bluuebunny/crossref_metadata_2025 huggingface dataset:
Three-dimensional visualization of flow pattern near transport airplane model with operating propellers in wind tunnel
Authors: Chernousov VI , Krutov A A , Pigusov E A
Published: December 2020

This paper presents the experiment results of three-dimensional visualization of flow pattern behind the wing and fuselage of the light transport aircraft (LTA) model with operating propellers in the T-102 TsAGI subsonic wind tunnel (WT). Studying the flow pattern, it is possible to recognize the features of the flow and aerodynamic interference of model elements. As a result of the analysis of the flow pattern and comparison with the previously obtained integral characteristics, the model elements for improving the aerodynamic perfection of the aircraft are revealed. It is shown that at operational angles of attack behind the main landing gear fairing, the vortex flow forms, increasing drag and, apparently, negatively affecting the longitudinal stability characteristics. Vortices are formed behind the flattened tail of the fuselage. Thus, the visualization of the flow with dacron ribbons is an effective method of obtaining flow pattern around the airplane model elements in WT.
Oscillatory solutions for a diode with counter-streaming electron and ion beams
Authors: Kuznetsov V I , Flegontova E Yu , Bakaleinikov L A
Published: December 2020

A plasma diode with counter-streaming electron and ion beams has as a rule more than one time-independent solution. Stability features of the steady state solution with ion reflection from a potential barrier are studied numerically. It was found that there is a threshold in the diode length beyond which nonlinear oscillations occur as an alternative instead of such solutions. Features of the oscillations are studied.
Heat flux measurement at the initial phase of normal shock wave reflection using the sensor on anisotropic thermoelements
Authors: Popov P A , Sakharov V A , Poniaev S A , Monakhov N A , Kotov M A
Published: December 2020

Thermal measurements were carried out using the sensors on anisotropic thermoelements during normal shock wave reflection with Mach number M = 3 … 5. The method of processing of sensor’s electric signal has been tested at low signal / noise ratio and characteristic time ∼0.1 μs.
Monte Carlo simulation of electron drift characteristics in an inert gas with mercury vapor
Authors: Kurbanismailov V S , Maiorov S A , Ragimkhanov G B , Khalikova Z R
Published: December 2020

The Monte Carlo method calculated the kinetic characteristics of electron drift in three inert gases (He, Ar, Xe) in the presence of small impurities (up to 1%) of mercury vapor at an electric field strength E/N = 1-2000 Td taking into account inelastic collisions and analyzed the effect of the concentration of metal vapor on the drift velocity, average electron energy, diffusion and mobility coefficients. In addition, the Townsend ionization coefficient and electron runaway, the electron energy distribution function, and their comparison with the Maxwell and Druvestein distributions are calculated. It has been shown that even insignificant additions of mercury atoms to an inert gas, starting with a fraction of a percent, strongly affect the discharge, in particular, the characteristics of inelastic processes and the charge composition.
Control of tokamak discharge parameters using a plasma jet
Authors: Goryainov V Yu , Voronin A V , Gusev V K , Minaev V B , Novokhatsky A N , Petrov Yu V , Sakharov N V
Published: December 2020

Results of the experimental study of the ability of plasma jet of coaxial accelerator to breakdown and ionization the working gas at the initial discharge phase in Globus-M2 spherical tokamak are presented. Studies of the development of the initial stage of discharge initiated with a plasma jet showed that the plasma current in the discharge began to grow earlier by 2 ms than using the standard inductive breakdown. The breakdown voltage decreased from 6.1 to 3.1 V (-49%) at 4.7 kV accelerator electrode voltage. The emission intensity of line Dα decreased during formation of the discharge with the help of plasma jet without additional gas puffing. Radiation level CIII in the discharge generated by the plasma jet was the same as the radiation in discharge produced by induction breakdown of the gas. At the stage of increase in the plasma current the most intense visible radiation of the plasma was found near duct through which the jet was injected. Discharge radiation decreased and spread out along the cross section of the plasma column during plasma current plateau.
Investigation of gasdynamic parameters of a supersonic flow near a body at various Mach numbers
Authors: Shevchenko A V , Yuriev A S , Poniaev S A , Zhitnikov T A , Panfilov E B , Rotermel A R
Published: December 2020

Interaction of a body with an incident supersonic flow is considered. By using numerical and experimental methods, gas-dynamic parameters of the supersonic flow near the body are determined for various Mach numbers. Theoretical calculations of the supersonic flow around a body are carried. The mathematical models used in the calculations are verified by the results of experimental studies performed in the IT-1M hypersonic impulse tube of the aerodynamic laboratory of the Mozhaysky Military Space Academy.
Investigation of the interaction of conical bodies with an supersonic flow at low angles of attack
Authors: Shevchenko A V , Yashkov S A , Zhitnikov T A , Rotermel A R , Poniaev S A , Prokopenko E A
Published: December 2020

