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Dataset

LOS LINFOCITOS VAN A CLASE: LAS VACUNAS

  • Casado, Marta
  • Esteban, Mariano
  • García Arriaza, Juan
  • CSIC - Instituto de Biomedicina de Valencia (IBV)
8º Vídeo de Divulgación Científica de la serie: "Un virus, mil preguntas" creada por Marta Casado y el Instituto de Biomedicina de Valencia: "Los linfocitos van a clase: las vacunas" 8,13 min. Guion y realización: Aprende con DANIO, En este nuevo vídeo de la serie vamos a explicar qué es una vacuna, porqué son importantes en el contexto de la pandemia, y se discutirá la estrategia de la vacuna diseñada por el equipo de los Dres. Mariano Esteban y Juan García Arriaza., Fundación General CSIC, Programa Cuenta la Ciencia., Peer reviewed

Proyecto: //

Dataset

DATA FROM: GENOME DATA FROM A 16TH CENTURY PIG ILLUMINATE MODERN BREED RELATIONSHIPS

  • Pérez-Enciso, Miguel
Ancient DNA (aDNA) provides direct evidence of historical events that have modeled the genome of modern individuals. In livestock, resolving the differences between the effects of initial domestication and of subsequent modern breeding is not straight forward without aDNA data. Here, we have obtained shotgun genome sequence data from a sixteenth century pig from Northeastern Spain (Montsoriu castle), the ancient pig was obtained from an extremely well-preserved and diverse assemblage. In addition, we provide the sequence of three new modern genomes from an Iberian pig, Spanish wild boar and a Guatemalan Creole pig. Comparison with both mitochondrial and autosomal genome data shows that the ancient pig is closely related to extant Iberian pigs and to European wild boar. Although the ancient sample was clearly domestic, admixture with wild boar also occurred, according to the D-statistics. The close relationship between Iberian, European wild boar and the ancient pig confirms that Asian introgression in modern Iberian pigs has not existed or has been negligible. In contrast, the Guatemalan Creole pig clusters apart from the Iberian pig genome, likely due to introgression from international breeds., Peer reviewed

Proyecto: //

Dataset

DATA FROM: ANALYSIS OF THE PORCINE APOA2 GENE EXPRESSION IN LIVER, POLYMORPHISMS IDENTIFICATION AND ASSOCIATION WITH FATTY ACID COMPOSITION TRAITS

  • Ballester, María
  • Revilla, Manuel
  • Puig-Oliveras, Anna
  • Marchesi, J.A.P.
  • Castelló, Anna
  • Corominas, Jordi
  • Fernández, Ana Isabel
  • Folch, Josep María
Usage Notes Porcine APOA2 gene expression in liver Data from Analysis of the porcine APOA2 gene expression in liver, polymorphisms identification and association with fatty acid composition traits. Contains SNP genotypes for GWAS and eGWAS studies, mRNA expression of APOA2 in liver, and fatty acid composition in backfat and muscle, APOA2 is a protein implicated in triglyceride, fatty acid and glucose metabolism. In pigs, the APOA2 gene is located on pig chromosome 4 (SSC4) in a QTL region affecting fatty acid composition, fatness and growth traits. In this study, we evaluated APOA2 as a candidate gene for meat quality traits in an Iberian × Landrace backcross population. The APOA2:c.131T>A polymorphism, located in exon 3 of APOA2 and determining a missense mutation, was associated with the percentage of hexadecenoic acid [C16:1(n–9)], linoleic acid [C18:2(n–6)], α-linolenic acid [C18:3(n–3)], dihomo-gamma-linolenic acid [C20:3(n–6)] and polyunsaturated fatty acids (PUFAs) in backfat. Furthermore, this SNP was associated with the global mRNA expression levels of APOA2 in liver and was used as a marker to determine allelic expression imbalance by pyrosequencing. We determined an overexpression of the T allele in heterozygous samples with a mean ratio of 2.8 (T/A), observing a high variability in the allelic expression among individuals. This result suggests that complex regulatory mechanisms, beyond a single polymorphism (e.g. epigenetic effects or multiple cis-acting polymorphisms), may be regulating APOA2 gene expression., Peer reviewed

