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  1. Article ; Online: A distance-based kernel for classification via Support Vector Machines.

    Amaya-Tejera, Nazhir / Gamarra, Margarita / Vélez, Jorge I / Zurek, Eduardo

    Frontiers in artificial intelligence

    2024  Volume 7, Page(s) 1287875

    Abstract: Support Vector Machines (SVMs) are a type of supervised machine learning algorithm widely used for classification tasks. In contrast to traditional methods that split the data into separate training and testing sets, here we propose an innovative ... ...

    Abstract Support Vector Machines (SVMs) are a type of supervised machine learning algorithm widely used for classification tasks. In contrast to traditional methods that split the data into separate training and testing sets, here we propose an innovative approach where subsets of the original data are randomly selected to train the model multiple times. This iterative training process aims to identify a representative data subset, leading to improved inferences about the population. Additionally, we introduce a novel distance-based kernel specifically designed for binary-type features based on a similarity matrix that efficiently handles both binary and multi-class classification problems. Computational experiments on publicly available datasets of varying sizes demonstrate that our proposed method significantly outperforms existing approaches in terms of classification accuracy. Furthermore, the distance-based kernel achieves superior performance compared to other well-known kernels from the literature and those used in previous studies on the same datasets. These findings validate the effectiveness of our proposed classification method and distance-based kernel for SVMs. By leveraging random subset selection and a unique kernel design, we achieve notable improvements in classification accuracy. These results have significant implications for diverse classification problems in Machine Learning and data analysis.
    Language English
    Publishing date 2024-02-26
    Publishing country Switzerland
    Document type Journal Article
    ISSN 2624-8212
    ISSN (online) 2624-8212
    DOI 10.3389/frai.2024.1287875
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Prediction of compound-target interaction using several artificial intelligence algorithms and comparison with a consensus-based strategy.

    Jimenes-Vargas, Karina / Pazos, Alejandro / Munteanu, Cristian R / Perez-Castillo, Yunierkis / Tejera, Eduardo

    Journal of cheminformatics

    2024  Volume 16, Issue 1, Page(s) 27

    Abstract: For understanding a chemical compound's mechanism of action and its side effects, as well as for drug discovery, it is crucial to predict its possible protein targets. This study examines 15 developed target-centric models (TCM) employing different ... ...

    Abstract For understanding a chemical compound's mechanism of action and its side effects, as well as for drug discovery, it is crucial to predict its possible protein targets. This study examines 15 developed target-centric models (TCM) employing different molecular descriptions and machine learning algorithms. They were contrasted with 17 third-party models implemented as web tools (WTCM). In both sets of models, consensus strategies were implemented as potential improvement over individual predictions. The findings indicate that TCM reach f1-score values greater than 0.8. Comparing both approaches, the best TCM achieves values of 0.75, 0.61, 0.25 and 0.38 for true positive/negative rates (TPR, TNR) and false negative/positive rates (FNR, FPR); outperforming the best WTCM. Moreover, the consensus strategy proves to have the most relevant results in the top
    Language English
    Publishing date 2024-03-07
    Publishing country England
    Document type Journal Article
    ZDB-ID 2486539-4
    ISSN 1758-2946
    ISSN 1758-2946
    DOI 10.1186/s13321-024-00816-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Cinnamomum

    Fernandez-Soto, Paulina / Celi, Diana / Tejera, Eduardo / Alvarez-Suarez, José Miguel / Machado, António

    Molecules (Basel, Switzerland)

    2023  Volume 28, Issue 2

    Abstract: Horchata, a herbal infusion drink from Ecuador containing a mixture of medicinal plants, has been reported to exhibit anti-inflammatory, analgesic, diuretic, and antioxidant activity. The antibacterial activity of each of the plants contained in the ... ...