The study of the interaction of conical bodies with an incident supersonic flow is carried out. In the presented theoretical and experimental studies, the parameters of the incident flow near the investigated bodies were determined at different Mach numbers. Experimental studies were carried out using a supersonic atmospheric-vacuum tube of the aerodynamic laboratory of the Mozhaysky Military Space Academy. The theoretical study is based on the model of a viscous perfect gas described by the Navier-Stokes equations.
Drastic change in surface electronic properties and creation of a new carbon-based nanostructure on the vicinal SiC(111)-4° surface
Authors: Timoshnev S N , Benemanskaya G V , Kukushkin S A
Published: December 2020

Novel carbon based nanostructure on the vicinal SiC(111)-4° surface has been found as effect of Cs adsorption. The SiC(111)-4°sample was grown by method of epitaxy of low-defect unstressed nanoscaled silicon carbide films on vicinal Si(111)-4° substrate. Electronic structure of the SiC(111)-4° surface and the Cs/SiC(111)-4°interface has been detailed studied in situ in an ultrahigh vacuum using synchrotron-based photoelectron spectroscopy. The C 1s and Si 2p core level spectra have been investigated as a function of Cs submonolayer coverage. A unique fine structure of the C 1s core level spectrum was revealed to appear under Cs atomic layer deposition. The effect was ascertained and shown to be originated from the interaction of the silicon vacancy with adsorbed Cs atoms that leads to both the redistribution of electron density and surface reconstruction with formation of a new type of the C-enriched aromatic-like nanostructure.
Laboratory sources of gravitational waves
Authors: Fomin I V , Gladyshev V O , Gorelik V S , Kauts V L , Kaytenko A V , Sharandin E A
Published: December 2020

We consider the possibility of generating and subsequently detecting artificial gravitational waves in a laboratory based on different approaches. As one of the methods for creating gravitational waves, we investigate oscillations of the ions of the crystal lattice of a dielectric under the influence of high-power laser radiation. The characteristics of gravitational waves obtained by this method are compared with the results of using the other approaches as well.
The influence of the Earth’s oblateness on the image motion velocity during the electro-optical survey of the planet’s surface
Authors: Nikulkina I M , Osipova L S , Shatina A V
Published: December 2020

In this paper we derive the formulas describing velocity of the planet’s surface orbital survey image in the focal plane, obtained via on-board electro-optical equipment in the nadir-viewing geometry, with consideration for the Earth’s oblateness. The Earth is modeled as a perfectly rigid spheroid uniformly rotating about its axis of symmetry. The orbit of the satellite’s mass center is perturbed because of the Earth’s oblateness in the direction of its rotation axis. The orbital camera’s prime focus is located in the satellite’s mass center. We present the graphs of image motion velocity vector coordinates in the focal plane depending on time (true anomaly) and the graphs of the velocity fields. The obtained results are compared to the results in case of a spherical Earth. In the latter case the satellite’s mass center moves along a Keplerian elliptic orbit. Key words: image motion velocity, focal plane, Earth’s satellite.
Possible solutions of inverse dynamical problems with regards for nonlinear constraint stabilization function
Authors: Kaspirovich I E , Mukharlyamov R G
Published: December 2020

Baumgarte’s method of constraint stabilization can be applied to find a stable numerical solution in relation for constraint equations during the numerical integration. According to this method full time derivatives of constraints are equated to their arbitrary linear form. Choosing values of the coefficients of this form allow us to obtain a stable solution. In this paper a method of constructing Lagrange equations of the second kind is considered with regard for a nonlinear homogeneous stabilization function. A necessity if introducing dissipative function to find a complete stabilization problem’s solution can be the main conclusion of the research.
Determination of critical Reynolds number in the jet based on the theory of stochastic equations and equivalence of measures
Authors: Dmitrenko A V
Published: December 2020

On the basis of the theory of stochastic equations and the theory of equivalence of measures, the flow in a plane jet is considered. As a result, in accordance with these theories, the analytical dependence for the critical Reynolds number and the expression for the critical point of the transition from the laminar flow to turbulent motion in the jet are derived. The calculations carried out using new formulas showed satisfactory agreement with the known experimental values of the critical Reynolds number.
The Spectrum of the turbulence based on theory of stochastic equations and equivalenceof measures
Authors: Dmitrenko A V
Published: December 2020

The formation of the spectrum of turbulence in the inertial interval on the basis of the new theory of stochastic hydrodynamics is presented. This theory is based on the theory of stochastic equations of continuum laws and equivalence of measures between random and deterministic movements. The purpose of the article is to present a solution based on these stochastic equations for the formation of the turbulence spectrum in the inertial interval in the form of the spectral function E(k)j depending on wave numbers k in form E(k)j∼kn. The results of analytical solutions showed a satisfactory correspondence of the obtained dependence with the classical Kolmogorov’s dependence in the form of E(k)j∼k5/3.
Estimation of the probable size of the lunar core based on geophysical and geochemical data
Authors: Kronrod E , Kuskov O , Matsumoto K , Kronrod V
Published: December 2020

