bluuebunny/crossref_metadata_2025 huggingface dataset:
Diagnosis of low-speed flows by particle shadow velocimetry method
Authors: Khant P T , Barinov V Yu
Published: December 2019

The method of particle shadow anemometry is one of the PIV modifications. LEDs are used as a radiation source. The application of particle shadow anemometry for diagnostics of low-speed vortex flows is considered in this article. The ability to obtain both visualization of the flow and numerical results was shown.
Prospects of applying the elastic light scattering effect for the development of an optical method to the colloidal solutions diagnositic
Authors: Sapronov M V , Skornyakova N M
Published: December 2019

In the paper the possibility of developing an optical method for colloidal solutions diagnostic based on elastic light scattering was investigated. The scheme of the experimental setup for light scattering indicatrix registration was presented, and the results of its work were demonstrated. The algorithm and the program of experimental data processing have been developed. Experimental light scattering indicatrices with 434, 546 and 656 nm wavelengths in a colloidal sulfur solution have been obtained. The scattering indicatrix models dynamics with changes in the scattering center size were presented. Qualitative comparison of the experimental and model results was carried out.
Application of computer vision and neural network analysis to study the structure and dynamics of turbulent jets
Authors: Abdurakipov S , Tokarev M , Butakov E , Dulin V
Published: December 2019

In this paper we solved the problem of detecting and detailed analysis of the characteristics of coherent structures in non-swirling and swirling turbulent jets from the 3D PIV experiment and DNS modelling database. To solve the problem intellectual approaches of computer vision based on deep neural networks were applied. It is shown that with the use of a generative competitive neural network, it is possible to reconstruct the structure and dynamics of a turbulent flow with an increased spatial resolution, which is important for analysis and interpretation. The approach is based on a modification of the loss function, which minimizes the residual part of the hydrodynamic equations (the continuity equations and the Poisson equation) for the reconstructed data. It is shown that generative models are more effective in the reconstruction of high moments of turbulent flow than conventional methods POD and DMD. Using a fully convolutional neural network, an automatic segmentation of the turbulent jet flow region and the external environment based on instantaneous velocity and pressure fields was carried out. For a swirling jet, the area of reversed flow is identified. It is shown that the complex of the developed machine learning algorithms successfully copes with the localization of coherent structures, the detection of their trajectory, characteristic size and phase propagation velocity. The obtained new fundamental information is important for a deeper understanding of the role of vortex structures in mixing processes in a jet flow. The developed complex of algorithms for the identification and analysis of characteristics of coherent structures can be applied to a database of measurements and numerical simulation of a wide class of hydrodynamic flows.
Peculiarities of the acousto-optical interactions of Bessel light beams in crystals
Authors: Belyi V N , Kulak G V , Krokh G V , Ropot P I , Shakin O V
Published: December 2019

The noncollinear acousto-optical filtration of diffracted Bessel light beams in uniaxial paratellurite crystals has been investigated. With the use of the method of overlap integrals it is shown that independently on the order of Bessel light beams in the conditions of transverse phase-matching of diffracted waves in the range of optical spectrum of 0.4-1.1 nm in paratellurite crystals the bandwidth of transmission of ∼0.52 nm is reached due to detuning from Bragg’s synchronism only. It is shown that in uniaxial gyrotropic crystals polarization-independent diffraction of Bessel light beams is possible, i.e. Bragg diffraction efficiency is independent of the polarization state of the incident beam. It has been stated that the physical reason of such diffraction is simultaneous realization of two processes of anisotropic scattering under which the Bragg synchronism conditions are realized for the orthogonally polarized elliptical Bessel beams.
Modeling pictures of the flow past rough and smooth surfaces in the program comsol multiphysics
Authors: Thu Win , Ilin D V
Published: December 2019

The aim of this work was to obtain simulated flow patterns of rough surfaces by aerodynamic flow at different speeds for comparison with the results obtained by anemometry from images of particles in a laboratory wind tunnel. The results obtained by the program Comsol Multiphysics, which is used to simulate complex high-turbulent flows characteristic of gas flows in aircraft engines and gas turbine plants.
Compact interferometer for precise shape testing of large-size convexaspherical mirrors
Authors: Gavlina A E , Novikov D A , Sergeeva M V
Published: December 2019

A model of an interferometer for testing of convex aspherical mirrors up to 250 mm in diameter based on the scheme of orthogonal rays is presented. An algorithm for interferogram processing has been developed. The results of measurements of the profile of a convex spherical mirror on the presented interferometer are presented.
Optical-acoustic diagnostics of cracks on the surface of solid bodies
Authors: Kazak N S , Kulak G V , Nikilaenko T V , Matveeva A G , Shakin O V
Published: December 2019

The features of optical-acoustic diagnostics of defects in the form of cracks on the surface of solid bodies in a pulsed mode are investigated. It has been established that pulsed surface Rayleigh waves should be used to detect cracks. The largest amplitude of the scattered surface acoustic wave is achieved at the optimum width of the laser spot, directed to the center of the crack.
Separate BOS-visualization of temperature and pressure distributions in a solid medium
Authors: Sychev D G
Published: December 2019

