scholarly journals pSiteExplorer: Visualization of the mass spectrometric data underlying phospho-site quantification

2021 ◽  
Author(s):  
Michael J. Plank
Keyword(s):  
Amino Acid Sequences ◽  
Peptide Ions ◽  
Mass Spectrometric Data ◽  
Spectrometric Data ◽  
Chromatographic Peaks ◽  
The Given ◽  
Insight Into ◽  
Individual Peptide ◽  
Selection Of

Mass spectrometry based phospho-proteomics is a widely used approach to assess protein phosphorylation. Intensities of phospho-peptide ions are obtained by integrating the MS signal over their chromatographic peaks. How individual peptide measurements mapping to the same phospho-site are combined for the quantification of the given site is, however, in most cases hidden from researchers conducting, reviewing, and reading these studies. I here describe pSiteExplorer, an R script that visualizes the peak intensities associated with phospho-sites in MaxQuant output tables. Barplots of MS intensities originating from phospho-peptides with distinct amino acid sequences due to missed cleavages, different numbers of phosphates and from all off-line chromatographic fractions and charge states are displayed. This tool will help gaining a deeper insight into phospho-site quantifications by contrasting individual and summed phospho-peptide intensities with the site-level values derived by MaxQuant. This will support the validation of quantification results, for example, for the selection of candidates for follow-up studies.

Vocal Repertoire for the Twenty-First Century, Volume 2

2021 ◽  
Author(s):  
Jane Manning
Keyword(s):  
Performance Guide ◽  
Art Songs ◽  
Song Cycles ◽  
First Century ◽  
Vocal Repertoire ◽  
Avant Garde ◽  
Twenty First Century ◽  
Insight Into ◽  
Selection Of

In this new follow-up to her highly regarded New Vocal Repertory, volumes 1 and 2, English concert and opera soprano Jane Manning provides a seasoned expert’s guidance and insight into the vocal genre she calls home. Manning’s comprehensive selection of contemporary art songs in Vocal Repertoire for the Twenty-First Century ranges from the avant-garde to the more easily accessible, including substantial song cycles, shorter encore pieces, and songs suitable for auditions and competitions. Each of the selections is accompanied by a highly detailed performance guide, music examples, levels of difficulty, and a brief encapsulation of vocal characteristics or challenges contained in the piece. A supplemental companion website provides composer biographies and an up-to-date list of recommended recordings. With a focus on younger composers in addition to prominent figures, Manning encourages singers to refresh and expand their recital repertoire into less familiar territory, and discover the rewards therein.

scholarly journals Sense Discrimination in Five English Learner’s Dictionaries

2013 ◽  
Vol 10 (1) ◽  
pp. 153-164
Author(s):  
Ana Halas
Keyword(s):  
Final Outcome ◽  
Polysemous Word ◽  
The Given ◽  
Insight Into ◽  
Selection Of ◽  
English Monolingual

Abstract This paper presents the comparison of sense discrimination strategies including the structure and organization of a polysemous word entry in five English monolingual learner’s dictionaries with the aim of gaining an insight into the aspects of sense division where the given dictionaries agree and disagree. The final outcome of the analysis is the selection of features contributing to the establishment of the user friendliest sense discrimination system in a pedagogical dictionary

Anacyclamide D8P, a prenylated cyanobactin from a Sphaerospermopsis sp. cyanobacterium

2017 ◽  
Author(s):  
Joana Martins ◽  
Niina Leikoski ◽  
Matti Wahlsten ◽  
Joana Azevedo ◽  
Jorge Antunes ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Cyclic Peptides ◽  
Biosynthetic Gene Cluster ◽  
The Novel ◽  
Tyrosine Residue ◽  
Biosynthetic Gene ◽  
Post Translational Modification ◽  
Biological Assays ◽  
Mass Spectrometric Data ◽  
Spectrometric Data