This study is devoted to estimations of the possible sizes of the lunar core, which were obtained with two independent approaches based on solving the inverse problem of determining the internal structure and composition of the Moon. For calculations Monte Carlo method was used taking into account geophysical and geochemical constraints on the models. In the first method, the inverse problem was solved for two different temperature models (“cold” and “hot”). In the second method, two different models of the bulk composition of the lunar mantle (Earthlike and enriched in Al2O3) were considered. Both approaches led to similar values for the radius of the lunar core. It was found that the radii of Fe-S core are in the range of 50-350 km with the most probable value of about 300 km (∼ 1% of the mass of the Moon) and are rather weakly dependent on the thermal regime and chemical composition of the lunar mantle.
Experimental solution of Buquoy’s problem
Authors: Domnyshev A A , Kalinichenko V A , Shkapov P M
Published: December 2020

This article addresses the problem in which a chain moves vertically upward from a horizontal plane under constant force – Buquoy’s problem. For the first time, an original technique is proposed for the experimental solution of this problem. The chain’s motion is studied in liquid (water), and the buoyancy force of the float attached to the chain serves as a constant force. The experiment reveals converging oscillation of the system at various displacements of the chain relative to the equilibrium position. The differential equation of chain motion which describes this variable mass system is solved by the numerical technique. A comparison of theoretical and experimental data is made.
Face Recognition and Temperature Data Acquisition for COVID-19 Patients in Honduras
Authors: Sorto A , Marquez T , Carrasco A , Ordoñez J
Published: December 2020

Honduras health workers are reduced; doctors and nurses are getting infected by COVID-19. The primary purpose of this project is the design and development of software that performs facial recognition and temperature registration for patients. The incremental model was used to develop the software. The algorithm was trained with 5 images per face for the first test and 10 images per face for the second, with a total sample of 80 participants. At a maximum distance of 1.4 meters from the camera, the system obtained 72% and 82% accuracy for each of the tests. Finally, the authors conclude that the system can be implemented in health areas such as laboratories, hospitals, and clinics so that contact between patients and doctors can be reduced.
Influence of nafen nanoparticles on the strength of nickel
Authors: Agureev L E , Ivanov B S , Savushkina S V , Laptev I N , Kanushkin A I , Sivtsova G V
Published: December 2020

The article presents the results of studies of the structure and properties of pure nickel with the addition of nanofibers of aluminum oxide – nafen. The samples were obtained by spark plasma sintering of mechanically activated metal powder. The effect of nanofibers on Young’s modulus and ultimate strength of nickel at 25 °C and elevated temperatures is considered.
Formation of the titanium-aluminum intermetallic compounds by ion-beam mixing
Authors: Bykov P V , Vorob’ev V L , Klimova I N , Kolotov A A , Drozdov A Yu , Bayankin V Ya , Alexandrova S S
Published: December 2020

The results of studying the X-ray photoelectron spectroscopy of the chemical composition formation of titanium surface layers with a deposited aluminum film after ion-beam mixing are presented. At the selected parameters of ion irradiation, the aluminum films 10 and 20 nm thick are mixed with a titanium substrate. TiAl compounds are formed during mixing.
The correlation of the parameters of the melt pool with the form of the track in the technology of laser metal deposition
Authors: Dubrov A V , Zavalov Yu N
Published: December 2020

The temporal dependence of parameters of the melt pool (MP) during the formation of the track in the process of laser metal deposition (LMD) was obtained. The video monitoring in the LMD process was used by the coaxial scheme with the frame rate of up to 3 kHz and the spatial resolution of down to 10 μm. The technique was developed to process video data, to analyse images of the illuminated area in LMD process and to determine the MP key characteristics. The method of the MP – contouring detects areas of solid material with high intensity due to differences in the emissivity of the material in images and to exclude them from consideration. 3D approximation of the tracks was made using the interferometric profilometer. The correlation analysis of the relationship between the geometric characteristics of the track and the characteristics of the MP was carried out. The maxima of the correlation of the height of the track profile and the MP width is detected on the scale of (0.1…1) mm. The additional conditions should be investigated to establish the reliable correlation between the deviations observed in the experiment.
Surface charge of polymer materials modified by nanostructured fluorocarbon coatings
Authors: Elinson V M , Shchur P A , Kukushkin D Yu
Published: December 2020

The paper presents the results of a study of the surface charge of polymer materials modified with fluorocarbon films formed by ion-plasma technology at different CF4 contents in the CF4 + CeH12 plasma mixture. Nanostructured fluorocarbon films formed on the surface of polyethyleneterephthalate and polystyrene have a positive charge in the region of “transient” processes, and films on the surface of polytetrafluoroethylene have a negative charge, which is associated with different topology of the relief on the surface of these polymers, as well as their polarity.
Methods for forecasting and control of the phase composition and residual voltage in Al-Cu-Li alloys in friction mixing welding
Authors: Gordeeva MI
Published: December 2020

One of the main directions for reducing the weight of structures of aerospace engineering products is the use of aluminum-lithium alloys, which have unique characteristics of strength, rigidity and fracture toughness [1–3]. Nevertheless, the manufacture of large-sized welded structures from high-strength aluminum-lithium alloys is associated with serious problems due to their softening under the influence of the thermal cycle of fusion welding, for which the joint strength coefficient (the ratio of the weld strength to the strength of the base material) is below 60% [4, 5]… It is possible to increase the operational characteristics of welded joints through the use of new effective technological processes, such as friction stir welding (FWW) [6].
The effect of plasma electrolytic polishing on the surface properties of nitrocarburised steel
Authors: Kusmanov S A , Tambovskiy I V , Silkin S A , Korableva S S , Belov R D , Belkin P N
Published: December 2020

