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  1. Article ; Online: Changing face of socio-economic vulnerability and COVID-19: An analysis of country wealth during the first two years of the pandemic.

    Pérez-Segura, Víctor / Caro-Carretero, Raquel / Rua, Antonio

    PloS one

    2023  Volume 18, Issue 8, Page(s) e0290529

    Abstract: There are numerous academic studies on the relationship between population wealth and the incidence of COVID-19. However, research developed shows contradictory results on their relationship. In accordance with this question, this work pursues two ... ...

    Abstract There are numerous academic studies on the relationship between population wealth and the incidence of COVID-19. However, research developed shows contradictory results on their relationship. In accordance with this question, this work pursues two objectives: on the one hand, to check whether wealth and disease incidence have a unidirectional and stable relationship. And on the other hand, to find out if the country's statistical production capacity is masking the real incidence of the COVID-19 pandemic. In order to achieve this objective, an ecological study has been designed at international level with the countries established as study units. The analytical strategy utilized involves the consecutive application of cross-sectional analysis, specifically employing multivariate linear regression daily throughout the first two years of the pandemic (from 03/14/2020 to 03/28/2022). The application of multiple cross-sectional analysis has shown that country wealth has a dynamic relationship with the incidence of COVID-19. Initially, it appears as a risk factor and, in the long term, as a protective element. In turn, statistical capacity appears as an explanatory variable for the number of published COVID-19 cases and deaths. Therefore, the inadequate statistical production capacity of low income countries may be masking the real incidence of the disease.
    MeSH term(s) Humans ; Pandemics ; COVID-19/epidemiology ; Cross-Sectional Studies ; Linear Models ; Socioeconomic Factors
    Language English
    Publishing date 2023-08-28
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0290529
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Multivariate Analysis of Risk Factors of the COVID-19 Pandemic in the Community of Madrid, Spain.

    Pérez-Segura, Víctor / Caro-Carretero, Raquel / Rua, Antonio

    International journal of environmental research and public health

    2021  Volume 18, Issue 17

    Abstract: It has been more than one year since Chinese authorities identified a deadly new strain of coronavirus, SARS-CoV-2. Since then, the scientific work regarding the transmission risk factors of COVID-19 has been intense. The relationship between COVID-19 ... ...

    Abstract It has been more than one year since Chinese authorities identified a deadly new strain of coronavirus, SARS-CoV-2. Since then, the scientific work regarding the transmission risk factors of COVID-19 has been intense. The relationship between COVID-19 and environmental conditions is becoming an increasingly popular research topic. Based on the findings of the early research, we focused on the community of Madrid, Spain, which is one of the world's most significant pandemic hotspots. We employed different multivariate statistical analyses, including principal component analysis, analysis of variance, clustering, and linear regression models. Principal component analysis was employed in order to reduce the number of risk factors down to three new components that explained 71% of the original variance. Cluster analysis was used to delimit the territory of Madrid according to these new risk components. An ANOVA test revealed different incidence rates between the territories delimited by the previously identified components. Finally, a set of linear models was applied to demonstrate how environmental factors present a greater influence on COVID-19 infections than socioeconomic dimensions. This type of local research provides valuable information that could help societies become more resilient in the face of future pandemics.
    MeSH term(s) COVID-19 ; Humans ; Multivariate Analysis ; Pandemics ; Risk Factors ; SARS-CoV-2 ; Spain/epidemiology
    Language English
    Publishing date 2021-09-01
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2175195-X
    ISSN 1660-4601 ; 1661-7827
    ISSN (online) 1660-4601
    ISSN 1661-7827
    DOI 10.3390/ijerph18179227
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: DeepMSPeptide: peptide detectability prediction using deep learning.

    Serrano, Guillermo / Guruceaga, Elizabeth / Segura, Victor

    Bioinformatics (Oxford, England)

    2019  Volume 36, Issue 4, Page(s) 1279–1280

    Abstract: Summary: The protein detection and quantification using high-throughput proteomic technologies is still challenging due to the stochastic nature of the peptide selection in the mass spectrometer, the difficulties in the statistical analysis of the ... ...