Cyanobactins are a family of linear and cyclic peptides produced through the post-translational modification of short precursor peptides. Anacyclamides are macrocyclic cyanobactins with a highly diverse sequence that are common in the genus <i>Anabaena</i>. A mass spectrometry-based screening of potential cyanobactin producers led to the discovery of a new prenylated member of this family of compounds, anacyclamide D8P (<b>1</b>), from <i>Sphaerospermopsis</i> sp. LEGE 00249. The anacyclamide biosynthetic gene cluster (<i>acy</i>) encoding the novel macrocyclic prenylated cyanobactin, was sequenced. Heterologous expression of the acy gene cluster in <i>Escherichia</i> <i>coli</i> established the connection between genomic and mass spectrometric data. Unambiguous establishment of the type and site of prenylation required the full structural elucidation of <b>1</b> using Nuclear Magnetic Resonance (NMR), which demonstrated that a forward prenylation occurred on the tyrosine residue. Compound <b>1</b> was tested in pharmacologically or ecologically relevant biological assays and revealed moderate antimicrobial activity towards the fouling bacterium <i>Halomonas aquamarina</i> CECT 5000.<br>

An Insight into Oligopeptide Transporter 3 (OPT3) family proteins

2020 ◽  
Vol 27 ◽  
Author(s):  
Fırat Kurt
Keyword(s):  
Stress Responses ◽  
Chelating Agent ◽  
Biological Processes ◽  
Biotic And Abiotic Stress ◽  
Oligopeptide Transporter ◽  
Binding Residues ◽  
Fe Homeostasis ◽  
Proteins Interactions ◽  
Insight Into ◽  
Selection Of

: Oligopeptide transporter 3 (OPT3) proteins are one of the subsets of OPT clade, yet little is known about these transporters. Therefore, homolog OPT3 proteins in several plant species were investigated and characterized using bioinformatical tools. Motif and co-expression analyses showed that OPT3 proteins may be involved in both biotic and abiotic stress responses as well as growth and developmental processes. AtOPT3 usually seemed to take part in Fe homeostasis whereas ZmOPT3 putatively interacted with proteins involved in various biological processes from plant defense system to stress responses. Glutathione (GSH), as a putative alternative chelating agent, was used in the AtOPT3 and ZmOPT3 docking analyses to identify their putative binding residues. The information given in this study will contribute to the understanding of OPT3 proteins’ interactions in various pathways and to the selection of potential ligands for OPT3s.

Mobile-Friendly Dashboards to Display Associations Between Cited-by and Similar Journals on Mobile Health Research: A Bibliometric Study (Preprint)

2018 ◽  
Author(s):  
Tsair-Wei Chien ◽  
Hsien-Yi Wang ◽  
Yang Shao ◽  
Willy Chou
Keyword(s):  
Social Network ◽  
Mobile Health ◽  
Health Research ◽  
Similarity Criteria ◽  
Network Density ◽  
Deep Insight ◽  
Density Indices ◽  
The Subject ◽  
The Given ◽  
Insight Into

BACKGROUND Researchers often spend a great deal of time and effort retrieving related journals for their studies and submissions. Authors often designate one article and then retrieve other articles that are related to the given one using PubMed’s service for finding cited-by or similar articles. However, to date, none present the association between cited-by and similar journals related to a given journal. Authors need one effective and efficient way to find related journals on the topic of mobile health research. OBJECTIVE This study aims (1) to show the related journals for a given journal by both cited-by and similarity criteria; (2) to present the association between cited-by and similarity journals related to a given journal; (3) to inspect the patterns of network density indices among clusters classified by social network analysis (SNA); (4) to investigate the feature of Kendall's coefficient(W) of concordance. METHODS We obtained 676 abstracts since 2013 from Medline based on the keywords of ("JMIR mHealth and uHealth"[Journal]) on June 30, 2018, and plotted the clusters of related journals on Google Maps by using MS Excel modules. The features of network density indices were examined. The Kendall coefficient (W) was used to assess the concordance of clusters across indices. RESULTS This study found that (1) the journals related to JMIR mHealth and uHealth are easily presented on dashboards; (2) a mild association(=0.14) exists between cited-by and similar journals related to JMIR mHealth and uHealth; (3) the median Impact Factor were 3.37 and 2.183 based on the representatives of top ten clusters grouped by the cited-by and similar journals, respectively; (4) all Kendall’s coefficients(i.e., 0.82, 0.89, 0.92, and 0.75) for the four sets of density centrality have a statistically significant concordance (p < 0.05). CONCLUSIONS SNA provides deep insight into the relationships of related journals to a given journal. The results of this research can provide readers with a knowledge and concept diagram to use with future submissions to a given journal in the subject category of Mobile Health Research. CLINICALTRIAL Not available

