Fast nonlinear Fourier transform algorithm for reconstruction of optical data from nonlinear spectra of the Manakov system.

We propose a high-precision algorithm for solving the three-component Gelfand-Levitan-Marchenko equations (GLME) associated with the Manakov system, which describes the behavior of light waves through the optical fibers. The algorithm generalizes the high-order generalized Toeplitz inner-bordering method for solving the two-component GLME associated with the nonlinear Schrödinger equation. Numerical experiments have shown that the proposed algorithm makes it possible to increase the accuracy of solving the GLME associated with Manakov system up to the sixth order.

Fast nonlinear Fourier transform algorithms for optical data processing.

The nonlinear Fourier transform (NFT) is an approach that is similar to a conventional Fourier transform. In particular, NFT allows to analyze the structure of a signal governed by the nonlinear Schrödinger equation (NLSE). Recently, NFT applied to NLSE has attracted special attention in applications of fiber-optic communication. Improving the speed and accuracy of the NFT algorithms remains an urgent problem in optics. We present an approach that allows to find all variants of symmetric exponential splitting schemes suitable for the fast NFT (FNFT) algorithms with low complexity. One of the obtained schemes showed good numerical results in computing the continuous spectrum compared with other fast fourth-order NFT schemes.

Generation of iPSCs from a Patient with the M694V Mutation in the MEFV Gene Associated with Familial Mediterranean Fever and Their Differentiation into Macrophages.

Familial Mediterranean fever (FMF) is a systemic autoinflammatory disorder caused by inherited mutations in the MEFV (Mediterranean FeVer) gene, located on chromosome 16 (16p13.3) and encoding the pyrin protein. Despite the existing data on MEFV mutations, the exact mechanism of their effect on the development of the pathological processes leading to the spontaneous and recurrent autoinflammatory attacks observed in FMF, remains unclear. Induced pluripotent stem cells (iPSCs) are considered an important tool to study the molecular genetic mechanisms of various diseases due to their ability to differentiate into any cell type, including macrophages, which contribute to the development of FMF. In this study, we developed iPSCs from an Armenian patient with FMF carrying the M694V, p.(Met694Val) (c.2080A>G, rs61752717) pathogenic mutation in exon 10 of the MEFV gene. As a result of direct differentiation, macrophages expressing CD14 and CD45 surface markers were obtained. We found that the morphology of macrophages derived from iPSCs of a patient with the MEFV mutation significantly differed from that of macrophages derived from iPSCs of a healthy donor carrying the wild-type MEFV gene.

A Model of iPSC-Derived Macrophages with TNFAIP3 Overexpression Reveals the Peculiarities of TNFAIP3 Protein Expression and Function in Human Macrophages.

Macrophages play a crucial role in the development and control of inflammation. Understanding the mechanisms balancing macrophage inflammatory activity is important to develop new strategies for treating inflammation-related diseases. TNF-α-induced protein 3 (TNFAIP3, A20) is a negative regulator of intracellular inflammatory cascades; its deficiency induces hyper-inflammatory reactions. Whether A20 overexpression can dampen macrophage inflammatory response remains unclear. Here, we generated human-induced pluripotent stem cells with tetracycline-inducible A20 expression and differentiated them into macrophages (A20-iMacs). A20-iMacs displayed morphology, phenotype, and phagocytic activity typical of macrophages, and they displayed upregulated A20 expression in response to doxycycline. A20 overexpression dampened the A20-iMac response to TNF-α, as shown by a decreased expression of IL1B and IL6 mRNA. A dynamic analysis of A20 expression following the generation of A20-iMacs and control iMacs showed that the expression declined in iMacs and that iMacs expressed a lower molecular weight form of the A20 protein (~70 kDa) compared with less differentiated cells (~90 kDa). A low-level expression of A20 and the predominance of a low-molecular-weight A20 form were also characteristic of monocyte-derived macrophages. The study for the first time developed a model for generating macrophages with an inducible expression of a target gene and identified the peculiarities of A20 expression in macrophages that likely underlie macrophage preparedness for inflammatory reactivity. It also suggested the possibility of mitigating inflammatory macrophage responses via A20 overexpression.

