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  1. Article: Beneficial Shifts in the Gut Bacterial Community of Gilthead Seabream (

    Rabelo-Ruiz, Miguel / Newman-Portela, Antonio M / Peralta-Sánchez, Juan Manuel / Martín-Platero, Antonio Manuel / Agraso, María Del Mar / Bermúdez, Laura / Aguinaga, María Arántzazu / Baños, Alberto / Maqueda, Mercedes / Valdivia, Eva / Martínez-Bueno, Manuel

    Animals : an open access journal from MDPI

    2022  Volume 12, Issue 14

    Abstract: This study analyzes the potential use of ... ...

    Abstract This study analyzes the potential use of an
    Language English
    Publishing date 2022-07-17
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2606558-7
    ISSN 2076-2615
    ISSN 2076-2615
    DOI 10.3390/ani12141821
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Biological Activity of Naphthoquinones Derivatives in the Search of Anticancer Lead Compounds.

    Durán, Alexandra G / Chinchilla, Nuria / Simonet, Ana M / Gutiérrez, M Teresa / Bolívar, Jorge / Valdivia, Manuel M / Molinillo, José M G / Macías, Francisco A

    Toxins

    2023  Volume 15, Issue 5

    Abstract: Naphthoquinones are a valuable source of secondary metabolites that are well known for their dye properties since ancient times. A wide range of biological activities have been described highlighting their cytotoxic activity, gaining the attention of ... ...

    Abstract Naphthoquinones are a valuable source of secondary metabolites that are well known for their dye properties since ancient times. A wide range of biological activities have been described highlighting their cytotoxic activity, gaining the attention of researchers in recent years. In addition, it is also worth mentioning that many anticancer drugs possess a naphthoquinone backbone in their structure. Considering this background, the work described herein reports the evaluation of the cytotoxicity of different acyl and alkyl derivatives from juglone and lawsone that showed the best activity results from a etiolated wheat coleoptile bioassay. This bioassay is rapid, highly sensitive to a wide spectrum of activities, and is a powerful tool for detecting biologically active natural products. A preliminary cell viability bioassay was performed on cervix carcinoma (HeLa) cells for 24 h. The most promising compounds were further tested for apoptosis on different tumoral (IGROV-1 and SK-MEL-28) and non-tumoral (HEK-293) cell lines by flow cytometry. Results reveal that derivatives from lawsone (particularly derivative
    MeSH term(s) Female ; Humans ; HEK293 Cells ; Naphthoquinones/pharmacology ; Naphthoquinones/metabolism ; Antineoplastic Agents/pharmacology ; Antineoplastic Agents/chemistry ; Etoposide ; Cell Line, Tumor
    Chemical Substances lawsone (TLH4A6LV1W) ; Naphthoquinones ; Antineoplastic Agents ; Etoposide (6PLQ3CP4P3)
    Language English
    Publishing date 2023-05-20
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2518395-3
    ISSN 2072-6651 ; 2072-6651
    ISSN (online) 2072-6651
    ISSN 2072-6651
    DOI 10.3390/toxins15050348
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Synergy of the Bacteriocin AS-48 and Antibiotics against Uropathogenic Enterococci.

    Montalbán-López, Manuel / Cebrián, Rubén / Galera, Rosa / Mingorance, Lidia / Martín-Platero, Antonio M / Valdivia, Eva / Martínez-Bueno, Manuel / Maqueda, Mercedes

    Antibiotics (Basel, Switzerland)

    2020  Volume 9, Issue 9

    Abstract: ... The ... ...

    Abstract The genus
    Language English
    Publishing date 2020-09-02
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2681345-2
    ISSN 2079-6382
    ISSN 2079-6382
    DOI 10.3390/antibiotics9090567
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Combining word embeddings to extract chemical and drug entities in biomedical literature.

    López-Úbeda, Pilar / Díaz-Galiano, Manuel Carlos / Ureña-López, L Alfonso / Martín-Valdivia, M Teresa

    BMC bioinformatics

    2021  Volume 22, Issue Suppl 1, Page(s) 599

    Abstract: Background: Natural language processing (NLP) and text mining technologies for the extraction and indexing of chemical and drug entities are key to improving the access and integration of information from unstructured data such as biomedical literature.! ...

