LIVIVO - Search results -

Search results

Result 1 - 10 of total 86

Search options

Article ; Online: Correction: Entamoeba lysyl-tRNA Synthetase Contains a Cytokine-Like Domain with Chemokine Activity towards Human Endothelial Cells.

de Moura, Manuel Castro / Miro, Francesc / Han, Jung Min / Kim, Sunghoon / Celada, Antonio / de Pouplana, Lluís Ribas

2024 Volume 18, Issue 3, Page(s) e0012047

Abstract: This corrects the article DOI: 10.1371/journal.pntd.0001398.]. ...

Abstract	[This corrects the article DOI: 10.1371/journal.pntd.0001398.].
Language	English
Publishing date	2024-03-19
Publishing country	United States
Document type	Published Erratum
ZDB-ID	2429704-5
ISSN	1935-2735 ; 1935-2735
ISSN (online)	1935-2735
ISSN	1935-2735
DOI	10.1371/journal.pntd.0012047
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

Book ; Online: XoveTIC 2020

de Moura Ramos, José / Puente-Castro, Alejandro / Loureiro, Javier / Penedo, Manuel / Penedo, Manuel

2021

Keywords	Technology: general issues ; T1-995 ; History of engineering & technology
Size	1 electronic resource (218 pages)
Publisher	MDPI - Multidisciplinary Digital Publishing Institute
Publishing place	Basel, Switzerland
Document type	Book ; Online
Note	English ; Open Access
HBZ-ID	HT021291718
ISBN	9783036508573 ; 3036508570
Database	ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: Cellular and clinical impact of protein phosphatase enzyme epigenetic silencing in multiple cancer tissues.

Wiltshire, Edward / de Moura, Manuel Castro / Piñeyro, David / Joshi, Ricky S

Human genomics

2024 Volume 18, Issue 1, Page(s) 24

Abstract: Background: Protein Phosphatase Enzymes (PPE) and protein kinases simultaneously control phosphorylation mechanisms that tightly regulate intracellular signalling pathways and stimulate cellular responses. In human malignancies, PPE and protein kinases ... ...

Abstract	Background: Protein Phosphatase Enzymes (PPE) and protein kinases simultaneously control phosphorylation mechanisms that tightly regulate intracellular signalling pathways and stimulate cellular responses. In human malignancies, PPE and protein kinases are frequently mutated resulting in uncontrolled kinase activity and PPE suppression, leading to cell proliferation, migration and resistance to anti-cancer therapies. Cancer associated DNA hypermethylation at PPE promoters gives rise to transcriptional silencing (epimutations) and is a hallmark of cancer. Despite recent advances in sequencing technologies, data availability and computational capabilities, only a fraction of PPE have been reported as transcriptionally inactive as a consequence of epimutations. Methods: In this study, we examined promoter-associated DNA methylation profiles in Protein Phosphatase Enzymes and their Interacting Proteins (PPEIP) in a cohort of 705 cancer patients in five tissues (Large intestine, Oesophagus, Lung, Pancreas and Stomach) in three cell models (primary tumours, cancer cell lines and 3D embedded cancer cell cultures). As a subset of PPEIP are known tumour suppressor genes, we analysed the impact of PPEIP promoter hypermethylation marks on gene expression, cellular networks and in a clinical setting. Results: Here, we report epimutations in PPEIP are a frequent occurrence in the cancer genome and manifest independent of transcriptional activity. We observed that different tumours have varying susceptibility to epimutations and identify specific cellular signalling networks that are primarily affected by epimutations. Additionally, RNA-seq analysis showed the negative impact of epimutations on most (not all) Protein Tyrosine Phosphatase transcription. Finally, we detected novel clinical biomarkers that inform on patient mortality and anti-cancer treatment sensitivity. Conclusions: We propose that DNA hypermethylation marks at PPEIP frequently contribute to the pathogenesis of malignancies and within the precision medicine space, hold promise as biomarkers to inform on clinical features such as patient survival and therapeutic response.
MeSH term(s)	Humans ; Epigenesis, Genetic ; DNA Methylation ; Neoplasms ; Phosphoprotein Phosphatases ; Protein Kinases ; Biomarkers ; DNA ; Gene Expression Regulation, Neoplastic
Chemical Substances	Phosphoprotein Phosphatases (EC 3.1.3.16) ; Protein Kinases (EC 2.7.-) ; Biomarkers ; DNA (9007-49-2)
Language	English
Publishing date	2024-03-12
Publishing country	England
Document type	Journal Article
ZDB-ID	2147618-4
ISSN	1479-7364 ; 1479-7364
ISSN (online)	1479-7364
ISSN	1479-7364
DOI	10.1186/s40246-024-00592-x
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: New insights into the pathogenesis and transmission of

