Energy of eigen-modes in magnetohydrodynamic flows of ideal fluids

Analytical expression for energy of eigen-modes in magnetohydrodynamic flows of ideal fluids is obtained. It is shown that the energy of unstable modes is zero, while the energy of stable oscillatory modes (waves) can assume both positive and negative values. Negative energy waves always correspond to non-symmetric eigen-modes -- modes that have a component of wave-vector along the equilibrium velocity. These results suggest that all non-symmetric instabilities in ideal MHD systems with flows are associated with coupling of positive and negative energy waves. As an example the energy of eigen-modes is calculated for incompressible conducting fluid rotating in axial magnetic field.Comment: 10 pages, 3 figure

A Lagrangian kinetic model for collisionless magnetic reconnection

A new fully kinetic system is proposed for modeling collisionless magnetic reconnection. The formulation relies on fundamental principles in Lagrangian dynamics, in which the inertia of the electron mean flow is neglected in the expression of the Lagrangian, rather then enforcing a zero electron mass in the equations of motion. This is done upon splitting the electron velocity into its mean and fluctuating parts, so that the latter naturally produce the corresponding pressure tensor. The model exhibits a new Coriolis force term, which emerges from a change of frame in the electron dynamics. Then, if the electron heat flux is neglected, the strong electron magnetization limit yields a hybrid model, in which the electron pressure tensor is frozen into the electron mean velocity.Comment: 15 pages, no figures. To Appear in Plasma Phys. Control. Fusio

Canonical description of ideal magnetohydrodynamic flows and integrals of motion

In the framework of the variational principle the canonical variables describing ideal magnetohydrodynamic (MHD) flows of general type (i.e., with spatially varying entropy and nonzero values of all topological invariants) are introduced. The corresponding complete velocity representation enables us not only to describe the general type flows in terms of single-valued functions, but also to solve the intriguing problem of the ``missing'' MHD integrals of motion. The set of hitherto known MHD local invariants and integrals of motion appears to be incomplete: for the vanishing magnetic field it does not reduce to the set of the conventional hydrodynamic invariants. And if the MHD analogs of the vorticity and helicity were discussed earlier for the particular cases, the analog of Ertel invariant has been so far unknown. It is found that on the basis of the new invariants introduced a wide set of high-order invariants can be constructed. The new invariants are relevant both for the deeper insight into the problem of the topological structure of the MHD flows as a whole and for the examination of the stability problems. The additional advantage of the proposed approach is that it enables one to deal with discontinuous flows, including all types of possible breaks.Comment: 16 page

Gene-centric coverage of the human liver transcriptome: QPCR, Illumina, and Oxford Nanopore RNA-Seq

It has been shown that the best coverage of the HepG2 cell line transcriptome encoded by genes of a single chromosome, chromosome 18, is achieved by a combination of two sequencing platforms, Illumina RNA-Seq and Oxford Nanopore Technologies (ONT), using cut-off levels of FPKM > 0 and TPM > 0, respectively. In this study, we investigated the extent to which the combination of these transcriptomic analysis methods makes it possible to achieve a high coverage of the transcriptome encoded by the genes of other human chromosomes. A comparative analysis of transcriptome coverage for various types of biological material was carried out, and the HepG2 cell line transcriptome was compared with the transcriptome of liver tissue cells. In addition, the contribution of variability in the coverage of expressed genes in human transcriptomes to the creation of a draft human transcriptome was evaluated. For human liver tissues, ONT makes an extremely insignificant contribution to the overall coverage of the transcriptome. Thus, to ensure maximum coverage of the liver tissue transcriptome, it is sufficient to apply only one technology: Illumina RNA-Seq (FPKM > 0)

The Size of the Human Proteome: The Width and Depth

This work discusses bioinformatics and experimental approaches to explore the human proteome, a constellation of proteins expressed in different tissues and organs. As the human proteome is not a static entity, it seems necessary to estimate the number of different protein species (proteoforms) and measure the number of copies of the same protein in a specific tissue. Here, meta-analysis of neXtProt knowledge base is proposed for theoretical prediction of the number of different proteoforms that arise from alternative splicing (AS), single amino acid polymorphisms (SAPs), and posttranslational modifications (PTMs). Three possible cases are considered: (1) PTMs and SAPs appear exclusively in the canonical sequences of proteins, but not in splice variants; (2) PTMs and SAPs can occur in both proteins encoded by canonical sequences and in splice variants; (3) all modification types (AS, SAP, and PTM) occur as independent events. Experimental validation of proteoforms is limited by the analytical sensitivity of proteomic technology. A bell-shaped distribution histogram was generated for proteins encoded by a single chromosome, with the estimation of copy numbers in plasma, liver, and HepG2 cell line. The proposed metabioinformatics approaches can be used for estimation of the number of different proteoforms for any group of protein-coding genes

Left Atrium Involvement in Lymphoma Patients: Single Center Observational Study

Aim. To assess the structure and performance of left atrium (LA) before and after 3 cycles of anticancer treatment in lymphoma patients, as well as the incidences of supraventricular arrhythmia (SVA) and the levels of biomarkers of inflammation.Material and Methods. This is a prospective observational study of patients with confirmed diagnosis of lymphoma [n=23; 57% men; median age 52 (34;64) years], who had no prior polychemotherapy. The comparison group included persons without lymphoma [n=18; 50% men; median age 43 (37; 54) years] comparable with the main group in terms of sex, age and risk factors for cardiovascular diseases. Patients with lymphoma underwent 24h-ECG monitoring and advanced transthoracic echocardiography at baseline and after 3 cycles (within 3 months) of anticancer treatment. Biomarkers of inflammation were measured. The results were compared with the data of the comparison group.Results. In lymphoma patients, LA reservoir, conduit, and booster function were found to be impaired at baseline but were comparable with these in matched controls. After 3 cycles of anticancer treatment, a trend to reduction of LA booster and conduit strain was found. The proportion of those with SVA was significantly higher in lymphoma patients before chemotherapy compared to those after anti-cancer treatment or controls: 57% vs 10% and 33% respectively (p<0.05). Lymphoma patients had a higher number of premature ventricular beats at baseline than after treatment or in control [183 (14;841) vs 38 (14;94) and 9 (4;38) respectively]. There were no associations found between the parameters of LA structure and function and SVA. Moderate positive correlation between ESR and supraventricular premature complexes was found (rS=0.44; p<0.05). A positive correlation between LA contractile function and inflammatory biomarkers were revealed: LA active ejection fraction (LA EFact) and ESR (rS=0.42, p<0.05); LA volume index and β-globulin (rS=0.43, p<0.05); LA EFact and neuregulin-1β (rS=0.42, p<0.05); LA expansion index and neuregulin-1β (rS=0.55, p<0.05).Conclusions. In lymphoma patients, LA phasic strain parameters were impaired regardless of anticancer treatment. The associations between inflammatory biomarkers with SVA and parameters of LA performance were found