    Abstract Background: Natural language processing (NLP) and text mining technologies for the extraction and indexing of chemical and drug entities are key to improving the access and integration of information from unstructured data such as biomedical literature.
    Methods: In this paper we evaluate two important tasks in NLP: the named entity recognition (NER) and Entity indexing using the SNOMED-CT terminology. For this purpose, we propose a combination of word embeddings in order to improve the results obtained in the PharmaCoNER challenge.
    Results: For the NER task we present a neural network composed of BiLSTM with a CRF sequential layer where different word embeddings are combined as an input to the architecture. A hybrid method combining supervised and unsupervised models is used for the concept indexing task. In the supervised model, we use the training set to find previously trained concepts, and the unsupervised model is based on a 6-step architecture. This architecture uses a dictionary of synonyms and the Levenshtein distance to assign the correct SNOMED-CT code.
    Conclusion: On the one hand, the combination of word embeddings helps to improve the recognition of chemicals and drugs in the biomedical literature. We achieved results of 91.41% for precision, 90.14% for recall, and 90.77% for F1-score using micro-averaging. On the other hand, our indexing system achieves a 92.67% F1-score, 92.44% for recall, and 92.91% for precision. With these results in a final ranking, we would be in the first position.
    MeSH term(s) Information Storage and Retrieval ; Medical Informatics/methods ; Pharmaceutical Preparations ; Semantics ; Unified Medical Language System
    Chemical Substances Pharmaceutical Preparations
    Language English
    Publishing date 2021-12-17
    Publishing country England
    Document type Journal Article
    ZDB-ID 2041484-5
    ISSN 1471-2105 ; 1471-2105
    ISSN (online) 1471-2105
    ISSN 1471-2105
    DOI 10.1186/s12859-021-04188-3
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Physiotherapy Interventions in Lung Cancer Patients: A Systematic Review.

    Valdivia-Martínez, Manuel / Fernández-Gualda, Miguel Ángel / Gallegos-García, Elena / Postigo-Martin, Paula / Fernández-González, María / Ortiz-Comino, Lucía

    Cancers

    2024  Volume 16, Issue 5

    Abstract: Background: Lung cancer is a very common disease and leads to a series of sequelae such as reduced lung capacity or reduced functional capacity in patients, which are associated not only with the disease itself, but also with medical treatment. Thus, ... ...

    Abstract Background: Lung cancer is a very common disease and leads to a series of sequelae such as reduced lung capacity or reduced functional capacity in patients, which are associated not only with the disease itself, but also with medical treatment. Thus, physiotherapeutic interventions are needed to improve quality of life and reduce these symptoms.
    Objectives: To find out the effects of physiotherapy on functional capacity, lung capacity, dyspnea, pain, and quality of life in lung cancer patients.
    Methods: A systematic review was carried out in five databases. Randomized clinical trials published between 2019-2023 were selected, in which the physiotherapeutic treatment was physical exercise and/or respiratory physiotherapy.
    Results: Nine articles were included, in which the total sample consisted of 635 lung cancer patients. When combined, respiratory physiotherapy and physical exercise improved functional capacity and lung capacity (
    Conclusions: Multimodal physiotherapy interventions may offer benefits for some lung cancer patients, but the extent and nature of these benefits may vary depending on the intervention applied. Therefore, it would be of great interest to carry out further scientific research to support this conclusion.
    Language English
    Publishing date 2024-02-25
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2527080-1
    ISSN 2072-6694
    ISSN 2072-6694
    DOI 10.3390/cancers16050924
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Enterocin Cross-Resistance Mediated by ABC Transport Systems.

    Teso-Pérez, Claudia / Martínez-Bueno, Manuel / Peralta-Sánchez, Juan Manuel / Valdivia, Eva / Maqueda, Mercedes / Fárez-Vidal, M Esther / Martín-Platero, Antonio M

    Microorganisms

    2021  Volume 9, Issue 7

    Abstract: In their struggle for life, bacteria frequently produce antagonistic substances against competitors. Antimicrobial peptides produced by bacteria (known as bacteriocins) are active against other bacteria, but harmless to their producer due to an ... ...