    Abstract Summary: The protein detection and quantification using high-throughput proteomic technologies is still challenging due to the stochastic nature of the peptide selection in the mass spectrometer, the difficulties in the statistical analysis of the results and the presence of degenerated peptides. However, considering in the analysis only those peptides that could be detected by mass spectrometry, also called proteotypic peptides, increases the accuracy of the results. Several approaches have been applied to predict peptide detectability based on the physicochemical properties of the peptides. In this manuscript, we present DeepMSPeptide, a bioinformatic tool that uses a deep learning method to predict proteotypic peptides exclusively based on the peptide amino acid sequences.
    Availability and implementation: DeepMSPeptide is available at https://github.com/vsegurar/DeepMSPeptide.
    Supplementary information: Supplementary data are available at Bioinformatics online.
    MeSH term(s) Deep Learning ; Mass Spectrometry ; Peptides ; Proteins ; Proteomics
    Chemical Substances Peptides ; Proteins
    Language English
    Publishing date 2019-09-16
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1422668-6
    ISSN 1367-4811 ; 1367-4803
    ISSN (online) 1367-4811
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btz708
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: MiTPeptideDB: a proteogenomic resource for the discovery of novel peptides.

    Guruceaga, Elizabeth / Garin-Muga, Alba / Segura, Victor

    Bioinformatics (Oxford, England)

    2019  Volume 36, Issue 1, Page(s) 205–211

    Abstract: Motivation: The principal lines of research in MS/MS based Proteomics have been directed toward the molecular characterization of the proteins including their biological functions and their implications in human diseases. Recent advances in this field ... ...

    Abstract Motivation: The principal lines of research in MS/MS based Proteomics have been directed toward the molecular characterization of the proteins including their biological functions and their implications in human diseases. Recent advances in this field have also allowed the first attempts to apply these techniques to the clinical practice. Nowadays, the main progress in Computational Proteomics is based on the integration of genomic, transcriptomic and proteomic experimental data, what is known as Proteogenomics. This methodology is being especially useful for the discovery of new clinical biomarkers, small open reading frames and microproteins, although their validation is still challenging.
    Results: We detected novel peptides following a proteogenomic workflow based on the MiTranscriptome human assembly and shotgun experiments. The annotation approach generated three custom databases with the corresponding peptides of known and novel transcripts of both protein coding genes and non-coding genes. In addition, we used a peptide detectability filter to improve the computational performance of the proteomic searches, the statistical analysis and the robustness of the results. These innovative additional filters are specially relevant when noisy next generation sequencing experiments are used to generate the databases. This resource, MiTPeptideDB, was validated using 43 cell lines for which RNA-Seq experiments and shotgun experiments were available.
    Availability and implementation: MiTPeptideDB is available at http://bit.ly/MiTPeptideDB.
    Supplementary information: Supplementary data are available at Bioinformatics online.
    MeSH term(s) Cell Line ; Humans ; Peptides/genetics ; Proteogenomics/methods ; Tandem Mass Spectrometry
    Chemical Substances Peptides
    Language English
    Publishing date 2019-06-26
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1422668-6
    ISSN 1367-4811 ; 1367-4803
    ISSN (online) 1367-4811
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btz530
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Proteogenomics in the context of the Human Proteome Project (HPP).

    González-Gomariz, José / Guruceaga, Elizabeth / López-Sánchez, Macarena / Segura, Victor

    Expert review of proteomics

    2019  Volume 16, Issue 3, Page(s) 267–275

    Abstract: Introduction: The technological and scientific progress performed in the Human Proteome Project (HPP) has provided to the scientific community a new set of experimental and bioinformatic methods in the challenging field of shotgun and SRM/MRM-based ... ...

    Abstract Introduction: The technological and scientific progress performed in the Human Proteome Project (HPP) has provided to the scientific community a new set of experimental and bioinformatic methods in the challenging field of shotgun and SRM/MRM-based Proteomics. The requirements for a protein to be considered experimentally validated are now well-established, and the information about the human proteome is available in the neXtProt database, while targeted proteomic assays are stored in SRMAtlas. However, the study of the missing proteins continues being an outstanding issue. Areas covered: This review is focused on the implementation of proteogenomic methods designed to improve the detection and validation of the missing proteins. The evolution of the methodological strategies based on the combination of different omic technologies and the use of huge publicly available datasets is shown taking the Chromosome 16 Consortium as reference. Expert commentary: Proteogenomics and other strategies of data analysis implemented within the C-HPP initiative could be used as guidance to complete in a near future the catalog of the human proteins. Besides, in the next years, we will probably witness their use in the B/D-HPP initiative to go a step forward on the implications of the proteins in the human biology and disease.
    MeSH term(s) Chromosomes, Human, Pair 16/genetics ; Databases, Protein ; Human Genome Project ; Humans ; Proteogenomics/trends ; Proteome/genetics ; Proteomics ; Reference Standards
    Chemical Substances Proteome
    Language English
    Publishing date 2019-01-28
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 2299100-1
    ISSN 1744-8387 ; 1478-9450
    ISSN (online) 1744-8387
    ISSN 1478-9450
    DOI 10.1080/14789450.2019.1571916
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Functional interpretation of microRNA-mRNA association in biological systems using R.

    Guruceaga, Elizabeth / Segura, Victor

    Computers in biology and medicine

    2014  Volume 44, Page(s) 124–131

    Abstract: The prediction of microRNA targets is a challenging task that has given rise to several prediction algorithms. Databases of predicted targets can be used in a microRNA target enrichment analysis, enhancing our capacity to extract functional information ... ...

    Abstract The prediction of microRNA targets is a challenging task that has given rise to several prediction algorithms. Databases of predicted targets can be used in a microRNA target enrichment analysis, enhancing our capacity to extract functional information from gene lists. However, the available tools in this field analyze gene sets one by one limiting their use in a meta-analysis. Here, we present an R system for miRNA enrichment analysis that is suitable for systems biology. These collection of R scripts and embedded data allow using predicted targets of public databases or a custom integration of them. As a proof-of-principle, we have successfully performed the challenging analysis of 2158 tumoral samples at a time. The obtained results have been summarized in a network where each cancer disease is linked to enriched miRNAs and overrepresented functions. These network connections have proven to be an invaluable resource for the study of biological and pathological causes and effects of the expression of miRNAs.
    MeSH term(s) Animals ; Databases, Nucleic Acid ; Humans ; MicroRNAs/genetics ; Neoplasms/genetics ; RNA, Messenger/genetics ; RNA, Neoplasm/genetics ; Systems Biology/methods
    Chemical Substances MicroRNAs ; RNA, Messenger ; RNA, Neoplasm
    Language English
    Publishing date 2014-01
    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.2013.11.001
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Venetoclax improves CD20 immunotherapy in a mouse model of MYC/BCL2 double-expressor diffuse large B-cell lymphoma.

    Melchor, Javier / Garcia-Lacarte, Marcos / Grijalba, Sara C / Arnaiz-Leché, Adrián / Pascual, Marién / Panizo, Carlos / Blanco, Oscar / Segura, Victor / Novo, Francisco J / Valero, Juan Garcia / Pérez-Galán, Patricia / Martinez-Climent, Jose A / Roa, Sergio

    Journal for immunotherapy of cancer

    2023  Volume 11, Issue 2

    Abstract: Background: Approximately one-third of diffuse large B cell lymphoma (DLBCL) patients exhibit co-expression of MYC and BCL2 (double-expressor lymphoma, DEL) and have a dismal prognosis. Targeted inhibition of the anti-apoptotic protein BCL2 with ... ...

    Abstract Background: Approximately one-third of diffuse large B cell lymphoma (DLBCL) patients exhibit co-expression of MYC and BCL2 (double-expressor lymphoma, DEL) and have a dismal prognosis. Targeted inhibition of the anti-apoptotic protein BCL2 with venetoclax (ABT-199) has been approved in multiple B-cell malignancies and is currently being investigated in clinical trials for DLBCL. Whether BCL2 anti-apoptotic function represents a multifaceted vulnerability for DEL-DLBCL, affecting both lymphoma B cells and T cells within the tumor microenvironment, remains to be elucidated.
    Methods: Here, we present novel genetically engineered mice that preclinically recapitulate DEL-DLBCL lymphomagenesis, and evaluate their sensitivity ex vivo and in vivo to the promising combination of venetoclax with anti-CD20-based standard immunotherapy.
    Results: Venetoclax treatment demonstrated specific killing of MYC
    Conclusions: These results suggest that the combination of anti-CD20-based immunotherapy and BCL2 inhibition leads to cooperative immunomodulatory effects and improved preclinical responses, which may offer promising therapeutic opportunities for DEL-DLBCL patients.
    MeSH term(s) Animals ; Mice ; Bridged Bicyclo Compounds, Heterocyclic/pharmacology ; Bridged Bicyclo Compounds, Heterocyclic/therapeutic use ; Disease Models, Animal ; Immunotherapy/methods ; Lymphoma, Large B-Cell, Diffuse/drug therapy ; Proto-Oncogene Proteins c-bcl-2 ; Tumor Microenvironment ; Proto-Oncogene Proteins c-myc
    Chemical Substances Bridged Bicyclo Compounds, Heterocyclic ; Proto-Oncogene Proteins c-bcl-2 ; venetoclax (N54AIC43PW) ; Proto-Oncogene Proteins c-myc
    Language English
    Publishing date 2023-02-28
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2719863-7
    ISSN 2051-1426 ; 2051-1426
    ISSN (online) 2051-1426
    ISSN 2051-1426
    DOI 10.1136/jitc-2022-006113
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Hospital El Salvador: broader questions remain - Authors' reply.

    Bello, Manuel / Segura, Víctor / Camputaro, Luis / Hoyos, William / Maza, Mauricio / Sandoval, Xochitl / Serpa, Magdalena / Coopersmith, Craig M

    The Lancet. Global health

    2021  Volume 9, Issue 4, Page(s) e407

    MeSH term(s) COVID-19 ; Central America ; Critical Care ; El Salvador/epidemiology ; Hospitals ; Humans ; SARS-CoV-2
    Language English
    Publishing date 2021-02-26
    Publishing country England
    Document type Letter ; Comment
    ZDB-ID 2723488-5
    ISSN 2214-109X ; 2214-109X
    ISSN (online) 2214-109X
    ISSN 2214-109X
    DOI 10.1016/S2214-109X(21)00058-9
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Long Noncoding RNA EGOT Responds to Stress Signals to Regulate Cell Inflammation and Growth.

    Barriocanal, Marina / Prior, Celia / Suarez, Beatriz / Unfried, Juan Pablo / Razquin, Nerea / Hervás-Stubbs, Sandra / Sangro, Bruno / Segura, Victor / Fortes, Puri

    Journal of immunology (Baltimore, Md. : 1950)

    2021  Volume 206, Issue 8, Page(s) 1932–1942

    Abstract: The cell has several mechanisms to sense and neutralize stress. Stress-related stimuli activate pathways that counteract danger, support cell survival, and activate the inflammatory response. We use human cells to show that these processes are modulated ... ...