IPSC-Derived Astrocytes Contribute to In Vitro Modeling of Parkinson's Disease Caused by the GBA1 N370S Mutation.

Parkinson's disease (PD) is a neurodegenerative disorder that ranks second in prevalence after Alzheimer's disease. The number of PD diagnoses increases annually. Nevertheless, modern PD treatments merely mitigate symptoms rather than preventing neurodegeneration progression. The creation of an appropriate model to thoroughly study the mechanisms of PD pathogenesis remains a current challenge in biomedicine. Recently, there has been an increase in data regarding the involvement of not only dopaminergic neurons of the substantia nigra but also astrocytes in the pathogenesis of PD. Cell models based on induced pluripotent stem cells (iPSCs) and their differentiated derivatives are a useful tool for studying the contribution and interaction of these two cell types in PD. Here, we generated two iPSC lines, ICGi034-B and ICGi034-C, by reprogramming peripheral blood mononuclear cells of a patient with a heterozygous mutation c.1226A>G (p.N370S) in the GBA1 gene by non-integrating episomal vectors encoding OCT4, KLF4, L-MYC, SOX2, LIN28, and mp53DD. The iPSC lines demonstrate the expression of pluripotency markers and are capable of differentiating into three germ layers. We differentiated the ICGi034-B and ICGi034-C iPSC lines into astrocytes. This resulting cell model can be used to study the involvement of astrocytes in the pathogenesis of GBA-associated PD.

Transcriptomic Analysis of CRISPR/Cas9-Mediated PARP1-Knockout Cells under the Influence of Topotecan and TDP1 Inhibitor.

Topoisomerase 1 (TOP1) is an enzyme that regulates DNA topology and is essential for replication, recombination, and other processes. The normal TOP1 catalytic cycle involves the formation of a short-lived covalent complex with the 3' end of DNA (TOP1 cleavage complex, TOP1cc), which can be stabilized, resulting in cell death. This fact substantiates the effectiveness of anticancer drugs-TOP1 poisons, such as topotecan, that block the relegation of DNA and fix TOP1cc. Tyrosyl-DNA phosphodiesterase 1 (TDP1) is able to eliminate TOP1cc. Thus, TDP1 interferes with the action of topotecan. Poly(ADP-ribose) polymerase 1 (PARP1) is a key regulator of many processes in the cell, such as maintaining the integrity of the genome, regulation of the cell cycle, cell death, and others. PARP1 also controls the repair of TOP1cc. We performed a transcriptomic analysis of wild type and PARP1 knockout HEK293A cells treated with topotecan and TDP1 inhibitor OL9-119 alone and in combination. The largest number of differentially expressed genes (DEGs, about 4000 both up- and down-regulated genes) was found in knockout cells. Topotecan and OL9-119 treatment elicited significantly fewer DEGs in WT cells and negligible DEGs in PARP1-KO cells. A significant part of the changes caused by PARP1-KO affected the synthesis and processing of proteins. Differences under the action of treatment with TOP1 or TDP1 inhibitors alone were found in the signaling pathways for the development of cancer, DNA repair, and the proteasome. The drug combination resulted in DEGs in the ribosome, proteasome, spliceosome, and oxidative phosphorylation pathways.

Biochemical Characteristics of iPSC-Derived Dopaminergic Neurons from N370S GBA Variant Carriers with and without Parkinson's Disease.

