| 1. |
- Viallon, Vivian, et al.
(author)
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A new pipeline for the normalization and pooling of metabolomics data
- 2021
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In: Metabolites. - : MDPI. - 2218-1989. ; 11:9
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Journal article (peer-reviewed)abstract
- Pooling metabolomics data across studies is often desirable to increase the statistical power of the analysis. However, this can raise methodological challenges as several preanalytical and analytical factors could introduce differences in measured concentrations and variability between datasets. Specifically, different studies may use variable sample types (e.g., serum versus plasma) collected, treated, and stored according to different protocols, and assayed in different laboratories using different instruments. To address these issues, a new pipeline was developed to normalize and pool metabolomics data through a set of sequential steps: (i) exclusions of the least informative observations and metabolites and removal of outliers; imputation of missing data; (ii) identification of the main sources of variability through principal component partial R-square (PC-PR2) analysis; (iii) application of linear mixed models to remove unwanted variability, including samples’ originating study and batch, and preserve biological variations while accounting for potential differences in the residual variances across studies. This pipeline was applied to targeted metabolomics data acquired using Biocrates AbsoluteIDQ kits in eight case-control studies nested within the European Prospective Investigation into Cancer and Nutrition (EPIC) cohort. Comprehensive examination of metabolomics measurements indicated that the pipeline improved the comparability of data across the studies. Our pipeline can be adapted to normalize other molecular data, including biomarkers as well as proteomics data, and could be used for pooling molecular datasets, for example in international consortia, to limit biases introduced by inter-study variability. This versatility of the pipeline makes our work of potential interest to molecular epidemiologists.
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| 2. |
- Jenab, S. M. Hosseini, et al.
(author)
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Head-on collision of nonlinear solitary solutions to Vlasov-Poisson equations
- 2019
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In: Physics of Plasmas. - : American Institute of Physics (AIP). - 1070-664X .- 1089-7674. ; 26:2
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Journal article (peer-reviewed)abstract
- Nonlinear solitary solutions to the Vlasov-Poisson set of equations are studied in order to investigate their stability by employing a fully kinetic simulation approach. This study is carried out in the ion-acoustic regime for a collisionless, electrostatic, and Maxwellian electron-ion plasma. The trapped population of electrons is modeled based on the well-known Schamel distribution function. Head-on mutual collisions of nonlinear solutions are performed in order to examine their collisional stability. The findings include three major aspects: (I) These nonlinear solutions are found to be divided into three categories based on their Mach numbers, i.e., stable, semi-stable, and unstable. Semi-stable solutions indicate a smooth transition from stable to unstable solutions for the increasing Mach number. (II) The stability of solutions is traced back to a condition imposed on averaged velocities, i.e., net neutrality. It is shown that a bipolar structure is produced in the flux of electrons, early in the temporal evolution. This bipolar structure acts as the seed of the net-neutrality instability, which tips off the energy balance of nonlinear solution during collisions. As the Mach number increases, the amplitude of the bipolar structure grows and results in a stronger instability. (III) It is established that during mutual collisions, a merging process of electron holes can occur to a variety of degrees, based on their velocity characteristics. Specifically, the number of rotations of electron holes around each other (in the merging phase) varies. Furthermore, it is observed that in the case of a non-integer number of rotations, two electron holes exchange their phase space cores.
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| 3. |
- Jenab, S. M. Hosseini, et al.
(author)
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Scattering of electron holes in the context of ion-acoustic regime
- 2019
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In: Physics of Plasmas. - : American Institute of Physics (AIP). - 1070-664X .- 1089-7674. ; 26:3
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Journal article (peer-reviewed)abstract
- Mutual collisions between ion-acoustic solitary waves are studied based on a fully kinetic simulation approach. Two cases, small and large relative velocities, are studied, and the effect of trapped electron population on the collision process is focused upon. It is shown that, for the case of small relative velocity, the repelling force between the trapped populations of electrons results in scattering of electron holes. However, this phenomenon cannot be witnessed if the relative velocity is considerably high since the impact of trapped population remains very weak.
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