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Metagenetics is a rapid and taxonomically comprehensive method for revealing community structures within environmental samples, based on large amounts of sequence data produced by high-throughput sequencers. Because community structures of planktonic copepods are important in the ocean owing to their high diversity and abundance, a metagenetic analysis of the 28S D2 region using Roche 454 was previously developed. However, the Illumina MiSeq platform with a high sequence output is being used more frequently...
Comparison between Roche and Xpert in HIV-1 RNA quantitation: A high concordance between the two techniques except for a CRF02_AG subtype variant with high viral load titters detected by Roche but undetected by Xpert.
HIV-1 viral load (VL) testing is important to predict viral progression and to monitor the response to antiretroviral therapy. New HIV-1 VL tests are continuously introduced to the market. Their performance is usually compared to Abbott and/or Roche HIV-1 VL assays, as reference. The Xpert HIV-1 VL test was recently introduced, but its performance compared to Roche has not been sufficiently studied.
High-throughput sequencing methods have become a routine analysis tool in environmental sciences as well as in public and private sector. These methods provide vast amount of data, which need to be analyzed in several steps. Although the bioinformatics may be applied using several public tools, many analytical pipelines allow too few options for the optimal analysis for more complicated or customized designs. Here, we introduce PipeCraft, a flexible and handy bioinformatics pipeline with a user friendly gra...
Illumina genotyping arrays have powered thousands of large-scale genome-wide association studies over the past decade. Yet, because of the tremendous volume and complicated genetic assumptions of Illumina genotyping data, processing and quality control (QC) of these data remain a challenge. Thorough QC ensures the accurate identification of single-nucleotide polymorphisms and is required for the correct interpretation of genetic association results. By processing genotyping data on > 100 000 subjects f...
After the introduction of high-throughput sequencing, genotyping arrays continue to be a viable source for conducting large-scale genetic studies. Currently, Illumina is one of the largest genotyping array manufacturers. One technical issue that has always plagued the post-processing of Illumina genotyping array data is the strand definition. Against convention, Illumina uses their own definition of strand, which is inconsistent with the standard reference forward and reverse definition. This issue has been...
A review of practical resources, including mnemonics, to aid in prevention and identification.
Pressure ulcers cause suffering to patients and costs to society. Reducing pressure at the interface between the patient's body and the support surface is a valid clinical intervention for reducing the risk of pressure ulcers. However, studies have shown that knowledge of how to reduce pressure and shear and to prevent pressure ulcers is lacking.
PIGSpro is a significant upgrade of the popular PIGS server for the prediction of the structure of immunoglobulins. The software has been completely rewritten in python following a similar pipeline as in the original method, but including, at various steps, relevant modifications found to improve its prediction accuracy, as demonstrated here. The steps of the pipeline include the selection of the appropriate framework for predicting the conserved regions of the molecule by homology; the target template alig...
The improvement in sensitive techniques has allowed the detection of tumor-specific aberrations in circulating tumor (ct) DNA. Amplification-refractory mutation system PCR has been used for the analysis of ctDNA to detect resistance-causing mutations in the epidermal growth factor receptor gene (eg, EGFR T790M) in lung cancer patients. So far, Streck tubes have been widely used as standard blood collection tubes. Here, we compared blood collection tubes manufactured by Streck with tubes from Roche and Qiage...
In recent years great emphasis has been placed on the role of central aortic blood pressure as measured non invasively using pulse wave analysis in pathophysiology of cardiovascular diseases and clinical aspects of hypertension. The difference of blood pressure between the central aorta and the brachial artery (amplification) is not constant but varies according to physiological, pathological and pharmacological mechanisms. Central aortic blood pressure is more strongly related to cardiovascular organ damag...
A numerical framework for interstitial fluid pressure imaging (IFPI) in biphasic materials is investigated based on three-dimensional nonlinear finite element poroelastic inversion. The objective is to reconstruct the time-harmonic pore-pressure field from tissue excitation in addition to the elastic parameters commonly associated with magnetic resonance elastography (MRE). The unknown pressure boundary conditions (PBCs) are estimated using the available full-volume displacement data from MRE. A subzone-bas...
In severe traumatic brain injury, cerebral perfusion pressure management based on cerebrovascular pressure reactivity index has the potential to provide a personalized treatment target to improve patient outcomes. So far, the methods have focused on identifying "one" autoregulation-guided cerebral perfusion pressure target-called "cerebral perfusion pressure optimal". We investigated whether a cerebral perfusion pressure autoregulation range-which uses a continuous estimation of the "lower" and "upper" cere...
We performed exome-wide association studies to identify genetic variants that influence systolic or diastolic blood pressure or confer susceptibility to hypertension in Japanese. The exome-wide association studies were performed with the use of Illumina HumanExome-12 DNA Analysis BeadChip or Infinium Exome-24 BeadChip arrays and with 14,678 subjects, including 8215 individuals with hypertension and 6463 controls. The relation of genotypes of 41,843 single nucleotide polymorphisms to systolic or diastolic bl...
Pressure ulcers may develop in different locations. Vulvar pressure ulcers can be easily misdiagnosed and, moreover, have been rarely reported in the literature. Surgical procedures that involve prolonged pressure on this area may trigger these lesions.
The pressure study was carried out to evaluate the hypotheses that ambulatory blood pressure (ABP) is superior to clinic blood pressure for ischemic stroke and that ABP is important to refine risk stratification.
The rupture of a high-pressure natural gas pipeline can pose a serious threat to human life and environment. In this research, a method has been proposed to simulate the release of natural gas from the rupture of high-pressure pipelines in any terrain. The process of gas releases from the rupture of a high-pressure pipeline is divided into three stages, namely the discharge, jet, and dispersion stages. Firstly, a discharge model is established to calculate the release rate of the orifice. Secondly, an impro...
Molecular dynamics simulations for the system of ubiquitin were performed with pressure simulated tempering to study pressure-induced conformational changes of ubiquitin. The pressure dependence of ubiquitin was analyzed in a wide range of pressure from atmospheric pressure (0.1 MPa) to 1.0 GPa. The fluctuation of the distance between amino-acid residues and the distribution of a largely fluctuating distance were calculated. The large fluctuation of the L8-E34 distance induced by pressure means that the con...
Several lines of evidence suggest that the pathogenesis of glaucoma may depend on an increased translaminar pressure gradient (TPG), the difference between intraocular and intracranial pressure (ICP), rather than on intraocular pressure (IOP) itself. It has also been suggested that high blood pressure might correlate with the incidence of glaucoma; however, the data are contradictory. Here, we studied the effect of arterial blood pressure and changes in body position on TPG in rats.