scholarly journals Comparison of errors between a differential and a classical abundance analysis

2017 ◽  
Vol 95 (9) ◽  
pp. 855-857
Author(s):  
Henrique Reggiani ◽  
Jorge Meléndez
Keyword(s):  
Measurement Errors ◽  
Signal To Noise Ratio ◽  
High Signal ◽  
Differential Analysis ◽  
Analysis Method ◽  
Chemical Abundances ◽  
Differential Abundance ◽  
Low Metallicity ◽  
Low Levels ◽  
Differential Abundance Analysis

The differential abundance analysis method can improve the precision of stellar chemical abundances. The method compares the equivalent widths of a certain line in a star with the same line in a star considered to be a standard representative of its class, using high resolution and high signal to noise ratio spectra. The method has achieved great results by reducing the measurement errors to unprecedentedly low levels. However, to date, there has not been a consistent analysis on the actual improvements of this method when compared to a classical analysis in metal-poor stars. Here we present a comparison between the errors of a classical stellar analysis and a differential analysis among low-metallicity stars.

scholarly journals MetaDEGalaxy: Galaxy workflow for differential abundance analysis of 16s metagenomic data

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 726
Author(s):  
Mike W.C. Thang ◽  
Xin-Yi Chua ◽  
Gareth Price ◽  
Dominique Gorse ◽  
Matt A. Field
Keyword(s):  
Microbial Communities ◽  
Sequence Data ◽  
Metagenomic Data ◽  
Marker Genes ◽  
Metagenomic Sequencing ◽  
Differential Analysis ◽  
Biomedical Sciences ◽  
Metagenomic Sequence ◽  
Differential Abundance ◽  
Differential Abundance Analysis

Metagenomic sequencing is an increasingly common tool in environmental and biomedical sciences.  While software for detailing the composition of microbial communities using 16S rRNA marker genes is relatively mature, increasingly researchers are interested in identifying changes exhibited within microbial communities under differing environmental conditions. In order to gain maximum value from metagenomic sequence data we must improve the existing analysis environment by providing accessible and scalable computational workflows able to generate reproducible results. Here we describe a complete end-to-end open-source metagenomics workflow running within Galaxy for 16S differential abundance analysis. The workflow accepts 454 or Illumina sequence data (either overlapping or non-overlapping paired end reads) and outputs lists of the operational taxonomic unit (OTUs) exhibiting the greatest change under differing conditions. A range of analysis steps and graphing options are available giving users a high-level of control over their data and analyses. Additionally, users are able to input complex sample-specific metadata information which can be incorporated into differential analysis and used for grouping / colouring within graphs.  Detailed tutorials containing sample data and existing workflows are available for three different input types: overlapping and non-overlapping read pairs as well as for pre-generated Biological Observation Matrix (BIOM) files. Using the Galaxy platform we developed MetaDEGalaxy, a complete metagenomics differential abundance analysis workflow. MetaDEGalaxy is designed for bench scientists working with 16S data who are interested in comparative metagenomics.  MetaDEGalaxy builds on momentum within the wider Galaxy metagenomics community with the hope that more tools will be added as existing methods mature.

scholarly journals A New Method for Measuring the Detailed Chemical Composition of Globular Clusters from High-Resolution, Integrated-Light Spectra

2002 ◽  
Vol 207 ◽  
pp. 739-742 ◽  
Author(s):  
Rebecca A. Bernstein ◽  
Andrew McWilliam
Keyword(s):  
Chemical Composition ◽  
High Resolution ◽  
Globular Clusters ◽  
Signal To Noise Ratio ◽  
High Signal ◽  
Analysis Method ◽  
Individual Stars ◽  
Light Spectra ◽  
History Of ◽  
Detailed Chemical

We are developing a method for measuring the detailed chemical composition and evolutionary history of extragalactic star clusters from high resolution spectra of their integrated light as one would from spectra of individual stars. In this paper, we show high signal-to-noise ratio echelle spectra of the integrated light of two Galactic globular clusters and equivalent-quality spectra of individual stars in those clusters in order to briefly illustrate some subtleties of the analysis method.