The effect of anodic plasma electrolytic polishing on the characteristics of low carbon steel (0.2 % C) after nitrocarburising was investigated. The formation of the modified layer including a hardened diffusion layer and a surface oxide layer occurs as a result of anodic plasma electrolytic nitrocarburising in an aqueous solution of glycerol (8 %), ammonium nitrate (5 %) and ammonium chloride (15 %) at 850 °C. Conducting a plasma electrolytic polishing of the surface leads to the removal of a loose part of the oxide layer (predominantly FeO), which affects the reduction the surface roughness of 2 times. The rate of the weight loss of steel in this process is 0.5 mg/s. The corrosion current density in a 3.5 % sodium chloride solution decreases from 41.0 μA/cm2 in an untreated sample to 32.6 μA/cm2 in the steel after nitrocarburising and polishing during 30 s and to 22–24 μA/cm2 when the second operation lasted 60-300 s due to the protective action of the nitride zone and the dense part of the oxide layer. Wear test shows that plasma electrolytic polishing enhances the wear resistance of a nitrocarburised sample by 1.8 times.
Interaction of cathode spots of a vacuum-arc discharge with a metal surface during its deactivation
Authors: Kuznetsov V G
Published: December 2020

For the first time, the possibility of deactivation of a metal surface by the dry method by means of treatment with cathode spots of a vacuum-arc discharge is shown. A high deactivation coefficient is obtained by squeezing the liquid phase of the metal from the cathode spot with a high pressure created by the plasma flow at the base of the cathode jet. Some principles of controlling the movement of cathode spots of a vacuum arc on the surface are shown.
Study of the influence of bias voltage on the texture and residual stresses of Mo coatings deposited on a Cu substrate by magnetron sputtering deposition
Authors: Lozovan A A , Betsofen S Ya , Labutin A A , Lenkovets A S , Bespalov A V , Grushin I A
Published: December 2020

The paper presents the results of studying the effect of the bias voltage on the structure, texture, and residual stresses of Mo coatings deposited on a copper substrate using an inverted magnetron. It is shown that variations in the bias voltage lead to changes in the texture and thickness of the Mo coatings. It was found that an increase in the bias voltage leads to an increase in the values of the compressive residual stresses.
Tribological properties of solid lubricating coatings of the TiN-Pb system at various Pb content
Authors: Lyakhovetskiy M A , Lozovan A A , Lesnevskiy L N , Nikolaev I A , Pavlov Yu S
Published: December 2020

The paper presents the results of the investigation of the solid lubricant coatings (SLC) tribological properties based on a TiN matrix with various content of Pb (13,16 and 22 at. %) in monolayer design. The results of the study of its morphology, elemental composition and tribological properties are provided. It is shown that the increase of the Pb content from 13 to 22 at. % lead to increase of CoF and decrease the wear resistance.
Integrated network analysis reveals new genes suggesting COVID-19 chronic effects and treatment
Authors: Pavel Alisa , del Giudice Giusy , Federico Antonio , Di Lieto Antonio , Kinaret Pia A S , Serra Angela , Greco Dario
Published: December 2020

The COVID-19 disease led to an unprecedented health emergency, still ongoing worldwide. Given the lack of a vaccine or a clear therapeutic strategy to counteract the infection as well as its secondary effects, there is currently a pressing need to generate new insights into the SARS-CoV-2 induced host response. Biomedical data can help to investigate new aspects of the COVID-19 pathogenesis, but source heterogeneity represents a major drawback and limitation. In this work, we applied data integration methods to develop a Unified Knowledge Space (UKS) and used it to identify a new set of genes associated with SARS-CoV-2 host response, both in vitro and in vivo. Functional analysis of these genes reveals possible long-term systemic effects of the infection, such as vascular remodelling and fibrosis. Finally, we identified a set of potentially relevant drugs targeting proteins involved in multiple steps of the host response to the virus.
Suppression of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) After a Second Wave in Victoria, Australia
Authors: Giles Michelle L , Wallace Euan M , Alpren Charles , Brady Nicole , Crouch Simon , Romanes Finn , Sutton Brett , Cheng Allen
Published: December 2020

Countries worldwide are experiencing a second wave of coronavirus disease 2019 (COVID-19), which is proving to be difficult to control. We describe the combination of physical distancing, mandatory mask wearing, movement restrictions, and enhanced test, trace, and isolation efforts that can be used to successfully suppress community transmission to zero.
Influence of Soil Moisture Zones on Rice Water Weevil (Coleoptera: Curculionidae) Populations in Furrow Irrigated Rice
Authors: Kelly F R , Gore J , Cook D , Catchot A L , Golden B R , Krutz L J , Crow W D , Towles T B
Published: December 2020