    Abstract Horchata, a herbal infusion drink from Ecuador containing a mixture of medicinal plants, has been reported to exhibit anti-inflammatory, analgesic, diuretic, and antioxidant activity. The antibacterial activity of each of the plants contained in the horchata mixture has not been fully evaluated. Thus, in this study, we analysed the antibacterial activity of 21 plants used in horchata, collected from the Ecuadorian Andes region, against bacterial strains of clinical importance. The methanolic extract of
    MeSH term(s) Staphylococcus aureus ; Pelargonium ; Cinnamomum/chemistry ; Methicillin-Resistant Staphylococcus aureus ; Plant Extracts/pharmacology ; Plant Extracts/chemistry ; Tandem Mass Spectrometry ; Gas Chromatography-Mass Spectrometry ; Anti-Bacterial Agents/pharmacology ; Anti-Bacterial Agents/chemistry ; Microbial Sensitivity Tests ; Tannins
    Chemical Substances Plant Extracts ; Anti-Bacterial Agents ; Tannins
    Language English
    Publishing date 2023-01-10
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 1413402-0
    ISSN 1420-3049 ; 1431-5165 ; 1420-3049
    ISSN (online) 1420-3049
    ISSN 1431-5165 ; 1420-3049
    DOI 10.3390/molecules28020693
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Prognostic significance of sentinel lymph node biopsy in elderly with cutaneous melanoma: systematic review and meta-analysis.

    Martínez Campayo, Nieves / Paradela de la Morena, Sabela / Pértega-Díaz, Sonia / Tejera Vaquerizo, Antonio / Fonseca, Eduardo

    International journal of dermatology

    2024  

    Abstract: Sentinel lymph node biopsy is the most powerful prognostic indicator to date for cutaneous melanoma. Even though elderly patients have a lower incidence of sentinel node involvement, its results are still necessary for access to adjuvant therapies. This ... ...

    Abstract Sentinel lymph node biopsy is the most powerful prognostic indicator to date for cutaneous melanoma. Even though elderly patients have a lower incidence of sentinel node involvement, its results are still necessary for access to adjuvant therapies. This is highly relevant considering that the Western population shows an aging trend, and the incidence of melanoma has grown exponentially over the years, making elderly patients more likely to die from melanoma than younger ones. We performed a systematic review to investigate the prognostic significance of sentinel lymph node biopsy in elderly patients with melanoma. The systematic review was conducted following the PRISMA guidelines and registered in PROSPERO. The authors searched the Cochrane Database, EMBASE, PubMed, and WOS. Eligible studies for the systematic review were clinical trials, observational population studies, clinical or hospital-based cohort studies, and case-control studies. The meta-analysis was conducted using the R software program applying the meta package. Six reports were identified to meet the inclusion criteria. All studies were retrospective, non-randomized cohorts. The results obtained in this systematic review show a statistically significant influence of sentinel lymph node biopsy on disease-specific survival (HR = 2.87; 95% CI: 1.73-4.74) but also suggest that a positive result negatively impacts disease-free survival (HR = 3.41; 95% CI: 0.96-12.11). This meta-analysis shows that a positive sentinel lymph node biopsy does not imply differences in overall survival but significantly influences disease-specific survival and suggests an unfavorable impact on disease-free survival.
    Language English
    Publishing date 2024-04-02
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 412254-9
    ISSN 1365-4632 ; 0011-9059 ; 1461-1244
    ISSN (online) 1365-4632
    ISSN 0011-9059 ; 1461-1244
    DOI 10.1111/ijd.17092
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Canonical or noncanonical? Structural plasticity of serine protease-binding loops in Kunitz-STI protease inhibitors.

    Guerra, Yasel / Armijos-Jaramillo, Vinicio / Pons, Tirso / Tejera, Eduardo / Berry, Colin

    Protein science : a publication of the Protein Society

    2023  Volume 32, Issue 2, Page(s) e4570

    Abstract: The Kunitz-Soybean Trypsin Inhibitor (Kunitz-STI) family is a large family of proteins with most of its members being protease inhibitors. The versatility of the inhibitory profile and the structural plasticity of these proteins, make this family a ... ...