Background Oriented Schlieren (BOS) is a technique widely used for visualizing disturbances in optically transparent objects. This method makes possible to visualize the variation of the refractive index, which depends on such physical parameters as temperature, pressure and concentration. Therefore, obtaining information about these parameters is also possible. In the course of the work, an experiment was conducted to visualize the optical inhomogeneity formed by changes in pressure and temperature in plane-parallel glass plate. Processing of experimental data has shown that under certain conditions it is possible to obtain information about the individual parameters of the environment which forms a complex inhomogeneity.
Micro-PTV technique application to velocity field measurements in immiscible liquid-liquid plug flow in microchannels
Authors: Kovalev A V , Yagodnitsyna A A , Bilsky A V
Published: December 2019

The present paper presents the results of micro-PTV technique application to velocity fields measurements in plug flow of immiscible liquids in T-shaped straight and curved microchannels. The data processing algorithms are described; the procedure for velocity circulation assessment was proposed and applied to measure velocity circulation in aqueous plugs at different flow rates. The comparison with micro-PIV technique application results is performed.
Elimination of distortions on images in the existence of turbulence
Authors: Belov S Yu
Published: December 2019

The aim of the study is to eliminate the influence of the turbulence model on the photographed images. This problem is solved by computer processing of images containing such distortions. In the course of the work, images with simulated turbulent distortions were obtained, and they were also post-processed using cascade filters.
Laser diagnostics of the instability onset in the confined vortex flows
Authors: Naumov I V , Tsoy M A
Published: December 2019

This paper focus is the application of optical methods of pulsating vortex flow diagnostics on the example of swirling flow instability in a cylinder with rotating lid and aspect ratio h = 3.3, 3.4. To obtain a complete picture of auto-generated pulsations development, long-term LDV measurements of the tangential velocity component were carried out with a continuous method of the Reynolds number variation from 2000 to 3500 over 8 hours (30,000 seconds). In the view of the smallness of the Reynolds number increase rate ΔRe / Δt = 0.05 s−1, this process can be considered as quasi-equilibrium. A comparison with the widely used discrete method of the Reynolds number variation is made, given range of the Reynolds numbers was studied with a step ΔRe = 50 for 20 minutes per point. It was found that at the same h, Re different vortex structures are formed depending on the Reynolds number variation method. In the case of discrete the Reynolds number variation, the development of pulsations may require up to 2000 rotating lid revolutions or 500 seconds, it should be considered conducting the experiments.
High speed visualization of self-oscillation of axisymmetric cavitating cavity in a square vortex chamber
Authors: Skripkin S G , Tsoy M A , Kuibin P A , Zuo Zhigang , Liu Shuhong
Published: December 2019

An experimental investigation of the multiphase turbulent flow in a square vortex chamber was carried out to examine the self-oscillation of a cavitating cavity in a wide range of flow rates and pressure conditions. Such phenomenon is observed behind turbine runner when the hydraulic units operate at full load regime at high flowrate, and leads to significant flowrate and pressure pulsations in the entire hydraulic system. The dynamics of the cavity over time, and the freaquency of the volumetric oscillations frequency was studied via high speed visualization. The grey-scale images of the vortex cavity were binarized. By assuming an axially symmetric flow, the volume of cavity for each frame was integrated, and further investigated using FFT. Quantitative information on the structure of a single-phase flow was also obtained using the PIV technique.
Compensation of spectral image shift in AOTF-based system
Authors: Bykov A A , Zinin P V , Bulatov K M , Khokhlov D D , Kutuza I B
Published: December 2019

Recently, it was shown that the use of a tandem acousto-optic tuneable filter (TAOTF) in combination with a camera allows one to measure the temperature distribution at the focus of a laser beam on an object’s surface. The TAOTF advantage is a reduction of aberrations and spatial distortions. Unfortunately, a TAOTF significantly reduces the intensity of the transmitted light beam, requires longer exposure time and often hampers temperature measurements below 1200 K. A single-crystal AOTF is free from this drawback and allows increasing the intensity of the incident radiation to the camera sensor. The paper presents experimental data for comparing measurements of the temperature distribution at the laser focus, obtained using single-crystal AOTF and TAOTF. A strong chromatic drift caused by AOTF-based system was compensated using the digital processing of the spectral images.
A review of non-polar liquids as materials for bulk acousto-optic devices operating with terahertz radiation
Authors: Nikitin P
Published: December 2019

In this paper, the acoustic and optical properties of a number of liquids transparent in the terahertz range are systematized. The acousto-optic quality is calculated for the quasi-orthogonal and collinear geometry of the acousto-optic interaction. The parameters of acousto-optic deflectors and filters of terahertz radiation are determined. The diagrams linking the resolution for the filter and the maximum number of resolvable elements for the deflector with the diffraction efficiency are given.
Application of the particle trajectory imaging for modelling dusty plasma levitation on the Moon
Authors: Poroykov A Yu , Bednyakov S A , Zaharov A V , Dolnikov G G , Lyash A N , Shashkova I A , Kuznetsov I A
Published: December 2019

