Search results for "Trim"
showing 10 items of 1942 documents
Loop diuretics decrease the renal elimination rate and increase the plasma levels of trimethylamine‐N‐oxide
2018
Aims Trimethylamine-N-oxide (TMAO) is a novel cardiovascular risk marker. We explored the association of commonly used cardiovascular medications with TMAO levels in patients and validated the identified associations in mice. Methods Detailed history of drug treatment was recorded in 300 patients with cardiovascular disease without diabetes in an observational, cross-sectional study. Animal study was performed in CD1 mice. Results Median plasma TMAO (interquartile range) level was 2.144 (1.570-3.104) μmol l-1 . Among nine cardiovascular drug groups, the use of loop diuretics (0.510 ± 0.296 in users vs. 0.336 ± 0.272 in nonusers, P = 0.008) and mineralocorticoid receptor antagonists (0.482 ±…
A practical method for barcoding and size-trimming PCR templates for amplicon sequencing
2016
Sample barcoding facilitates the analysis of tens or even hundreds of samples in a single next-generation sequencing (NGS) run, but more efficient methods are needed for high-throughput barcoding and size-trimming of long PCR products. Here we present a two-step PCR approach for barcoding followed by pool shearing, adapter ligation, and 5′ end selection for trimming sets of DNA templates of any size. Our new trimming method offers clear benefits for phylogenetic studies, since targeting exactly the same region maximizes the alignment and enables the use of operational taxonomic unit (OTU)-based algorithms.
CntA oxygenase substrate profile comparison and oxygen dependency of TMA production in Providencia rettgeri.
2017
CntA oxygenase is a Rieske 2S-2Fe cluster-containing protein that has been previously described as able to produce trimethylamine (TMA) from carnitine, gamma-butyrobetaine, glycine betaine, and in one case, choline. TMA found in humans is exclusively of bacterial origin, and its metabolite, trimethylamine oxide (TMAO), has been associated with atherosclerosis and heart and renal failure. We isolated four different Rieske oxygenases and determined that there are no significant differences in their substrate panels. All three had high activity toward carnitine/gamma-butyrobetaine, medium activity toward glycine betaine, and very low activity toward choline. We tested the influence of low oxyg…
Microbiota-Derived Trimethylamine
2018
Associating HIV-1 envelope glycoprotein structures with states on the virus observed by smFRET
2019
The HIV-1 envelope glycoprotein (Env) trimer mediates cell entry and is conformationally dynamic1-8. Imaging by single-molecule fluorescence resonance energy transfer (smFRET) has revealed that, on the surface of intact virions, mature pre-fusion Env transitions from a pre-triggered conformation (state 1) through a default intermediate conformation (state 2) to a conformation in which it is bound to three CD4 receptor molecules (state 3)8-10. It is currently unclear how these states relate to known structures. Breakthroughs in the structural characterization of the HIV-1 Env trimer have previously been achieved by generating soluble and proteolytically cleaved trimers of gp140 Env that are …
Graphical Workflow System for Modification Calling by Machine Learning of Reverse Transcription Signatures
2019
Modification mapping from cDNA data has become a tremendously important approach in epitranscriptomics. So-called reverse transcription signatures in cDNA contain information on the position and nature of their causative RNA modifications. Data mining of, e.g. Illumina-based high-throughput sequencing data, is therefore fast growing in importance, and the field is still lacking effective tools. Here we present a versatile user-friendly graphical workflow system for modification calling based on machine learning. The workflow commences with a principal module for trimming, mapping, and postprocessing. The latter includes a quantification of mismatch and arrest rates with single-nucleotide re…
Automatic detection and measurement of nuchal translucency.
2017
In this paper we propose a new methodology to support the physician both to identify automatically the nuchal region and to obtain a correct thickness measurement of the nuchal translucency. The thickness of the nuchal translucency is one of the main markers for screening of chromosomal defects such as trisomy 13, 18 and 21. Its measurement is performed during ultrasound scanning in the first trimester of pregnancy. The proposed methodology is mainly based on wavelet and multi resolution analysis. The performance of our method was analysed on 382 random frames, representing mid-sagittal sections, uniformly extracted from real clinical ultrasound videos of 12 patients. According to the groun…
CCDC 2211279: Experimental Crystal Structure Determination
2023
Related Article: Anssi Peuronen, Anni Taponen, Elina Kalenius, Ari Lehtonen, Manu Lahtinen|2023|Angew.Chem.,Int.Ed.|62|e202215689|doi:10.1002/anie.202215689
CCDC 2057072: Experimental Crystal Structure Determination
2021
Related Article: Maciej Bujak, Hans-Georg Stammler, Yury V. Vishnevskiy, Norbert W. Mitzel|2022|CrystEngComm|24|70|doi:10.1039/D1CE01268A
CCDC 2057071: Experimental Crystal Structure Determination
2021
Related Article: Maciej Bujak, Hans-Georg Stammler, Yury V. Vishnevskiy, Norbert W. Mitzel|2022|CrystEngComm|24|70|doi:10.1039/D1CE01268A