Water conservation is an important factor for production of rice in the United States because of declining aquifer levels, but little research has been done to evaluate insect management in rice systems integrating water conservation practices. Rice water weevil, Lissorhoptrus oryzophilus Kuschel, is an important insect pest of rice in the U.S. Rice water weevil is a semiaquatic species that relies on flooded conditions to complete larval development, so water conservation practices are likely to impact their pest status. The study was conducted across the Mississippi River alluvial floodplain to compare rice water weevil population densities in different zones of a furrow irrigated rice field to a conventionally flooded rice field. All locations were sampled at 3, 4, and 5 wk after the initial irrigation. Larval densities were greatest in the lower end of furrow irrigated fields and in the adjacent flooded rice field compared with the upper and middle sections that did not hold standing water when averaged across three sample dates. Also, rice water weevil densities were greater during week five than week three. In terms of rice yields, the top third of furrow irrigated rice fields, the section that remained mostly dry, produced lower rough rice yields than all other sections and the flooded field. These results suggest that rice water weevil populations can be lower in a furrow irrigated rice system. As a result, more research is needed to determine whether a spatial management plan can be developed based on soil moisture zones in furrow irrigated rice.
Mesalazine-induced myopericarditis: a case report
Authors: Shergill Simran
Published: December 2020

Background

Mesalazine is a well-established 1st line treatment for inflammatory bowel disease (IBD). Cardiotoxicity following 5-aminosalicyclic-acid therapy remains a rare yet serious complication and can often be challenging to distinguish from myocarditis presenting as an extra-intestinal manifestation of IBD.

Case summary

We present a case of a 22-year-old man with a background of ulcerative colitis commenced on a mesalazine preparation for disease progression. He presented to our hospital 12 days following drug initiation with acute chest pain, peak troponin-T of 242 ng/L, dynamic electrocardiogram changes, and severe left ventricular systolic dysfunction on transthoracic echocardiogram. The clinical diagnosis of myopericarditis was suspected and mesalazine was stopped shortly after. Outpatient cardiac magnetic resonance performed 2 weeks following mesalazine cessation demonstrated a recovery of cardiac function with associated symptom and biochemical resolution.

Discussion

Clinicians should be aware of this potentially fatal adverse effect of a commonly prescribed medication. Symptoms of myocarditis often occur within the early stages of mesalazine initiation, which aids the clinical diagnosis. The mainstay of treatment is to simply discontinue the drug with rapid resolution of symptoms seen without any permanent or long-term cardiac dysfunction. Close liaison with the gastroenterology team is key, as 2nd line IBD therapies are often required for the ongoing management of the patient’s colitis.
Dento-skeletal effects produced by rapid versus slow maxillary expansion using fixed jackscrew expanders: a systematic review and meta-analysis
Authors: Rutili Valentina , Mrakic Giorgia , Nieri Michele , Franceschi Debora , Pierleoni Felicita , Giuntini Veronica , Franchi Lorenzo
Published: December 2020

Background

No systematic review and meta-analysis of dento-skeletal effects following rapid maxillary expansion (RME) and slow maxillary expansion (SME) using the same jackscrew expander with different activation protocols is available.

Objective

To compare dento-skeletal effects produced by RME with those induced by SME using the same fixed jackscrew expanders in growing patients.

Search methods

PubMed (MEDLINE), Cochrane Library, Scopus, Embase, and OpenGrey were searched with no language or publication date restrictions.

Selection criteria

Only randomized controlled trials (RCTs) were selected and the following inclusion criteria were used: growing patients in mixed or permanent dentition, with maxillary transverse discrepancy, dental crowding, and treated with fixed jackscrew maxillary expander (e.g. Hyrax, Haas) activated to achieve either RME or SME.

Data collection and analysis

Data were extracted by two independent reviewers. The quality of the included RCTs was assessed according to the Cochrane risk-of-bias tool for randomized trials (RoB 2.0). For the aggregation of continuous data, the mean of the differences (MD) between treatments was used. A random effect model was applied.

Results

From 4855 retrieved articles, 3 studies were selected, 1 at unclear risk and 2 at high risk of bias. Maxillary intermolar distance showed no significant differences between the two modalities of expansion [pooled MD = 0.99 mm favouring RME, with 95% confidence interval (CI) = −2.09 to 4.06, P = 0.53, I2 = 90%]. As for maxillary molar inclination measured as the angle formed by the axes passing through the disto-buccal cusps and the apexes of the palatine root of the first upper molars, it was significantly smaller in the SME group (MD = −11.51°, with 95% CI = −15.23 to −7.79, P < 0.0001). Posterior maxillary expansion was significantly greater in RME than SME (pooled MD = 0.75 mm, with 95% CI = 0.27–1.23, P = 0.002, I2 = 0%).

Conclusions

Both RME and SME produce an effective dento-skeletal expansion of the maxilla. RME is slightly more effective in increasing the posterior transverse skeletal width of the maxilla while SME induces smaller molar inclination.

