On the Accuracy of Equivalent Antenna Representations

The accuracy of two equivalent antenna representations, near-field sources and far-field sources, are evaluated for an antenna installed on a simplified platform in a series of case studies using different configurations of equivalent antenna representations. The accuracy is evaluated in terms of installed far-fields and surface currents on the platform. The results show large variations between configurations. The root-mean-square installed far-field error is 4.4% for the most accurate equivalent representation. When using far-field sources, the design parameters have a large influence of the achieved accuracy. There is also a varying accuracy depending on the type of numerical method used. Based on the results, some recommendations on the choice of sub-domain for the equivalent antenna representation are given. In industrial antenna applications, the accuracy in determining e.g. installed far-fields and antenna isolation on large platforms are critical. Equivalent representations can reduce the fine-detail complexity of antennas and thus give an efficient numerical descriptions to be used in large-scale simulations. The results in this paper can be used as a guideline by antenna designers or system engineers when using equivalent sources

DIANA—algorithmic improvements for analysis of data-independent acquisition MS data

Motivation: Data independent acquisition mass spectrometry has emerged as a reproducible and sensitive alternative in quantitative proteomics, where parsing the highly complex tandem mass spectra requires dedicated algorithms. Recently, targeted data extraction was proposed as a novel analysis strategy for this type of data, but it is important to further develop these concepts to provide quality-controlled, interference-adjusted and sensitive peptide quantification. Results: We here present the algorithm DIANA and the classifier PyProphet, which are based on new probabilistic sub-scores to classify the chromatographic peaks in targeted data-independent acquisition data analysis. The algorithm is capable of providing accurate quantitative values and increased recall at a controlled false discovery rate, in a complex gold standard dataset. Importantly, we further demonstrate increased confidence gained by the use of two complementary data-independent acquisition targeted analysis algorithms, as well as increased numbers of quantified peptide precursors in complex biological samples. Availability and implementation: DIANA is implemented in scala and python and available as open source (Apache 2.0 license) or pre-compiled binaries from http://quantitativeproteomics.org/diana. PyProphet can be installed from PyPi (https://pypi.python.org/pypi/pyprophet). Supplementary information: Supplementary data are available at Bioinformatics onlin

Efficient visualization of high-throughput targeted proteomics experiments: TAPIR

Motivation: Targeted mass spectrometry comprises a set of powerful methods to obtain accurate and consistent protein quantification in complex samples. To fully exploit these techniques, a cross-platform and open-source software stack based on standardized data exchange formats is required. Results: We present TAPIR, a fast and efficient Python visualization software for chromatograms and peaks identified in targeted proteomics experiments. The input formats are open, community-driven standardized data formats (mzML for raw data storage and TraML encoding the hierarchical relationships between transitions, peptides and proteins). TAPIR is scalable to proteome-wide targeted proteomics studies (as enabled by SWATH-MS), allowing researchers to visualize high-throughput datasets. The framework integrates well with existing automated analysis pipelines and can be extended beyond targeted proteomics to other types of analyses. Availability and implementation: TAPIR is available for all computing platforms under the 3-clause BSD license at https://github.com/msproteomicstools/msproteomicstools. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics onlin

aLFQ: an R-package for estimating absolute protein quantities from label-free LC-MS/MS proteomics data

Motivation: The determination of absolute quantities of proteins in biological samples is necessary for multiple types of scientific inquiry. While relative quantification has been commonly used in proteomics, few proteomic datasets measuring absolute protein quantities have been reported to date. Various technologies have been applied using different types of input data, e.g. ion intensities or spectral counts, as well as different absolute normalization strategies. To date, a user-friendly and transparent software supporting large-scale absolute protein quantification has been lacking. Results: We present a bioinformatics tool, termed aLFQ, which supports the commonly used absolute label-free protein abundance estimation methods (TopN, iBAQ, APEX, NSAF and SCAMPI) for LC-MS/MS proteomics data, together with validation algorithms enabling automated data analysis and error estimation. Availability and implementation: aLFQ is written in R and freely available under the GPLv3 from CRAN (http://www.cran.r-project.org). Instructions and example data are provided in the R-package. The raw data can be obtained from the PeptideAtlas raw data repository (PASS00321). Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics onlin

