scholarly journals Priors for Genotyping Polyploids

2019 ◽  
Author(s):  
David Gerard ◽  
Luís Felipe Ventorim Ferrão
Keyword(s):  
Empirical Bayes ◽  
A Priori ◽  
Real Data ◽  
R Package ◽  
Complete Characterization ◽  
Genotype Distribution ◽  
Link Type ◽  
Systematic Biases ◽  
Technical Artifacts

AbstractMotivationEmpirical Bayes techniques to genotype polyploid organisms usually either (i) assume technical artifacts are known a priori or (ii) estimate technical artifacts simultaneously with the prior genotype distribution. Case (i) is unappealing as it places the onus on the researcher to estimate these artifacts, or to ensure that there are no systematic biases in the data. However, as we demonstrate with a few empirical examples, case (ii) makes choosing the class of prior genotype distributions extremely important. Choosing a class that is either too flexible or too restrictive results in poor genotyping performance.ResultsWe propose two classes of prior genotype distributions that are of intermediate levels of flexibility: the class of proportional normal distributions and the class of unimodal distributions. We provide a complete characterization of and optimization details for the class of unimodal distributions. We demonstrate, using both simulated and real data, that using these classes results in superior genotyping performance.Availability and ImplementationGenotyping methods that use these priors are implemented in the updog R package available on the Comprehensive R Archive Network: https://cran.r-project.org/package=updog. All code needed to reproduce the results of this paper is available on GitHub: https://github.com/dcgerard/[email protected]

scholarly journals Priors for Genotyping Polyploids

2019 ◽  
Author(s):  
David Gerard ◽  
Luís Felipe Ventorim Ferrão
Keyword(s):  
Empirical Bayes ◽  
A Priori ◽  
Real Data ◽  
R Package ◽  
Complete Characterization ◽  
Supplementary Information ◽  
Genotype Distribution ◽  
Systematic Biases ◽  
Technical Artifacts

Abstract Motivation Empirical Bayes techniques to genotype polyploid organisms usually either (i) assume technical artifacts are known a priori or (ii) estimate technical artifacts simultaneously with the prior genotype distribution. Case (i) is unappealing as it places the onus on the researcher to estimate these artifacts, or to ensure that there are no systematic biases in the data. However, as we demonstrate with a few empirical examples, case (ii) makes choosing the class of prior genotype distributions extremely important. Choosing a class that is either too flexible or too restrictive results in poor genotyping performance. Results We propose two classes of prior genotype distributions that are of intermediate levels of flexibility: the class of proportional normal distributions and the class of unimodal distributions. We provide a complete characterization of and optimization details for the class of unimodal distributions. We demonstrate, using both simulated and real data, that using these classes results in superior genotyping performance. Availability and implementation Genotyping methods that use these priors are implemented in the updog R package available on the Comprehensive R Archive Network: https://cran.r-project.org/package=updog. All code needed to reproduce the results of this paper is available on GitHub: https://github.com/dcgerard/reproduce\_prior\_sims. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Bayesian wavelet de-noising with the caravan prior

2019 ◽  
Vol 23 ◽  
pp. 947-978
Author(s):  
Shota Gugushvili ◽  
Frank van der Meulen ◽  
Moritz Schauer ◽  
Peter Spreij
Keyword(s):  
Empirical Bayes ◽  
Expert Knowledge ◽  
Estimation Error ◽  
A Priori ◽  
Real Data ◽  
Detailed Comparison ◽  
Wavelet Coefficients ◽  
Visual Appearance ◽  
Bayesian Wavelet ◽  
Clustering Patterns

According to both domain expert knowledge and empirical evidence, wavelet coefficients of real signals tend to exhibit clustering patterns, in that they contain connected regions of coefficients of similar magnitude (large or small). A wavelet de-noising approach that takes into account such a feature of the signal may in practice outperform other, more vanilla methods, both in terms of the estimation error and visual appearance of the estimates. Motivated by this observation, we present a Bayesian approach to wavelet de-noising, where dependencies between neighbouring wavelet coefficients are a priori modelled via a Markov chain-based prior, that we term the caravan prior. Posterior computations in our method are performed via the Gibbs sampler. Using representative synthetic and real data examples, we conduct a detailed comparison of our approach with a benchmark empirical Bayes de-noising method (due to Johnstone and Silverman). We show that the caravan prior fares well and is therefore a useful addition to the wavelet de-noising toolbox.