Registration

PROSPERO CDR42018105530.
Parliament2: Accurate structural variant calling at scale
Authors: Zarate Samantha , Carroll Andrew , Mahmoud Medhat , Krasheninina Olga , Jun Goo , Salerno William J , Schatz Michael C , Boerwinkle Eric , Gibbs Richard A , Sedlazeck Fritz J
Published: December 2020

Background

Structural variants (SVs) are critical contributors to genetic diversity and genomic disease. To predict the phenotypic impact of SVs, there is a need for better estimates of both the occurrence and frequency of SVs, preferably from large, ethnically diverse cohorts. Thus, the current standard approach requires the use of short paired-end reads, which remain challenging to detect, especially at the scale of hundreds to thousands of samples.

Findings

We present Parliament2, a consensus SV framework that leverages multiple best-in-class methods to identify high-quality SVs from short-read DNA sequence data at scale. Parliament2 incorporates pre-installed SV callers that are optimized for efficient execution in parallel to reduce the overall runtime and costs. We demonstrate the accuracy of Parliament2 when applied to data from NovaSeq and HiSeq X platforms with the Genome in a Bottle (GIAB) SV call set across all size classes. The reported quality score per SV is calibrated across different SV types and size classes. Parliament2 has the highest F1 score (74.27%) measured across the independent gold standard from GIAB. We illustrate the compute performance by processing all 1000 Genomes samples (2,691 samples) in <1 day on GRCH38. Parliament2 improves the runtime performance of individual methods and is open source (https://github.com/slzarate/parliament2), and a Docker image, as well as a WDL implementation, is available.

Conclusion

Parliament2 provides both a highly accurate single-sample SV call set from short-read DNA sequence data and enables cost-efficient application over cloud or cluster environments, processing thousands of samples.
Relative earthquake location procedure for clustered seismicity with a single station
Authors: Grigoli Francesco , Ellsworth William L , Zhang Miao , Mousavi Mostafa , Cesca Simone , Satriano Claudio , Beroza Gregory C , Wiemer Stefan
Published: December 2020

Earthquake location is one of the oldest problems in seismology, yet remains an active research topic. With dense seismic monitoring networks, it is possible to obtain reliable locations for microearthquakes; however, in many cases dense networks are lacking, limiting the location accuracy, or preventing location when there are too few observations. For small events in all settings, recording may be sparse and location may be difficult due to low signal-to-noise ratio. In this work, we introduce a new, distance-geometry-based method to locate seismicity clusters using only one or two seismic stations. A distance geometry problem consists in determining the location of sets of points based only on the distances between member pairs. Applied to seismology, our approach allows earthquake location using the interevent distance between earthquake pairs, which can be estimated using only one or two seismic stations. We first validate the method with synthetic data that resemble common cluster shapes, and then test the method with two seismic sequences in California: the August 2014   Mw 6.0 Napa earthquake and the July 2019 Mw 6.4 Ridgecrest earthquake sequence. We demonstrate that our approach provides robust and reliable results even for a single station. When using two seismic stations, the results capture the same structures recovered with high-resolution double-difference locations based on multiple stations. The proposed method is particularly useful for poorly monitored areas, where only a limited number of stations are available.
Synergistic Effects of the Red Light and Blue Traps on Control of Thrips palmi (Thysanoptera: Thripidae)
Authors: Murata Mika , Yamahama Yumi , Hariyama Takahiko
Published: December 2020

The melon thrips (Thrips palmi) is a serious insect pest of vegetables and ornamental plants. To control and monitor this thrips, blue traps are widely used. We previously reported that irradiation of cucumber plants with red light-emitting diodes (660 nm) causes T. palmi to avoid the plants. Here, we evaluated the responses of T. palmi adults to a cucumber plant in an experimental arena with either a transparent sticky trap or a blue sticky trap, without or with illumination by a red LED panel. When T. palmi were introduced into the arena, the number of thrips attracted to the plant was lowest in treatments using the red light and blue trap. On the other hand, when T. palmi were inoculated on plants first, most thrips stayed put on the plants. Placing both red LEDs and blue sticky traps in greenhouses before the thrips invade the greenhouse from the outside might effectively control T. palmi.
Leiomyosarcoma of the spermatic cord presenting as an incarcerated inguinal hernia: a rare presentation of a rare condition
Authors: Christodoulidis Gregory , Samara Athina Α , Perivoliotis Konstantinos , Floros Theodoros , Volakakis Georgios , Magouliotis Dimitrios E , Papamichali Roidoula , Tepetes Konstantinos
Published: December 2020

Leiomyosarcomas of the spermatic cord are rare malignancies with only sporadic cases (less than 150) reported in the literature. Preoperative diagnosis of a paratestical leiomyosarcoma is challenging. Clinicians do not typically consider inguinoscrotal lumps as underlying sarcomas due to their relatively low prevalence compared with hernias. As a result the diagnosis of a sarcoma of the paratesticular area is often hard to reach. Herein, we report a rare case of a leiomyosarcoma originating from the spermatic cord, masquerading as a strangulated inguinal hernia. Intraoperatively, a mass arising from the spermatic cord was found and excised. A supplementary orchiectomy with high ligation of the spermatic cord was also performed.
Assessing the response of odonates (dragonflies and damselflies) to a tropical urbanization gradient
Authors: Jere Arjit , Darshetkar Apeksha , Patwardhan Ankur , Koparde Pankaj
Published: December 2020