    Abstract The Kunitz-Soybean Trypsin Inhibitor (Kunitz-STI) family is a large family of proteins with most of its members being protease inhibitors. The versatility of the inhibitory profile and the structural plasticity of these proteins, make this family a promising scaffold for designing new multifunctional proteins. Historically, Kunitz-STI inhibitors have been classified as canonical serine protease inhibitors, but new inhibitors with novel inhibition mechanisms have been described in recent years. Different inhibition mechanisms could be the result of different evolutionary pathways. In the present work, we performed a structural analysis of all the crystallographic structures available for Kunitz-STI inhibitors to characterize serine protease-binding loop structural features and locations. Our study suggests a relationship between the conformation of serine protease-binding loops and the inhibition mechanism, their location in the β-trefoil fold, and the plant source of the inhibitors. The classical canonical inhibitors of this family are restricted to plants from the Fabales order and bind their targets via the β4-β5 loop, whereas serine protease-binding loops in inhibitors from other plants lie mainly in the β5-β6 and β9-β10 loops. In addition, we found that the β5-β6 loop is used to inhibit two different families of serine proteases through a steric blockade inhibition mechanism. This work will help to change the general perception that all Kunitz-STI inhibitors are canonical inhibitors and proteins with protease-binding loops adopting noncanonical conformations are exceptions. Additionally, our results will help in the identification of protease-binding loops in uncharacterized or newly discovered inhibitors, and in the design of multifunctional proteins.
    MeSH term(s) Serine Proteases ; Trypsin Inhibitor, Kunitz Soybean/chemistry ; Serine ; Amino Acid Sequence ; Serine Endopeptidases ; Serine Proteinase Inhibitors/pharmacology ; Serine Proteinase Inhibitors/chemistry
    Chemical Substances Serine Proteases (EC 3.4.-) ; Trypsin Inhibitor, Kunitz Soybean (9088-41-9) ; Serine (452VLY9402) ; Serine Endopeptidases (EC 3.4.21.-) ; Serine Proteinase Inhibitors
    Language English
    Publishing date 2023-01-20
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1106283-6
    ISSN 1469-896X ; 0961-8368
    ISSN (online) 1469-896X
    ISSN 0961-8368
    DOI 10.1002/pro.4570
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: The search for molecular mimicry in proteins carried by extracellular vesicles secreted by cells infected with

    Armijos-Jaramillo, Vinicio / Mosquera, Andrea / Rojas, Brian / Tejera, Eduardo

    Communicative & integrative biology

    2021  Volume 14, Issue 1, Page(s) 212–220

    Abstract: Red blood cells infected ... ...

    Abstract Red blood cells infected with
    Language English
    Publishing date 2021-09-08
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2451097-X
    ISSN 1942-0889
    ISSN 1942-0889
    DOI 10.1080/19420889.2021.1972523
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Effect of time to sentinel lymph node biopsy on cutaneous melanoma survival: a matter of discussion.

    Tejera-Vaquerizo, Antonio / Nagore, Eduardo

    American journal of surgery

    2017  Volume 213, Issue 1, Page(s) 204–205

    MeSH term(s) Humans ; Lymph Nodes ; Lymphatic Metastasis ; Melanoma ; Sentinel Lymph Node ; Sentinel Lymph Node Biopsy ; Skin Neoplasms
    Language English
    Publishing date 2017
    Publishing country United States
    Document type Letter ; Comment
    ZDB-ID 2953-1
    ISSN 1879-1883 ; 0002-9610
    ISSN (online) 1879-1883
    ISSN 0002-9610
    DOI 10.1016/j.amjsurg.2016.06.014
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Evolutionary analysis of endogenous intronic retroviruses in primates reveals an enrichment in transcription binding sites associated with key regulatory processes.

    Calero-Layana, Melissa / López-Cruz, Carmen / Ocaña, Agustín / Tejera, Eduardo / Armijos-Jaramillo, Vinicio

    PeerJ

    2022  Volume 10, Page(s) e14431

    Abstract: Background: Endogenous retroviruses (ERVs) are the result of the integration of retroviruses into host DNA following germline infection. Endogenous retroviruses are made up of three main genes: : Results: In this work, we studied the evolutionary ... ...