GBA variants increase the risk of Parkinson's disease (PD) by 10 times. The GBA gene encodes the lysosomal enzyme glucocerebrosidase (GCase). The p.N370S substitution causes a violation of the enzyme conformation, which affects its stability in the cell. We studied the biochemical characteristics of dopaminergic (DA) neurons generated from induced pluripotent stem cells (iPSCs) from a PD patient with the GBA p.N370S mutation (GBA-PD), an asymptomatic GBA p.N370S carrier (GBA-carrier), and two healthy donors (control). Using liquid chromatography with tandem mass spectrometry (LC-MS/MS), we measured the activity of six lysosomal enzymes (GCase, galactocerebrosidase (GALC), alpha-glucosidase (GAA), alpha-galactosidase (GLA), sphingomyelinase (ASM), and alpha-iduronidase (IDUA)) in iPSC-derived DA neurons from the GBA-PD and GBA-carrier. DA neurons from the GBA mutation carrier demonstrated decreased GCase activity compared to the control. The decrease was not associated with any changes in GBA expression levels in DA neurons. GCase activity was more markedly decreased in the DA neurons of GBA-PD patient compared to the GBA-carrier. The amount of GCase protein was decreased only in GBA-PD neurons. Additionally, alterations in the activity of the other lysosomal enzymes (GLA and IDUA) were found in GBA-PD neurons compared to GBA-carrier and control neurons. Further study of the molecular differences between the GBA-PD and the GBA-carrier is essential to investigate whether genetic factors or external conditions are the causes of the penetrance of the p.N370S GBA variant.

New Hybrid Compounds Combining Fragments of Usnic Acid and Thioether Are Inhibitors of Human Enzymes TDP1, TDP2 and PARP1.

Tyrosyl-DNA phosphodiesterase 1 (TDP1) catalyzes the cleavage of the phosphodiester bond between the tyrosine residue of topoisomerase 1 (TOP1) and the 3' phosphate of DNA in the single-strand break generated by TOP1. TDP1 promotes the cleavage of the stable DNA-TOP1 complexes with the TOP1 inhibitor topotecan, which is a clinically used anticancer drug. This article reports the synthesis and study of usnic acid thioether and sulfoxide derivatives that efficiently suppress TDP1 activity, with IC50 values in the 1.4-25.2 µM range. The structure of the heterocyclic substituent introduced into the dibenzofuran core affects the TDP1 inhibitory efficiency of the compounds. A five-membered heterocyclic fragment was shown to be most pharmacophoric among the others. Sulfoxide derivatives were less cytotoxic than their thioester analogs. We observed an uncompetitive type of inhibition for the four most effective inhibitors of TDP1. The anticancer effect of TOP1 inhibitors can be enhanced by the simultaneous inhibition of PARP1, TDP1, and TDP2. Some of the compounds inhibited not only TDP1 but also TDP2 and/or PARP1, but at significantly higher concentration ranges than TDP1. Leader compound 10a showed promising synergy on HeLa cells in conjunction with the TOP1 inhibitor topotecan.

Exponential fourth order schemes for direct Zakharov-Shabat problem.

Nowadays, improving the accuracy of computational methods to solve the initial value problem of the Zakharov-Shabat system remains an urgent problem in optics. In particular, increasing the approximation order of the methods is important, especially in problems where it is necessary to analyze the structure of complex waveforms. In this work, we propose two finite-difference algorithms of fourth order of approximation in the time variable. Both schemes have the exponential form and conserve the quadratic invariant of Zakharov-Shabat system. The second scheme allows applying fast algorithms with low computational complexity (fast nonlinear Fourier transform).

Conservative multi-exponential scheme for solving the direct Zakharov-Shabat scattering problem.

The direct Zakharov-Shabat scattering problem has recently gained significant attention in various applications of fiber optics. The development of accurate and fast algorithms with low computational complexity to solve the Zakharov-Shabat problem (ZSP) remains an urgent problem in optics. In this Letter, a fourth-order multi-exponential scheme is proposed for the Zakharov-Shabat system. The construction of the scheme is based on a fourth-order three-exponential scheme and Suzuki factorization. This allows one to apply the fast algorithms with low complexity to calculate the ZSP for a large number of spectral parameters. The scheme conserves the quadratic invariant for real spectral parameters, which is important for various telecommunication problems related to information coding.

An autologous humanized patient-derived-xenograft platform to evaluate immunotherapy in ovarian cancer.