The future robotic and human lunar landing missions to the Moon has many factors which turn them into difficult technology and science tasks. One of these factors is the influence of the dust. Upper layers of the regolith are an insulator. The regolith exposed to permanent bombardment by micrometeorites and acquire a charge due to solar wind fluxes and solar UV radiation. These factors create a charge distribution on the surface of the Moon: positive on the illuminated side and negative on the night side. On the day side of the Moon near the surface layer exists possibility of formation an electric field. Charged dust particles of micron and submicron sizes can take off and levitate over the surface. The aim of the work is to get visualization of the dynamic of dust particles under a charged surface with simultaneously estimating its parameters as accurately as possible. The experimental setup based on vacuum chamber for physical modelling of dusty plasma levitation is described. For visualization of the dust particles trajectory a stereo system of two cameras with a laser as source of illumination is used. Image processing techniques for estimating the particle trajectory in three dimensional coordinates and examples of processing results are presented.
Computer modeling of acoustic standing waves in the coolant of nuclear power plants
Authors: Proskuryakov K N , Anikeev A V , Afshar E
Published: December 2019

In nuclear power plants (NPPs), the dynamic interactions of the coolant with the structures are among the main factors determining the dynamic loads on the equipments, its service life and reliability. The most hazardous is the resonant interaction of vibrations of the equipment with acoustic standing waves (ASW) that arise in accidental conditions. It is pointed out that the study of accident conditions on a full-scale object model is not possible and, accordingly, the development of adequate computer models to simulate the conditions is of prime importance. The analysis of acoustic systems with single-phase and two-phase fluid media is based on the theory of elastic wave propagation in liquids and gases. The analysis is based on the equations of fluid state, equations of motion, continuity equation and the equation expressing the law of conservation of energy. It is shown that in view of the unity of the differential equations of acoustic and electrical systems, the study of the propagation of the volume flow rate of one-dimensional pulsating flow of a compressible single-phase or two-phase fluid in the acoustic system can be replaced by the study of the propagation of electric current in the lines of electrical circuits. The paper presents an acoustic scheme of the NPP coolant circuit formed by acoustic elements considering their inherent thermal-hydraulic and geometric parameters. It is shown that the results of calculations of the frequencies of the ASW are confirmed by the measurements carried out at the NPP.
Determination of parameters of the compelled capillary disintegration of liquid jets
Authors: Boukharov A V , Kukanov S I
Published: December 2019

The technique of the automated precision parameters diagnostics of the compelled capillary disintegration of liquid jet is developed for the solution of heat-physical problems of receiving the stable monodisperse drop streams. The analysis of the images received from two digital cameras, located at the angle ninety degrees to each other is the basic of this procedure. One of cameras fixes the image of a drop flow in plane X, another - in plane Y. The minimum time of storing images is ∼0.1 microsecond. By means of specially developed software in the “on line” mode it is possible to process images and to determine the following parameters: jets speed, drops speed, jets length, jets diameter and drops diameter. Testing on objects with the known geometrical sizes confirmed working capacity and efficiency of the technique and the software. The relative error of parameters determination does not exceed 0.5% for jets with length of several millimeters. The developed technique and the software allow to increase the accuracy and reliability of parameters determination of compelled capillary disintegration of liquid jets and drop streams and expand possibilities of parameters control of setups for receiving monodisperse streams.
Visualization and PIV-study of the formation of a cooling film when flowing around the leading edge of the gas turbine nozzle blade
Authors: Veretennikov S V , Evdokimov O A
Published: December 2019

The results of particle image velocimetry near the perforated leading edge of the nozzle vane of gas turbine are presented. Visualization of the formation of cooling film on the surface of the blade with determination of its thickness is carried out. On the basis of the obtained results, the influence of the blown cooling air mass flow rate on the formation of the film is analyzed.
Estimating the quality of stereoscopic endoscopic systems
Authors: Naumov A A , Gorevoy A V , Machikhin A S , Batshev V I , Pozha V E
Published: December 2019

Stereoscopic video endoscopic systems are widely used for the control of hard-to-reach objects at the stages of production, assembly and testing of various devices. Using a stereoscopic endoscope as a measuring tool requires its geometrical calibration. The effectiveness of such systems is largely determined by the quality of an image, based on modulation transfer function (MTF) of the optical system. In this paper, we describe and test an algorithm for automatic calculating the MTF for images of a plane test object with chessboard pattern. Experimental data was obtained using two self-developed prism-based endoscopic stereoscopic systems. Coincidence of computer simulation results and results of applying the proposed algorithm shows its effectiveness for estimating the image quality provided by stereoscopic endoscopic systems.
On computer modelling of operations, geometric characteristics and methods of pulsed optical tomography of nuclear fuel microobjects
Authors: Domoratskiy E P , Baybikova T N
Published: December 2019

