scholarly journals Haplotype assembly of autotetraploid potato using integer linear programing

2019 ◽  
Vol 35 (18) ◽  
pp. 3279-3286 ◽  
Author(s):  
Enrico Siragusa ◽  
Niina Haiminen ◽  
Richard Finkers ◽  
Richard Visser ◽  
Laxmi Parida

Abstract Summary Haplotype assembly of polyploids is an open issue in plant genomics. Recent experimental studies on highly heterozygous autotetraploid potato have shown that available methods do not deliver satisfying results in practice. We propose an optimal method to assemble haplotypes of highly heterozygous polyploids from Illumina short-sequencing reads. Our method is based on a generalization of the existing minimum fragment removal model to the polyploid case and on new integer linear programs to reconstruct optimal haplotypes. We validate our methods experimentally by means of a combined evaluation on simulated and experimental data based on 83 previously sequenced autotetraploid potato cultivars. Results on simulated data show that our methods produce highly accurate haplotype assemblies, while results on experimental data confirm a sensible improvement over the state of the art. Availability and implementation Executables for Linux at http://github.com/Computational Genomics/HaplotypeAssembler. Supplementary information Supplementary data are available at Bioinformatics online.

2018 ◽  
Author(s):  
Enrico Siragusa ◽  
Richard Finkers ◽  
Laxmi Parida

AbstractHaplotype assembly of polyploids is an open issue in plant genomics. Recent experimental studies on highly heterozygous autotetraploid potato have shown that available methods are not delivering satisfying results in practice. We propose an optimal method to assemble haplotypes of highly heterozygous polyploids from Illumina short sequencing reads. Our method is based on a generalization of the existing minimum fragment removal (MFR) model to the polyploid case and on new integer linear programs (ILPs) to reconstruct optimal haplotypes. We validate our methods experimentally by means of a combined evaluation on simulated and real data based on 83 previously sequenced autotetraploid potato cultivars. Results on simulated data show that our methods produce highly accurate haplotype assemblies, while results on real data confirm a sensible improvement over the state of the art. Binaries for Linux are available at: http://github.com/ComputationalGenomics/HaplotypeAssembler.


Author(s):  
Wei Huang ◽  
Ping Zheng ◽  
Zhenhai Cui ◽  
Zhuo Li ◽  
Yifeng Gao ◽  
...  

  Accurately predicting phenotypes from genotypes holds great promise to improve health management in humans and animals, and breeding efficiency in animals and plants. Although many prediction methods have been developed, the optimal method differs across datasets due to multiple factors, including species, environments, populations and traits of interest. Studies have demonstrated that the number of genes underlying a trait and its heritability are the two key factors that determine which method fits the trait the best. In many cases, however, these two factors are unknown for the traits of interest. We developed a cloud computing platform for Mining the Maximum Accuracy of Predicting phenotypes from genotypes (MMAP) using unsupervised learning on publicly available real data and simulated data. MMAP provides a user interface to upload input data, manage projects and analyses and download the output results. The platform is free for the public to conduct computations for predicting phenotypes and genetic merit using the best prediction method optimized from many available ones, including Ridge Regression, gBLUP, compressed BLUP, Bayesian LASSO, Bayes A, B, Cpi and many more. Users can also use the platform to conduct data analyses with any methods of their choice. It is expected that extensive usage of MMAP would enrich the training data, which in turn results in continual improvement of the identification of the best method for use with particular traits. Availability and implementation The MMAP user manual, tutorials and example datasets are available at http://zzlab.net/MMAP. Supplementary information Supplementary data are available at Bioinformatics online.


2018 ◽  
Vol 84 (10) ◽  
pp. 23-28
Author(s):  
D. A. Golentsov ◽  
A. G. Gulin ◽  
Vladimir A. Likhter ◽  
K. E. Ulybyshev

Destruction of bodies is accompanied by formation of both large and microscopic fragments. Numerous experiments on the rupture of different samples show that those fragments carry a positive electric charge. his phenomenon is of interest from the viewpoint of its potential application to contactless diagnostics of the early stage of destruction of the elements in various technical devices. However, the lack of understanding the nature of this phenomenon restricts the possibility of its practical applications. Experimental studies were carried out using an apparatus that allowed direct measurements of the total charge of the microparticles formed upon sample rupture and determination of their size and quantity. The results of rupture tests of duralumin and electrical steel showed that the size of microparticles is several tens of microns, the particle charge per particle is on the order of 10–14 C, and their amount can be estimated as the ratio of the cross-sectional area of the sample at the point of discontinuity to the square of the microparticle size. A model of charge formation on the microparticles is developed proceeding from the experimental data and current concept of the electron gas in metals. The model makes it possible to determine the charge of the microparticle using data on the particle size and mechanical and electrical properties of the material. Model estimates of the total charge of particles show order-of-magnitude agreement with the experimental data.