    Abstract In their struggle for life, bacteria frequently produce antagonistic substances against competitors. Antimicrobial peptides produced by bacteria (known as bacteriocins) are active against other bacteria, but harmless to their producer due to an associated immunity gene that prevents self-inhibition. However, knowledge of cross-resistance between different types of bacteriocin producer remains very limited. The immune function of certain bacteriocins produced by the
    Language English
    Publishing date 2021-06-30
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2720891-6
    ISSN 2076-2607
    ISSN 2076-2607
    DOI 10.3390/microorganisms9071411
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Circular and L50-like leaderless enterocins share a common ABC-transporter immunity gene.

    Teso-Pérez, Claudia / Martínez-Bueno, Manuel / Peralta Sánchez, Juan Manuel / Valdivia, Eva / Fárez-Vidal, María Esther / Martín-Platero, Antonio Manuel

    BMC genomics

    2023  Volume 24, Issue 1, Page(s) 639

    Abstract: Microbes live within complex communities of interacting populations, either free-living in waters and soils or symbionts of animals and plants. Their interactions include the production of antimicrobial peptides (bacteriocins) to antagonize competitors, ... ...

    Abstract Microbes live within complex communities of interacting populations, either free-living in waters and soils or symbionts of animals and plants. Their interactions include the production of antimicrobial peptides (bacteriocins) to antagonize competitors, and these producers must carry their own immunity gene for self-protection. Whether other coexisting populations are sensitive or resistant to the bacteriocin producer will be key for the population dynamics within the microbial community. The immunity gene frequently consists of an ABC transporter to repel its own bacteriocin but rarely protects against a nonrelated bacteriocin. A case where this cross-resistance occurs mediated by a shared ABC transporter has been shown between enterocins MR10A/B and AS-48. The first is an L50-like leaderless enterocin, while AS-48 is a circular enterocin. In addition, L50-like enterocins such as MR10A/B have been found in E. faecalis and E. faecium, but AS-48 appears only in E. faecalis. Thus, using the ABC transporter of the enterocin MR10A/B gene cluster of Enterococcus faecalis MRR10-3 as a cross-resistance model, we aimed to unravel to what extent a particular ABC transporter can be shared across multiple bacteriocinogenic bacterial populations. To this end, we screened the MR10A/B-ABC transporters in available microbial genomes and analyzed their sequence homologies and distribution. Overall, our main findings are as follows: (i) the MR10A/B-ABC transporter is associated with multiple enterocin gene clusters; (ii) the different enterocins associated with this transporter have a saposin-like fold in common; (iii) the Mr10E component of the transporter is more conserved within its associated enterocin, while the Mr10FGH components are more conserved within the carrying species. This is the least known component of the transporter, but it has shown the greatest specificity to its corresponding enterocin. Bacteriocins are now being investigated as an alternative to antibiotics; hence, the wider or narrower distribution of the particular immunity gene should be taken into account for clinical applications to avoid the selection of resistant strains. Further research will be needed to investigate the mechanistic interactions between the Mr10E transporter component and the bacteriocin as well as the specific ecological and evolutionary mechanisms involved in the spread of the immunity transporter across multiple bacteriocins.
    MeSH term(s) Animals ; Enterococcus faecium/genetics ; ATP-Binding Cassette Transporters/genetics ; Bacteriocins ; Anti-Bacterial Agents
    Chemical Substances ATP-Binding Cassette Transporters ; enterocin (59678-46-5) ; Bacteriocins ; Anti-Bacterial Agents
    Language English
    Publishing date 2023-10-24
    Publishing country England
    Document type Journal Article
    ZDB-ID 2041499-7
    ISSN 1471-2164 ; 1471-2164
    ISSN (online) 1471-2164
    ISSN 1471-2164
    DOI 10.1186/s12864-023-09750-2
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: CARES: A Corpus for classification of Spanish Radiological reports.