The structure of human dermatan sulfate epimerase 1 emphasizes the importance of C5 epimerization of glucuronic acid in higher organisms

Dermatan sulfate epimerase 1 DS epi1, EC 5.1.3.19 catalyzes the conversion of D glucuronic acid to L iduronic acid on the polymer level, a key step in the biosynthesis of the glycosaminoglycan dermatan sulfate. Here, we present the first crystal structure of the catalytic domains of DS epi1, solved at 2.4 resolution, as well as a model of the full length luminal protein obtained by a combination of macromolecular crystallography and targeted cross linking mass spectrometry. Based on docking studies and molecular dynamics simulations of the protein structure and a chondroitin substrate, we suggest a novel mechanism of DS epi1, involving a His double Tyr motif. Our work uncovers detailed information about the domain architecture, active site, metal coordinating center and pattern of N glycosylation of the protein. Additionally, the structure of DS epi1 reveals a high structural similarity to proteins from several families of bacterial polysaccharide lyases. DS epi1 is of great importance in a range of diseases, and the structure provides a necessary starting point for design of active site inhibitor

Immunohistology and remodeling in fatal pediatric and adolescent asthma

Background: Thickening of reticular basement membrane, increased airway smooth muscle mass and eosinophilic inflammation are found in adult fatal asthma. At the present study the histopathology of fatal paediatric and adolescent asthma is evaluated. Methods: Post-mortem lung autopsies from 12 fatal asthma cases and 8 non-asthmatic control subjects were examined. Thickness of reticular basement membrane (RBM) and percentage of airway smooth muscle (ASM%) mass area were measured and inflammatory cells were counted. Patient records were reviewed for clinical history. Results: The age range of the cases was from 0.9 to 19.5 years, eight were males and five had received inhaled corticosteroids. Thickened RBM was detected in majority of the cases without any correlation to treatment delay, age at onset of symptoms or diagnosis. In the large airways ASM was clearly increased in one third of the cases whereas the median ASM% did not differ from that in healthy controls (14.0% vs. 14.0%). In small airways no increase of ASM was found, instead mucous plugs were seen in fatal asthma. The number of eosinophils, plasmacytoid dendritic cells, macrophages, and B-cells were significantly increased in fatal asthma cases compared with controls and the two latter correlated with the length of the fatal exacerbation. Conclusions: The findings highlight the strong presence of eosinophils and mucous plugs even in small airways in children and adolescents with fatal asthma. Thickened RBM was obvious in majority of the patients. Contrary to our hypothesis, increased ASM% was detected in only one third of the patients.Peer reviewe

Swath-ms: a new data independent acquisition LC-MS methodology for quantitative complete proteome analysis

Comunicaciones a congreso

It is important that the process goes quickly, isn't it?” A qualitative multi-country study of colorectal or lung cancer patients’ narratives of the timeliness of diagnosis and quality of care

Purpose: The emphasis on early diagnosis to improve cancer survival has been a key factor in the development of cancer pathways across Europe. The aim of this analysis was to explore how the emphasis on early diagnosis and timely treatment is reflected in patient's accounts of care, from the first suspicion of colorectal or lung cancer to their treatment in Denmark, England and Sweden. Method: We recruited 155 patients in Denmark, England and Sweden who were within six months of being diagnosed with lung or colorectal cancer. Data were collected via semi-structured narrative interviews and analysed using a thematic approach. Results: Participants’ accounts of quality of care were closely related to how quickly (or not) diagnosis, treatment and/or healthcare processes went. Kinetic metaphors as a description of care (such as treadmill) could be interpreted positively as participants were willing to forgo some degree of control and accept disruption to their lives to ensure more timely care. Drawing on wider cultural expectations of the benefits of diagnosing and treating cancer quickly, some participants were concerned that the waiting times between interventions might allow time for the cancer to grow. Conclusions: Initiatives emphasising the timeliness of diagnosis and treatment are reflected in the ways some patients experience their care. However, these accounts were open to further contextualisation about what speed of healthcare processes meant for evaluating the quality of their care. Healthcare professionals could therefore be an important patient resource in providing reassurance and support about the timeliness of diagnosis or treatment