A Spherically Bent Crystal X-Ray Specteometer with Variable Curvature

1973 ◽  
Vol 17 ◽  
pp. 521-530
Author(s):  
Donald L. Parker
Keyword(s):  
Signal To Noise Ratio ◽  
Three Dimensional ◽  
High Signal ◽  
X Rays ◽  
X Ray ◽  
Bent Crystal ◽  
Variable Curvature ◽  
The Face ◽  
Low Levels ◽  
And Performance

AbstractThe design and performance of a spherically bent crystal x-ray spectrometer with variable curvature are given. A thin crystal with the diffracting planes parallel to the face is mounted on a vacuum chuck consisting of an O-ring in a brass mounting. A controlled partial vacuum is applied behind the crystal to cause spherical deformation of the lattice. Thus, rays from a point source on the focusing circle are diffracted to a line image also on the focusing circle. The differential pressure is automatically varied such that the source-to-crystal and crystal-to-image distances are equal and constant for all Bragg angles and hence the simple θ-2θ motion of a one flat crystal spectrometer is used.The data are accumulated by a scanning proportional counter tube placed behind a vertical slit (perpendicular to the scattering plane) located at the image line. The fixed chord length is 22 cm and the instrument is designed to scan from zero up to 120° 2θ. Crystals are easily interchanged and the automatic vacuum regulator has sufficient flexibility to allow tailoring the spherical bending to crystals of materials of various thicknesses. The resolution is easily adjusted by either the size of the x-ray source or the width of the detector slit. The performance of the spectrometer has been evaluated by characteristic x-rays produced by various samples placed in a demountable x-ray tube. The main advantages of this three-dimensional focusing instrument are the very high signal-to-noise ratio and the very low levels of x-ray flux required.

scholarly journals Censcyt: censored covariates in differential abundance analysis in cytometry

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Reto Gerber ◽  
Mark D. Robinson
Keyword(s):  
Error Control ◽  
Proportional Hazards ◽  
Proportional Hazards Model ◽  
Cox Proportional Hazards ◽  
Cox Proportional Hazards Model ◽  
Measured Quantity ◽  
Differential Analysis ◽  
Differential Abundance ◽  
Study Results ◽  
Differential Abundance Analysis

Abstract Background Innovations in single cell technologies have lead to a flurry of datasets and computational tools to process and interpret them, including analyses of cell composition changes and transition in cell states. The diffcyt workflow for differential discovery in cytometry data consist of several steps, including preprocessing, cell population identification and differential testing for an association with a binary or continuous covariate. However, the commonly measured quantity of survival time in clinical studies often results in a censored covariate where classical differential testing is inapplicable. Results To overcome this limitation, multiple methods to directly include censored covariates in differential abundance analysis were examined with the use of simulation studies and a case study. Results show that multiple imputation based methods offer on-par performance with the Cox proportional hazards model in terms of sensitivity and error control, while offering flexibility to account for covariates. The tested methods are implemented in the package censcyt as an extension of diffcyt and are available at https://bioconductor.org/packages/censcyt. Conclusion Methods for the direct inclusion of a censored variable as a predictor in GLMMs are a valid alternative to classical survival analysis methods, such as the Cox proportional hazard model, while allowing for more flexibility in the differential analysis.

scholarly journals A Spectroscopic Study of Barium Stars

2008 ◽  
Vol 4 (S252) ◽  
pp. 425-426
Author(s):  
G. Q. Liu ◽  
Y. C. Liang ◽  
L. Deng
Keyword(s):  
Neutron Capture ◽  
Binary Systems ◽  
Signal To Noise Ratio ◽  
High Signal ◽  
Agb Stars ◽  
Atmospheric Parameters ◽  
Chemical Abundances ◽  
Capture Process ◽  
Abundance Patterns ◽  
Process Elements

AbstractWe present an analysis of eight barium stars, providing their atmospheric parameters (Teff, log g, [Fe/H], ξt) and chemical abundances, based on the high signal-to-noise ratio and high resolution Echelle spectra. The s-process elements Y, Zr, Ba, La, Eu show obvious overabundance relative to the Sun. And Na, Mg, Al, Si, Ca, Sc, Ti, V, Cr, Mn, Ni show comparable abundances to the Solar ones. The results of theoretical model of wind accretion for binary systems can explain the observed abundance patterns of the neutron capture process elements in these Ba stars, which means that their overabundant heavy-elements could be caused by accreting the ejecta of AGB stars, the progenitors of the present white dwarf companions in the binary systems.