    Abstract Background: Endogenous retroviruses (ERVs) are the result of the integration of retroviruses into host DNA following germline infection. Endogenous retroviruses are made up of three main genes:
    Results: In this work, we studied the evolutionary history of endogenous retroviruses associated with five human genes (
    Conclusions: With the data collected, and by observing the transcription factors annotated inside ERVs, we propose that these elements play a relevant role in gene expression regulation and they probably possess important features for tumorigenesis control.
    MeSH term(s) Animals ; Humans ; Endogenous Retroviruses/genetics ; Phylogeny ; Introns/genetics ; Primates/genetics ; Binding Sites
    Language English
    Publishing date 2022-12-22
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2703241-3
    ISSN 2167-8359 ; 2167-8359
    ISSN (online) 2167-8359
    ISSN 2167-8359
    DOI 10.7717/peerj.14431
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: Comparative Effectiveness of Treatments for Bacterial Vaginosis: A Network Meta-Analysis.

    Muñoz-Barreno, Alison / Cabezas-Mera, Fausto / Tejera, Eduardo / Machado, António

    Antibiotics (Basel, Switzerland)

    2021  Volume 10, Issue 8

    Abstract: Bacterial vaginosis (BV) is a common vaginal dysbiosis in women of reproductive age. However, the cure rate for BV varies considerably and many women experience a relapse after the initial treatment. The present meta-analysis aimed to evaluate the ... ...

    Abstract Bacterial vaginosis (BV) is a common vaginal dysbiosis in women of reproductive age. However, the cure rate for BV varies considerably and many women experience a relapse after the initial treatment. The present meta-analysis aimed to evaluate the clinical cure rates (CCRs) in randomized controlled trials (RCTs) through different therapies and administration routes. This meta-analysis included a final set of 25 eligible studies with a total of 57 RCTs and compared the effectiveness of BV treatments among non-pregnant and pregnant women. The initial range of CCRs varied greatly from 46.75% to 96.20% and the final pooled CCR was 75.5% (CI: 69.4-80.8) using the random model. The heterogeneity indices were Q = 418.91, I2 = 94.27%, and τ = 0.7498 (
    Language English
    Publishing date 2021-08-13
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2681345-2
    ISSN 2079-6382
    ISSN 2079-6382
    DOI 10.3390/antibiotics10080978
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  10. Article: Comparative organizational network analysis considering formal power-based networks and organizational hierarchies.

    Ramos, Valentina / Pazmiño, Pablo / Franco-Crespo, Antonio / Ramos-Galarza, Carlos / Tejera, Eduardo

    Heliyon

    2022  Volume 8, Issue 1, Page(s) e08661

    Abstract: Comparative organizational network analysis makes it possible to identify the similarities and differences between organizations according to the content of their networks. This research is a comparative study of organizational networks based on formal ... ...

    Abstract Comparative organizational network analysis makes it possible to identify the similarities and differences between organizations according to the content of their networks. This research is a comparative study of organizational networks based on formal power. To accomplish this goal, networks were developed in three organizations from different sectors with workers distributed in high, middle and operational levels in the organizational hierarchy. For the study, 100% of the workers within the identified networks were included. The results indicated that, considering centrality and connectivity network indices, there were no statistically significant differences between organizations according to formal power network behavior. However, we obtained statistically significant differences in terms connectivity and centrality considering the workers' hierarchy. The representative nodes of high and middle hierarchical levels had higher indices of connectivity and centrality than the nodes representative of the operational level. This study makes it possible to identify the formal roles within networks based on legitimate power, which can serve as a basis for decision-making processes and resource allocations, for the strategic use of the networks created.
    Language English
    Publishing date 2022-01-05
    Publishing country England
    Document type Journal Article
    ZDB-ID 2835763-2
    ISSN 2405-8440
    ISSN 2405-8440
    DOI 10.1016/j.heliyon.2021.e08661
    Database MEDical Literature Analysis and Retrieval System OnLINE

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