Understanding species responses to urbanization is important to realize their specific conservation needs. Odonates (dragonflies and damselflies) are freshwater insects perceived as good ecological indicators. To investigate responses of tropical odonates to an urbanization gradient, we sampled adult odonates along an urbanization gradient at six sites along the Mula River across Pune City, Maharashtra, India. For species–habitat analysis, we first performed a variable reduction using principal component analysis. we analyzed species–habitat data using redundancy analysis and canonical correspondence analysis. We documented 15 odonates across 6 sites. Our statistical analyses on patterns of odonate assemblages across sites and environmental variables did not return significant results. However, we detected site-exclusivity in a few species based on occurrence data and identified urban sensitive, urban tolerant and generalist species. We found that the odonate diversity was highest at a moderately urbanized site. We believe that increase in diversity due to moderate amounts of disturbance can be explained by the intermediate disturbance hypothesis. Based on our data, we suggest that for the conservation of odonates in the urban context, anthropogenic disturbance needs to be regulated. Here, we demonstrate that understanding species–habitat associations is the first step towards understanding their ecological and conservation requirements. To conserve odonates and rivers in metropolitan cities like Pune, restoring original river-side habitat and reducing the disturbance at highly urbanized sites to at least intermediate levels needs to be done on an urgent basis.
enckehh: an integrator for gravitational dynamics with a dominant mass that achieves optimal error behaviour
Authors: Hernandez David M , Holman Matthew J
Published: December 2020

We present enckehh, a new, highly accurate code for orbital dynamics of perturbed Keplerian systems such as planetary systems or galactic centre systems. It solves Encke’s equations of motion, which assume perturbed Keplerian orbits. By incorporating numerical techniques, we have made the code follow optimal roundoff error growth. In a 1012 d integration of the outer Solar system, enckehh was 3.5 orders of magnitude more accurate than ias15 in a fixed timestep test. Adaptive steps are recommended for ias15. Through study of efficiency plots, we show that enckehh reaches significantly higher accuracy than the rebound integrators ias15 and whckl for fixed step size.
Revisiting the gas kinematics in SSA22 Lyman-α Blob 1 with radiative transfer modelling in a multiphase, clumpy medium
Authors: Li Zhihui , Steidel Charles C , Gronke Max , Chen Yuguang
Published: December 2020

We present new observations of Lyman-α (Lyα) Blob 1 (LAB1) in the SSA22 protocluster region (z = 3.09) using the Keck Cosmic Web Imager and Keck Multi-object Spectrometer for Infrared Exploration. We have created a narrow-band Lyα image and identified several prominent features. By comparing the spatial distributions and intensities of Lyα and Hβ, we find that recombination of photo-ionized H i gas followed by resonant scattering is sufficient to explain all the observed Lyα/Hβ ratios. We further decode the spatially resolved Lyα profiles using both moment maps and radiative transfer modelling. By fitting a set of multiphase, ‘clumpy’ models to the observed Lyα profiles, we manage to reasonably constrain many parameters, namely the H i number density in the interclump medium (ICM), the cloud volume filling factor, the random velocity and outflow velocity of the clumps, the H i outflow velocity of the ICM, and the local systemic redshift. Our model has successfully reproduced the diverse Lyα morphologies, and the main results are: (1) the observed Lyα spectra require relatively few clumps per line of sight as they have significant fluxes at the line centre; (2) the velocity dispersion of the clumps yields a significant broadening of the spectra as observed; (3) the clump bulk outflow can also cause additional broadening if the H i in the ICM is optically thick; (4) and the H i in the ICM is responsible for the absorption feature close to the Lyα line centre.
Vicarious Responsibility and the Problem of ‘Too Much’: Moral Luck from the Perspective of Ordinary Ethics
Authors: Kuan Teresa
Published: December 2020

This paper explores vicarious responsibility and circumstantial luck from a first-person perspective, drawing on ethnographic research on parenting in Reform Era China. The paper focuses on how informants drew boundaries between what they could and could not control in raising a child who might thrive in a hypercompetitive society. In doing so, the paper engages the question, “What kind of moral agent do we want?” by proposing that we also ask, “What kind of moral agent do we find?” In contrast to the hypothetical figure of a walled-off agent who must be convinced of the duty to take on responsibilities in a circumstance of moral luck, empirical research finds instead a vulnerable agent who has taken on ‘too much’.
Dual inhibition of DNA-PK and DNA polymerase theta overcomes radiation resistance induced by p53 deficiency
Authors: Kumar Rashmi J , Chao Hui Xiao , Simpson Dennis A , Feng Wanjuan , Cho Min-Guk , Roberts Victoria R , Sullivan Aurora R , Shah Sonam J , Wozny Anne-Sophie , Fagan-Solis Katerina , Kumar Sunil , Luthman Adam , Ramsden Dale A , Purvis Jeremy E , Gupta Gaorav P
Published: December 2020