OBJECTIVE: The aim of this study was to "humanize" ovarian cancer patient-derived xenograft (PDX) models by autologous transfer of patient-matched tumor infiltrating lymphocytes (TILs) to evaluate immunotherapies. METHODS: Orthotopic high-grade serous ovarian cancer (HGSOC) PDX models were established from three patient donors. Models were molecularly and histologically validated by immunohistochemistry. TILs were expanded from donor tumors using a rapid expansion protocol. Ex vivo TIL and tumor co-cultures were performed to validate TIL reactivity against patient-matched autologous tumor cells. Expression of TIL activation markers and cytokine secretion was quantitated by flow cytometry and ELISA. As proof of concept, the efficacy of anti-PD-1 monotherapy was tested in autologous TIL/tumor HGSOC PDX models. RESULTS: Evaluation of T-cell activation in autologous TIL/tumor co-cultures resulted in an increase in HLA-dependent IFNγ production and T-cell activation. In response to increased IFNγ production, tumor cell expression of PD-L1 was increased. Addition of anti-PD-1 antibody to TIL/tumor co-cultures increased autologous tumor lysis in a CCNE1 amplified model. Orthotopic HGSOC PDX models from parallel patient-matched tumors maintained their original morphology and molecular marker profile. Autologous tumor-reactive TIL administration in patient-matched PDX models resulted in reduced tumor burden and increased survival, in groups that also received anti-PD-1 therapy. CONCLUSIONS: This study validates a novel, clinically relevant model system for in vivo testing of immunomodulating therapeutic strategies for ovarian cancer, and provides a unique platform for assessing patient-specific T-cell response to immunotherapy.

CellCountCV-A Web-Application for Accurate Cell Counting and Automated Batch Processing of Microscopic Images Using Fully Convolutional Neural Networks.

In vitro cellular models are promising tools for studying normal and pathological conditions. One of their important applications is the development of genetically engineered biosensor systems to investigate, in real time, the processes occurring in living cells. At present, there are fluorescence, protein-based, sensory systems for detecting various substances in living cells (for example, hydrogen peroxide, ATP, Ca2+ etc.,) or for detecting processes such as endoplasmic reticulum stress. Such systems help to study the mechanisms underlying the pathogenic processes and diseases and to screen for potential therapeutic compounds. It is also necessary to develop new tools for the processing and analysis of obtained microimages. Here, we present our web-application CellCountCV for automation of microscopic cell images analysis, which is based on fully convolutional deep neural networks. This approach can efficiently deal with non-convex overlapping objects, that are virtually inseparable with conventional image processing methods. The cell counts predicted with CellCountCV were very close to expert estimates (the average error rate was < 4%). CellCountCV was used to analyze large series of microscopic images obtained in experimental studies and it was able to demonstrate endoplasmic reticulum stress development and to catch the dose-dependent effect of tunicamycin.

Design, Synthesis, and Biological Investigation of Novel Classes of 3-Carene-Derived Potent Inhibitors of TDP1.

Two novel structural types of tyrosyl-DNA phosphodiesterase 1 (TDP1) inhibitors with hexahydroisobenzofuran 11 and 3-oxabicyclo [3.3.1]nonane 12 scaffolds were discovered. These monoterpene-derived compounds were synthesized through preliminary isomerization of (+)-3-carene to (+)-2-carene followed by reaction with heteroaromatic aldehydes. All the compounds inhibit the TDP1 enzyme at micro- and submicromolar levels, with the most potent compound having an IC50 value of 0.65 µM. TDP1 is an important DNA repair enzyme and a promising target for the development of new chemosensitizing agents. A panel of isogenic clones of the HEK293FT cell line knockout for the TDP1 gene was created using the CRISPR-Cas9 system. Cytotoxic effects of topotecan (Tpc) and non-cytotoxic compounds of the new structures were investigated separately and jointly in the TDP1 gene knockout cells. For two TDP1 inhibitors, 11h and 12k, a synergistic effect was observed with Tpc in the HEK293FT cells but was not found in TDP1 -/- cells. Thus, it is likely that the synergistic effect is caused by inhibition of TDP1. Synergy was also found for 11h in other cancer cell lines. Thus, sensitizing cancer cells using a non-cytotoxic drug can enhance the efficacy of currently used pharmaceuticals and, concomitantly, reduce toxic side effects.

