Optimizing the generation of polarization squeezed light in nonlinear optical fibers driven by femtosecond pulses.

Bright squeezed light can be generated in optical fibers utilizing the Kerr effect for ultrashort laser pulses. However, pulse propagation in a fiber is subject to nonconservative effects that deteriorate the squeezing. Here, we analyze two-mode polarization squeezing, which is SU(2)-invariant, robust against technical perturbations, and can be generated in a polarization-maintaining fiber. We perform a rigorous numerical optimization of the process and the pulse parameters using our advanced model of quantum pulse evolution in the fiber that includes various nonconservative effects and real fiber data. Numerical results are consistent with experimental results.

Implementation of rapid microwave sintering using a 24 GHz gyrotron system.

Rapid microwave sintering of different oxide ceramics with heating rates up to 300 °C/min and zero hold time has been implemented using a 24 GHz gyrotron-based system for high-temperature processing of materials. The design of the system, principle of operation, and process control are described. Particular attention is given to the design of thermal insulation assemblies and the implementation of temperature measurement in an environment with intense electromagnetic fields. A description of an optical system for dilatometry and temperature measurement is presented. The interrelation between the automatically regulated output power of the gyrotron and the microwave power absorbed volumetrically in the sample is analyzed on the basis of energy balance considerations. The analysis is illustrated by considering examples of rapid sintering processes with ZnO-based and BaTiO3 ceramic samples making use of direct and susceptor-assisted microwave heating. It is demonstrated that an increase in the volumetrically absorbed power leads to the development of a controlled thermal instability, which results in a lower temperature of the densification onset.

[Analysis of phosphatidylcholines alterations in human glioblastoma multiform tissues ex vivo]. / Analiz izmenenii sostava fosfatidilkholinov v glioblastomakh cheloveka ex vivo.

Significant metabolism alteration is accompanying the cell malignization process. Energy metabolism disturbance leads to the activation of de novo synthesis and beta-oxidation processes of lipids and fatty acids in a cancer cell, which becomes an indicator of pathological processes inside the cell. The majority of studies dealing with lipid metabolism alterations in glial tumors are performed using the cell lines in vitro or animal models. However, such conditions do not entirely represent the physiological conditions of cell growth or possible cells natural variability. This work presents the results of the data obtained by applying ambient mass spectrometry to human glioblastoma multiform tissues. By analyzing a relatively large cohort of primary and secondary glioblastoma samples, we identify the alterations in cells lipid composition, which accompanied the development of grade IV brain tumors. We demonstrate that primary glioblastomas, as well as ones developed from astrocytomas, are enriched with mono- and diunsaturated phosphatidylcholines (PC 26:1, 30:2, 32:1, 32:2, 34:1, 34:2). Simultaneously, the saturated and polyunsaturated phosphatidylcholines and phosphatidylethanolamines decrease. These alterations are obviously linked to the availability of the polyunsaturated fatty acids and activation of the de novo lipid synthesis and beta-oxidation pathways under the anaerobic conditions in the tumor core.

The software for interactive evaluation of mass spectra stability and reproducibility.

SUMMARY: Mass spectrometry (MS) methods are widely used for the analysis of biological and medical samples. Recently developed methods, such as DESI, REIMS and NESI allow fast analyses without sample preparation at the cost of higher variability of spectra. In biology and medicine, MS profiles are often used with machine learning (classification, regression, etc.) algorithms and statistical analysis, which are sensitive to outliers and intraclass variability. Here, we present spectra similarity matrix (SSM) Display software, a tool for fast visual outlier detection and variance estimation in mass spectrometric profiles. The tool speeds up the process of manual spectra inspection, improves accuracy and explainability of outlier detection, and decreases the requirements to the operator experience. It was shown that the batch effect could be revealed through SSM analysis and that the SSM calculation can also be used for tuning novel ion sources concerning the quality of obtained mass spectra. AVAILABILITY AND IMPLEMENTATION: Source code, example datasets, binaries and other information are available at https://github.com/EvgenyZhvansky/R_matrix. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

[The role of lipids in the classification of astrocytoma and glioblastoma using MS tumor profiling]. / Rol' lipidov pri klassifikatsii astrotsitomy i glioblastomy pri pomoshchi mass-spektrometricheskogo profilirovaniia opukholei.