Vargas-Castro, Ignacio / Crespo-Picazo, José Luis / Fayos, Manena / Jiménez-Martínez, María de Los Ángeles / Torre-Fuentes, Laura / Álvarez, Julio / Moura, André E / Hernández, Marta / Buendía, Aranzazu / Barroso-Arévalo, Sandra / García-Seco, Teresa / Pérez-Sancho, Marta / De Miguel, María Jesús / Andrés-Barranco, Sara / Marco-Cabedo, Vicente / Peñin-Villahoz, Gaizka / Muñoz, Pilar María / Domínguez, Lucas / García-Párraga, Daniel /

Sánchez-Vizcaíno, José Manuel

Microbiology spectrum

2023 Volume 11, Issue 6, Page(s) e0199723

Abstract: Importance: ... ...

Abstract	Importance: Brucella
MeSH term(s)	Animals ; Humans ; Female ; Bottle-Nosed Dolphin ; Brucellosis/veterinary ; Brucella ; Sepsis
Language	English
Publishing date	2023-10-06
Publishing country	United States
Document type	Journal Article
ZDB-ID	2807133-5
ISSN	2165-0497 ; 2165-0497
ISSN (online)	2165-0497
ISSN	2165-0497
DOI	10.1128/spectrum.01997-23
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: Time series causal relationships discovery through feature importance and ensemble models.

Castro, Manuel / Mendes Júnior, Pedro Ribeiro / Soriano-Vargas, Aurea / de Oliveira Werneck, Rafael / Moreira Gonçalves, Maiara / Lusquino Filho, Leopoldo / Moura, Renato / Zampieri, Marcelo / Linares, Oscar / Ferreira, Vitor / Ferreira, Alexandre / Davólio, Alessandra / Schiozer, Denis / Rocha, Anderson

Scientific reports

2023 Volume 13, Issue 1, Page(s) 11402

Abstract: Inferring causal relationships from observational data is a key challenge in understanding the interpretability of Machine Learning models. Given the ever-increasing amount of observational data available in many areas, Machine Learning algorithms used ... ...

Abstract	Inferring causal relationships from observational data is a key challenge in understanding the interpretability of Machine Learning models. Given the ever-increasing amount of observational data available in many areas, Machine Learning algorithms used for forecasting have become more complex, leading to a less understandable path of how a decision is made by the model. To address this issue, we propose leveraging ensemble models, e.g., Random Forest, to assess which input features the trained model prioritizes when making a forecast and, in this way, establish causal relationships between the variables. The advantage of these algorithms lies in their ability to provide feature importance, which allows us to build the causal network. We present our methodology to estimate causality in time series from oil field production. As it is difficult to extract causal relations from a real field, we also included a synthetic oil production dataset and a weather dataset, which is also synthetic, to provide the ground truth. We aim to perform causal discovery, i.e., establish the existing connections between the variables in each dataset. Through an iterative process of improving the forecasting of a target's value, we evaluate whether the forecasting improves by adding information from a new potential driver; if so, we state that the driver causally affects the target. On the oil field-related datasets, our causal analysis results agree with the interwell connections already confirmed by tracer information; whenever the tracer data are available, we used it as our ground truth. This consistency between both estimated and confirmed connections provides us the confidence about the effectiveness of our proposed methodology. To our knowledge, this is the first time causal analysis using solely production data is employed to discover interwell connections in an oil field dataset.
MeSH term(s)	Time Factors ; Causality ; Algorithms ; Forecasting ; Random Forest
Language	English
Publishing date	2023-07-14
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-37929-w
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article: The Curcumin Supplementation with Piperine Can Influence the Acute Elevation of Exercise-Induced Cytokines: Double-Blind Crossover Study.

