112,707 research outputs found
The prediction of organelle-targeting peptides in eukaryotic proteins with Grammatical-Restrained Hidden Conditional Random Fields.
No full textMOTIVATION:
Targeting peptides are the most important signal controlling the import of nuclear encoded proteins into mitochondria and plastids. In the lack of experimental information, their prediction is an essential step when proteomes are annotated for inferring both the localization and the sequence of mature proteins.
RESULTS:
We developed TPpred a new predictor of organelle-targeting peptides based on Grammatical-Restrained Hidden Conditional Random Fields. TPpred is trained on a non-redundant dataset of proteins where the presence of a target peptide was experimentally validated, comprising 297 sequences. When tested on the 297 positive and some other 8010 negative examples, TPpred outperformed available methods in both accuracy and Matthews correlation index (96% and 0.58, respectively). Given its very low-false-positive rate (3.0%), TPpred is, therefore, well suited for large-scale analyses at the proteome level. We predicted that from ∼4 to 9% of the sequences of human, Arabidopsis thaliana and yeast proteomes contain targeting peptides and are, therefore, likely to be localized in mitochondria and plastids. TPpred predictions correlate to a good extent with the experimental annotation of the subcellular localization, when available. TPpred was also trained and tested to predict the cleavage site of the organelle-targeting peptide: on this task, the average error of TPpred on mitochondrial and plastidic proteins is 7 and 15 residues, respectively. This value is lower than the error reported by other methods currently available.
AVAILABILITY:
The TPpred datasets are available at http://biocomp.unibo.it/valentina/TPpred/. TPpred is available on request from the authors
The murals of Estrada Courts. Leopard crouching in a tree, Los Angeles, 1975
No full textThe murals of Estrada Courts. Leopard crouching in a tree, Los Angeles, 1975, 3281 East Olympic Boulevard (walkway). In acrylic on stucco, 32' x 24' by Indio and V. Cholo -- Dunitz, Street gallery, p. 298, #28 T. "The murals were produced by a number of Chicano artists from Los Angeles, San Diego, and Northern California between 1972 and 1978, during the height of the Chicano civil rights and art movements" -- Estrada Courts at http://www.heritagepreservation.org/RPM/archive.html (viewed on Dec. 2, 2012)
author-bios-SRD-19-0063.R1 – Supplemental material for The Network Structure of Police Misconduct
No full textSupplemental material, author-bios-SRD-19-0063.R1 for The Network Structure of Police Misconduct by George Wood, Daria Roithmayr and Andrew V. Papachristos in Socius</p
Al indio constitucional, un ciudadano español intimo suyo
No full textResponse to 'El indio constitucional', which urges indigenous populations and Creoles alike to support the Spanish Constitution and its attendant freedoms from tyranny, with a focus on the points raised by 'El indio constitucional', in particular the liberty of the press, openness in political debates, and restraint when dealing with questions of religion and morality. See also 9770.bb.3.(54.
MemPype: a pipeline for the annotation of eukaryotic membrane proteins
No full textMemPype is a Python-based pipeline including previously published methods for the prediction of signal peptides (SPEP), glycophosphatidylinositol (GPI) anchors (PredGPI), all-alpha membrane topology (ENSEMBLE), and a recent method (MemLoci) that specifically discriminates the localization of eukaryotic membrane proteins in: 'cell membrane', 'internal membranes', 'organelle membranes'. MemLoci scores with accuracy of 70% and generalized correlation coefficient (GCC) of 0.50 on a rigorous homology-unbiased validation set and overpasses other predictors for subcellular localization. The annotation process is based both on inheritance through homology and computational methods. Each submitted protein first retrieves, when available, up to 25 similar proteins (with sequence identity ≥50% and alignment coverage ≥50% on both sequences). This helps the identification of membrane-associated proteins and detailed localization tags. Each protein is also filtered for the presence of a GPI anchor [0.8% false positive rate (FPR)]. A positive score of GPI anchor prediction labels the sequence as exposed to 'Cell surface'. Concomitantly the sequence is analysed for the presence of a signal peptide and classified with MemLoci into one of three discriminated classes. Finally the sequence is filtered for predicting its putative all-alpha protein membrane topology (FPR <1%). The web server is available at: http://mu2py.biocomp.unibo.it/mempype
The Identity of PDGFRA D842V-Mutant Gastrointestinal Stromal Tumors (GIST)
No full textThe majority of gastrointestinal stromal tumors (GIST) carry a sensitive primary KIT mutation, but approximately 5% to 10% of cases harbor activating mutations of platelet-derived growth factor receptor (PDGFRA), mainly involving the A-loop encoded by exon 18 (~5%), or more rarely the JM domain, encoded by exon 12 (~1%), or the ATP binding domain encoded by exon 14 (<1%). The most frequent mutation is the substitution at position 842 in the A-loop of an aspartic acid (D) with a valine (V) in exon 18, widely recognized as D842V. This mutation, as well known, provides primary resistance to imatinib and sunitinib. Thus, until few years ago, no active drugs were available for this subtype of GIST. Conversely, recent years have witnessed the development of a new specific inhibitor—avapritinib—that has been studied in in vitro and clinical setting with promising results. In light of this primary resistance to conventional therapies, the biological background of D842V-mutant GIST has been deeply investigated to better understand what features characterize this peculiar subset of GIST, and some promising insights have emerged. Hereinafter, we present a comprehensive overview on the clinical features and the molecular background of this rare subtype of GIST
Going Beyond Counting First Authors in Author Co-citation Analysis
No full textThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
V. Lombardo Toledano, El problema del indio. Selección de textos de Marcela Lombardo, con una introducción de G. Aguirre Beltrán
No full textDehouve Danièle. V. Lombardo Toledano, El problema del indio. Selección de textos de Marcela Lombardo, con una introducción de G. Aguirre Beltrán. In: L'Homme, 1976, tome 16 n°1. pp. 168-169
V. Lombardo Toledano, El problema del indio. Selección de textos de Marcela Lombardo, con una introducción de G. Aguirre Beltrán
No full textDehouve Danièle. V. Lombardo Toledano, El problema del indio. Selección de textos de Marcela Lombardo, con una introducción de G. Aguirre Beltrán. In: L'Homme, 1976, tome 16 n°1. pp. 168-169
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