    Chizhikova, Mariia / López-Úbeda, Pilar / Collado-Montañez, Jaime / Martín-Noguerol, Teodoro / Díaz-Galiano, Manuel C / Luna, Antonio / Ureña-López, L Alfonso / Martín-Valdivia, M Teresa

    Computers in biology and medicine

    2023  Volume 154, Page(s) 106581

    Abstract: This paper presents a new corpus of radiology medical reports written in Spanish and labeled with ICD-10. CARES (Corpus of Anonymised Radiological Evidences in Spanish) is a high-quality corpus manually labeled and reviewed by radiologists that is freely ...

    Abstract This paper presents a new corpus of radiology medical reports written in Spanish and labeled with ICD-10. CARES (Corpus of Anonymised Radiological Evidences in Spanish) is a high-quality corpus manually labeled and reviewed by radiologists that is freely available for the research community on HuggingFace. These types of resources are essential for developing automatic text classification tools as they are necessary for training and tuning computational systems. However, in the medical domain these are very difficult to obtain for different reasons including privacy and data protection issues or the involvement of medical specialists in the generation of these resources. We present a corpus labeled and reviewed by radiologists in their daily practice that is available for research purposes. In addition, after describing the corpus and explaining how it has been generated, a first experimental approach is carried out using several machine learning algorithms based on transformer language models such as BioBERT and RoBERTa to test the validity of this linguistic resource. The best performing classifier achieved 0.8676 micro and 0.8328 macro f1-score and these results encourage us to continue working in this research line.
    MeSH term(s) Natural Language Processing ; Language ; Machine Learning ; Algorithms ; Radiology
    Language English
    Publishing date 2023-01-23
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 127557-4
    ISSN 1879-0534 ; 0010-4825
    ISSN (online) 1879-0534
    ISSN 0010-4825
    DOI 10.1016/j.compbiomed.2023.106581
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: Beneficial Shifts in the Gut Bacterial Community of Gilthead Seabream (Sparus aurata) Juveniles Supplemented with Allium-Derived Compound Propyl Propane Thiosulfonate (PTSO)

    Rabelo-Ruiz, Miguel / Newman-Portela, Antonio M. / Peralta-Sánchez, Juan Manuel / Martín-Platero, Antonio Manuel / Agraso, María del Mar / Bermúdez, Laura / Aguinaga, María Arántzazu / Baños, Alberto / Maqueda, Mercedes / Valdivia, Eva / Martínez-Bueno, Manuel

    Animals. 2022 July 17, v. 12, no. 14

    2022  

    Abstract: This study analyzes the potential use of an Allium-derived compound, propyl propane thiosulfonate (PTSO), as a functional feed additive in aquaculture. Gilthead seabream (Sparus aurata) juveniles had their diet supplemented with this Allium-derived ... ...

    Abstract This study analyzes the potential use of an Allium-derived compound, propyl propane thiosulfonate (PTSO), as a functional feed additive in aquaculture. Gilthead seabream (Sparus aurata) juveniles had their diet supplemented with this Allium-derived compound (150 mg/kg of PTSO) and were compared with control fish. The effects of this organosulfur compound were tested by measuring the body weight and analyzing the gut microbiota after 12 weeks. The relative abundance of potentially pathogenic Vibrio and Pseudomonas in the foregut and hindgut of supplemented fish significantly decreased, while potentially beneficial Lactobacillus increased compared to in the control fish. Shannon’s alpha diversity index significantly increased in both gut regions of fish fed with a PTSO-supplemented diet. Regarding beta diversity, significant differences between treatments only appeared in the hindgut when minority ASVs were taken into account. No differences occurred in body weight during the experiment. These results indicate that supplementing the diet with Allium-derived PTSO produced beneficial changes in the intestinal microbiota while maintaining the productive parameters of gilthead seabream juveniles.
    Keywords Lactobacillus ; Pseudomonas ; Sparus aurata ; Vibrio ; aquaculture ; bacterial communities ; body weight ; diet ; feed additives ; fish ; foregut ; hindgut ; intestinal microorganisms ; propane ; species diversity
    Language English
    Dates of publication 2022-0717
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article
    ZDB-ID 2606558-7
    ISSN 2076-2615
    ISSN 2076-2615
    DOI 10.3390/ani12141821
    Database NAL-Catalogue (AGRICOLA)

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  10. Article ; Online: Predictive factors for decompensating events in patients with cirrhosis with primary biliary cholangitis under different lines of therapy.