The paper refers to the area of morphological processing of projection images and its goal is to design some computer models of basic operations, geometric properties and methods of pulsed optical tomography which provide a high-speed production operational control and sorting of each microobjet (MO) of nuclear fuel in their flow according to their size and shape. Based on the proposed computer models, a precision laser method of industrial differential control and quality control of an MO flow of nuclear fuel was developed and experimentally tested. The method uses the statistical reconstruction of the size (D) and shape (K) of each microobject and takes into account the overall dimensions of the outlines of three mutually orthogonal two-dimensional pulsed discrete projection images of a microobject. The processing speed of this method is 100 MO/s in the diameter range of 400–1500 µm. The relative error of an MO diameter control is no more than 0.25% (at the reliability of PD
= 0.7 and K = 1.3 relative units), and the relative error of the non-sphericity coefficient control lies in the range of 2.3% (PK
= 0.7 and K = 1.3) to 0.6% (PK
= 0.96 and K = 1.05).
Study of convective structures and phase transition induced in a water layer by non-stationary boundary conditions
Authors: Dubnishchev Yu N , Arbuzov V A , Arbuzov E V , Berdnikov V S , Zolotukhina O S , Kislitsin S A
Published: December 2019

The problem of reconstructing interference and Hilbert structures from a numerical model of the evolution of the thermal field of convective flows in a water layer bounded by flat heat-exchanging surfaces under unsteady boundary conditions in the monotonic cooling mode and taking into account density inversion at a temperature of +4 °C was solved. The simulation of the thermal fields of convective flows in the form of the dynamic structure of isotherms was carried out taking into account the nonlinear dependence of thermal conductivity and water density on temperature. The field of the phase function, its Hilbert image and the interference field, which are compared with the results of the interference and Hilbert visualization of the fields of phase optical density obtained in the experiment, were reconstructed from the isotherms field supplemented by calculating of the velocity field and of the temperature gradients field. The presented films illustrate the qualitative adequacy of the coevolution of numerical models and real processes.
Infrared fiber based on AgCl-AgBr and AgBr-TlI crystals to transfer thermal radiation in pulsed
Authors: Shmygalev A S , Korsakov A S , Zhilkin B P , Turabi A
Published: December 2019

The our research objective is to study IR energy transfer in pulsed and continuous mode through optical fibers produced from crystals of silver halide and a monovalent thallium solid solutions. It is assumed that the transfer of infrared radiation in the pulsed mode will significantly reduce losses. We designed the experimental setup, determined its operational parameters, and obtained the dependence of the detector’s received radiation on the frequency of the pulses of thermal radiation. As a research subjects we used two different fibers compositions namely AgCl0.25Br0.75 and Ag0.95Tl0.05Br0.95I0.05.
Experimental study of the multiphase flow in a pore doublet model
Authors: Zamula Yu S , Batyrshin E S , Latypova R R , Abramova O A , Pityuk Yu A
Published: December 2019

The paper presents the results of an experimental study of the properties of single-and multiphase flows in a “pore doublet model” (PDM) using microfluidic and optical microscopy techniques. Polymer based microfluidic devices containing pore doublet were fabricated using soft lithography methods. The average cross-section of the microchannels was in the order of 100 μm, and the length reached several millimeters. A bubble generator in the form of a T-junction microchannel was fabricated to study the multiphase flows. High speed imaging and tracer visualization methods were used to study the flow patterns. The properties of multiphase flows were studied during liquid-gas displacement and bubbly liquid flow through pore doublet. The flow patterns were visualized using polymer micro particles suspended in flowing liquids.
The method of compensation for local displacements of images of capillaries in the evaluation of capillary blood flow parameters
Authors: Volkov M V , Margaryants N B , Potemkin A V , Gurov I P
Published: December 2019

The paper discusses the features of applying the method of local compensation of video frame displacements in the study of microcirculation parameters by the methods of video capillaroscopy (VCS) and microphotoplethysmography (micro-PPG). The results of the assessment and compensation of local displacements of images of the capillary network in the region of the hand of a conditionally healthy volunteer are presented. The result of the computation of the synthesized image of capillaries with equalized contrast based on the processing of a locally-combined sequence of video frames is shown. An example of capillary visualization using the frequency analysis of locally aligned video frames is given. The effectiveness of the method of local image stabilization within the study of the capillary network of mucous membranes using a laparoscope is demonstrated.
Installation for investigation of optical and mechanical system of fiber optical sensors of parameters of liquid or air flows
Authors: Badeeva E , Shachneva E , Murashkina T , Kukushkin A
Published: December 2019

A special measuring unit has been developed for experimental studies of micro-optomechanical systems of fiber-optic micro-angle transducers based on a bellows and micrometer, which are the basic elements of fiber-optic sensors of aerodynamic angles, imitating the physical effect of the flux on the sensing element.
Medical control of a pulse wave fiber optic sensors
Authors: Gerashchenko M , Badeeva E , Murashkina T , Gerashchenko S
Published: December 2019