scholarly journals Analytical modelling of period spacings across the HR diagram

2019 ◽  
Vol 490 (1) ◽  
pp. 909-926 ◽  
Author(s):  
M S Cunha ◽  
P P Avelino ◽  
J Christensen-Dalsgaard ◽  
D Stello ◽  
M Vrard ◽  
...  
Keyword(s):  
Mixed Mode ◽  
Chemical Elements ◽  
A Priori ◽  
Real Data ◽  
Relative Difference ◽  
Model Data ◽  
Analytical Expression ◽  
Chemical Gradients ◽  
Red Giant

ABSTRACT The characterization of stellar cores may be accomplished through the modelling of asteroseismic data from stars exhibiting either gravity-mode or mixed-mode pulsations, potentially shedding light on the physical processes responsible for the production, mixing, and segregation of chemical elements. In this work, we validate against model data an analytical expression for the period spacing that will facilitate the inference of the properties of stellar cores, including the detection and characterization of buoyancy glitches (strong chemical gradients). This asymptotically based analytical expression is tested both in models with and without buoyancy glitches. It does not assume that glitches are small and, consequently, predicts non-sinusoidal glitch-induced period-spacing variations, as often seen in model and real data. We show that the glitch position and width inferred from the fitting of the analytical expression to model data consisting of pure gravity modes are in close agreement (typically better than 7 ${{\ \rm per\ cent}}$ relative difference) with the properties measured directly from the stellar models. In the case of fitting mixed-mode model data, the same expression is shown to reproduce well the numerical results, when the glitch properties are known a priori. In addition, the fits performed to mixed-mode model data reveal a frequency dependence of the coupling coefficient, q, for a moderate-luminosity red-giant-branch model star. Finally, we find that fitting the analytical expression to the mixed-mode period spacings may provide a way to infer the frequencies of the pure acoustic dipole modes that would exist if no coupling took place between acoustic and gravity waves.

scholarly journals Complete Characterization of Incorrect Orthology Assignments in Best Match Graphs

2021 ◽  
Vol 82 (3) ◽  
Author(s):  
David Schaller ◽  
Manuela Geiß ◽  
Peter F. Stadler ◽  
Marc Hellmuth
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
A Priori ◽  
Gene Tree ◽  
Polynomial Time Algorithm ◽  
Time Algorithm ◽  
Complete Characterization ◽  
Species Trees ◽  
Genome Scale

AbstractGenome-scale orthology assignments are usually based on reciprocal best matches. In the absence of horizontal gene transfer (HGT), every pair of orthologs forms a reciprocal best match. Incorrect orthology assignments therefore are always false positives in the reciprocal best match graph. We consider duplication/loss scenarios and characterize unambiguous false-positive (u-fp) orthology assignments, that is, edges in the best match graphs (BMGs) that cannot correspond to orthologs for any gene tree that explains the BMG. Moreover, we provide a polynomial-time algorithm to identify all u-fp orthology assignments in a BMG. Simulations show that at least $$75\%$$ 75 % of all incorrect orthology assignments can be detected in this manner. All results rely only on the structure of the BMGs and not on any a priori knowledge about underlying gene or species trees.

scholarly journals Postsynaptic α-Neurotoxin Gene of the Spitting Cobra, Naja naja sputatrix: Structure, Organization, and Phylogenetic Analysis

1999 ◽  
Vol 9 (3) ◽  
pp. 259-266
Author(s):  
Fatemeh Afifiyan ◽  
Arunmoziarasi Armugam ◽  
Chee Hong Tan ◽  
Ponnampalam Gopalakrishnakone ◽  
Kandiah Jeyaseelan
Keyword(s):  
Dna Sequences ◽  
Dna Amplification ◽  
Complete Characterization ◽  
Long Distance ◽  
Ancestral Gene ◽  
Naja Naja ◽  
Link Type ◽  
Transcription Sites ◽  
Ccaat Box

The venom of the spitting cobra, Naja naja sputatrixcontains highly potent α-neurotoxins (NTXs) in addition to phospholipase A2 (PLA2) and cardiotoxin (CTX). In this study, we report the complete characterization of three genes that are responsible for the synthesis of three isoforms of α-NTX in the venom of a single spitting cobra. DNA amplification by long-distance polymerase chain reaction (LD-PCR) and genome walking have provided information on the gene structure including their promoter and 5′ and 3′ UTRs. Each NTX isoform is ∼4 kb in size and contains three exons and two introns. The sequence homology among these isoforms was found to be 99%. Two possible transcription sites were identified by primer extension analysis and they corresponded to the adenine (A) nucleotide at positions +1 and −45. The promoter also contains two TATA boxes and a CCAAT box. Putative binding sites for transcriptional factors AP-2 and GATA are also present. The high percentage of similarity observed among the NTX gene isoforms of N. n. sputatrix as well as with the α-NTX and κ-NTX genes from other land snakes suggests that the NTX gene has probably evolved from a common ancestral gene.[The genomic DNA sequences reported in this paper have been submitted to GenBank databases under accession nos. AF096999 to AF097001.]

Experimental Characterization of Mechanical Behavior of Cord-Rubber Composites

1982 ◽  
Vol 10 (1) ◽  
pp. 37-54 ◽  
Author(s):  
M. Kumar ◽  
C. W. Bert
Keyword(s):  
Response Characteristic ◽  
Cord Compression ◽  
Complete Characterization ◽  
Strain Response ◽  
Strain Gages ◽  
Experimental Characterization ◽  
Rubber Composites ◽  
Stress Strain ◽  
Strain Data

Abstract Unidirectional cord-rubber specimens in the form of tensile coupons and sandwich beams were used. Using specimens with the cords oriented at 0°, 45°, and 90° to the loading direction and appropriate data reduction, we were able to obtain complete characterization for the in-plane stress-strain response of single-ply, unidirectional cord-rubber composites. All strains were measured by means of liquid mercury strain gages, for which the nonlinear strain response characteristic was obtained by calibration. Stress-strain data were obtained for the cases of both cord tension and cord compression. Materials investigated were aramid-rubber, polyester-rubber, and steel-rubber.

Characterization of CMOS Structures (0.6 µm process) Submitted to HBM and COM ESD Stress Tests

1997 ◽  
Author(s):  
G. Meneghesso ◽  
E. Zanoni ◽  
P. Colombo ◽  
M. Brambilla ◽  
R. Annunziata ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Electrostatic Discharge ◽  
Stress Test ◽  
Complete Characterization ◽  
Stress Tests ◽  
Test Procedures ◽  
Emission Microscopy ◽  
Fast Rise ◽  
Scanning Electron

Abstract In this work, we present new results concerning electrostatic discharge (ESD) robustness of 0.6 μm CMOS structures. Devices have been tested according to both HBM and socketed CDM (sCDM) ESD test procedures. Test structures have been submitted to a complete characterization consisting in: 1) measurement of the tum-on time of the protection structures submitted to pulses with very fast rise times; 2) ESD stress test with the HBM and sCDM models; 3) failure analysis based on emission microscopy (EMMI) and Scanning Electron Microscopy (SEM).

scholarly journals Complete characterization of spin chains with two Ising symmetries

2019 ◽  
Vol 125 (1) ◽  
pp. 10008 ◽  
Author(s):  
Bat-el Friedman ◽  
Atanu Rajak ◽  
Emanuele G. Dalla Torre
Keyword(s):  
Complete Characterization ◽  
Spin Chains

scholarly journals On the star forest polytope for trees and cycles

2019 ◽  
Vol 53 (5) ◽  
pp. 1763-1773
Author(s):  
Meziane Aider ◽  
Lamia Aoudia ◽  
Mourad Baïou ◽  
A. Ridha Mahjoub ◽  
Viet Hung Nguyen
Keyword(s):  
Undirected Graph ◽  
Dominating Set ◽  
Discrete Math ◽  
Complete Characterization ◽  
Facial Structure ◽  
Maximum Weight ◽  
Single Node ◽  
End Node ◽  
Vertex Disjoint

Let G = (V, E) be an undirected graph where the edges in E have non-negative weights. A star in G is either a single node of G or a subgraph of G where all the edges share one common end-node. A star forest is a collection of vertex-disjoint stars in G. The weight of a star forest is the sum of the weights of its edges. This paper deals with the problem of finding a Maximum Weight Spanning Star Forest (MWSFP) in G. This problem is NP-hard but can be solved in polynomial time when G is a cactus [Nguyen, Discrete Math. Algorithms App. 7 (2015) 1550018]. In this paper, we present a polyhedral investigation of the MWSFP. More precisely, we study the facial structure of the star forest polytope, denoted by SFP(G), which is the convex hull of the incidence vectors of the star forests of G. First, we prove several basic properties of SFP(G) and propose an integer programming formulation for MWSFP. Then, we give a class of facet-defining inequalities, called M-tree inequalities, for SFP(G). We show that for the case when G is a tree, the M-tree and the nonnegativity inequalities give a complete characterization of SFP(G). Finally, based on the description of the dominating set polytope on cycles given by Bouchakour et al. [Eur. J. Combin. 29 (2008) 652–661], we give a complete linear description of SFP(G) when G is a cycle.

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