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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

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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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
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Zs.MO 81: Show issues

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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
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Zs.A 3407: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
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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 Jan., v. 8, no. 1

2022

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.
Keywords	comparative study ; decision making ; objectives ; resource allocation
Language	English
Dates of publication	2022-01
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	2835763-2
ISSN	2405-8440
ISSN	2405-8440
DOI	10.1016/j.heliyon.2021.e08661
Database	NAL-Catalogue (AGRICOLA)

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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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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
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Article ; Online: Prevalence of biofilms in Candida spp. bloodstream infections: A meta-analysis.

Atiencia-Carrera, María Belén / Cabezas-Mera, Fausto Sebastián / Tejera, Eduardo / Machado, António

PloS one

2022 Volume 17, Issue 2, Page(s) e0263522

Abstract: Context: Candida-related infections are nowadays a serious Public Health Problem emerging multidrug-resistant strains. Candida biofilm also leads bloodstream infections to invasive systemic infections.: Objective: The present meta-analysis aimed to ... ...

Abstract	Context: Candida-related infections are nowadays a serious Public Health Problem emerging multidrug-resistant strains. Candida biofilm also leads bloodstream infections to invasive systemic infections. Objective: The present meta-analysis aimed to analyze Candida biofilm rate, type, and antifungal resistance among hospitalized patients between 1995 and 2020. Data sources: Web of Science, Scopus, PubMed, and Google Scholar databases were searched for English papers using the following medical subject heading terms (MESH): "invasive candidiasis"; "bloodstream infections"; "biofilm formation"; "biofilm-related infections"; "mortality"; and "prevalence". Study selection: The major inclusion criteria included reporting the rate of biofilm formation and the prevalence of biofilm-related to Candida species, including observational studies (more exactly, cohort, retrospective, and case-control studies). Furthermore, data regarding the mortality rate, the geographical location of the study set, and the use of anti-fungal agents in clinical isolates were also extracted from the studies. Data extraction: Independent extraction of articles by 2 authors using predefined data fields, including study quality indicators. Data synthesis: A total of 31 studies from publicly available databases met our inclusion criteria. The biofilm formation in the data set varied greatly from 16 to 100% in blood samples. Most of the studies belonged to Europe (17/31) and Asia (9/31). Forest plot showed a pooled rate of biofilm formation of 80.0% (CI: 67-90), with high heterogeneity (Q = 2567.45, I2 = 98.83, τ2 = 0.150) in random effects model (p < 0.001). The funnel plot and Egger's linear regression test failed to find publication bias (p = 0.896). The mortality rate in Candida-related bloodstream infections was 37.9% of which 70.0% were from biofilm-associated infections. Furthermore, Candida isolates were also characterized in low, intermediate, or high biofilm formers through their level of biofilm mass (crystal violet staining or XTT assays) after a 24h growth. When comparing between countries, statistical differences were obtained (p = 0.0074), showing the lower and higher biofilm prevalence values in Italy and Spain, respectively. The prevalence of low, intermediate, and high biofilms were 36.2, 18.9, and 35.0% (p < 0.0001), respectively. C. tropicalis was the prevalent species in high biofilm formation (67.5%) showing statistically significant differences when compared to other Candida species, except for C. krusei and C. glabrata. Finally, the rates of antifungal resistance to fluconazole, voriconazole, and caspofungin related to biofilm were 70.5, 67.9 and 72.8% (p < 0.001), respectively. Conclusions: Early detection of biofilms and a better characterization of Candida spp. bloodstream infections should be considered, which eventually will help preserve public health resources and ultimately diminish mortality among patients.
MeSH term(s)	Biofilms ; Candida ; Candidemia/blood ; Candidemia/microbiology ; Candidiasis/blood ; Candidiasis/microbiology ; Caspofungin/pharmacology ; Drug Resistance, Fungal ; Fluconazole/pharmacology ; Hospitalization ; Humans ; Prevalence ; Sepsis/blood ; Sepsis/microbiology ; Voriconazole/pharmacology
Chemical Substances	Fluconazole (8VZV102JFY) ; Caspofungin (F0XDI6ZL63) ; Voriconazole (JFU09I87TR)
Language	English
Publishing date	2022-02-03
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0263522
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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 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
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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
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Article ; Online: A population-based study of preeclampsia and eclampsia in Ecuador: ethnic, geographical and altitudes differences.

Tejera, Eduardo / Sánchez, Maria Eugenia / Henríquez-Trujillo, Aquiles R / Pérez-Castillo, Yunierkis / Coral-Almeida, Marco

BMC pregnancy and childbirth

2021 Volume 21, Issue 1, Page(s) 116

Abstract: Background: In Ecuador eclampsia and preeclampsia were identified as the third cause of maternal death. Like other Latin-American countries, Ecuador has human settlements living from 0 to more than 4000 m of altitude and comprising a wide ethnic- ... ...

Abstract	Background: In Ecuador eclampsia and preeclampsia were identified as the third cause of maternal death. Like other Latin-American countries, Ecuador has human settlements living from 0 to more than 4000 m of altitude and comprising a wide ethnic-diversity across all these altitude changes. These characteristics offer the possibility to study a wide variety of possible risk factors for preeclampsia and eclampsia. Methods: We conducted a population-based retrospective study of all deliveries in Ecuador from 2015 through 2017. The main variables analyzed were: altitude, ethnic self-identification, geographic location, and maternal age. The data comes from the Ecuadorian National Institute of Statistics and Census (INEC) and the Ecuadorian Ministry of Health. Data information regarding maternal parity and socioeconomic status was not available from official records. Logistic regression analysis was used to study the relationship between preeclampsia and eclampsia with the variable of interest. Geospatial statistical analysis was done to identify statistically significant spatial clusters of preeclampsia and eclampsia cases. Results: The incidence of preeclampsia was estimated between 5.11 (5.05-5.18) and 6.23 (6.16-6.30), and 0.25 (0.23-0.26) for eclampsia. Native American have a lower incidence regarding preeclampsia compared to other ethnic groups. High altitude has a significant odds ratio (OR = 2.31, 1.93-2.78) of preeclampsia. Montubio residing in middle altitude (1500-3500 m) have the highest risk of preeclampsia (OR = 18.13, 9.53-34.50). Afro-Ecuadorians also have an increased risk of preeclampsia associated with altitude (OR = 2.36, 1.78-3.14). Ethnicity was not identified as a risk factor for eclampsia. Early and older maternal age was associated with an increased risk of preeclampsia and eclampsia. Women living more than 20 km from the obstetric unit have an OR = 2.61 (2.32-2.95, p-value< 0.01) and OR = 1.87 (1.82-1.92, p-value< 0.01) of developing eclampsia and preeclampsia respectively. Conclusions: Preeclampsia is widespread across low and high-altitude areas, while eclampsia is mostly located at lower altitudes. Montubios living at middle or high altitudes represents the ethnic group with a higher risk of preeclampsia. No ethnic effect was identified as a potential risk factor for eclampsia. Moreover, in eclampsia the associated risk of young women seems to be higher than in preeclampsia.
MeSH term(s)	Adolescent ; Adult ; Altitude ; Child ; Eclampsia/epidemiology ; Ecuador/epidemiology ; Ethnic Groups ; Female ; Humans ; Incidence ; Maternal Age ; Middle Aged ; Pre-Eclampsia/epidemiology ; Pregnancy ; Registries ; Retrospective Studies ; Young Adult
Language	English
Publishing date	2021-02-09
Publishing country	England
Document type	Journal Article
ISSN	1471-2393
ISSN (online)	1471-2393
DOI	10.1186/s12884-021-03602-1
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