The modern level of development of systems of measurement, processing and data transmission promote creation of optical multiple parameter medical diagnostic systems. One of intensively developed directions is creation of fiber-optical diagnostic systems on the basis of fiber optic sensors. Fiber optic sensors are characterized by high sensitivity to mechanical oscillations of a surface of a body of the patient under power influence of a blood flow. This property creates premises for design miniature, steady against noises, safe sensors of micromovements. Their fixing on a body of the patient allows to reveal a number of the vital parameters characterizing normal and critical condition of the patient. Results of a research of fiber optic sensors of pressure on the basis of standard single-mode optical SMF-28 fiber are presented in article. The principle of operation of sensors consists in use of physical properties of the fiber - the impact which had in some pressure point on throughput characteristic. The purpose of the real work is the research of a possibility of use of fiber optic sensors of the tunnel, flexural and microflexural types on Bragg’s grid for control of a pulse wave providing more exact determination of parameters of a pulse wave. The offered monitoring systems of a status of patients on the basis of fiber optic sensors in medicine are very perspective.
Optical methods for droplets evaporation on graphene nanocomposite surfaces
Authors: Babenko D D , Dmitriev A S
Published: December 2019

We study the evaporation of water droplets on the surface of graphene nanocomposites of different compositions. Methods for manufacturing samples of nanocomposites, optical methods for studying contact angles and evaporation dynamics are described. New experimental data are presented on the behavior of contact angles and evaporation rates at various temperatures for samples of nanocomposites in both the constant contact line mode and the constant contact angle mode. The features of evaporation for nanocomposites with inclusions of boron nitride and aluminum nitride nanoparticles inside graphene samples are noted.
The combination of PIV and heat flux measurement in study of flow and heat transfer near a circular finned cylinder
Authors: Sapozhnikov S Z , Mityakov V Yu , Seroshtanov V V , Gusakov A A
Published: December 2019

The flow and heat transfer of the finned cylinder are investigated by the methods of PIV, gradient heat flux measurement and thermometry. On the hollow model of a circular cylinder heated by saturated water vapor at atmospheric pressure, five annular fins of 20 mm high and of 10 mm thick are mounted. For the first model, the “acting” fin was hollow, for the second, it was solid and made of titanium alloy VT22. The remaining four fins simulated flow blockage. To visualize the flow in the intercostal space, the fin simulators were made of Perspex. Battery gradient heat flux sensors (GHFSs) with volt-watt sensitivity of 10 mV/W, were installed on the “acting” fin at different distances from the surface of the carrier cylinder. The cylinder rotated around its axis at an angle of φ = 0…180°, which made it possible to obtain the distribution of heat flux over the surface of the fin. By combining PIV diagnostics and gradient heat flux measurement, it was possible to obtain a complex 3D structure of the flow in the intercostal space and the distribution of heat flux on the surface of the fin. The values of the local heat transfer coefficients (HTCs) were also obtained. The dependence of HTC on flow mode and intercostal space is revealed. Comparison of the obtained characteristics for models with hollow and solid fins allowed us to determine in experiment fin efficiency for different intercostal spaces and free-stream velocities. The combination of all three technologies opens up new possibilities in study of flow and convective heat transfer.
Design features of the glossmeter system
Authors: Beliaeva A S , Romanova G E
Published: December 2019

The paper discusses the stages of development of the glossmeter device. Possible options are analysed and the choice of the optical scheme is justified, as well as the choice and matching of the source and detector. The issues of ensuring the linearity of the device characteristics are considered. The results of the device testing are given.
Immersion laser-induced ultrasound imaging of solids with complex macroscopic geometry of surface
Authors: Zarubin V , Bychkov A , Simonova V , Cherepetskaya E , Karabutov A
Published: December 2019

In this paper a real-time experimental system and algorithms for immersion two-dimensional laser ultrasonic imaging of solids with complex geometry of surface are presented. Wideband probe ultrasonic pulse is generated photoacoustically in an opaque plate, which absorbs pulsed laser radiation. The back-scattered acoustic field is recorded by a multi-element piezoelectric array. The signals are used to reconstruct refraction-corrected ultrasonic images, which are post-processed to determine positions of the external and internal boundaries of the object. The numerical simulations are carried out to verify the developed algorithms. The proposed approach allowed measuring the positions of the boundaries of the polymethyl methacrylate (PMMA) sample with accuracy of ∼0.1 mm in the direction of the probe beam propagation, and ~0.2-0.3 mm in the perpendicular direction.
Acoustic properties of LNM crystal
Authors: Velikovskii D Yu , Kokshaiskii A I , Milkov M G , Sukharev V A
Published: December 2019

We report linear acoustic and acousto-optical properties of LiNa5Mo9O30 (LNM) single crystal. This relatively new crystal, known for its complex crystallographic structure, is optically biaxial with high birefringence of 0.2545 at 450.2 nm, and crystals that consist of molybdates are widely used in different applications, from cintillators, double β-decay detectors, “dark matter” sensors to electro optics. The lowest measured propagation velocity of shear wave was 1200 m/s, and for the longitudinal mode it was 4100 m/s, which are a relatively low value for crystalline media. The maximum attenuation of the longitudinal wave at a frequency of 180 MHz was moderate and equal 20 dB/cm·GHz2. The values of the acousto-optic figure of merit for light diffraction on a longitudinal acoustic wave were also determined, the maximum value of the coefficient was 13 c.u., which exceeds the efficiency of the one used in AO devices material α-SiO2. Thus, the set of measured acoustic and elastic-optical properties shows a new promising optically biaxial material for acousto-optics, which needs for further researching.
Selective scheme of gas concentration measurement based on acousto-optic spectral filters with multi-frequency control signal
Authors: Pisarevsky Yu V , Kolesnikov S A , Lomonov V A , Vinogradov A V
Published: December 2019

A scheme for measuring the concentration of components of gas mixtures improving the selectivity of conventional optical absorption spectroscopy is proposed. The scheme is based on the use of acousto-optic spectral filter as a dispersion element which is fed simultaneously several control signals with frequencies corresponding to the maxima and minima of absorption in the optical spectrum of the measured gas. The scheme is implemented on the basis of the acousto-optic filter based on paratellurite TeO2 crystal, providing the high resolution achieved by reducing the absorption of ultrasound due to the special technology of the growth of high quality crystals and the use of absorption anisotropy of ultrasound in paratellurite. Experimental verification of this approach with measuring the concentration of nitrogen dioxide has confirmed the effectiveness of the proposed scheme.
Estimation of the image quality correction efficiency in optical measurement systems under Scheimpflug condition
Authors: Pechinskaya O V
Published: December 2019

A criterion for evaluating the image quality correction efficiency in optical systems under Scheimpflug conditions is proposed. The limits of applicability of the geometric optics approximation are clarified for the sensor tilt angle calculating. The results of a simulation optical stereoscopic system arm for three cases: normal, oblique system not under the Scheimpflug condition and oblique system under the Scheimpflug condition are presented. The quantitative estimation of the image quality correction efficiency is performed. The ranges of object distances and viewing angles, providing the maximum image quality correction without loss of accuracy due to perspective distortion are defined.
Novel fibrillar structure in the inversin compartment of primary cilia revealed by 3D single-molecule superresolution microscopy
Authors: Bennett Henrietta W. , Gustavsson Anna-Karin , Bayas Camille A. , Petrov Petar N. , Mooney Nancie , Moerner W. E. , Jackson Peter K.
Published: January 2020

Using three-dimensional single-molecule superresolution imaging and systematic analysis of knockout cell lines, we have determined the molecular structure and composition of the inversin compartment in primary cilia. INVS establishes fibrillar structures that recruit ANKS6-NEK8 complexes to sequester NPHP3 in this unique periaxonemal compartment.
UDSMProt: universal deep sequence models for protein classification
Authors: Strodthoff Nils , Wagner Patrick , Wenzel Markus , Samek Wojciech
Published: January 2020

Motivation

Inferring the properties of a protein from its amino acid sequence is one of the key problems in bioinformatics. Most state-of-the-art approaches for protein classification are tailored to single classification tasks and rely on handcrafted features, such as position-specific-scoring matrices from expensive database searches. We argue that this level of performance can be reached or even be surpassed by learning a task-agnostic representation once, using self-supervised language modeling, and transferring it to specific tasks by a simple fine-tuning step.

Results

We put forward a universal deep sequence model that is pre-trained on unlabeled protein sequences from Swiss-Prot and fine-tuned on protein classification tasks. We apply it to three prototypical tasks, namely enzyme class prediction, gene ontology prediction and remote homology and fold detection. The proposed method performs on par with state-of-the-art algorithms that were tailored to these specific tasks or, for two out of three tasks, even outperforms them. These results stress the possibility of inferring protein properties from the sequence alone and, on more general grounds, the prospects of modern natural language processing methods in omics. Moreover, we illustrate the prospects for explainable machine learning methods in this field by selected case studies.

Availability and implementation

Source code is available under https://github.com/nstrodt/UDSMProt.

Supplementary information

Supplementary data are available at Bioinformatics online.
A U-statistics for integrative analysis of multilayer omics data
Authors: Wang Xiaqiong , Wen Yalu
Published: January 2020

Motivation

The emerging multilayer omics data provide unprecedented opportunities for detecting biomarkers that are associated with complex diseases at various molecular levels. However, the high-dimensionality of multiomics data and the complex disease etiologies have brought tremendous analytical challenges.

Results

We developed a U-statistics-based non-parametric framework for the association analysis of multilayer omics data, where consensus and permutation-based weighting schemes are developed to account for various types of disease models. Our proposed method is flexible for analyzing different types of outcomes as it makes no assumptions about their distributions. Moreover, it explicitly accounts for various types of underlying disease models through weighting schemes and thus provides robust performance against them. Through extensive simulations and the application to dataset obtained from the Alzheimer’s Disease Neuroimaging Initiatives, we demonstrated that our method outperformed the commonly used kernel regression-based methods.

Availability and implementation

The R-package is available at https://github.com/YaluWen/Uomic.

Supplementary information

Supplementary data are available at Bioinformatics online.
A mixed-model approach for powerful testing of genetic associations with cancer risk incorporating tumor characteristics
Authors: Zhang Haoyu , Zhao Ni , Ahearn Thomas U , Wheeler William , García-Closas Montserrat , Chatterjee Nilanjan
Published: January 2020

Cancers are routinely classified into subtypes according to various features, including histopathological characteristics and molecular markers. Previous genome-wide association studies have reported heterogeneous associations between loci and cancer subtypes. However, it is not evident what is the optimal modeling strategy for handling correlated tumor features, missing data, and increased degrees-of-freedom in the underlying tests of associations. We propose to test for genetic associations using a mixed-effect two-stage polytomous model score test (MTOP). In the first stage, a standard polytomous model is used to specify all possible subtypes defined by the cross-classification of the tumor characteristics. In the second stage, the subtype-specific case–control odds ratios are specified using a more parsimonious model based on the case–control odds ratio for a baseline subtype, and the case–case parameters associated with tumor markers. Further, to reduce the degrees-of-freedom, we specify case–case parameters for additional exploratory markers using a random-effect model. We use the Expectation–Maximization algorithm to account for missing data on tumor markers. Through simulations across a range of realistic scenarios and data from the Polish Breast Cancer Study (PBCS), we show MTOP outperforms alternative methods for identifying heterogeneous associations between risk loci and tumor subtypes. The proposed methods have been implemented in a user-friendly and high-speed R statistical package called TOP (https://github.com/andrewhaoyu/TOP)
The Practice of States on Air Defense Identification Zones: Geographical Scope, Object of Identification, and Identification Measures
Authors: Su Jinyuan
Published: January 2020

This note provides a survey of the practice of States on ADIZs. It is found that while some ADIZs are entirely within territorial airspace, most extend beyond the outer limit into the airspace above the EEZs and even the high seas; and in the part beyond territorial airspace, transiting aircraft are prevalently subject to identification. Transiting military aircraft, which most of the time refuse to identify themselves voluntarily by submitting a flight plan or reporting their positions, may nevertheless be identified passively through radar detection, radio communication or close visual check. As most ADIZs are within the claiming State’s FIRs, transiting civil aircraft can be identified “unconsciously” through civil air traffic control. Where an ADIZ extends beyond the claiming State’s FIRs, most transiting civil aircraft comply with voluntary identification measures, presumably due to the light extra burden incurred. The non-compliant are easy to identify through passive means such as radar detection and radio communication, with the use of close visual check highly unnecessary.
Influenza Vaccine Effectiveness Against Influenza-Related Mortality in Australian Hospitalized Patients: A Propensity Score Analysis
Authors: Nation Monica L , Moss Robert , Spittal Matthew J , Kotsimbos Tom , Kelly Paul M , Cheng Allen C
Published: January 2020

Background

Data on influenza vaccine effectiveness (IVE) against mortality are limited, with no Australian data to guide vaccine uptake. We aimed to assess IVE against influenza-related mortality in Australian hospitalized patients, assess residual confounding in the association between influenza vaccination and mortality, and assess whether influenza vaccination reduces the severity of influenza illness.

Methods

Data were collected between 2010 and 2017 from a national Australian hospital-based sentinel surveillance system using a case-control design. Adults and children admitted to the 17 study hospitals with acute respiratory symptoms were tested for influenza using nucleic acid testing; all eligible test-positive cases, and a subset of test-negative controls, were included. Propensity score analysis and multivariable logistic regression were used to determine the adjusted odds ratio (aOR) of vaccination, with IVE = 1 – aOR × 100%. Residual confounding was assessed by examining mortality in controls.

Results

Over 8 seasons, 14038 patients were admitted with laboratory-confirmed influenza. The primary analysis included 9298 cases and 6451 controls, with 194 cases and 136 controls dying during hospitalization. Vaccination was associated with a 31% (95% confidence interval [CI], 3%–51%; P = .033) reduction in influenza-related mortality, with similar estimates in the National Immunisation Program target group. Residual confounding was identified in patients ≥65 years old (aOR, 1.92 [95% CI, 1.06–3.46]; P = .031). There was no evidence that vaccination reduced the severity of influenza illness (aOR, 1.07 [95% CI, .76–1.50]; P = .713).

Conclusions

Influenza vaccination is associated with a moderate reduction in influenza-related mortality. This finding reinforces the utility of the Australian vaccination program in protecting those most at risk of influenza-related deaths.
Assessment of the Potential of Vaccination to Combat Antibiotic Resistance in Gonorrhea: A Modeling Analysis to Determine Preferred Product Characteristics
Authors: Whittles Lilith K , White Peter J , Didelot Xavier
Published: January 2020

Background

Gonorrhea incidence is increasing rapidly in many countries, while antibiotic resistance is making treatment more difficult. Combined with evidence that two meningococcal vaccines are likely partially protective against gonorrhea, this has renewed interest in a gonococcal vaccine, and several candidates are in development. Key questions are how protective and long-lasting a vaccine needs to be, and how to target it. We assessed vaccination’s potential impact and the feasibility of achieving the World Health Organization’s (WHO) target of reducing gonorrhea incidence by 90% during 2018–2030, by comparing realistic vaccination strategies under a range of scenarios of vaccine efficacy and duration of protection, and emergence of extensively-resistant gonorrhea.

Methods

We developed a stochastic transmission-dynamic model, incorporating asymptomatic and symptomatic infection and heterogeneous sexual behavior in men who have sex with men (MSM). We used data from England, which has a comprehensive, consistent nationwide surveillance system. Using particle Markov chain Monte Carlo methods, we fitted to gonorrhea incidence in 2008–2017, then used Bayesian forecasting to examine an extensive range of scenarios.

