Search results for "Detection"
showing 10 items of 2543 documents
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…
Quantitative patterns of Hsps in tubular adenoma compared with normal and tumor tissues reveal the value of Hsp10 and Hsp60 in early diagnosis of lar…
2016
Large bowel carcinogenesis involves accumulation of genetic alterations leading to transformation of normal mucosa into dysplasia and, lastly, adenocarcinoma. It is pertinent to elucidate the molecular changes occurring in the pre-neoplastic lesions to facilitate early diagnosis and treatment. Heat shock proteins (Hsps), many of which are molecular chaperones, are implicated in carcinogenesis, and their variations with tumor progression encourage their study as biomarkers. There are many reports on Hsps and cancer but none to our knowledge on their systematic quantification in pre-neoplastic lesions of the large bowel. We performed immunohistochemical determinations of Hsp10, Hsp60, Hsp70, …
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…
Mineral Profile of Children’s Fast Food Menu Samples
2017
Abstract Children’s fast food menus, including hamburgers served with french fries, dessert, and a soft drink, were analyzed to obtain the mineral profile of trace elements. The developed analytical methodology involved sample digestion under pressure inside a microwave oven with a mixture of HNO3 and H2O2 and inductively coupled plasma-optical emission spectrometry. The method was validated by carrying out the analysis of certified reference materials (NIST 1570a spinach leaves, NCS ZC73016 chicken, and NIST 1568a rice flour) and using recovery experiments. Repeatability was verified by analyzing replicate samples. Twenty-six elements were studied, 12 of which—aluminum, barium, calcium, co…
Cholesterol Content in Human Milk during Lactation: A Comparative Study of Enzymatic and Chromatographic Methods.
2018
This study validates a gas chromatography (GC) method for determining the sterol profile of human milk (HM) and compares it with an enzymatic-spectrophotometric (E-S) method. Good linearity ( r > 0.97) and low limits of detection and quantification were obtained with the GC method (<1.8 and <6 μg/100 g of HM, respectively). Suitable intra- and interassay precisions (all <18%) and satisfactory recovery percentages (80-109%) were obtained for both methods. In addition, both methodologies were used to assess cholesterol evolution in HM during lactation, showing a 50% decrease at 6 months versus colostrum. The E-S method overestimated cholesterol content by <20% versus the GC method. The result…
Reliable determination of new lipid peroxidation compounds as potential early Alzheimer Disease biomarkers.
2018
Lipid peroxidation plays an important role in Alzheimer Disease, so corresponding metabolites found in urine samples could be potential biomarkers. The aim of this work is to develop a reliable ultra-performance liquid chromatography-tandem mass spectrometry analytical method to determine a new set of lipid peroxidation compounds in urine samples. Excellent sensitivity was achieved with limits of detection between 0.08 and 17 nmol L-1, which renders this method suitable to monitor analytes concentrations in real samples. The method's precision was satisfactory with coefficients of variation around 5-17% (infra-day) and 8-19% (inter-day). The accuracy of the method was assessed by analysis o…
Deep learning in next-generation sequencing
2020
Highlights • Machine learning increasingly important for NGS. • Deep learning can improve many NGS applications.
Prospective Image Quality and Lesion Assessment in the Setting of MR-Guided Radiation Therapy of Prostate Cancer on an MR-Linac at 1.5 T: A Compariso…
2021
The objective of this study is to conduct a qualitative and a quantitative image quality and lesion evaluation in patients undergoing MR-guided radiation therapy (MRgRT) for prostate cancer on a hybrid magnetic resonance imaging and linear accelerator system (MR-Linac or MRL) at 1.5 Tesla. This prospective study was approved by the institutional review board. A total of 13 consecutive patients with biopsy-confirmed prostate cancer and an indication for MRgRT were included. Prior to radiation therapy, each patient underwent an MR-examination on an MRL and on a standard MRI scanner at 3 Tesla (MRI3T). Three readers (two radiologists and a radiation oncologist) conducted an independent qualita…
Determination of meropenem in endotracheal tubes by in-tube solid phase microextraction coupled to capillary liquid chromatography with diode array d…
2017
Meropenem is a widely used antimicrobial for the treatment of infections associated with the use of invasive medical devices in intensive care unit patients. These treatments are not always effective, in fact, in-vitro studies have demonstrated the difficulty of antimicrobials to penetrate into the biofilm, however in-vivo studies of the effect of these compounds is a trend, mostly because of the complexity of pulmonary samples extracted from ETTs. Therefore, the objective of this study was to evaluate in-tube solid phase microextraction (in-tube SPME) coupled to capillary liquid chromatography (CapLC) with DAD to determine meropenem in Errs in order to estimate the penetration capability i…
Sterols in infant formulas: validation of a gas chromatographic method.
2017
AbstractSterols are components present in the fat fraction of infant formulas (IFs). Their characterization is therefore of interest, though there are no official reference methods for their analysis in these matrices.Aim: To validate a gas chromatographic method with flame ionization detection for the determination of animal (cholesterol and desmosterol) and plant sterols (brassicasterol, campesterol, stigmasterol, β-sitosterol and sitostanol) found in IFs.All correlation coefficients obtained for the calibration curves of sterols studied were >0.99. Limits of detection (<1 μg/100 mL) and quantification (<4 μg/100 mL) are suitable for sterols determination in IFs. The within-assay precisio…