Miranda-Castro, Stéfani / Aidar, Felipe J / de Moura, Samara Silva / Marcucci-Barbosa, Lucas / Lobo, Lázaro Fernandes / de Assis Dias Martins-Júnior, Francisco / da Silva Filha, Roberta / Vaz de Castro, Pedro Alves Soares / Simões E Silva, Ana Cristina / da Glória de Souza, Danielle / da Silva, Siomara Aparecida / de Castro Pinto, Kelerson Mauro / de Paula Costa, Guilherme / Silva, Ana Filipa / Clemente, Filipe Manuel / Pereira, William Valadares Campos / Nunes-Silva, Albená

Biology

2022 Volume 11, Issue 4

Abstract: Background: to evaluate the effects of one week of supplementation with curcumin combined with piperine on physical performance, immune system cell counts, muscle damage, and plasma levels of inflammatory markers after a treadmill running training ... ...

Abstract	Background: to evaluate the effects of one week of supplementation with curcumin combined with piperine on physical performance, immune system cell counts, muscle damage, and plasma levels of inflammatory markers after a treadmill running training session. Methods: This study is a double-blind, crossover-balanced clinical trial with a three-week intervention. Sixteen male runners with a mean age of 36 ± 9 years and VO2 max of 60.6 ± 9.03 mL.kg Results: curcumin and piperine supplementation could not change the physical performance, immune cell counts, and muscle damage; however, the aerobic fatiguing exercise protocol inhibited the elevation of the plasmatic levels of some cytokines. The running exercise protocol could elevate the circulating levels of IL-2 (from 49.7 to 59.3 pg/mL), TNF-α (from 48.5 to 51.5 pg/mL), INF (from 128.8 to 165.0 pg/mL), IL-6 (from 63.1 to 77.3 pg/mL), and IL-10 (from 48.9 to 59.6 pg/mL) 1 h after the end of the running protocol. However, the curcumin and piperine supplementation could inhibit this elevation. Conclusions: curcumin and piperine supplementation had no effect on physical performance, immune cell counts, or muscle damage; however, the supplementation could modulate the kinetics of IL-2, TNF-α, INF, IL-6, and IL-10 1 h after the end of exercise.
Language	English
Publishing date	2022-04-10
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2661517-4
ISSN	2079-7737
ISSN	2079-7737
DOI	10.3390/biology11040573
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: Time series causal relationships discovery through feature importance and ensemble models

Manuel Castro / Pedro Ribeiro Mendes Júnior / Aurea Soriano-Vargas / Rafael de Oliveira Werneck / Maiara Moreira Gonçalves / Leopoldo Lusquino Filho / Renato Moura / Marcelo Zampieri / Oscar Linares / Vitor Ferreira / Alexandre Ferreira / Alessandra Davólio / Denis Schiozer / Anderson Rocha

Scientific Reports, Vol 13, Iss 1, Pp 1-

2023 Volume 18

Abstract: Abstract Inferring causal relationships from observational data is a key challenge in understanding the interpretability of Machine Learning models. Given the ever-increasing amount of observational data available in many areas, Machine Learning ... ...

Abstract	Abstract Inferring causal relationships from observational data is a key challenge in understanding the interpretability of Machine Learning models. Given the ever-increasing amount of observational data available in many areas, Machine Learning algorithms used for forecasting have become more complex, leading to a less understandable path of how a decision is made by the model. To address this issue, we propose leveraging ensemble models, e.g., Random Forest, to assess which input features the trained model prioritizes when making a forecast and, in this way, establish causal relationships between the variables. The advantage of these algorithms lies in their ability to provide feature importance, which allows us to build the causal network. We present our methodology to estimate causality in time series from oil field production. As it is difficult to extract causal relations from a real field, we also included a synthetic oil production dataset and a weather dataset, which is also synthetic, to provide the ground truth. We aim to perform causal discovery, i.e., establish the existing connections between the variables in each dataset. Through an iterative process of improving the forecasting of a target’s value, we evaluate whether the forecasting improves by adding information from a new potential driver; if so, we state that the driver causally affects the target. On the oil field-related datasets, our causal analysis results agree with the interwell connections already confirmed by tracer information; whenever the tracer data are available, we used it as our ground truth. This consistency between both estimated and confirmed connections provides us the confidence about the effectiveness of our proposed methodology. To our knowledge, this is the first time causal analysis using solely production data is employed to discover interwell connections in an oil field dataset.
Keywords	Medicine ; R ; Science ; Q
Subject code	006
Language	English
Publishing date	2023-07-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: Genetically predicted telomere length and Alzheimer's disease endophenotypes: a Mendelian randomization study.

