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Sitio web CIRAH. Nuevo espacio de trabajo para el centro

Elsa Ramona Regalado Miranda, Marlene Ferrer Arrocha, Maylín Alonso Martínez, José Emilio Fernández-Britto Rodríguez
2014 Revista Habanera de Ciencias Médicas  
Introducción: el CIRAH es una institución de postgrado que contribuye a la actualización permanente del personal de la salud en sus conocimientos sobre la enfermedad aterosclerótica, sus factores de riesgo y sus consecuencias orgánicas. Desarrolla la Carrera Certificativa de Investigación en Aterosclerosis que oferta a todo el país dividida en tres etapas: Diplomado, Maestría y Doctorado. Coordinar este proceso es complejo y el centro cuenta con muy poco personal para ello. Objetivo: crear un
more » ... tio web para el CIRAH que facilite la gestión de información y el proceso docente-investigativo de la Carrera Certificativa de Investigaciones de Aterosclerosis. Material y Método: se comenzó por realizar un trabajo de mesa para definir los contenidos del sitio analizando la misión y visión de la institución. Se revisaron sitios web temáticos, de centros de investigación y educacionales. Se seleccionó la información del centro, se hizo el diseño estructural y gráfico del sitio, se definió la plataforma a utilizar y las herramientas a emplear. Por último, se montaron todos los contenidos. Resultados: se publicó el sitio institucional CIRAH. Mostró la estructura, contenidos y resultados del trabajo desarrollado. Se colocaron variadas secciones para facilitar el acceso a la información bibliográfica. Ofreció tutoriales y herramientas útiles para el trabajo. Respondió a las dos líneas fundamentales de trabajo: docencia-investigación sobre aterosclerosis. Centralizó el acceso a la información del centro. Conclusiones: el sitio web CIRAH resultó una nueva vía de organización y gestión de información para el centro. Su lanzamiento inició una nueva forma de trabajo colaborativo para sus trabajadores. <span style="font-family: Verdana,Arial,Helvetica,sans-serif; font-size: x-sma [...]
doaj:5aa7322c0c114dc1ba52d710e018fada fatcat:m57waptyyvd45nsbvy3ay6l6sa

Apoptosis Induction by Activator Protein 2α Involves Transcriptional Repression of Bcl-2

Narendra Wajapeyee, Ramona Britto, Halasahalli M. Ravishankar, Kumaravel Somasundaram
2006 Journal of Biological Chemistry  
Activator protein 2␣ (AP-2␣) induces cytotoxicity by inducing cell cycle arrest and apoptosis. In this study we investigated the mechanism of apoptosis induction by AP-2␣. We found that AP-2␣ induced apoptosis efficiently in cells treated with benzyloxycarbonyl-IETD-fluoromethyl ketone or FADD-silenced cells but failed to do so in benzyloxycarbonyl-LEHD-fluoromethyl ketone-treated or apoptosis protease activation factor-1 (Apaf1)-silenced cells, suggesting the central role of mitochondria in
more » ... 2␣-induced apoptosis. In good correlation, cells overexpressing AP-2␣ showed a reduction in mitochondrial membrane potential (⌬ m ), cytochrome c and Smac/DIABLO release into cytosol, and Bax translocation into mitochondria. We found that the pro-apoptotic protein Bax is important for AP-2␣-induced apoptosis as adenovirus AP2 failed to induce apoptosis in HCT116 Bax ؊/؊ cells. However, we found the IAP (inhibitor of apoptosis) inhibitor Smac/DIABLO may have a limited role in AP-2␣-induced apoptosis as we found the IAP member Survivin down-regulated by AP-2␣. Although the total Bax level remains unaltered, we found a time-dependent increase in the activated form of Bax in adenovirus AP2-infected cells. In addition, we show that AP-2␣ transcriptionally represses Bcl-2 by binding to its promoter both in vitro and in vivo and that this is essential for AP-2␣-induced apoptosis as ectopic expression of Bcl-2 efficiently inhibited apoptosis induced by AP-2␣ . Furthermore, we show that chemotherapy-induced endogenous AP-2␣ down-regulates Bcl-2 and induces apoptosis in an AP-2␣-dependent manner. Moreover, we demonstrate that inhibition of okadaic acid or staurosporine-sensitive pathways in AP-2␣ overexpressing breast cancer cells resulted in AP-2␣-dependent apoptosis induction. These results suggest that AP-2␣ induces apoptosis by down-regulating Bcl-2 and utilizing a bax/ cytochrome c/Apaf1/caspase 9-dependent mitochondrial pathway. Activator protein 2␣ (AP-2␣) 3 is a sequence-specific DNA binding transcription factor that is required for normal growth and morphogenesis (1-3). AP-2␣ has a conserved C-terminal DNA binding motif with an integral helix-span-helix homodimerization motif and a less-con-
doi:10.1074/jbc.m600539200 pmid:16533807 fatcat:elo5uvnrmbdxfirdsf73z7kkda

Minimizing proteome redundancy in the UniProt Knowledgebase

Borisas Bursteinas, Ramona Britto, Benoit Bely, Andrea Auchincloss, Catherine Rivoire, Nicole Redaschi, Claire O'Donovan, Maria Jesus Martin
2016 Database: The Journal of Biological Databases and Curation  
Advances in high-throughput sequencing have led to an unprecedented growth in genome sequences being submitted to biological databases. In particular, the sequencing of large numbers of nearly identical bacterial genomes during infection outbreaks and for other large-scale studies has resulted in a high level of redundancy in nucleotide databases and consequently in the UniProt Knowledgebase (UniProtKB). Redundancy negatively impacts on database searches by causing slower searches, an increase
more » ... n statistical bias and cumbersome result analysis. The redundancy combined with the large data volume increases the computational costs for most reuses of UniProtKB data. All of this poses challenges for effective discovery in this wealth of data. With the continuing development of sequencing technologies, it is clear that finding ways to minimize redundancy is crucial to maintaining UniProt's essential contribution to data interpretation by our users. We have developed a methodology to identify and remove highly redundant proteomes from UniProtKB. The procedure identifies redundant proteomes by performing pairwise alignments of sets of sequences for pairs of proteomes and subsequently, applies graph theory to find dominating sets that provide a set of non-redundant proteomes with a minimal loss of information. This method was implemented for bacteria in mid-2015, resulting in a removal of 50 million proteins in UniProtKB. With every new release, this procedure is used to filter new incoming proteomes, resulting in a more scalable and scientifically valuable growth of UniProtKB. Database URL: http://www.uniprot.org/proteomes/ V C The Author(s)
doi:10.1093/database/baw139 pmid:28025334 pmcid:PMC5199198 fatcat:kava4a7cobh2tasps3cmvmix4i

Modelo CCa, plantilla de Word para el montaje de documentos de tesis

Elsa Ramona Regalado Miranda, Ana Mary Fernández Milán, José Emilio Fernández-Britto Rodríguez
2015 Revista Cubana de Informática Médica  
El Centro de Investigaciones y Referencias de Aterosclerosis de la Habana desarrolla la Carrera Certificativa de Investigaciones en Aterosclerosis que incluye: Diplomado, Maestría y Doctorado. La elaboración de documentos de tesis presente, ha sido un problema para los implicados en el proceso. Propósito: Crear una plantilla de Word que sirva de guía a maestrantes y doctorantes en la elaboración de sus documentos de tesis. Método: se realizó trabajo búsqueda de lo legislado sobre la creación de
more » ... los documentos de tesis, se investigaron las deficiencias ya presentadas, se elaboró la plantilla de Word y un manual, se distribuyó para su validación. Resultados: Se creó el "Modelo CCa", plantilla de Word totalmente modificable que contiene la estructura de la tesis e incluye las orientaciones metodológicas en el mismo lugar donde se inserta el contenido. Se publicó en el sitio web del centro. Conclusiones: La plantilla facilitó el desarrollo del proceso educativo, ayudó al perfeccionamiento científico de los alumnos y creó condiciones para un uso más práctico de la tecnología.
doaj:7774a1764d1148e4a297dedd8217d9b3 fatcat:l3drr6tvb5h7bdbgohp4arp64y

GPSy: a cross-species gene prioritization system for conserved biological processes—application in male gamete development

Ramona Britto, Olivier Sallou, Olivier Collin, Grégoire Michaux, Michael Primig, Frédéric Chalmel
2012 Nucleic Acids Research  
We present gene prioritization system (GPSy), a cross-species gene prioritization system that facilitates the arduous but critical task of prioritizing genes for follow-up functional analyses. GPSy's modular design with regard to species, data sets and scoring strategies enables users to formulate queries in a highly flexible manner. Currently, the system encompasses 20 topics related to conserved biological processes including male gamete development discussed in this article. The web
more » ... sed tool is freely available at http://gpsy. genouest.org.
doi:10.1093/nar/gks380 pmid:22570409 pmcid:PMC3394256 fatcat:on67qjod2ndkpl5o5anlxaavi4

Quality Matters: Biocuration Experts on the Impact of Duplication and Other Data Quality Issues in Biological Databases [article]

Qingyu Chen, Ramona Britto, Ivan Erill, Constance J Jeffery, Arthur Liberzon, Michele Magrane, Jun-ichi Onami, Marc Robinson-Rechavi, Jana Sponarova, Justin Zobel, Karin Verspoor
2019 bioRxiv   pre-print
The volume of biological database records is growing rapidly, populated by complex records drawn from heterogeneous sources. A specific challenge is duplication, that is, the presence of redundancy (records with high similarity) or inconsistency (dissimilar records that correspond to the same entity). The characteristics (which records are duplicates), impact (why duplicates are significant), and solutions (how to address duplication), are not well understood. Studies on the topic are neither
more » ... cent nor comprehensive. In addition, other data quality issues, such as inconsistencies and inaccuracies, are also of concern in the context of biological databases. A primary focus of this paper is to present and consolidate the opinions of over 20 experts and practitioners on the topic of duplication in biological sequence databases. The results reveal that survey participants believe that duplicate records are diverse; that the negative impacts of duplicates are severe, while positive impacts depend on correct identification of duplicates; and that duplicate detection methods need to be more precise, scalable, and robust. A secondary focus is to consider other quality issues. We observe that biocuration is the key mechanism used to ensure the quality of this data, and explore the issues through a case study of curation in UniProtKB/Swiss-Prot as well as an interview with an experienced biocurator. While biocuration is a vital solution for handling of data quality issues, a broader community effort is needed to provide adequate support for thorough biocuration in the face of widespread quality concerns.
doi:10.1101/788034 fatcat:nhcgdtct4bd5de4x4s7ewyqf54

Upregulation of ASCL1 and inhibition of Notch signaling pathway characterize progressive astrocytoma

Kumaravel Somasundaram, Sreekanth P Reddy, Katyayni Vinnakota, Ramona Britto, Madhavan Subbarayan, Sandeep Nambiar, Aparna Hebbar, Cini Samuel, Mitesh Shetty, Hari Kishore Sreepathi, Vani Santosh, Alangar Sathyaranjandas Hegde (+3 others)
2005 Oncogene  
doi:10.1038/sj.onc.1208865 pmid:16103883 fatcat:j63aoopuwfaoriyzoxcahkkzbi

Quality Matters: Biocuration Experts on the Impact of Duplication and Other Data Quality Issues in Biological Databases

Qingyu Chen, Ramona Britto, Ivan Erill, Constance J. Jeffery, Arthur Liberzon, Michele Magrane, Jun-ichi Onami, Marc Robinson-Rechavi, Jana Sponarova, Justin Zobel, Karin Verspoor
2020 Genomics, Proteomics & Bioinformatics  
doi:10.1016/j.gpb.2018.11.006 pmid:32652120 pmcid:PMC7646089 fatcat:k3r3wplhtravxlkom6gd7kfsxy

Expediente /Editorial Board / Cuerpo Editorial

Rev. Bras. Ext. Univ.
2014 Revista Brasileira de Extensão Universitária  
-UFFS, Brasil Marco Aurélio Spohn, Universidade Federal da Fronteira Sul -UFFS, Brasil Maria Salete Marcon Gomes Vaz, Universidade Estadual de Ponta Grossa -UEPG, Brasil Maria Teresa Seabra Soares de Britto  ...  Transformación en la orden metabólica social del capital: la teoría y la praxis de extensión en comunidades agrarias en el municipio de Colares, Pará, Amazonía Oriental 5 Editorial 7 Jaquiel Salvi Fernandes, Ramona  ... 
doaj:56291001a48449bc976c4fb77999cb9f fatcat:3x2klruqlfc5rb37gndnlkw5ee

Quality Matters: Biocuration Experts on the Impact of Duplication and Other Data Quality Issues in Biological Databases [article]

Qingyu Chen, Ramona Britto, Ivan Erill, Constance J. Jeffery, Arthur Liberzon, Michele Magrane, Jun-Ichi Onami, Marc Robinson-Rechavi, Jana Sponarova, Justin Zobel, Karin Verspoor, Maryland Shared Open Access Repository
2022
Biological databases represent an extraordinary collective volume of work. Diligently built up over decades and comprising many millions of contributions from the biomedical research community, biological databases provide worldwide access to a massive number of records (also known as entries) [1]. Starting from individual laboratories, genomes are sequenced, assembled, annotated, and ultimately submitted to primary nucleotide databases such as GenBank [2], European Nucleotide Archive (ENA)
more » ... and DNA Data Bank of Japan (DDBJ) [4] (collectively known as the International Nucleotide Sequence Database Collaboration, INSDC). Protein records, which are the translations of these nucleotide records, are deposited into central protein databases such as the UniProt KnowledgeBase (UniProtKB) [5] and the Protein Data Bank (PDB) [6]. Sequence records are further accumulated into different databases for more specialized purposes: RFam [7] and PFam [8] for RNA and protein families, respectively; DictyBase [9] and PomBase [10] for model organisms; as well as ArrayExpress [11] and Gene Expression Omnibus (GEO) [12] for gene expression profiles. These databases are selected as examples; the list is not intended to be exhaustive. However, they are representative of biological databases that have been named in the "golden set" of the 24th Nucleic Acids Research database issue (in 2016). The introduction of that issue highlights the databases that "consistently served as authoritative, comprehensive, and convenient data resources widely used by the entire community and offer some lessons on what makes a successful database" [13]. In addition, the associated information about sequences is also propagated into non-sequence databases, such as PubMed (https://www.ncbi.nlm.nih.gov/pubmed/) for scientific literature or Gene Ontology (GO) [14] for function annotations. These databases in turn benefit individual studies, many of which use these publicly available records as the basis for their own research. Inevitably, given the scale of [...]
doi:10.13016/m2j4my-ztnw fatcat:6llk2qetgndcrgwnlgqaclwtta

Page 2738 of Psychological Abstracts Vol. 93, Issue 7 [page]

2006 Psychological Abstracts  
Ramona, 18818 Bock, Kathryn, 19090 Boden, Joseph M., 20016 Bodenhorn, Nancy, 20966 Bodenmann, Guy, 18512 Bodnar, Susan, 20563 Bodor, Tamas, 21406 Boehm, Stephan G., 18827 Boer, Erwin, 18670 Boer, Harry  ...  G., 18927 Britto, Pia Rebello, 19377 Britton, Jennifer C., 19031 Brizzolara, Daniela, 20072 Broad, Robert D., 19758 Broadbent, Nicola J., 18953 Brock, Adrian C., 18490 Brockington, I., 20165 Brody, Gene  ... 

A tradução de títulos das Histórias em Quadrinhos: o caso de Violent Cases e Repeteco

Francisca Ysabelle Manríquez Reyes Silveira, Gilles Jean Abes
2017 Revista Fronteiras : Estudos Midiáticos  
Scott Pilgrim e Ramona Flowers jantam lá) e deseja passar um tom descolado.  ...  Acho que a opinião geral de tradução é vista dessa forma, como o Britto coloca: é muito real, mas para quem pensa assim foge do próprio senso comum.  ... 
doi:10.4013/fem.2017.193.06 fatcat:y427e4bejzbfhmzzgxecrpi7dy

UniProt: the universal protein knowledgebase in 2021

The UniProt Consortium, Alex Bateman, Maria-Jesus Martin, Sandra Orchard, Michele Magrane, Rahat Agivetova, Shadab Ahmad, Emanuele Alpi, Emily H Bowler-Barnett, Ramona Britto, Borisas Bursteinas, Hema Bye-A-Jee (+122 others)
2020 Nucleic Acids Research  
The aim of the UniProt Knowledgebase is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information. In this article, we describe significant updates that we have made over the last two years to the resource. The number of sequences in UniProtKB has risen to approximately 190 million, despite continued work to reduce sequence redundancy at the proteome level. We have adopted new methods of assessing proteome
more » ... s and quality. We continue to extract detailed annotations from the literature to add to reviewed entries and supplement these in unreviewed entries with annotations provided by automated systems such as the newly implemented Association-Rule-Based Annotator (ARBA). We have developed a credit-based publication submission interface to allow the community to contribute publications and annotations to UniProt entries. We describe how UniProtKB responded to the COVID-19 pandemic through expert curation of relevant entries that were rapidly made available to the research community through a dedicated portal. UniProt resources are available under a CC-BY (4.0) license via the web at https://www.uniprot.org/.
doi:10.1093/nar/gkaa1100 pmid:33237286 pmcid:PMC7778908 fatcat:6rwvp6l5uzb3li4lygf2gny6qq

A crowdsourcing open platform for literature curation in UniProt

Yuqi Wang, Qinghua Wang, Hongzhan Huang, Wei Huang, Yongxing Chen, Peter B. McGarvey, Cathy H. Wu, Cecilia N. Arighi, on behalf of the UniProt Consortium
2021 PLoS Biology  
Bowler-Barnett, Ramona Britto, Borisas Bursteinas, Hema Bye-A-Jee, Ray Coetzee, Austra Cukura, Alan Da Silva, Paul Denny, Tunca Dogan, ThankGod Ebenezer, Jun Fan, Leyla Garcia Castro, Penelope Garmiri,  ... 
doi:10.1371/journal.pbio.3001464 pmid:34871295 pmcid:PMC8675915 fatcat:6tsqu5evlre45ocilvfp4ad2ca

AP-2α expression in papillary thyroid carcinoma predicts tumor progression and poor prognosis

Wu HR, Zhang J
2018 Cancer Management and Research  
Ramona Britto et al 21 found that decreased nuclear expression was indicative of a better prognosis, and observed the shift in localization of this protein from the nucleus to the cytoplasm with increasing  ...  Britto R, Umesh S, Hegde AS, et al. Shift in AP-2alpha localization characterizes astrocytoma progression. Zeng C, Liu Z, Zhang J, et al.  ... 
doaj:d1624e3b78f24e468ee231419ec8c0fe fatcat:ovlvkzdrwbfrladnmdqy2kk6fu
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