2019 ◽  
Vol 108 (1) ◽  
pp. 11-17
Author(s):  
Mert Şekerci ◽  
Hasan Özdoğan ◽  
Abdullah Kaplan

Abstract One of the methods used to treat different cancer diseases is the employment of therapeutic radioisotopes. Therefore, many clinical, theoretical and experimental studies are being carried out on those radioisotopes. In this study, the effects of level density models and gamma ray strength functions on the theoretical production cross-section calculations for the therapeutic radioisotopes 90Y, 153Sm, 169Er, 177Lu and 186Re in the (n,γ) route have been investigated. TALYS 1.9 code has been used by employing different level density models and gamma ray strength functions. The theoretically obtained data were compared with the experimental data taken from the literature. The results are presented graphically for better interpretation.


1981 ◽  
Vol 21 (06) ◽  
pp. 747-762 ◽  
Author(s):  
Karl E. Bennett ◽  
Craig H.K. Phelps ◽  
H. Ted Davis ◽  
L.E. Scriven

Abstract The phase behavior of microemulsions of brine, hydrocarbon, alcohol, and a pure alkyl aryl sulfonate-sodium 4-(1-heptylnonyl) benzenesulfonate (SHBS or Texas 1) was investigated as a function of the concentration of salt (NaCl, MgCl2, or CaCl2), the hydrocarbon (n-alkanes, octane to hexadecane), the alcohol (butyl and amyl isomers), the concentration of surfactant, and temperature. The phase behavior mimics that of similar systems with the commercial surfactant Witco TRS 10–80. The phase volumes follow published trends, though with exceptions.A mathematical framework is presented for modeling phase behavior in a manner consistent with the thermodynamically required critical tie lines and plait point progressions from the critical endpoints. Hand's scheme for modeling binodals and Pope and Nelson's approach to modeling the evolution of the surfactant-rich third phase are extended to satisfy these requirements.An examination of model-generated progressions of ternary phase diagrams enhances understanding of the experimental data and reveals correlations of relative phase volumes (volume uptakes) with location of the mixing point (overall composition) relative to the height of the three-phase region and the locations of the critical tie lines (critical endpoints and conjugate phases). The correlations account, on thermodynamic grounds, for cases in which the surfactant is present in more than one phase or the phase volumes change discontinuously, both cases being observed in the experimental study. Introduction The phase behavior of a surfactant-based micellar formulation is one of the major factors governing the displacement efficiency of any chemical flooding process employing that formulation. Knowledge of phase behavior is, thus, important for the interpretation of laboratory core floods, the design of flooding processes, and the evaluation of field tests. Phase behavior is connected intimately with other determinants of the flooding process, such as interfacial tension and viscosity. Since the number of equilibrium phases and their volumes and appearances are easier to measure and observe than phase compositions, viscosities, and interfacial tensions, there is great interest in understanding the phase-volume/phase-property relationships. Commercial surfactants, such as Witco TRS 10-80, are sulfonates of crude or partially refined oil. While they seem to be the most economically practicable surfactants for micellar flooding, their behavior, particularly with crude oils and reservoir brines, can be difficult to interpret, the phases varying with time and from batch to batch. Phase behavior studies with a small number of components, in conjunction with a theoretical understanding of phase behavior progressions, can aid in understanding more complex behavior. In particular, one can begin to appreciate which seemingly abnormal experimental observations (e.g., surfactant present in more than one phase or a discontinuity in phase volume trends) are merely features of certain regions of any phase diagram and which are peculiar to the specific crude oil or commercial surfactant used in the study.We report here experimental studies of the phase behavior of microemulsions of a pure sulfonate surfactant (Texas 1), a single normal alkane hydrocarbon, a simple brine, and a small amount of a suitable alcohol as cosurfactant or cosolvent. The controlled variables are hydrocarbon chain length, alcohol, salinity, salt type (NaCl, MgCl2, or CaCl2), surfactant purity, surfactant concentration, and temperature. Many of these experimental data were presented earlier. SPEJ P. 747^


Author(s):  
Patrick J. Migliorini ◽  
Alexandrina Untaroiu ◽  
William C. Witt ◽  
Neal R. Morgan ◽  
Houston G. Wood