Application of the turbidity ratio method in the spherical particle size determination in the range m ∈ and α ∈

1979 ◽  
Vol 44 (7) ◽  
pp. 2064-2078 ◽  
Author(s):  
Blahoslav Sedláček ◽  
Břetislav Verner ◽  
Miroslav Bárta ◽  
Karel Zimmermann
Keyword(s):  
Refractive Index ◽  
Spherical Particle ◽  
Ratio Method ◽  
Refractive Indices ◽  
Relative Refractive Index ◽  
Particle Size Determination ◽  
The Individual ◽  
The Given ◽  
Turbidity Ratio ◽  
Selection Of

Basic scattering functions were used in a novel calculation of the turbidity ratios for particles having the relative refractive index m = 1.001, 1.005 (0.005) 1.315 and the size α = 0.05 (0.05) 6.00 (0.10) 15.00 (0.50) 70.00 (1.00) 100, where α = πL/λ, L is the diameter of the spherical particle, λ = Λ/μ1 is the wavelength of light in a medium with the refractive index μ1 and Λ is the wavelength of light in vacuo. The data are tabulated for the wavelength λ = 546.1/μw = 409.357 nm, where μw is the refractive index of water. A procedure has been suggested how to extend the applicability of Tables to various refractive indices of the medium and to various turbidity ratios τa/τb obtained with the individual pairs of wavelengths λa and λb. The selection of these pairs is bound to the sequence condition λa = λ0χa and λb = λ0χb, in which b-a = δ = 1, 2, 3; a = -2, -1, 0, 1, 2, ..., b = a + δ = -1, 0, 1, 2, ...; λ0 = λa=0 = 326.675 nm; χ = 546.1 : 435.8 = 1.2531 is the quotient of the given sequence.

Discovery of five new Galactic symbiotic stars in the VPHAS+ survey

2021 ◽  
Vol 502 (2) ◽  
pp. 2513-2517
Author(s):  
Stavros Akras ◽  
Denise R Gonçalves ◽  
Alvaro Alvarez-Candal ◽  
Claudio B Pereira
Keyword(s):  
Spectroscopic Data ◽  
Selection Criterion ◽  
Optical Spectra ◽  
Emission Lines ◽  
High Rate ◽  
Symbiotic Stars ◽  
Selection Of

ABSTRACT We report the validation of a recently proposed infrared (IR) selection criterion for symbiotic stars (SySts). Spectroscopic data were obtained for seven candidates, selected from the SySt candidates of Akras et al. by employing the new supplementary IR selection criterion for SySts in the VST/OmegaCAM Photometric H-Alpha Survey. Five of them turned out to be genuine SySts after the detection of H α, He ii, and [O iii] emission lines as well as TiO molecular bands. The characteristic O vi Raman-scattered line is also detected in one of these SySts. According to their IR colours and optical spectra, all five newly discovered SySts are classified as S-type. The high rate of true SySts detections of this work demonstrates that the combination of the H α emission and the new IR criterion improves the selection of target lists for follow-up observations by minimizing the number of contaminants and optimizing the observing time.

scholarly journals Age-dependency in mortality of Finnish family caregivers: a nationwide register-based study

2020 ◽  
Vol 30 (Supplement_5) ◽  
Author(s):  
T M Mikkola ◽  
H Kautiainen ◽  
M Mänty ◽  
M B von Bonsdorff ◽  
T Kröger ◽  
...  
Keyword(s):  
General Population ◽  
Family Caregivers ◽  
Family Caregiver ◽  
Causes Of Death ◽  
Lower Mortality ◽  
All Cause Mortality ◽  
The Difference ◽  
Caregiver Role ◽  
Selection Of

Abstract Purpose Mortality appears to be lower in family caregivers than in the general population. However, there is lack of knowledge whether the difference in mortality between family caregivers and the general population is dependent on age. The purpose of this study was to analyze all-cause mortality in relation to age in family caregivers and to study their cause-specific mortality using data from multiple Finnish national registers. Methods The data included all individuals, who received family caregiver's allowance in Finland in 2012 (n = 42 256, mean age 67 years, 71% women) and a control population matched for age, sex, and municipality of residence (n = 83 618). Information on dates and causes of death between 2012 and 2017 were obtained from the Finnish Causes of Death Register. Flexible parametric survival modeling and competing risk regression adjusted for socioeconomic status were used. Results The total follow-up time was 717 877 person-years. Family caregivers had lower all-cause mortality than the controls over the follow-up (8.1% vs. 11.6%) both among women (hazard ratio [HR]: 0.64, 95% CI: 0.61-0.68) and men (HR: 0.73, 95% CI: 0.70-0.77). Younger adult caregivers had equal or only slightly lower mortality than their controls, but after age 60, the difference increased markedly resulting in over 10% lower mortality in favor of the caregivers in the oldest age groups. Caregivers had lower mortality for all the causes of death studied, namely cardiovascular, cancer, neurological, external, respiratory, gastrointestinal and dementia than the controls. Of these, the lowest was the risk for dementia (subhazard ratio=0.29, 95%CI: 0.25-0.34). Conclusions Older family caregivers have lower mortality than the age-matched controls from the general population while younger caregivers have similar mortality to their peers. This age-dependent advantage in mortality is likely to reflect selection of healthier individuals into the family caregiver role. Key messages The difference in mortality between family caregivers and the age-matched general population varies considerably with age. Advantage in mortality observed in family caregiver studies is likely to reflect the selection of healthier individuals into the caregiver role, which underestimates the adverse effects of caregiving.

scholarly journals How to Use Online Tools to Generate New Hypotheses for Mammary Gland Biology Research: A Case Study for Wnt7b

2021 ◽  
Author(s):  
Yorick Bernardus Cornelis van de Grift ◽  
Nika Heijmans ◽  
Renée van Amerongen
Keyword(s):  
Mammary Gland ◽  
In Silico ◽  
Online Tools ◽  
Mammary Gland Biology ◽  
User Friendly ◽  
In Silico Analyses ◽  
Biology Research ◽  
Selection Of

AbstractAn increasing number of ‘-omics’ datasets, generated by labs all across the world, are becoming available. They contain a wealth of data that are largely unexplored. Not every scientist, however, will have access to the required resources and expertise to analyze such data from scratch. Fortunately, a growing number of investigators is dedicating their time and effort to the development of user friendly, online applications that allow researchers to use and investigate these datasets. Here, we will illustrate the usefulness of such an approach. Using regulation of Wnt7b expression as an example, we will highlight a selection of accessible tools and resources that are available to researchers in the area of mammary gland biology. We show how they can be used for in silico analyses of gene regulatory mechanisms, resulting in new hypotheses and providing leads for experimental follow up. We also call out to the mammary gland community to join forces in a coordinated effort to generate and share additional tissue-specific ‘-omics’ datasets and thereby expand the in silico toolbox.

scholarly journals Good Idea But Not Here! A Pilot Study of Swedish Tourism Stakeholders’ Perceptions of Halal Tourism

2021 ◽  
Vol 13 (5) ◽  
pp. 2646
Author(s):  
Saeid Abbasian
Keyword(s):  
Content Analysis ◽  
Pilot Study ◽  
Tourism Industry ◽  
Target Group ◽  
Exploratory Research ◽  
Swedish Study ◽  
Increased Risk ◽  
Insight Into

The following study is the first Swedish study on Halal tourism in Sweden. The purpose of this exploratory research is to get insight into the perception of Halal tourism in Sweden among representatives of tourism stakeholders. The overall methodology approach in this research is qualitative, consisting of 25 qualitative questionnaires, 21 short letters, four follow-up interviews, and a web observation, and content analysis was employed. The results indicate that there is a low knowledge of Halal tourism in Sweden including Swedish tourism industry. The concept is very challenging, and profits are low. It might result in problem scenarios such as detrimental effects on non-Halal tourism, cultural difficulties and increased risk of xenophobia, anti-Islamism, and tension in the society. There is low interest for Sweden among Muslim tourists as the interest and priority for Halal tourism is rather low from Swedish tourism industry. Despite Halal tourism’s importance internationally, these representatives are rather cautious and doubtful about promotion of Sweden towards this niche. Still, a majority seems to be positive to a lighter version of Muslim-friendly tourism with secular/moderate Muslims as a target group.

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