Express MS identification of biological tissues has become a much more accessible research method due to the application of direct specimen ionization at atmospheric pressure. In contrast to traditional methods of analysis employing GC-MS methods for determining the molecular composition of the analyzed objects it eliminates the influence of mutual ion suppression. Despite significant progress in the field of direct MS of biological tissues, the question of mass spectrometric profile attribution to a certain type of tissue still remains open. The use of modern machine learning methods and protocols (e.g., "random forests") enables us to trace possible relationships between the components of the sample MS profile and the result of brain tumor tissue classification (astrocytoma or glioblastoma). It has been shown that the most pronounced differences in the mass spectrometric profiles of these tumors are due to their lipid composition. Detection of statistically significant differences in lipid profiles of astrocytoma and glioblastoma may be used to perform an express test during surgery and inform the neurosurgeon what type of malignant tissue he is working with. The ability to accurately determine the boundaries of the neoplastic growth significantly improves the quality of both surgical intervention and postoperative rehabilitation, as well as the duration and quality of life of patients.

Metrics for evaluating the stability and reproducibility of mass spectra.

In this work, we demonstrate a new approach for assessing the stability and reproducibility of mass spectra obtained via ambient ionization methods. This method is suitable for both comparing experiments during which only one mass spectrum is measured and for evaluating the internal homogeneity of mass spectra collected over a period of time. The approach uses Pearson's r coefficient and the cosine measure to compare the spectra. It is based on the visualization of dissimilarities between measurements, thus leading to the analysis of dissimilarity patterns. The cosine measure and correlations are compared to obtain better metrics for spectra homogeneity. The method filters out unreliable scans to prevent the analyzed sample from being wrongly characterized. The applicability of the method is demonstrated on a set of brain tumor samples. The developed method could be employed in neurosurgical applications, where mass spectrometry is used to monitor the intraoperative tumor border.

Unified representation of high- and low-resolution spectra to facilitate application of mass spectrometric techniques in clinical practice.

The majority of research in the biomedical sciences is carried out with the highest resolution accessible to the scientist, but, in the clinic, cost constraints necessitate the use of low-resolution devices. Here, we compare high- and low-resolution direct mass spectrometry profiling data and propose a simple pre-processing technique that makes high-resolution data suitable for the development of classification and regression techniques applicable to low-resolution data, while retaining high accuracy of analysis. This work demonstrates an approach to de-noising spectra to make the same representation for both high- and low-resolution spectra. This approach uses noise threshold detection based on the Tversky index, which compares spectra with different resolutions, and minimizes the percentage of resolution-specific peaks. The presented method provides an avenue for the development of analytical algorithms using high-resolution mass spectrometry data, while applying these algorithms in the clinic using low-resolution mass spectrometers.

[Destabilization of the DNA Duplex of Actively Replicating Promoters of T7-Like Bacteriophages].

The relation between the processes of replication and transcription has been actively studied over several decades, but detailed mechanisms for their interaction have not been established reliably. Among the initiating transcription promoters of bacteria and bacteriophages, there are both promoters having an additional function of the secondary origin of replication (OR) and promoters not participating in this process. In this paper, we describe the stability of DNA by Stress-Induced Duplex Destabilization (SIDD) profiles for a complete set of promoters and the primary OR of the bacteriophage T7 genome. It has been shown that, among the native T7 promoters, only those that have an additional function of secondary OR are characterized by high destabilization. These include the phiOL and phiOR promoters adjoining the 5' and 3' terminal repeats of bacteriophage T7, and of six other T7 group phages. In each case, these two promoters are located in the regions of DNA with high destabilization of the duplex. Additionally, the genomes of seven representatives of the T7 group without annotated phiOL and phiOR have been considered. For three of them, high peaks of SIDD profiles have been found near the ends of the genomic DNA that may be due to the presence of similar phiOL and phiOR promoters. Probably, such promoters can be found in the genomes of other bacteriophages. Thus, for the promoters of bacteriophages, we have a confirmation of the relationship of SIDD as a DNA duplex parameter and the DNA replication initiation on promoters, serving as secondary OR.

