Search results for "ROUGH"
showing 10 items of 1198 documents
Surface Characteristics of Machined Polystyrene with 3D Printed Thermoplastic Tool
2020
An effort is made in this work to appraise the surface characteristics of machined expandable polystyrene (EPS) with a novel 3D printed thermoplastic acrylonitrile-butadiene-styrene (ABS) tool. Linear grooves on EPS were made on a vertical milling machine that was modified to conduct experiments in the laboratory. The tests were designed as per the Taguchi L9 based factorial design of experimentation while varying process parameters such as depth of cut, spindle speed, and feed rate. The machining responses dimensional accuracy and surface roughness of the machined grooves were studied. Furthermore, the surface topography of the machined specimens was considered to investigate the mechanism…
Rough Set Theory for Optimization of Packet Management Mechanism in IP Routers
2020
Bandwidth and consequently optimum overall efficiency of network system relies greatly on mechanism of packet management in IP routers. Our research objective is to implement rough set theory to minimizing number of the network system attributes responsible for decision making in selection of those packets, which improve its transmission. Such an approach is called priority queuing system model, as we assign priority to the packets selected, following rough set theory. Regardless of the file format, for all the routers, packets are transmitted in sequence one-by-one. Nonetheless, quality of streaming data largely depends on how much the packet loss is minimized, or eliminated at all, if pos…
SPECTR
2018
Modern high throughput sequencing platforms can produce large amounts of short read DNA data at low cost. Error correction is an important but time-consuming initial step when processing this data in order to improve the quality of downstream analyses. In this paper, we present a Scalable Parallel Error CorrecToR designed to improve the throughput of DNA error correction for Illumina reads on various parallel platforms. Our design is based on a k-spectrum approach where a Bloom filter is frequently probed as a key operation and is optimized towards AVX-512-based multi-core CPUs, Xeon Phi many-cores (both KNC and KNL), and heterogeneous compute clusters. A number of architecture-specific opt…
Next‐Generation Sequencing‐Based RiboMethSeq Protocol for Analysis of tRNA 2′‐O‐Methylation
2017
Analysis of RNA modifications by traditional physico‐chemical approaches is labor intensive, requires substantial amounts of input material and only allows site‐by‐site measurements. The recent development of qualitative and quantitative approaches based on next‐generation sequencing (NGS) opens new perspectives for the analysis of various cellular RNA species. The Illumina sequencing‐based RiboMethSeq protocol was initially developed and successfully applied for mapping of ribosomal RNA (rRNA) 2′‐O‐methylations. This method also gives excellent results in the quantitative analysis of rRNA modifications in different species and under varying growth condi…
Computational processing and quality control of Hi-C, capture Hi-C and capture-C data
2019
Hi-C, capture Hi-C (CHC) and Capture-C have contributed greatly to our present understanding of the three-dimensional organization of genomes in the context of transcriptional regulation by characterizing the roles of topological associated domains, enhancer promoter loops and other three-dimensional genomic interactions. The analysis is based on counts of chimeric read pairs that map to interacting regions of the genome. However, the processing and quality control presents a number of unique challenges. We review here the experimental and computational foundations and explain how the characteristics of restriction digests, sonication fragments and read pairs can be exploited to distinguish…
High-throughput sequencing for 1-methyladenosine (m1A) mapping in RNA
2016
Abstract Detection and mapping of modified nucleotides in RNAs is a difficult and laborious task. Several physico-chemical approaches based on differential properties of modified nucleotides can be used, however, most of these methods do not allow high-throughput analysis. Here we describe in details a method for mapping of rather common 1-methyladenosine (m1A) residues using high-throughput next generation sequencing (NGS). Since m1A residues block primer extension during reverse transcription (RT), the accumulation of abortive products as well as the nucleotide misincorporation can be detected in the sequencing data. The described library preparation protocol allows to capture both types …
Engineering of a DNA Polymerase for Direct m6A Sequencing
2017
Methods for the detection of RNA modifications are of fundamental importance for advancing epitranscriptomics. N6-methyladenosine (m6A) is the most abundant RNA modification in mammalian mRNA and is involved in the regulation of gene expression. Current detection techniques are laborious and rely on antibody-based enrichment of m6A-containing RNA prior to sequencing, since m6A modifications are generally "erased" during reverse transcription (RT). To overcome the drawbacks associated with indirect detection, we aimed to generate novel DNA polymerase variants for direct m6A sequencing. Therefore, we developed a screen to evolve an RT-active KlenTaq DNA polymerase variant that sets a mark for…
Genome-Wide Estimation of the Spontaneous Mutation Rate of Human Adenovirus 5 by High-Fidelity Deep Sequencing
2016
Rates of spontaneous mutation determine the ability of viruses to evolve, infect new hosts, evade immunity and undergo drug resistance. Contrarily to RNA viruses, few mutation rate estimates have been obtained for DNA viruses, because their high replication fidelity implies that new mutations typically fall below the detection limits of Sanger and standard next-generation sequencing. Here, we have used a recently developed high-fidelity deep sequencing technique (Duplex Sequencing) to score spontaneous mutations in human adenovirus 5 under conditions of minimal selection. Based on >200 single-base spontaneous mutations detected throughout the entire viral genome, we infer an average mutatio…
Dynamic clonal remodelling in breast cancer metastases is associated with subtype conversion
2019
Background: Changes in the clinical subtype (CS) and intrinsic subtype (IS) between breast cancer (BC) metastases and corresponding primary tumours have been reported. However, their relationship with tumour genomic changes remains poorly characterised. Here, we analysed the association between genomic remodelling and subtype conversion in paired primary and metastatic BC samples. Methods: A total of 57 paired primary and metastatic tumours from GEICAM/2009-03 (ConvertHER, NCT01377363) study participants with centrally assessed CS (n = 57) and IS (n = 46) were analysed. Targeted capture and next-generation sequencing of 202 genes on formalin-fixed paraffin-embedded samples was performed. Th…
Molecular diagnosis of PIK3CA-related overgrowth spectrum (PROS) in 162 patients and recommendations for genetic testing.
2017
Postzygotic activating mutations of PIK3CA cause a wide range of mosaic disorders collectively referred to as PIK3CA-related overgrowth spectrum (PROS). We describe the diagnostic yield and characteristics of PIK3CA sequencing in PROS. We performed ultradeep next-generation sequencing (NGS) of PIK3CA in various tissues from 162 patients referred to our clinical laboratory and assessed diagnostic yield by phenotype and tissue tested. We identified disease-causing mutations in 66.7% (108/162) of patients, with mutant allele levels as low as 1%. The diagnostic rate was higher (74%) in syndromic than in isolated cases (35.5%; P = 9.03 × 10−5). We identified 40 different mutations and found stro…