    Ampuero, Javier / Lucena, Ana / Berenguer, Marina / Hernández-Guerra, Manuel / Molina, Esther / Gómez-Camarero, Judith / Valdivia, Carlos / Gómez, Elena / Casado, Marta / Álvarez-Navascuez, Carmen / Jorquera, Francisco / García-Buey, Luisa / Díaz-González, Álvaro / Morillas, Rosa / García-Retortillo, Montserrat / Sousa, Jose M / Pérez-Medrano, Indhira / Simón, Miguel Á / Martínez, Javier /
    Arenas, Juan / Londoño, María Carlota / Olveira, Antonio / Fernández-Rodríguez, Conrado

    Hepatology (Baltimore, Md.)

    2024  

    Abstract: Background and aims: The landscape in primary biliary cholangitis (PBC) has changed with the advent of second-line treatments. However, the use of obeticholic acid (OCA) and fibrates in PBC-related cirrhosis is challenging. We assessed the impact of ... ...

    Abstract Background and aims: The landscape in primary biliary cholangitis (PBC) has changed with the advent of second-line treatments. However, the use of obeticholic acid (OCA) and fibrates in PBC-related cirrhosis is challenging. We assessed the impact of receiving a second-line therapy as a risk factor for decompensated cirrhosis in a real-world population with cirrhosis and PBC, and identify the predictive factors for decompensated cirrhosis in these patients.
    Approach and results: Multicenter study enrolling 388 patients with PBC-cirrhosis from the Spanish ColHai registry. Biopsy (20%), ultrasound (59%), or transient elastography (21%) defined cirrhosis, and the presence of varices and splenomegaly defined clinically significant portal hypertension (CSPH). Paris-II and PBC OCA international study of efficacy criteria determined the response to ursodeoxycholic acid (UDCA), fibrates (n=93), and OCA (n=104). The incidence of decompensated cirrhosis decreased for UDCA versus OCA or fibrates in the real-world population, but they were similar considering the propensity score-matched cohort (UDCA 3.77 vs. second-line therapy 4.5 100 persons-year, respectively), as patients on second-line therapy exhibited advanced liver disease. Consequently, GGT, albumin, platelets, clinically significant portal hypertension, and UDCA response were associated with a decompensating event. OCA response (achieved in 52% of patients) was associated with bilirubin (OR 0.21 [95% CI: 0.06-0.73]) and AST (OR 0.97 [95% CI: 0.95-0.99]), while fibrate response (achieved in 55% of patients) with AST [OR 0.96 (95% CI: 0.95-0.98]). In patients treated with OCA, drug response (sHR 0.23 [95% CI: 0.08-0.64]), diabetes (sHR 5.62 [95% CI: 2.02-15.68]), albumin (sHR 0.34 [95% CI: 0.13-0.89]), and platelets (sHR 0.99 [95% CI: 0.98-1.00]) were related to decompensation. In patients treated with fibrate, drug response (sHR 0.36 (95% CI: 0.14-0.95]), albumin (sHR 0.36 (95% CI: 0.16-0.81]), and clinically significant portal hypertension (sHR 3.70 (95% CI: 1.17-11.70]) were associated with decompensated cirrhosis.
    Conclusions: Advanced PBC, rather than OCA and fibrates, was found to be associated with decompensating events. Therefore, biochemical and clinical variables should be considered when making decisions about the management of these drugs. Moreover, a positive response to OCA and fibrates reduced the risk of decompensation.
    Language English
    Publishing date 2024-03-06
    Publishing country United States
    Document type Journal Article
    ZDB-ID 604603-4
    ISSN 1527-3350 ; 0270-9139
    ISSN (online) 1527-3350
    ISSN 0270-9139
    DOI 10.1097/HEP.0000000000000826
    Database MEDical Literature Analysis and Retrieval System OnLINE

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