Alzheimer's research & therapy

2022 Volume 14, Issue 1, Page(s) 167

Abstract: Telomere length (TL) is associated with biological aging, consequently influencing the risk of age-related diseases such as Alzheimer's disease (AD). We aimed to evaluate the potential causal role of TL in AD endophenotypes (i.e., cognitive performance, ... ...

Abstract	Telomere length (TL) is associated with biological aging, consequently influencing the risk of age-related diseases such as Alzheimer's disease (AD). We aimed to evaluate the potential causal role of TL in AD endophenotypes (i.e., cognitive performance, N = 2233; brain age and AD-related signatures, N = 1134; and cerebrospinal fluid biomarkers (CSF) of AD and neurodegeneration, N = 304) through a Mendelian randomization (MR) analysis. Our analysis was conducted in the context of the ALFA (ALzheimer and FAmilies) study, a population of cognitively healthy individuals at risk of AD. A total of 20 single nucleotide polymorphisms associated with TL were used to determine the effect of TL on AD endophenotypes. Analyses were adjusted by age, sex, and years of education. Stratified analyses by APOE-ɛ4 status and polygenic risk score of AD were conducted. MR analysis revealed significant associations between genetically predicted longer TL and lower levels of CSF Aβ and higher levels of CSF NfL only in APOE-ɛ4 non-carriers. Moreover, inheriting longer TL was associated with greater cortical thickness in age and AD-related brain signatures and lower levels of CSF p-tau among individuals at a high genetic predisposition to AD. Further observational analyses are warranted to better understand these associations.
MeSH term(s)	Humans ; Alzheimer Disease/cerebrospinal fluid ; Mendelian Randomization Analysis ; Endophenotypes ; Biomarkers/cerebrospinal fluid ; Apolipoproteins E/genetics ; Telomere ; tau Proteins/cerebrospinal fluid ; Amyloid beta-Peptides/cerebrospinal fluid
Chemical Substances	Biomarkers ; Apolipoproteins E ; tau Proteins ; Amyloid beta-Peptides
Language	English
Publishing date	2022-11-07
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2506521-X
ISSN	1758-9193 ; 1758-9193
ISSN (online)	1758-9193
ISSN	1758-9193
DOI	10.1186/s13195-022-01101-9
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: Crystal structures of Entamoeba histolytica lysyl-tRNA synthetase reveal conformational changes upon lysine binding and a specific helix bundle domain.

Bonnefond, Luc / Castro de Moura, Manuel / Ribas de Pouplana, Lluis / Nureki, Osamu

FEBS letters

2014 Volume 588, Issue 23, Page(s) 4478–4486

Abstract: The class II lysyl-tRNA synthetases (KRS) are conserved aminoacyl-tRNA synthetases that attach lysine to the cognate tRNA in a two-step mechanism. The enzyme from the parasitic protozoan Entamoeba histolytica was crystallized in the presence of small ... ...

Abstract	The class II lysyl-tRNA synthetases (KRS) are conserved aminoacyl-tRNA synthetases that attach lysine to the cognate tRNA in a two-step mechanism. The enzyme from the parasitic protozoan Entamoeba histolytica was crystallized in the presence of small ligands to generate snapshots of the lysine-adenylate formation. The residues involved in lysine activation are highly conserved and the active site closes around the lysyl-adenylate, as observed in bacterial KRS. The Entamoeba EMAPII-like polypeptide is not resolved in the crystals, but another Entamoeba-specific insertion could be modeled as a small helix bundle that may contribute to tRNA binding through interaction with the tRNA hinge.
MeSH term(s)	Amino Acid Sequence ; Apoenzymes/chemistry ; Apoenzymes/metabolism ; Catalytic Domain/drug effects ; Crystallography, X-Ray ; Entamoeba histolytica/enzymology ; Lysine/metabolism ; Lysine/pharmacology ; Lysine-tRNA Ligase/chemistry ; Lysine-tRNA Ligase/metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Binding ; Protein Structure, Secondary/drug effects ; RNA, Transfer/metabolism
Chemical Substances	Apoenzymes ; RNA, Transfer (9014-25-9) ; Lysine-tRNA Ligase (EC 6.1.1.6) ; Lysine (K3Z4F929H6)
Language	English
Publishing date	2014-11-28
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	212746-5
ISSN	1873-3468 ; 0014-5793
ISSN (online)	1873-3468
ISSN	0014-5793
DOI	10.1016/j.febslet.2014.10.019
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Accessible to users with ZB MED library card

In stock of ZB MED Cologne/Königswinter

Zs.B 282: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾

Article ; Online: Epigenome-wide association study of COVID-19 severity with respiratory failure.