Proyecto: //

Dataset

DATA FROM: GENOME-WIDE SNP DATA UNVEILS THE GLOBALIZATION OF DOMESTICATED PIGS

  • Yang, Bin
  • Cui, Leilei
  • Pérez-Enciso, Miguel
  • Traspov, Aleksei
  • Crooijmans, Richard P. M. A.
  • Zinovieva, Natalia
  • Schook, Lawrence B.
  • Archibald, Alan L.
  • Gatphayak, Kesinee
  • Knorr, Christophe
  • Triantafyllidis, Alex
  • Alexandri, Panoraia
  • Semiadi, Gono
  • Hanotte, Olivier
  • Dias, Deodália
  • Dovč, Peter
  • Uimari, Pekka
  • Iacolina, Laura
  • Scandura, Massimo
  • Groenen, Martien A. M.
  • Huang, Lusheng
  • Megens, Hendrik-Jan
Usage Notes: Description_data_GSE_Global_pigs Table describing the samples. Note that the submitted data includes a few animals that were removed from the paper due to additional constraints applied in the review process. GSE_global_pigs.map PLINK MAP file, describing the SNPs used. GSE_global_pigs.ped Genotype data used in PLINK PED file format., [Background]: Pigs were domesticated independently in Eastern and Western Eurasia early during the agricultural revolution, and have since been transported and traded across the globe. Here, we present a worldwide survey on 60K genome-wide single nucleotide polymorphism (SNP) data for 2093 pigs, including 1839 domestic pigs representing 122 local and commercial breeds, 215 wild boars, and 39 out-group suids, from Asia, Europe, America, Oceania and Africa. The aim of this study was to infer global patterns in pig domestication and diversity related to demography, migration, and selection., [Results]: A deep phylogeographic division reflects the dichotomy between early domestication centers. In the core Eastern and Western domestication regions, Chinese pigs show differentiation between breeds due to geographic isolation, whereas this is less pronounced in European pigs. The inferred European origin of pigs in the Americas, Africa, and Australia reflects European expansion during the sixteenth to nineteenth centuries. Human-mediated introgression, which is due, in particular, to importing Chinese pigs into the UK during the eighteenth and nineteenth centuries, played an important role in the formation of modern pig breeds. Inbreeding levels vary markedly between populations, from almost no runs of homozygosity (ROH) in a number of Asian wild boar populations, to up to 20% of the genome covered by ROH in a number of Southern European breeds. Commercial populations show moderate ROH statistics. For domesticated pigs and wild boars in Asia and Europe, we identified highly differentiated loci that include candidate genes related to muscle and body development, central nervous system, reproduction, and energy balance, which are putatively under artificial selection., [Conclusions]: Key events related to domestication, dispersal, and mixing of pigs from different regions are reflected in the 60K SNP data, including the globalization that has recently become full circle since Chinese pig breeders in the past decades started selecting Western breeds to improve local Chinese pigs. Furthermore, signatures of ongoing and past selection, acting at different times and on different genetic backgrounds, enhance our insight in the mechanism of domestication and selection. The global diversity statistics presented here highlight concerns for maintaining agrodiversity, but also provide a necessary framework for directing genetic conservation., Peer reviewed

Proyecto: //

Dataset

A COMPREHENSIVE PHYLOGENOMIC PLATFORM FOR EXPLORING THE ANGIOSPERM TREE OF LIFE

  • Baker, William J.
  • Bailey, Paul
  • Barber, Vanessa
  • Barker, Abigail
  • Bellot, Sidonie
  • Bishop, David
  • Botigue, Laura
  • Brewer, Grace
  • Carruthers, Tom
  • Clarkson, James
  • Cook, Jeffrey
  • Cowan, Robyn
  • Dodsworth, Steven
  • Epitawalage, Niroshini
  • Françoso, Elaine
  • Gallego, Berta
  • Johnson, Matthew
  • Kim, Jan
  • Leempoel, Kevin
  • Maurin, Olivier
  • McGinnie, Catherine
  • Pokorny, Lisa
  • Roy, Shyamali
  • Stone, Malcolm
  • Toledo, Eduardo
  • Wickett, Norman
  • Zuntini, Alexandre
  • Eiserhardt, Wolf
  • Kersey, Paul
  • Leitch, Ilia
  • Forest, Félix
Software https://treeoflife.kew.org https://github.com/RBGKew/KewTreeOfLife, The tree of life is the fundamental biological roadmap for navigating the evolution and properties of life on Earth, and yet remains largely unknown. Even angiosperms (flowering plants) are fraught with data gaps, despite their critical role in sustaining terrestrial life. Today, high-throughput sequencing promises to significantly deepen our understanding of evolutionary relationships. Here, we describe a comprehensive phylogenomic platform for exploring the angiosperm tree of life, comprising a set of open tools and data based on the 353 nuclear genes targeted by the universal Angiosperms353 sequence capture probes. The primary goals of this paper are to (i) document our methods, (ii) describe our first data release and (iii) present a novel open data portal, the Kew Tree of Life Explorer (https://treeoflife.kew.org). We aim to generate novel target sequence capture data for all genera of flowering plants, exploiting natural history collections such as herbarium specimens, and augment it with mined public data. Our first data release, described here, is the most extensive nuclear phylogenomic dataset for angiosperms to date, comprising 3,099 samples validated by DNA barcode and phylogenetic tests, representing all 64 orders, 404 families (96%) and 2,333 genera (17%). A “first pass” angiosperm tree of life was inferred from the data, which totalled 824,878 sequences, 489,086,049 base pairs, and 532,260 alignment columns, for interactive presentation in the Kew Tree of Life Explorer. This species tree was generated using methods that were rigorous, yet tractable at our scale of operation. Despite limitations pertaining to taxon and gene sampling, gene recovery, models of sequence evolution and paralogy, the tree strongly supports existing taxonomy, while challenging numerous hypothesized relationships among orders and placing many genera for the first time. The validated dataset, species tree and all intermediates are openly accessible via the Kew Tree of Life Explorer and will be updated as further data become available. This major milestone towards a complete tree of life for all flowering plant species opens doors to a highly integrated future for angiosperm phylogenomics through the systematic sequencing of standardised nuclear markers. Our approach has the potential to serve as a much-needed bridge between the growing movement to sequence the genomes of all life on Earth and the vast phylogenomic potential of the world’s natural history collections., Calleva Foundation. Sackler Trust. Garfield Weston Foundation, Peer reviewed

Proyecto: //

Dataset

GENOMIC PATTERNS OF HOMOZYGOSITY AND INBREEDING DEPRESSION IN MURCIANO-GRANADINA GOATS

  • Luigi-Sierra, Maria Gracia
Genotypic data from 1,040 Murciano-Granadina female goats genotyped with the Goat SNP50 BeadChip, as well as milk production records of 817 Murciano-Granadina goats for the traits milk yield measured in kilograms at 210 days (MY210), 240 days (MY240) and 305 days (MY305), the natural logarithm of the somatic cell count divided by 1,000 (lnSCC, to convert this value into a somatic cell count please use the formula: elnSCC × 103 cells/mL), fat percentage (FP), protein percentage (PP) and lactose percentage (LP)., Peer reviewed

Proyecto: //

Dataset

FULL-FIELD NUMERICAL SIMULATIONS OF ICE VISCOPLASTIC DEFORMATION DURING TWO DEFORMATION EVENTS

  • Llorens, Maria-Gema
  • Griera, A.
  • Bons, P. D.
  • Weikusat, Ilka
  • Prior, D. J.
  • Gómez-Rivas, E.
  • de Riese, Tamara
  • Jimenez-Munt, Ivone
  • García-Castellanos, Daniel
  • Lebensohn, R. A.
This data set contains the output files with the crystal orientation of each simulation presented in the article (run using the open-source software platform ELLE; Bons et al., 2008). For the visualization of the crystallographic preferred orientation the information contained in these output files can be loaded to the software toolbox MTEX (Bachmann, F., Hielscher, R. and Schaeben, H. Grain detection from 2d and 3d EBSD data—Specification of the MTEX algorithm. Ultramicroscopy, 111(12), pp.1720-1733. 2011)., Beca Juan de la Cierva-Incorporación (IJC2018-036826-I), financiada por MCIN/AEI/10.13039/501100011033. Beca Ramón y Cajal (RYC2018-026335-I), financiada por MCIN/AEI/10.13039/501100011033 and the FSE. Beca HFG no.VH-NG-802. Proyecto GeoCAM (PGC2018-095154-B-100), financiado por el Gobierno de España., Peer reviewed


Dataset

CLARA-MED CORPUS

  • Campillos-Llanos, Leonardo
  • Terroba Reinares, Ana Rosa
  • Zakhir Puig, Sofía
  • Valverde Mateos, Ana
  • Capllonch Carrión, Adrián
A collection of 24.298 pairs of professional and simplified texts (>96 million tokens): 1) Drug leaflets and summaries of product characteristics (10 211 pairs of texts, >82M words); 2) Cancer-related information summaries (201 pairs of texts, >3M tokens); and 2) Clinical trials announcements (5748 pairs of texts, 451 690 tokens). The dataset also contains a parallel corpus with a subset of 3800 sentence pairs of professional and laymen variants (149 862 tokens). This is a benchmark for medical text simplification. The latest download of files was in February 2022., A collection of 24 298 pairs of professional and simplified texts (>96 million tokens) for automatic medical text simplification in Spanish. A parallel corpus with a subset of 3800 sentence pairs of professional and laymen variants (149 862 tokens) is released as a benchmark for medical text simplification. This dataset was collected in the CLARA-MeD project, with the goal of simplifying medical texts in the Spanish language and reducing the language barrier to patient's informed decision making. In particular, the project aims at developing linguistic resources for automatic medical term simplification in Spanish; and conducting experiments in automatic text simplification., This dataset was collected in the CLARA-MeD project (PID2020- 116001RA-C33), with funding from the Spanish government by MCIN/AEI/10.13039/501100011033/, in project call: “Proyectos I+D+i Retos Investigación”., Folders: 1) Comparable corpus: the data of each source can be found in the corresponding folder. Each folder contains two other subfolders: - source: professional, specialized texts (".src" file extension) - target: simplified texts (".trg" file extension). 2) Aligned sentences: these can be found file "aligned.tsv" (in folder "aligned"). The folder structure is as follows: - aligned/ - aligned.tsv - cima/ - source/ - target/ - eudract/ - source/ - target/ - nci/ - source/ - target/., Peer reviewed


Dataset

MEDICAL LEXICON FOR SPANISH (MEDLEXSP)

  • Campillos-Llanos, Leonardo
- MedLexSp.dsv: a delimiter-separated value file, with the following data fields: Field 1 is the UMLS CUI of the entity; field 2, the lemma; field 3, the variant forms; field 4, the part-of-speech; field 5, the semantic types(s); and field 6, the semantic group. - MedLexSp.xml: an XML-encoded version using the Lexical Markup Framework (LMF), which includes the morphological data (number, gender, verb tense and person, and information about affix/abbreviation data). The Document Type Definition file is also provided (lmf.dtd). - Lexical Record files: in subfolder "LR/": · LR_abr.dsv: list of equivalences between acronyms/abbreviations and full forms. · LR_affix.dsv: provides the equivalence between affixes/roots and their meanings. · LR_n_v.dsv: list of deverbal nouns. · LR_adj_n.dsv: list of adjectives derived from nouns. - Spacy lemmatizer (in subfolder "spacy_lemmatizer/"): lemmatizer.py - Stanza lemmatizer (in subfolder "stanza_lemmatizer/"): ancora-medlexsp.pt, File List: 1) MedLexSp.dsv; 2) MedLexSp.xml and lmf.dtd (Document Type Definition); 3) Lexical Record files: in subfolder "LR/": 3.1) LR_abr.dsv; 3.2) LR_affix.dsv; 3.3) LR_n_v.dsv; 3.4) LR_adj_n.dsv; 4) Spacy lemmatizer (in subfolder "spacy_lemmatizer/"): lemmatizer.py 5) Stanza lemmatizer (in subfolder "stanza_lemmatizer/"): ancora-medlexsp.pt See more information about the format below. Companion code and files can be found in the github repository: https://github.com/lcampillos/MedLexSp, MedLexSp is an unified medical lexicon for Medical Natural Language Processing in Spanish. It includes terms and inflected word forms with part-of-speech information and Unified Medical Language System (UMLS) semantic types, groups and Concept Unique Identifiers (CUIs). To create it, we used Natural Language Processing techniques and domain corpora (e.g. MedlinePlus). We also collected terms from the Dictionary of Medical Terms from the Spanish Royal Academy of Medicine, the Medical Subject Headings (MeSH), the Systematized Nomenclature of Medicine – Clinical Terms (SNOMED-CT), the Medical Dictionary for Regulatory Activities Terminology (MedDRA), the International Classification of Diseases vs 10, the Anatomical Therapeutical Classification, the National Cancer Institute (NCI) Dictionary, the Online Mendelian Inheritance in Man (OMIM) and OrphaData. Terms related to COVID-19 were assembled by applying a similarity-based approach with word embeddings trained on a large corpus. This dataset was collected during the NLPMedTerm project and the CLARA-MeD project, with the goal of creating a lexical resource for medical text processing in the Spanish language., MedLexSp is an unified medical lexicon for Medical Natural Language Processing in Spanish. It includes 100 887 lemmas, 302 543 inflected forms (conjugated verbs, and number/gender variants), and 42 958 Unified Medical Language System (UMLS) Concept Unique Identifiers (CUIs)., Spain, Latin America and United States of America (data from MedlinePlus Spanish and the Spanish version of the National Cancer Institute Dictionary of Medical Terms)., This dataset was collected in the NLPMedTerm project, funded by the European Union’s Horizon 2020 research programme under the Marie Skodowska-Curie grant agreement nº. 713366 (InterTalentum UAM), and the CLARA-MeD project (PID2020-116001RA-C33), funded by MCIN/AEI/10.13039/501100011033/, in project call: "Proyectos I+D+i Retos Investigación"., Peer reviewed


Dataset

BORDALLO – SQUALIUS CAROLITERTII (DOADRIO, 1987)

  • Perea, Silvia
Peces - Orden Cypriniformes - Familia Leuciscidae en la Enciclopedia Virtual de Vertebrados Españoles, http://www.vertebradosibericos.org/., A comprehensive review of the natural history of the northern Iberian chub Squalius carolitertii in Spain., Peer reviewed

Proyecto: //

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