scholarly journals Omega Centauri: weak MgH band in red giants directly traces the helium content

2020 ◽  
Vol 495 (1) ◽  
pp. 383-401
Author(s):  
Arumalla B S Reddy
Keyword(s):  
Signal To Noise Ratio ◽  
Asymptotic Giant Branch ◽  
High Spectral Resolution ◽  
High Signal ◽  
Synthetic Spectrum ◽  
Red Giants ◽  
Chemical Abundances ◽  
Rich Cluster ◽  
Red Giant ◽  
The Impact

ABSTRACT High spectral resolution and high signal-to-noise ratio optical spectra of red giants in the globular cluster Omega Centauri are analysed for stellar parameters and chemical abundances of 15 elements including helium by either line equivalent widths or synthetic spectrum analyses. The simultaneous abundance analysis of MgH and Mg lines adopting theoretical photospheres and a combination of He/H ratios proved to be the only powerful probe to evaluate helium abundances of red giants cooler than 4400 K, wherein otherwise helium line transitions (He i 10830 and 5876 Å) present for a direct spectral line analysis. The impact of helium-enhanced model photospheres on the resulting abundance ratios is smaller than 0.15 dex, in agreement with past studies. The first indirect spectroscopic helium abundances measured in this paper for the most metal-rich cluster members reveal the discovery of seven He-enhanced giants ($\Delta Y=+0.15 \pm 0.04$), the largest such sample found spectroscopically to date. The average metallicity of −0.79 ± 0.06 dex and abundances for O, Na, Al, Si, Ca, Ti, Ni, Ba, and La are consistent with values found for the red giant branch (RGB-a) and subgiant branch (SGB-a) populations of Omega Centauri, suggesting an evolutionary connection among samples. The He enhancement in giants is associated with larger s-process elemental abundances, which correlate with Al and anticorrelate with O. These results support the formation of He-enhanced, metal-rich population of Omega Centauri out of the interstellar medium enriched with the ejecta of fast rotating massive stars, binaries exploding as supernovae, and asymptotic giant branch (AGB) stars.

scholarly journals MetaDEGalaxy: Galaxy workflow for differential abundance analysis of 16s metagenomic data

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 726 ◽  
Author(s):  
Mike W.C. Thang ◽  
Xin-Yi Chua ◽  
Gareth Price ◽  
Dominique Gorse ◽  
Matt A. Field
Keyword(s):  
Microbial Communities ◽  
Sequence Data ◽  
Metagenomic Data ◽  
Marker Genes ◽  
Metagenomic Sequencing ◽  
Differential Analysis ◽  
Biomedical Sciences ◽  
Metagenomic Sequence ◽  
Differential Abundance ◽  
Differential Abundance Analysis

Metagenomic sequencing is an increasingly common tool in environmental and biomedical sciences yet analysis workflows remain immature relative to other field such as DNASeq and RNASeq analysis pipelines.  While software for detailing the composition of microbial communities using 16S rRNA marker genes is constantly improving, increasingly researchers are interested in identifying changes exhibited within microbial communities under differing environmental conditions. In order to gain maximum value from metagenomic sequence data we must improve the existing analysis environment by providing accessible and scalable computational workflows able to generate reproducible results. Here we describe a complete end-to-end open-source metagenomics workflow running within Galaxy for 16S differential abundance analysis. The workflow accepts 454 or Illumina sequence data (either overlapping or non-overlapping paired end reads) and outputs lists of the operational taxonomic unit (OTUs) exhibiting the greatest change under differing conditions. A range of analysis steps and graphing options are available giving users a high-level of control over their data and analyses. Additionally, users are able to input complex sample-specific metadata information which can be incorporated into differential analysis and used for grouping / colouring within graphs.  Detailed tutorials containing sample data and existing workflows are available for three different input types: overlapping and non-overlapping read pairs as well as for pre-generated Biological Observation Matrix (BIOM) files. Using the Galaxy platform we developed MetaDEGalaxy, a complete metagenomics differential abundance analysis workflow. MetaDEGalaxy is designed for bench scientists working with 16S data who are interested in comparative metagenomics.  MetaDEGalaxy builds on momentum within the wider Galaxy metagenomics community with the hope that more tools will be added as existing methods mature.