A Room-Temperature Verwey-type Transition in Iron Oxide, Fe5 O6.

Functional oxides whose physicochemical properties may be reversibly changed at standard conditions are potential candidates for the use in next-generation nanoelectronic devices. To date, vanadium dioxide (VO2 ) is the only known simple transition-metal oxide that demonstrates a near-room-temperature metal-insulator transition that may be used in such appliances. In this work, we synthesized and investigated the crystals of a novel mixed-valent iron oxide with an unconventional Fe5 O6 stoichiometry. Near 275 K, Fe5 O6 undergoes a Verwey-type charge-ordering transition that is concurrent with a dimerization in the iron chains and a following formation of new Fe-Fe chemical bonds. This unique feature highlights Fe5 O6 as a promising candidate for the use in innovative applications. We established that the minimal Fe-Fe distance in the octahedral chains is a key parameter that determines the type and temperature of charge ordering. This model provides new insights into charge-ordering phenomena in transition-metal oxides in general.

Impact of Xist RNA on chromatin modifications and transcriptional silencing maintenance at different stages of imprinted X chromosome inactivation in vole Microtus levis.

In vole Microtus levis, cells of preimplantation embryo and extraembryonic tissues undergo imprinted X chromosome inactivation (iXCI) which is triggered by a long non-coding nuclear RNA, Xist. At early stages of iXCI, chromatin of vole inactive X chromosome is enriched with the HP1 heterochromatin-specific protein, trimethylated H3K9 and H4K20 attributable to constitutive heterochromatin. In the study, using vole trophoblast stem (TS) cells as a model of iXCI, we further investigated chromatin of the inactive X chromosome of M. levis and tried to find out the role of Xist RNA. We demonstrated that chromatin of the inactive X chromosome in vole TS cells also contained the SETDB1 histone methyltransferase and KAP1 protein. In addition, we observed that Xist RNA did not contribute significantly to maintenance of X chromosome inactive state during iXCI in vole TS cells. Xist repression affected neither transcriptional silencing caused by iXCI nor maintenance of trimethylated H3K9 and H4K20 as well as HP1, KAP1, and SETDB1 on the inactive X chromosome. Moreover, the unique repertoire of chromatin modifications on the inactive X chromosome in vole TS cells could be disrupted by a chemical compound, DZNep, and then restored even in the absence of Xist RNA. However, Xist transcript was necessary for recruitment of an additional repressive histone modification, trimethylated H3K27, to the inactive X chromosome during vole TS cell differentiation.

Numerical algorithm with fourth-order accuracy for the direct Zakharov-Shabat problem.

We propose a finite-difference algorithm for solving the initial problem for the Zakharov-Shabat system. This method has the fourth order of accuracy and represents a generalization of the second-order Boffetta-Osborne scheme. Our method permits the Zakharov-Shabat spectral problem to be solved more effectively for continuous and discrete spectra.

Hamiltonian approach for optimization of phase-sensitive double-pumped parametric amplifiers.

In this work we applied a Hamiltonian formalism to simplify the equations of non-degenerate nonlinear four-wave mixing to the one-degree-of-freedom Hamiltonian equations with a three-parameter Hamiltonian. Thereby, a problem of signal amplification in a phase-sensitive double-pumped parametric fiber amplifier with pump depletion was reduced to a geometrical study of the phase portraits of the one-degree-of-freedom Hamiltonian system. For a symmetric case of equal pump powers and equal signal and idler powers at the fiber input, it has been shown that the theoretical maximum gain occurs on the extremal trajectories. However, to reduce the nonlinear interaction of waves, we proposed to choose the separatrix as the optimal trajectory on the phase plane. Analytical expressions were found for the maximum amplification, as well as the length of optical fiber and the relative phase of interacting waves allowing this amplification. Using the proposed approach, we optimized of the phase-sensitive parametric amplifier. As a result, the optimal parameters of the phase-sensitive amplifier were found and the maximum possible signal amplification was realized in a broad range of signal wavelengths.