High-resolution mass spectra processing for the identification of different pathological tissue types of brain tumors.

The purpose of the work is to demonstrate the possibilities of identifying the different types of pathological tissue identification directly through tissue mass spectrometry. Glioblastoma parts dissected during neurosurgical operation were investigated. Tumor fragments were investigated by the immunohistochemistry method and were identified as necrotic tissue with necrotized vessels, necrotic tissue with tumor stain, tumor with necrosis (tumor tissue as major), tumor, necrotized tumor (necrotic tissues as major), parts of tumor cells, boundary brain tissue, and brain tissue hyperplasia. The technique of classification of tumor tissues based on mass spectrometric profile data processing is suggested in this paper. Classifiers dividing the researched sample to the corresponding tissue type were created as a result of the processing. Classifiers of necrotic and tumor tissues are shown to yield a combined result when the tissue is heterogeneous and consists of both tumor cells and necrotic tissue.

Absolute pulse energy measurements of soft x-rays at the Linac Coherent Light Source.

This paper reports novel measurements of x-ray optical radiation on an absolute scale from the intense and ultra-short radiation generated in the soft x-ray regime of a free electron laser. We give a brief description of the detection principle for radiation measurements which was specifically adapted for this photon energy range. We present data characterizing the soft x-ray instrument at the Linac Coherent Light Source (LCLS) with respect to the radiant power output and transmission by using an absolute detector temporarily placed at the downstream end of the instrument. This provides an estimation of the reflectivity of all x-ray optical elements in the beamline and provides the absolute photon number per bandwidth per pulse. This parameter is important for many experiments that need to understand the trade-offs between high energy resolution and high flux, such as experiments focused on studying materials via resonant processes. Furthermore, the results are compared with the LCLS diagnostic gas detectors to test the limits of linearity, and observations are reported on radiation contamination from spontaneous undulator radiation and higher harmonic content.

Electrostatic map of T7 DNA: comparative analysis of functional and electrostatic properties of T7 RNA polymerase-specific promoters.

The entire T7 bacteriophage genome contains 39937 base pairs (Database NCBI RefSeq N1001604). Here, electrostatic potential distribution around double helical T7 DNA was calculated by Coulomb method using the computer program of Sorokin A.A. (lptolik@gmail.com). Electrostatic profiles of 17 promoters recognized by T7 phage-specific RNA polymerase were analyzed. It was shown that electrostatic profiles of all T7 RNA polymerase-specific promoters can be characterized by distinctive motifs which are specific for each promoter class. Comparative analysis of electrostatic profiles of native T7 promoters of different classes demonstrates that T7 RNA polymerase can differentiate them due to their electrostatic features.

Two-photon inner-shell ionization in the extreme ultraviolet.

We have observed the simultaneous inner-shell absorption of two extreme-ultraviolet photons by a Xe atom in an experiment performed at the short-wavelength free electron laser facility FLASH. Photoelectron spectroscopy permitted us to unambiguously identify a feature resulting from the ionization of a single electron of the 4d subshell of Xe by two photons each of energy (93±1) eV. The feature's intensity has a quadratic dependence on the pulse energy. The results are discussed and interpreted within the framework of recent results of ion spectroscopy experiments of Xe obtained at ultrahigh irradiance in the extreme-ultraviolet regime.

Extreme ultraviolet laser excites atomic giant resonance.

Exceptional behavior of light-matter interaction in the extreme ultraviolet is demonstrated. The photoionization of different rare gases was compared at the free-electron laser in Hamburg, FLASH, by applying ion spectroscopy at the wavelength of 13.7 nm and irradiance levels of thousands of terawatts per square centimeter. In the case of xenon, the degree of nonlinear photoionization was found to be significantly higher than for neon, argon, and krypton. This target specific behavior cannot be explained by the standard theories developed for optical strong-field phenomena. We suspect that the collective giant 4d resonance of xenon is the driving force behind the effect that arises in this spectral range.

