Search results for "Cripto"

Proteomic profiling of Trastuzumab (Herceptin(R))-sensitive and -resistant SKBR-3 breast cancer cells.

2013

BACKGROUND: The Human Epidermal Growth Factor Receptor 2 (HER-2), overexpressed in 25-30% of breast carcinomas (BC), is the therapeutic target for trastuzumab, a recombinant humanized monoclonal antibody. The initial response to trastuzumab is often followed by drug-insensitivity within one year. Several hypotheses have been raised to explain this event, but the mechanisms behind the responses to trastuzumab are still unclear. Aim: To study the effects of short and prolonged trastuzumab treatment on the proteomic profiles of HER-2-overexpressing SKBR-3 BC cells. MATERIALS AND METHODS: Cells were treated with trastuzumab to obtain sensitive and resistant clones. The drug effects were evaluat…

QSPR/QSAR Studies of 2-Furylethylenes Using Bond-Level Quadratic Indices and Comparison with Other Computational Approaches

2017

The recently introduced, non-stochastic and stochastic quadratic indices (Marrero-Ponce <em>et al. J. Comp. Aided Mol. Des.</em> 2006, 20, 685-701) were applied to QSAR/QSPR studies of heteroatomic molecules. These novel bond-based molecular descriptors (MDs) were used for the prediction of the partition coefficient (log P), and the antibacterial activity of 34 derivatives of 2-furylethylenes. Two statistically significant QSPR models using non-stochastic and stochastic bond-based quadratic indices were obtained (R<sup>2</sup> = 0.971, s = 0.137 and R<sup>2</sup> = 0.986, s = 0.096). These models showed good stability to data variation in leave-one-out (L…

A Comparative Study of Nonlinear Machine Learning for the "In Silico" Depiction of Tyrosinase Inhibitory Activity from Molecular Structure.

2011

In the preset report, for the first time, support vector machine (SVM), artificial neural network (ANN), Baye- sian networks (BNs), k-nearest neighbor (k-NN) are applied and compared on two "in-house" datasets to describe the tyrosinase inhibitory activity from the molecular structure. The data set Data I is used for the identification of tyrosi- nase inhibitors (TIs) including 701 active and 728 inactive compounds. Data II consists of active chemicals for potency estimation of TIs. The 2D TOMOCOMD-CARDD atom-based quadratic indices are used as molecular descriptors. The de- rived models show rather encouraging results with the areas under the Receiver Operating Characteristic (AURC) curve …

Applying pattern recognition methods plus quantum and physico-chemical molecular descriptors to analyze the anabolic activity of structurally diverse…

2008

The great cost associated with the development of new anabolic-androgenic steroid (AASs) makes necessary the development of computational methods that shorten the drug discovery pipeline. Toward this end, quantum, and physicochemical molecular descriptors, plus linear discriminant analysis (LDA) were used to analyze the anabolic/androgenic activity of structurally diverse steroids and to discover novel AASs, as well as also to give a structural interpretation of their anabolic-androgenic ratio (AAR). The obtained models are able to correctly classify 91.67% (86.27%) of the AASs in the training (test) sets, respectively. The results of predictions on the 10% full-out cross-validation test al…

In Silico Prediction of Caco-2 Cell Permeability by a Classification QSAR Approach

2011

In the present study, 21 validated QSAR models that discriminate compounds with high Caco-2 permeability (Papp ≥8×10(-6)  cm/s) from those with moderate-poor permeability (Papp <8×10(-6)  cm/s) were developed on a novel large dataset of 674 compounds. 20 DRAGON descriptor families were used. The global accuracies of obtained models were ranking between 78-82 %. A general model combining all types of molecular descriptors was developed and it classified correctly 81.56 % and 83.94 % for training and test sets, respectively. An external set of 10 compounds was predicted and 80 % was correctly assessed by in vitro Caco-2 assays. The potential use of the final model was evaluated by a virtual s…

2014

Codebook is an effective image representation method. By clustering in local image descriptors, a codebook is shown to be a distinctive image feature and widely applied in object classification. In almost all existing works on codebooks, the building of the visual vocabulary follows a basic routine, that is, extracting local image descriptors and clustering with a user-designated number of clusters. The problem with this routine lies in that building a codebook for each single dataset is not efficient. In order to deal with this problem, we investigate the influence of vocabulary sizes on classification performance and vocabulary universality with the kNN classifier. Experimental results in…

iGEMS : an integrated model for identification of alternative exon usage events

2016

DNA microarrays and RNAseq are complementary methods for studying RNA molecules. Current computational methods to determine alternative exon usage (AEU) using such data require impractical visual inspection and still yield high false-positive rates. Integrated Gene and Exon Model of Splicing (iGEMS) adapts a gene-level residuals model with a gene size adjusted false discovery rate and exon-level analysis to circumvent these limitations. iGEMS was applied to two new DNA microarray datasets, including the high coverage Human Transcriptome Arrays 2.0 and performance was validated using RT-qPCR. First, AEU was studied in adipocytes treated with (n = 9) or without (n = 8) the anti-diabetes drug,…

Comprehensive dataset of shotgun metagenomes from oxygen stratified freshwater lakes and ponds

2021

Stratified lakes and ponds featuring steep oxygen gradients are significant net sources of greenhouse gases and hotspots in the carbon cycle. Despite their significant biogeochemical roles, the microbial communities, especially in the oxygen depleted compartments, are poorly known. Here, we present a comprehensive dataset including 267 shotgun metagenomes from 41 stratified lakes and ponds mainly located in the boreal and subarctic regions, but also including one tropical reservoir and one temperate lake. For most lakes and ponds, the data includes a vertical sample set spanning from the oxic surface to the anoxic bottom layer. The majority of the samples were collected during the open wate…

Effects of postharvest partial dehydration and prolonged treatments with ethylene on transcript profiling in skins of wine grape berries.

2010

For certain food products, postharvest controlled stresses or treatments with specific elicitors are applied to induce desired physical/chemical changes and/or to positively affect phytochemical content. This is the case of wine grapes where both strategies, singularly applied or coupled, can be used to modulate berry composition and, as a consequence, affect wine quality traits. Since the knowledge of the effects of these postharvest treatments on berry metabolism and the regulation of gene expression is very limited, a large-scale transcriptome analysis has been carried out, using an oligo-based microarray (14,562 probes) on skins of wine grape (Vitis vinifera L.) berries subjected to deh…

RNACache: Fast Mapping of RNA-Seq Reads to Transcriptomes Using MinHashing

2021

The alignment of reads to a transcriptome is an important initial step in a variety of bioinformatics RNA-seq pipelines. As traditional alignment-based tools suffer from high runtimes, alternative, alignment-free methods have recently gained increasing importance. We present a novel approach to the detection of local similarities between transcriptomes and RNA-seq reads based on context-aware minhashing. We introduce RNACache, a three-step processing pipeline consisting of minhashing of k-mers, match-based (online) filtering, and coverage-based filtering in order to identify truly expressed transcript isoforms. Our performance evaluation shows that RNACache produces transcriptomic mappings …