Annular seals are used in turbomachinery to reduce secondary flow between regions of high and low pressure. In a vibrating rotor system, the non-axisymmetric pressure field developed in the small clearance between the rotor and the seal generate reactionary forces that can affect the stability of the entire rotor system. Traditionally, two analyses have been used to study the fluid flow in seals, bulk-flow analysis and computational fluid dynamics (CFD). Bulk-flow methods are computational inexpensive, but solve simplified equations that rely on empirically derived coefficients and are moderately accurate. CFD analyses generally provide more accurate results than bulk-flow codes, but solution time can vary between days and weeks. For gas damper seals, these analyses have been developed with the assumption that the flow can be treated as isothermal. Some experimental studies show that the difference between the inlet and outlet temperature temperatures is less than 5% but initial CFD studies show that there can be a significant temperature change which can have an effect on the density field. Thus, a comprehensive analysis requires the solution of an energy equation. Recently, a new hybrid method that employs a CFD analysis for the base state, unperturbed flow and a bulk-flow analysis for the first order, perturbed flow has been developed. This method has shown to compare well with full CFD analysis and experimental data while being computationally efficient. In this study, the previously developed hybrid method is extended to include the effects of non-isothermal flow. The hybrid method with energy equation is then compared with the isothermal hybrid method and experimental data for several test cases of hole-pattern seals and the importance of the use of energy equation is studied.


Author(s):  
Longxin Zhang ◽  
Shaowen Chen ◽  
Hao Xu ◽  
Jun Ding ◽  
Songtao Wang

Compared with suction slots, suction holes are (1) flexible in distribution; (2) alterable in size; (3) easy to fabricate and (4) high in strength. In this paper, the numerical and experimental studies for a high turning compressor cascade with suction air removed by using suction holes in the end-wall at a low Mach numbers are carried out. The main objective of the investigation is to study the influence of different suction distributions on the aerodynamic performance of the compressor cascade and to find a better compound suction scheme. A numerical model was first made and validated by comparing with the experimental results. The computed flow visualization and exit parameter distribution showed a good agreement with experimental data. Second, the model was then used to simulate the influence of different suction distributions on the aerodynamic performance of the compressor cascade. A better compound suction scheme was obtained by summarizing numerical results and tested in a low speed wind tunnel. As a result, the compound suction scheme can be used to significantly improve the performance of the compressor cascade because the corner separation gets further suppressed.


Author(s):  
A. Semenov ◽  
T. Sakhno ◽  
Y. Sakhno

Purpose: The article aims to study the photobiological safety of ultraviolet radiation of UV lamps in agriculture. Design/methodology/approach: The research and analysis of the lighting characteristics of samples of LUF 80 and LE 30 lamps, which are the most widely used in the agrarian complex. Findings: Experimental studies have shown that the photobiological safety of LUF 80 lamps belongs to the low-risk group RG1, while LE 30 lamps show high risk and are thus assigned to group RG3. Research limitations/implications: It is advisable to continue studying the characteristics of lamps and lamp systems for various fields of agriculture on the market in Ukraine to assess their compliance with safety requirements. Practical implications: The application of the proposed approach allows increasing the level of labor safety in commercial greenhouses or any other industry by choosing the suitable lamps for agriculture that at present are not regulated by additional safety measures. Originality/value: The originality of the article is showing the results of the experimental data of the studies of light-technical characteristics of ultraviolet lamps for agriculture.


2021 ◽  
Vol 1022 ◽  
pp. 194-202
Author(s):  
R.Kh. Dadashev ◽  
R.A. Kutuev

The experimental study results of the melts concentration dependence of the surface tension of the four-component indium-tin-lead-bismuth system and its constituent binary systems of indium-tin, indium-lead, indium-bismuth, tin-lead, tin-bismuth, lead-bismuth are presented in the paper. It is shown that the concentration dependence of the melts surface tension of the In-Sn-Pb-Bi four-component system can be predicted from the data on ST (surface tension) values of lateral binary systems. Features in the ST isotherms in the form of a minimum are observed only in the indium-tin lateral system from all lateral binaries. A distinctive feature of the detected minimum is that the minimum depth slightly exceeds the experimental error. Therefore, in addition to the fact that the area of average compositions was studied more thoroughly, we carried out the surface tension measurements by two independent methods. The experimental data obtained by both methods coincide within the experimental error and indicate the extremum availability on ST isotherms. Thus, ST experimental studies by two independent methods confirmed the presence of a flat minimum on ST isotherms of the indium-tin binary system increasing the reliability of the obtained data. The obtained outcomes and their comparison with experimental data have shown that the considered models for predicting surface properties based on data due to similar properties of lateral binary systems adequately reflect the experimental dependences. However, the prediction model based on Kohler's method of excess values describes the experimental curves more accurately.


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