability in forest ecosystems. The exotic Phytophthora cinnamomi is one of the most aggressive pathogens of woody species and, together with drought, is considered to be one of the main drivers of holm oak decline. The effect of and response to P. cinnamomi inoculation were studied in the offspring of mother trees from two Andalusian populations, Cordoba and Huelva. At the two locations, acorns collected from both symptomatic (damaged) and asymptomatic (apparently healthy) trees were sampled. Damage symptoms, mortality, and chlorophyll fluorescence were evaluated in seedlings inoculated under humid and drought conditions. The effect and response depended on the population and were more apparent in Huelva than in Cordoba. An integrated proteomic and metabolomic analysis revealed the involvement of different metabolic pathways in response to the pathogen in both populations, including amino acid metabolism pathways in Huelva, and terpenoid and flavonoid biosynthesis in Cordoba. However, no differential response was observed between seedlings inoculated under humid and drought conditions. A protective mechanism of the photosynthetic apparatus was activated in response to defective photosynthetic activity in inoculated plants, which seemed to be more efficient in the Cordoba population. In addition, enzymes and metabolites of the phenylpropanoid and flavonoid biosynthesis pathways may have conferred higher resistance in the Cordoba population. Some enzymes are proposed as markers of resilience, among which glyoxalase I, glutathione reductase, thioredoxin reductase, and cinnamyl alcohol dehydrogenase are candidates.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Holm oak (Quercus ilex) is considered to be one of the major structural elements of Mediterranean forests and the agrosilvopastoral Spanish “dehesa”, making it an outstanding example of ecological and socioeconomic sustainability in forest ecosystems. The exotic Phytophthora cinnamomi is one of the most aggressive pathogens of woody species and, together with drought, is considered to be one of the main drivers of holm oak decline. The effect of and response to P. cinnamomi inoculation were studied in the offspring of mother trees from two Andalusian populations, Cordoba and Huelva. At the two locations, acorns collected from both symptomatic (damaged) and asymptomatic (apparently healthy) trees were sampled. Damage symptoms, mortality, and chlorophyll fluorescence were evaluated in seedlings inoculated under humid and drought conditions. The effect and response depended on the population and were more apparent in Huelva than in Cordoba. An integrated proteomic and metabolomic analysis revealed the involvement of different metabolic pathways in response to the pathogen in both populations, including amino acid metabolism pathways in Huelva, and terpenoid and flavonoid biosynthesis in Cordoba. However, no differential response was observed between seedlings inoculated under humid and drought conditions. A protective mechanism of the photosynthetic apparatus was activated in response to defective photosynthetic activity in inoculated plants, which seemed to be more efficient in the Cordoba population. In addition, enzymes and metabolites of the phenylpropanoid and flavonoid biosynthesis pathways may have conferred higher resistance in the Cordoba population. Some enzymes are proposed as markers of resilience, among which glyoxalase I, glutathione reductase, thioredoxin reductase, and cinnamyl alcohol dehydrogenase are candidates.
Silva, Maria J. S. A.; Zhang, Yiyi; Vinck, Robin; Santos, Fábio M. F.; António, João P. M.; Gourdon-Grünewaldt, Lisa; Zaouter, Charlotte; Castonguay, Annie; Patten, Shunmoogum A.; Cariou, Kevin; Boscá, Francisco; Nájera, Francisco; Arteaga, Jesús F.; Gasser, Gilles; Pischel, Uwe; Gois, Pedro M. P.
BASHY Dyes Are Highly Efficient Lipid Droplet-Targeting Photosensitizers that Induce Ferroptosis through Lipid Peroxidation Artículo de revista
En: Bioconjugate Chem., vol. 34, no 12, pp. 2337–2344, 2023, ISSN: 1520-4812.
@article{Silva2023,
title = {BASHY Dyes Are Highly Efficient Lipid Droplet-Targeting Photosensitizers that Induce Ferroptosis through Lipid Peroxidation},
author = {Maria J. S. A. Silva and Yiyi Zhang and Robin Vinck and Fábio M. F. Santos and João P. M. António and Lisa Gourdon-Grünewaldt and Charlotte Zaouter and Annie Castonguay and Shunmoogum A. Patten and Kevin Cariou and Francisco Boscá and Francisco Nájera and Jesús F. Arteaga and Gilles Gasser and Uwe Pischel and Pedro M. P. Gois},
doi = {10.1021/acs.bioconjchem.3c00449},
issn = {1520-4812},
year = {2023},
date = {2023-12-20},
journal = {Bioconjugate Chem.},
volume = {34},
number = {12},
pages = {2337--2344},
publisher = {American Chemical Society (ACS)},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Royo, Raquel; Mainik, Philipp; Benitez‐Martin, Carlos; Andreu, Raquel; Blasco, Eva; Najera, Francisco; Villacampa, Belén
Highly Efficient Photoninitiators Based on 4H‐Pyranylidene Derivatives for Two‐Photon Laser Printing Artículo de revista
En: Adv Materials Technologies, vol. 8, no 23, 2023, ISSN: 2365-709X.
@article{Royo2023,
title = {Highly Efficient Photoninitiators Based on 4\textit{H}‐Pyranylidene Derivatives for Two‐Photon Laser Printing},
author = {Raquel Royo and Philipp Mainik and Carlos Benitez‐Martin and Raquel Andreu and Eva Blasco and Francisco Najera and Belén Villacampa},
doi = {10.1002/admt.202300571},
issn = {2365-709X},
year = {2023},
date = {2023-12-00},
journal = {Adv Materials Technologies},
volume = {8},
number = {23},
publisher = {Wiley},
abstract = {Abstract A series of four donor–acceptor–donor derivatives bearing 4H ‐pyranylidene and 4‐methylcyclohexan‐1‐one units as donor and acceptor groups respectively is designed, synthesized, and photophysically characterized. Both experimental and theoretical studies reveal good two‐photon absorption (2PA) properties for these systems. Decoration of the exocyclic position of the 4H ‐pyranylidene moiety with a thiophene ring results in high 2PA cross‐section values (σ 2PA ) ≈700 nm, and remarkably, in the region between 900 and 1000 nm. Furthermore, all chromophores are evaluated as photoinitiators (PIs) for two‐photon‐laser printing at 780 nm, showing superior performance compared to the commonly used commercially available PI, phenylbis(2,4,6‐trimethylbenzoyl)phosphine oxide. Among the studied PIs, the ones equipped with a thiophene unit at the exocyclic position of the 4H ‐pyranylidene moiety exhibit the highest efficiency, enabling fast printing using low laser powers with even lower concentrations of PI. Overall, this study shows the great potential of this new class of PIs for application in the field of 3D nanoprinting. },
keywords = {},
pubstate = {published},
tppubtype = {article}
}