Castro de Moura, Manuel / Davalos, Veronica / Planas-Serra, Laura / Alvarez-Errico, Damiana / Arribas, Carles / Ruiz, Montserrat / Aguilera-Albesa, Sergio / Troya, Jesús / Valencia-Ramos, Juan / Vélez-Santamaria, Valentina / Rodríguez-Palmero, Agustí / Villar-Garcia, Judit / Horcajada, Juan P / Albu, Sergiu / Casasnovas, Carlos / Rull, Anna / Reverte, Laia / Dietl, Beatriz / Dalmau, David /

Arranz, Maria J / Llucià-Carol, Laia / Planas, Anna M / Pérez-Tur, Jordi / Fernandez-Cadenas, Israel / Villares, Paula / Tenorio, Jair / Colobran, Roger / Martin-Nalda, Andrea / Soler-Palacin, Pere / Vidal, Francesc / Pujol, Aurora / Esteller, Manel

EBioMedicine

2021 Volume 66, Page(s) 103339

Abstract: ... Foundation and the CERCA Programme/Generalitat de Catalunya. ...

Abstract	Background: Patients infected with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for the coronavirus disease 2019 (COVID-19), exhibit a wide spectrum of disease behaviour. Since DNA methylation has been implicated in the regulation of viral infections and the immune system, we performed an epigenome-wide association study (EWAS) to identify candidate loci regulated by this epigenetic mark that could be involved in the onset of COVID-19 in patients without comorbidities. Methods: Peripheral blood samples were obtained from 407 confirmed COVID-19 patients ≤ 61 years of age and without comorbidities, 194 (47.7%) of whom had mild symptomatology that did not involve hospitalization and 213 (52.3%) had a severe clinical course that required respiratory support. The set of cases was divided into discovery (n = 207) and validation (n = 200) cohorts, balanced for age and sex of individuals. We analysed the DNA methylation status of 850,000 CpG sites in these patients. Findings: The DNA methylation status of 44 CpG sites was associated with the clinical severity of COVID-19. Of these loci, 23 (52.3%) were located in 20 annotated coding genes. These genes, such as the inflammasome component Absent in Melanoma 2 (AIM2) and the Major Histocompatibility Complex, class I C (HLA-C) candidates, were mainly involved in the response of interferon to viral infection. We used the EWAS-identified sites to establish a DNA methylation signature (EPICOVID) that is associated with the severity of the disease. Interpretation: We identified DNA methylation sites as epigenetic susceptibility loci for respiratory failure in COVID-19 patients. These candidate biomarkers, combined with other clinical, cellular and genetic factors, could be useful in the clinical stratification and management of patients infected with the SARS-CoV-2. Funding: The Unstoppable campaign of the Josep Carreras Leukaemia Foundation, the Cellex Foundation and the CERCA Programme/Generalitat de Catalunya.
MeSH term(s)	Adult ; COVID-19/etiology ; COVID-19/genetics ; Cohort Studies ; CpG Islands ; DNA Methylation ; Epigenome ; Female ; Genome-Wide Association Study ; Humans ; Interferons/genetics ; Interferons/metabolism ; Male ; Middle Aged ; Reproducibility of Results ; Respiratory Insufficiency/genetics ; Respiratory Insufficiency/virology ; Severity of Illness Index ; Spain ; Young Adult
Chemical Substances	Interferons (9008-11-1)
Language	English
Publishing date	2021-04-15
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2851331-9
ISSN	2352-3964
ISSN (online)	2352-3964
DOI	10.1016/j.ebiom.2021.103339
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 7090: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

To top

More links

Kategorien

Order via subito

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

Order via subito

More links

Kategorien

Order via subito

More links

Kategorien

Order via subito

More links

Kategorien

Order via subito

Full text online

More links

Kategorien

Inter-library loan at ZB MED

More links

Kategorien

Order via subito

Full text online

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito