Search results for "methods [Proteomics]"

The Making of the New European Wind Atlas - Part 2: production and evaluation

2020

This is the second of two papers that document the creation of the New European Wind Atlas (NEWA). In Part 1, we described the sensitivity experiments and accompanying evaluation done to arrive at the final mesoscale model setup used to produce the mesoscale wind atlas. In this paper, Part 2, we document how we made the final wind atlas product, covering both the production of the mesoscale climatology generated with the Weather Research and Forecasting (WRF) model and the microscale climatology generated with the Wind Atlas Analysis and Applications Program (WAsP). The paper includes a detailed description of the technical and practical aspects that went into running the mesoscale simulati…

Visible implant elastomer (VIE) success in early larval stages of a tropical amphibian species

2020

AbstractAnimals are often difficult to distinguish at an individual level, but being able to identify individuals can be crucial in ecological or behavioral studies. In response to this challenge, biologists have developed a range of marking (tattoos, brands, toe-clips) and tagging (PIT, VIA, VIE) methods to identify individuals and cohorts. Animals with complex life cycles are notoriously hard to mark because of the distortion or loss of the tag across metamorphosis. In frogs, few studies have attempted larval tagging and none have been conducted on a tropical species. Here, we present the first successful account of VIE tagging in early larval stages (Gosner stage 25) of the dyeing poison…

Preparation prerequisites for effective irrigation of apical root canal : a critical review

2017

Background It is well recognized that disinfection of the complex root canal system at the apical root canal remains the most critical therapeutic measure to treat apical periodontitis. Material and Methods Observational and experimental data in relation to the anatomy of the apical root canal in different tooth types and the cross sectional diameters of the apical part of the most commonly used hand and rotary files are critically reviewed. Results The present data analysis confirm that the challenging issue of antibacterial efficacy of modern preparation protocols in non-surgical endodontics requires more attention to apical root canal irrigation as a balance between safety and effectiven…

A computational method for studying the relation between alternative splicing and DNA methylation.

2015

Alternative splicing is an important mechanism in eukaryotes that expands the transcriptome and proteome significantly. It plays an important role in a number of biological processes. Understanding its regulation is hence an important challenge. Recently, increasing evidence has been collected that supports an involvement of intragenic DNA methylation in the regulation of alternative splicing. The exact mechanisms of regulation, however, are largely unknown, and speculated to be complex: different methylation profiles might exist, each of which could be associated with a different regulation mechanism. We present a computational technique that is able to determine such stable methylation pa…

NOseq: amplicon sequencing evaluation method for RNA m6A sites after chemical deamination

2020

Abstract Methods for the detection of m6A by RNA-Seq technologies are increasingly sought after. We here present NOseq, a method to detect m6A residues in defined amplicons by virtue of their resistance to chemical deamination, effected by nitrous acid. Partial deamination in NOseq affects all exocyclic amino groups present in nucleobases and thus also changes sequence information. The method uses a mapping algorithm specifically adapted to the sequence degeneration caused by deamination events. Thus, m6A sites with partial modification levels of ∼50% were detected in defined amplicons, and this threshold can be lowered to ∼10% by combination with m6A immunoprecipitation. NOseq faithfully d…

iGEMS: an integrated model for identification of alternative exon usage events.

2016

Abstract DNA microarrays and RNAseq are complementary methods for studying RNA molecules. Current computational methods to determine alternative exon usage (AEU) using such data require impractical visual inspection and still yield high false-positive rates. Integrated Gene and Exon Model of Splicing (iGEMS) adapts a gene-level residuals model with a gene size adjusted false discovery rate and exon-level analysis to circumvent these limitations. iGEMS was applied to two new DNA microarray datasets, including the high coverage Human Transcriptome Arrays 2.0 and performance was validated using RT-qPCR. First, AEU was studied in adipocytes treated with (n = 9) or without (n = 8) the anti-diabe…

Contour integration with corners.

2016

Contour integration refers to the ability of the visual system to bind disjoint local elements into coherent global shapes. In cluttered images containing randomly oriented elements a contour becomes salient when its elements are coaligned with a smooth global trajectory, as described by the Gestalt law of good continuation. Abrupt changes of curvature strongly diminish contour salience. Here we show that by inserting local corner elements at points of angular discontinuity, a jagged contour becomes as salient as a straight one. We report results from detection experiments for contours with and without corner elements which indicate their psychophysical equivalence. This presents a challeng…

Diagnostic performance of gadobenate dimeglumine enhanced MR angiography of the iliofemoral and calf arteries: a large-scale multicenter trial

2007

OBJECTIVE. The purpose of this study was to compare gadobenate dimeglumine–enhanced MR angiography and unenhanced time-of-flight MR angiography for the detection of significant peripheral arterial occlusive disease using digital subtraction angiography as our reference standard. SUBJECTS AND METHODS. Two hundred seventy-two patients underwent MR angiography and digital subtraction angiography of the iliofemoral arteries. MR angiography was performed before (2D time-of-flight acquisitions) and after (spoiled gradient-echo acquisitions) the administration of 0.1 mmol/kg of gadobenate dimeglumine at 1–2 mL/s. Contrast-enhanced MR angiography and digital subtraction angiography of the calf arte…

The Rise and Fall of Business Firms: A Stochastic Framework on Innovation, Creative

2021

Absolute and relative quantification of RNA modifications via biosynthetic isotopomers

2014

In the resurging field of RNA modifications, quantification is a bottleneck blocking many exciting avenues. With currently over 150 known nucleoside alterations, detection and quantification methods must encompass multiple modifications for a comprehensive profile. LC-MS/MS approaches offer a perspective for comprehensive parallel quantification of all the various modifications found in total RNA of a given organism. By feeding (13)C-glucose as sole carbon source, we have generated a stable isotope-labeled internal standard (SIL-IS) for bacterial RNA, which facilitates relative comparison of all modifications. While conventional SIL-IS approaches require the chemical synthesis of single mod…