Search results for " generation"
showing 10 items of 1135 documents
KRAS mutations testing in non-small cell lung cancer: the role of Liquid biopsy in the basal setting
2020
In advanced stage non-small cell lung cancer (NSCLC) patients, Kirsten Rat Sarcoma Viral Oncogene Homolog (KRAS) testing may soon acquire a predictive significance to select patients for AMG510 treatment. Since tissue samples are not always available, liquid biopsy may represent a viable option for KRAS testing. Here, we review the last three years clinical practice performed on 194 plasma based liquid biopsies by next generation sequencing (NGS) SiRe(®) panel. In particular, 36 (18.6%) KRAS mutated cases were identified, with an overall median allelic frequency of 5.0% (ranging between 0.2% and 46.8%). No concomitant mutations were observed in the other NSCLC clinical relevant genes includ…
Whole genome semiconductor based sequencing of farmed European sea bass (Dicentrarchus labrax) Mediterranean genetic stocks using a DNA pooling appro…
2016
European sea bass (Dicentrarchus labrax) is an important marine species for commercial and sport fisheries and aquaculture production. Recently, the European sea bass genome has been sequenced and assembled. This resource can open new opportunities to evaluate and monitor variability and identify variants that could contribute to the adaptation to farming conditions. In this work, two DNA pools constructed from cultivated European sea bass were sequenced using a next generation semiconductor sequencing approach based on Ion Proton sequencer. Using the first draft version of the D. labrax genome as reference, sequenced reads obtained a total of about 1.6 million of single nucleotide polymorp…
Functional analyses of a novel splice variant in the CHD7 gene, found by next generation sequencing, Confirm Its pathogenicity in a Spanish patient a…
2018
Mutations in CHD7 have been shown to be a major cause of CHARGE syndrome, which presents many symptoms and features common to other syndromes making its diagnosis difficult. Next generation sequencing (NGS) of a panel of intellectual disability related genes was performed in an adult patient without molecular diagnosis. A splice donor variant in CHD7 (c.5665 + 1G > T) was identified. To study its potential pathogenicity, exons and flanking intronic sequences were amplified from patient DNA and cloned into the pSAD® splicing vector. HeLa cells were transfected with this construct and a wild-type minigene and functional analysis were performed. The construct with the c.5665 + 1G > T variant p…
Methods for RNA Modification Mapping Using Deep Sequencing: Established and New Emerging Technologies
2019
New analytics of post-transcriptional RNA modifications have paved the way for a tremendous upswing of the biological and biomedical research in this field. This especially applies to methods that included RNA-Seq techniques, and which typically result in what is termed global scale modification mapping. In this process, positions inside a cell`s transcriptome are receiving a status of potential modification sites (so called modification calling), typically based on a score of some kind that issues from the particular method applied. The resulting data are thought to represent information that goes beyond what is contained in typical transcriptome data, and hence the field has taken to use …
FROM EPIGENETICS TO ANTI-DOPING APPLICATION: A NEW TOOL OF DETECTION
2017
Eukaryotic genomes transcribe up to 90% of the genomic DNA but only 1–2% of these transcripts encode for proteins, whereas the vast majority are transcribed as non-coding RNAs (ncRNAs). They are divided into short ncRNA, particularly microRNA (miRNA) and small interference RNA (siRNA), and long ncRNAs. Noteworthy, they are unexpectedly stable since they are protected from degradation through different mechanisms: package in exosomes/microvesicles structures, in apoptotic bodies, in HDL lipoprotein, or by RNA binding proteins. For several years already, biomarkers have been used to detect biological disease; in the last years, a requirement appeared to find some of them to unearth the signs …
Tumor Heterogeneity, Single-Cell Sequencing, and Drug Resistance
2016
Tumor heterogeneity has been compared with Darwinian evolution and survival of the fittest. The evolutionary ecosystem of tumors consisting of heterogeneous tumor cell populations represents a considerable challenge to tumor therapy, since all genetically and phenotypically different subpopulations have to be efficiently killed by therapy. Otherwise, even small surviving subpopulations may cause repopulation and refractory tumors. Single-cell sequencing allows for a better understanding of the genomic principles of tumor heterogeneity and represents the basis for more successful tumor treatments. The isolation and sequencing of single tumor cells still represents a considerable technical ch…
Do shifts in life strategies explain microbial community responses to increasing nitrogen in tundra soil?
2016
Subarctic tundra soils store large quantities of the global organic carbon (C) pool as the decomposition of plant litter and soil organic matter is limited by low temperatures and limiting nutrients. Mechanisms that drive organic matter decomposition are still poorly understood due to our limited knowledge of microbial communities and their responses to changing conditions. In subarctic tundra large grazers, in particular reindeer, exert a strong effect on vegetation and nutrient availability causing drastic nutrient pulses in the soils located along the migratory routes. Here we studied the effect of increased nitrogen (N) availability on microbial community structure and activities by lab…
Generating Executable Code from High-Level Social or Socio-Ecological Model Descriptions
2019
Agent-Based Modelling has been used for social simulation because of the several benefits it entails. Social models are often constructed by inter-disciplinary teams that include subject-matter experts with no programming skills. These experts are typically involved in the creation of the conceptual model, but not the verification or validation of the simulation model. The Overview, Design concepts, and Details (ODD) protocol has emerged as a way of presenting a model at a high level of abstraction and as an effort towards improving the reproducibility of Agent-Based Models (ABMs) but it is typically written after a model has been completed. This paper reverses the process and provides non-…
Recycling a genre for news automation: The production of Valtteri the Election Bot
2020
Abstract The amount of available digital data is increasing at a tremendous rate. These data, however, are of limited use unless converted into a user-friendly form. We took on this task and built a natural language generation (NLG) driven system that generates journalistic news stories about elections without human intervention. In this paper, after presenting an overview of state-of-the-art technologies in NLG, we explain systematically how we identified and then recontextualized the determinant aspects of the genre of an online news story in the algorithm of our NLG software. In the discussion, we introduce the key results of a user test we carried out and some improvements that these re…
Contributions to Branch-and-Price-and-Cut Algorithms for Routing Problems
2019
This article deals with new exact branch-and-price-and-cut algorithms for the solution of routing problems. Specialized methods for the pickup-and-delivery problem (PDP), the truck-and-trailer routing problem (TTRP), the periodic vehicle routing problem (PVRP) and a service network design and hub location problem (SNDHLP) are presented. We develop a new technique for the acceleration of bidirectional labeling algorithms by a dynamic choice of the merge point. Moreover, for variants of the PDP, the bidirectional labeling can be effectively applied for the first time. In the TTRP, we model the extension to a 2 days planning horizon and the consideration of a quantity-dependent transfer time. …