    Abstract The cell has several mechanisms to sense and neutralize stress. Stress-related stimuli activate pathways that counteract danger, support cell survival, and activate the inflammatory response. We use human cells to show that these processes are modulated by EGOT, a long noncoding RNA highly induced by viral infection, whose inhibition results in increased levels of antiviral IFN-stimulated genes (ISGs) and decreased viral replication. We now show that EGOT is induced in response to cell stress, viral replication, or the presence of pathogen-associated molecular patterns via the PI3K/AKT, MAPKs, and NF-κB pathways, which lead to cell survival and inflammation. Transcriptome analysis and validation experiments show that EGOT modulates PI3K/AKT and NF-κB responses. On the one hand, EGOT inhibition decreases expression of PI3K/AKT-induced cellular receptors and cell proliferation. In fact, EGOT levels are increased in several tumors. On the other hand, EGOT inhibition results in decreased levels of key NF-κB target genes, including those required for inflammation and ISGs in those cells that build an antiviral response. Mechanistically, EGOT depletion decreases the levels of the key coactivator TBLR1, essential for transcription by NF-κB. In summary, EGOT is induced in response to stress and may function as a switch that represses ISG transcription until a proper antiviral or stress response is initiated. EGOT then helps PI3K/AKT, MAPKs, and NF-κB pathways to activate the antiviral response, cell inflammation, and growth. We believe that modulation of EGOT levels could be used as a therapy for the treatment of certain viral infections, immune diseases, and cancer.
    MeSH term(s) Cell Growth Processes ; Cell Line ; Gene Expression Profiling ; Gene Knockdown Techniques ; Hepacivirus/physiology ; Hepatitis C/immunology ; Humans ; Inflammation/genetics ; NF-kappa B/metabolism ; Phosphatidylinositol 3-Kinases/metabolism ; Proto-Oncogene Proteins c-akt/metabolism ; RNA, Long Noncoding/genetics ; Receptors, Cytoplasmic and Nuclear/genetics ; Receptors, Cytoplasmic and Nuclear/metabolism ; Repressor Proteins/genetics ; Repressor Proteins/metabolism ; Signal Transduction ; Stress, Physiological/immunology
    Chemical Substances NF-kappa B ; RNA, Long Noncoding ; Receptors, Cytoplasmic and Nuclear ; Repressor Proteins ; TBL1XR1 protein, human ; Proto-Oncogene Proteins c-akt (EC 2.7.11.1)
    Language English
    Publishing date 2021-03-31
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 3056-9
    ISSN 1550-6606 ; 0022-1767 ; 1048-3233 ; 1047-7381
    ISSN (online) 1550-6606
    ISSN 0022-1767 ; 1048-3233 ; 1047-7381
    DOI 10.4049/jimmunol.1900776
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  10. Article: Proteogenomic Analysis of Single Amino Acid Polymorphisms in Cancer Research.

    Garin-Muga, Alba / Corrales, Fernando J / Segura, Victor

    Advances in experimental medicine and biology

    2016  Volume 926, Page(s) 93–113

    Abstract: The integration of genomics and proteomics has led to the emergence of proteogenomics, a field of research successfully applied to the characterization of cancer samples. The diagnosis, prognosis and response to therapy of cancer patients will largely ... ...

    Abstract The integration of genomics and proteomics has led to the emergence of proteogenomics, a field of research successfully applied to the characterization of cancer samples. The diagnosis, prognosis and response to therapy of cancer patients will largely benefit from the identification of mutations present in their genome. The current state of the art of high throughput experiments for genome-wide detection of somatic mutations in cancer samples has allowed the development of projects such as the TCGA, in which hundreds of cancer genomes have been sequenced. This huge amount of data can be used to generate protein sequence databases in which each entry corresponds to a mutated peptide associated with certain cancer types. In this chapter, we describe a bioinformatics workflow for creating these databases and detecting mutated peptides in cancer samples from proteomic shotgun experiments. The performance of the proposed method has been evaluated using publicly available datasets from four cancer cell lines.
    MeSH term(s) Amino Acid Sequence ; Amino Acid Substitution ; Cell Line, Tumor ; Databases, Protein ; Gene Expression ; Genome-Wide Association Study ; High-Throughput Nucleotide Sequencing ; Humans ; Molecular Sequence Annotation ; Mutant Proteins/genetics ; Mutant Proteins/metabolism ; Mutation ; Neoplasm Proteins/genetics ; Neoplasm Proteins/metabolism ; Neoplasms/genetics ; Neoplasms/metabolism ; Neoplasms/pathology ; Proteogenomics/methods
    Chemical Substances Mutant Proteins ; Neoplasm Proteins
    Language English
    Publishing date 2016
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 2214-8019 ; 0065-2598
    ISSN (online) 2214-8019
    ISSN 0065-2598
    DOI 10.1007/978-3-319-42316-6_7
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