A FPGA-PC Based Acoustic Emission System with Logarithmic Preamplifier for Fracture Monitoring

2013 ◽  
Vol 592-593 ◽  
pp. 541-544 ◽  
Author(s):  
Marek Vondra ◽  
Gabriel Cséfalvay ◽  
Petr Sedlak
Keyword(s):  
Acoustic Emission ◽  
Dynamic Range ◽  
Signal To Noise Ratio ◽  
Quantization Noise ◽  
High Signal ◽  
Source Characterization ◽  
Nondestructive Technique ◽  
Emission System ◽  
Low Levels ◽  
Input Gain

Acoustic emission (AE) is one of the most used nondestructive technique since it offers a great potential due to its ability of quantitative evaluation such as source location and source characterization. A common set of recorded acoustic emission signals has an extraordinarily wide dynamic range. Thus, the input gain of the A/D converter plays a key role due in information loss considering limitation of high signal amplitudes and domination of quantization noise at low levels. The usage of a logarithmic preamplifier extends the dynamic range of conventional A/D converters, thus increases the accuracy and signal-to-noise ratio of weak acoustic emission signals.

scholarly journals censcyt: censored covariates in differential abundance analysis in cytometry

2020 ◽  
Author(s):  
Reto Gerber ◽  
Mark D. Robinson
Keyword(s):  
Error Control ◽  
R Package ◽  
Measured Quantity ◽  
Differential Analysis ◽  
Differential Abundance ◽  
Cox Proportional Hazard ◽  
Study Results ◽  
Differential Abundance Analysis ◽  
Composition Changes

AbstractInnovations in single cell technologies have lead to a flurry of datasets and computational tools to process and interpret them, including analyses of cell composition changes and transition in cell states. The diffcyt workflow for differential discovery in cytometry data consist of several steps, including preprocessing, cell population identification and differential testing for an association with a binary or continuous covariate. However, the commonly measured quantity of survival time in clinical studies often results in a censored covariate where classical differential testing is inapplicable. To overcome this limitation, multiple methods to directly include censored covariates in differential abundance analysis were examined with the use of simulation studies and a case study. Results show high error control and decent sensitivity for a subset of the methods. The tested methods are implemented in the R package censcyt as an extension of diffcyt and are available at https://github.com/retogerber/censcyt. Methods for the direct inclusion of a censored variable as a predictor in GLMMs are a valid alternative to classical survival analysis methods, such as the Cox proportional hazard model, while allowing for more flexibility in the differential analysis.

scholarly journals Detailed chemical compositions of planet-hosting stars – I. Exploration of possible planet signatures

2020 ◽  
Vol 495 (4) ◽  
pp. 3961-3973 ◽  
Author(s):  
F Liu ◽  
D Yong ◽  
M Asplund ◽  
H S Wang ◽  
L Spina ◽  
...  
Keyword(s):  
High Precision ◽  
Chemical Evolution ◽  
Planet Formation ◽  
Scale Efficiency ◽  
High Signal ◽  
Chemical Compositions ◽  
Condensation Temperature ◽  
Differential Analysis ◽  
Chemical Abundances ◽  
Comparison Stars

ABSTRACT We present a line-by-line differential analysis of a sample of 16 planet-hosting stars and 68 comparison stars using high-resolution, high signal-to-noise ratio spectra gathered using Keck. We obtained accurate stellar parameters and high-precision relative chemical abundances with average uncertainties in Teff, log g, [Fe/H], and [X/H] of 15 K, 0.034 cm s−2 , 0.012 dex, and 0.025 dex, respectively. For each planet host, we identify a set of comparison stars and examine the abundance differences (corrected for Galactic chemical evolution effect) as a function of the dust condensation temperature, Tcond, of the individual elements. While we confirm that the Sun exhibits a negative trend between abundance and Tcond, we also confirm that the remaining planet hosts exhibit a variety of abundance–Tcond trends with no clear dependence upon age, metallicity, or Teff. The diversity in the chemical compositions of planet-hosting stars relative to their comparison stars could reflect the range of possible planet-induced effects present in these planet hosts, from the sequestration of rocky material (refractory poor) to the possible ingestion of planets (refractory rich). Other possible explanations include differences in the time-scale, efficiency and degree of planet formation, or inhomogeneous chemical evolution. Although we do not find an unambiguous chemical signature of planet formation among our sample, the high-precision chemical abundances of the host stars are essential for constraining the composition and structure of their exoplanets.

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