Results

Even in the worst-case scenario of untreatable infection emerging, the WHO target is achievable if all MSM attending sexual health clinics receive a vaccine offering ≥ 52% protection for ≥ 6 years. A vaccine conferring 31% protection (as estimated for MeNZB) for 2–4 years could reduce incidence in 2030 by 45% in the worst-case scenario, and by 75% if > 70% of resistant gonorrhea remains treatable.

Conclusions

Even a partially-protective vaccine, delivered through a realistic targeting strategy, could substantially reduce gonorrhea incidence, despite antibiotic resistance.
Effects of Influenza Vaccination in the United States During the 2018–2019 Influenza Season
Authors: Chung Jessie R , Rolfes Melissa A , Flannery Brendan , Prasad Pragati , O’Halloran Alissa , Garg Shikha , Fry Alicia M , Singleton James A , Patel Manish , Reed Carrie ,   US Influenza Vaccine Effectiveness Network, the Influenza Hospitalization Surveillance Network, and the Assessment Branch, Immunization Services Division, Centers for Disease Control and Prevention, Kim Sara S , Martin Emily T , Monto Arnold S , Jackson Michael L , Jackson Lisa A , McLean Huong Q , Belongia Edward A , King Jennifer P , Zimmerman Richard K , Nowalk Mary Patricia , Balasubramani G K , Bear Todd M , Hickey Robert , Raviotta Jonathan M , Suyama Joe , Weissman Alexandra J , Williams John V , Gaglani Manjusha , Raiyani Chandni , Smith Michael , Murthy Kempapura , Clipper Lydia , Reis Michael , Rao Arundhati , Walker Kimberly , Volz Marcus , Mutnal Manohar , Cummings Charisse N , Yousey-Hindes Kimberly , McMullen Chelsea , Chai Shua J , Anderson Evan J , Monroe Maya L , Risk Ilene , Herlihy Rachel , Kim Sue , Spina Nancy , Billing Laurie , Schaffner William , Keipp Talbot H , Thomas Ann , McMahon Melissa
Published: January 2020

Background

Multivalent influenza vaccine products provide protection against influenza A(H1N1)pdm09, A(H3N2), and B lineage viruses. The 2018–2019 influenza season in the United States included prolonged circulation of A(H1N1)pdm09 viruses well-matched to the vaccine strain and A(H3N2) viruses, the majority of which were mismatched to the vaccine. We estimated the number of vaccine-prevented influenza-associated illnesses, medical visits, hospitalizations, and deaths for the season.

Methods

We used a mathematical model and Monte Carlo algorithm to estimate numbers and 95% uncertainty intervals (UIs) of influenza-associated outcomes prevented by vaccination in the United States. The model incorporated age-specific estimates of national 2018–2019 influenza vaccine coverage, influenza virus–specific vaccine effectiveness from the US Influenza Vaccine Effectiveness Network, and disease burden estimated from population-based rates of influenza-associated hospitalizations through the Influenza Hospitalization Surveillance Network.

Results

Influenza vaccination prevented an estimated 4.4 million (95%UI, 3.4 million–7.1 million) illnesses, 2.3 million (95%UI, 1.8 million–3.8 million) medical visits, 58 000 (95%UI, 30 000–156 000) hospitalizations, and 3500 (95%UI, 1000–13 000) deaths due to influenza viruses during the US 2018–2019 influenza season. Vaccination prevented 14% of projected hospitalizations associated with A(H1N1)pdm09 overall and 43% among children aged 6 months–4 years.

Conclusions

Influenza vaccination averted substantial influenza-associated disease including hospitalizations and deaths in the United States, primarily due to effectiveness against A(H1N1)pdm09. Our findings underscore the value of influenza vaccination, highlighting that vaccines measurably decrease illness and associated healthcare utilization even in a season in which a vaccine component does not match to a circulating virus.
Clinical Utility of Universal Broad-Range Polymerase Chain Reaction Amplicon Sequencing for Pathogen Identification: A Retrospective Cohort Study
Authors: Kerkhoff Andrew D , Rutishauser Rachel L , Miller Steve , Babik Jennifer M
Published: January 2020

We assessed the real-world utility of universal broad-range polymerase chain reaction sequencing for pathogen detection. Among 1062 clinical samples, 107/1062 (10.1%) had a clinically significant, positive result, with substantial variation by specimen type. Clinical management was changed in 44/1062 (4.1%). These data can help maximize utility of this emerging diagnostic.
Calciphylaxis or vascular oxalosis?
Authors: El-Saygeh Skye , Roese Douglas , Moe Sharon M
Published: January 2020

We report the case of a 31-year-old female with primary hyperoxaluria type 1 with end-stage kidney disease who developed severe peripheral vascular disease leading to limb amputation initially thought to be secondary to calciphylaxis. However, polarized review of the pathologic specimen revealed calcium oxalate deposition in the lumen of blood vessels. This unusual presentation of systemic oxalosis demonstrates the adverse consequences of elevations of serum oxalate in patients with hyperoxaluria and that levels can acutely worsen with abrupt onset of kidney failure.