More Than 50 Years after Its Discovery in SiO2 Octahedral Coordination Has Also Been Established in SiS2 at High Pressure.

SiO2 exhibits a high-pressure-high-temperature polymorphism, leading to an increase in silicon coordination number and density. However, for the related compound SiS2 such pressure-induced behavior has not been observed with tetrahedral coordination yet. All four crystal structures of SiS2 known so far contain silicon with tetrahedral coordination. In the orthorhombic, ambient-pressure phase these tetrahedra share edges and achieve only low space filling and density. Up to 4 GPa and 1473 K, three phases can be quenched as metastable phases from high-pressure high-temperature to ambient conditions. Space occupancy and density are increased first by edge and corner sharing and then by corner sharing alone. The structural situation of SiS2 up to the current study resembles that of SiO2 in 1960: Then, in its polymorphs only Si-O4 tetrahedra were known. But in 1961, a polymorph with rutile structure was discovered: octahedral Si-O6 coordination was established. Now, 50 years later, we report here on the transition from 4-fold to 6-fold coordination in SiS2, the sulfur analogue of silica.

Transparent dense sodium.

Under pressure, metals exhibit increasingly shorter interatomic distances. Intuitively, this response is expected to be accompanied by an increase in the widths of the valence and conduction bands and hence a more pronounced free-electron-like behaviour. But at the densities that can now be achieved experimentally, compression can be so substantial that core electrons overlap. This effect dramatically alters electronic properties from those typically associated with simple free-electron metals such as lithium (Li; refs 1-3) and sodium (Na; refs 4, 5), leading in turn to structurally complex phases and superconductivity with a high critical temperature. But the most intriguing prediction-that the seemingly simple metals Li (ref. 1) and Na (ref. 4) will transform under pressure into insulating states, owing to pairing of alkali atoms-has yet to be experimentally confirmed. Here we report experimental observations of a pressure-induced transformation of Na into an optically transparent phase at approximately 200 GPa (corresponding to approximately 5.0-fold compression). Experimental and computational data identify the new phase as a wide bandgap dielectric with a six-coordinated, highly distorted double-hexagonal close-packed structure. We attribute the emergence of this dense insulating state not to atom pairing, but to p-d hybridizations of valence electrons and their repulsion by core electrons into the lattice interstices. We expect that such insulating states may also form in other elements and compounds when compression is sufficiently strong that atomic cores start to overlap strongly.

Stress-induced electrolyte leakage: the role of K+-permeable channels and involvement in programmed cell death and metabolic adjustment.

Electrolyte leakage accompanies plant response to stresses, such as salinity, pathogen attack, drought, heavy metals, hyperthermia, and hypothermia; however, the mechanism and physiological role of this phenomenon have only recently been clarified. Accumulating evidence shows that electrolyte leakage is mainly related to K(+) efflux from plant cells, which is mediated by plasma membrane cation conductances. Recent studies have demonstrated that these conductances include components with different kinetics of activation and cation selectivity. Most probably they are encoded by GORK, SKOR, and annexin genes. Hypothetically, cyclic nucleotide-gated channels and ionotropic glutamate receptors can also be involved. The stress-induced electrolyte leakage is usually accompanied by accumulation of reactive oxygen species (ROS) and often results in programmed cell death (PCD). Recent data strongly suggest that these reactions are linked to each other. ROS have been shown to activate GORK, SKOR, and annexins. ROS-activated K(+) efflux through GORK channels results in dramatic K(+) loss from plant cells, which stimulates proteases and endonucleases, and promotes PCD. This mechanism is likely to trigger plant PCD under severe stress. However, in moderate stress conditions, K(+) efflux could play an essential role as a 'metabolic switch' in anabolic reactions, stimulating catabolic processes and saving 'metabolic' energy for adaptation and repair needs.