[Electrostatic map of bacteriophage T7 genome. Comparative analysis of electrostatic properties of sigma70-specific T7 DNA promoters recognized by RNA-polymerase of Escherichia coli].

The distribution of the electrostatic potential of T7 bacteriophage genome has been calculated. Promoter sites were localized in the electrostatic profile of T7-DNA. The electrostatic patterns of sigma70-specific promoters interacting with Escherichia coli RNA-polymerase were analyzed and compared with their functional behavior. Some specific electrostatic motifs were found in the upstream region of the promoters that may be involved in the differential recognition of promoter DNA by RNA-polymerase.

Spatio-temporal coherence of free electron laser pulses in the soft x-ray regime.

The temporal coherence properties of soft x-ray free electron laser pulses at FLASH are measured at 23.9 nm by interfering two time-delayed partial beams directly on a CCD camera. The partial beams are obtained by wave front beam splitting in an autocorrelator operating at photon energies from h nu = 30 to 200 eV. At zero delay a visibility of (0.63+/- 0.04) is measured. The delay of one partial beam reveals a coherence time of 6 fs at 23.9 nm. The visibility further displays a non-monotonic decay, which can be rationalized by the presence of multiple pulse structure.

[Analysis of the distribution of the nucleotide sequence and electrostatic potential of the Escherichia coli genome].

The oligonucleotide composition of the E. coli genome and its sigma70-specific promoters has been analyzed. The promoter DNA was shown to contain mainly AT-rich hexanucleotides having functionally important physical properties such as the ability to form easily melting sites and induce the bending of the double helix. A comparative analysis of the electrostatic characteristics of hexanucleotides within the whole sequence of the E. coli genome and its promoter regions was made. Hexanucleotides possessing a more electronegative surrounding were found to predominate in the nucleotide sequence of the promoter DNA.

[Regulation of promoter activity through electrostatic interactions with RNA-polymerase].

Electrostatic profiles for sigma70-specific promoters of T4 bacteriophage and four consensus-like synthetic promoters have been calculated. It was shown that the promoters can be classified according to the presence of some specific electrostatic elements located in the far upstream region of their DNAs. A correlation between the electrostatic elements specific for promoters and their functional behaviour was established. A general scheme of promotor activity regulation through electrostatic interactions between the upstream region of promoter DNA and the RNA-polymerase a-subunit was suggested.

Photoelectric effect at ultrahigh intensities.

In the spectral range of the extreme ultraviolet at a wavelength of 13.3 nm, we have studied the photoionization of xenon at ultrahigh intensities. For our ion mass-to-charge spectroscopy experiments, irradiance levels from 10(12) to 10(16) W cm(-2) were achieved at the new free-electron laser in Hamburg FLASH by strong beam focusing with the aid of a spherical multilayer mirror. Ion charges up to Xe21+ were observed and investigated as a function of irradiance. Our surprising results are discussed in terms of a perturbative and nonperturbative description.

Electrostatic potentials of E.coli genome DNA.

Distribution of electrostatic potential of the complete sequence of E. coli genome was calculated. Comparative analysis of electrostatic patterns for 359 promoter and nonpromoter nucleotide sequences was carried out. It is found that nonpromoter regions are characterized by more homogeneous distribution of electrostatic potential with no common specific elements. Electrostatic patterns of promoter DNAs can be specified due to the presence of some distinctive motifs which may be involved as promoter signal elements in RNA-polymerase-promoter recognition.

[Some principles in the organization of sigma70-specific promoters on the E. coli genome on the basis of electrostatic patterns of promoter DNA].

The distribution of electrostatic potential of the complete sequence of the E. coli genome was calculated. It was found that DNA is not a uniformly charged molecule. There are some local inhomogeneities in its electrostatic profile, which correlate with the position of promoters in the genome. Electrostatic patterns of promoter DNAs can be specified due to the presence of some distinctive motifs, which may be involved as promoter signal elements in RNA-polymerase-promoter recognition.