TP53 deficiency in cancer is associated with poor patient outcomes and resistance to DNA damaging therapies. However, the mechanisms underlying treatment resistance in p53-deficient cells remain poorly characterized. Using live cell imaging of DNA double-strand breaks (DSBs) and cell cycle state transitions, we show that p53-deficient cells exhibit accelerated repair of radiomimetic-induced DSBs arising in S phase. Low-dose DNA-dependent protein kinase (DNA-PK) inhibition increases the S-phase DSB burden in p53-deficient cells, resulting in elevated rates of mitotic catastrophe. However, a subset of p53-deficient cells exhibits intrinsic resistance to radiomimetic-induced DSBs despite DNA-PK inhibition. We show that p53-deficient cells under DNA-PK inhibition utilize DNA polymerase theta (Pol θ)-mediated end joining repair to promote their viability in response to therapy-induced DSBs. Pol θ inhibition selectively increases S-phase DSB burden after radiomimetic therapy and promotes prolonged G2 arrest. Dual inhibition of DNA-PK and Pol θ restores radiation sensitivity in p53-deficient cells as well as in p53-mutant breast cancer cell lines. Thus, combination targeting of DNA-PK- and Pol θ-dependent end joining repair represents a promising strategy for overcoming resistance to DNA damaging therapies in p53-deficient cancers.
The incidence of brain metastases among patients with metastatic breast cancer: a systematic review and meta-analysis
Authors: Kuksis Markus , Gao Yizhuo , Tran William , Hoey Christianne , Kiss Alex , Komorowski Adam S , Dhaliwal Aman J , Sahgal Arjun , Das Sunit , Chan Kelvin K , Jerzak Katarzyna J
Published: December 2020

Background

Patients with metastatic breast cancer (MBC) are living longer, but the development of brain metastases often limits their survival. We conducted a systematic review and meta-analysis to determine the incidence of brain metastases in this patient population.

Methods

Articles published from January 2000 to January 2020 were compiled from four databases using search terms related to breast cancer, brain metastasis, and incidence. The overall and per patient-year incidence of brain metastases were extracted from studies including patients with human epidermal growth factor receptor-2 positive (HER2+), triple negative, and hormone receptor (HR)+/hormone receptor negative (HER2−) MBC; pooled overall estimates for incidence were calculated using random effects models.

Results

937 articles were compiled, and 25 were included in the meta-analysis. Incidence of brain metastases in patients with HER2+ MBC, triple negative MBC, and HR+/HER2− MBC was reported in 17, 6, and 4 studies, respectively. The pooled cumulative incidence of brain metastases was 31% for the HER2+ subgroup (median follow-up: 30.7 months, IQR: 24.0–34.0), 32% for the triple negative subgroup (median follow-up: 32.8 months, IQR: 18.5–40.6), and 15% among patients with HR+/HER2− MBC (median follow-up: 33.0 months, IQR: 31.9–36.2). The corresponding incidences per patient-year were 0.13 (95% CI: 0.10–0.16) for the HER2+ subgroup, 0.13 (95%CI: 0.09–0.20) for the triple negative subgroup, and only 0.05 (95%CI: 0.03–0.08) for patients with HR+/HER2− MBC.

Conclusion

There is a high incidence of brain metastases among patients with HER2+ and triple negative MBC. The utility of a brain metastases screening program warrants investigation in these populations.
The nature of bright C-complex asteroids
Authors: Hasegawa Sunao , Kasuga Toshihiro , Usui Fumihiko , Kuroda Daisuke
Published: December 2020

Most C-complex asteroids have albedo values less than 0.1, but there are some high-albedo (bright) C-complex asteroids with albedo values exceeding 0.1. To reveal the nature and origin of bright C-complex asteroids, we conducted spectroscopic observations of the asteroids at visible and near-infrared wavelengths. As a result, the bright B-, C-, and Ch-type (Bus) asteroids, which are subclasses of the Bus C-complex, are classified as DeMeo C-type asteroids with concave curvature, B-, Xn-, and K-type asteroids. Analogue meteorites and material (CV/CK chondrites, enstatite chondrites/achondrites, and salts) associated with these spectral types of asteroids are thought to be composed of minerals and material exposed to high temperatures. A comparison of the results obtained in this study with the SDSS photometric data suggests that salts may have occurred in the parent bodies of 24 Themis and 10 Hygiea, as well as 2 Pallas. The bright C-complex asteroids in other C-complex families were likely caused by impact heating. Bright C-complex asteroids that do not belong to any families are likely to be impact-metamorphosed carbonaceous chondrites, CV/CK chondrites, or enstatite chondrites/achondrites.
Surviving Capitalism: Affordability as a Racial “Wage” in Contemporary Housing Markets
Authors: Robinson John N
Published: December 2020

In a time of growing inequality, analysts and commentators increasingly highlight the unaffordability of everyday living under capitalism as a convenient language for diagnosing today’s problems and devising policy solutions. This article reconsiders the notion of an “affordability crisis” by drawing on Du Bois’ conceptualization of the racial “wage” to theorize the uneven development of markets: a racial stratification process that renders capitalism affordable and livable for some non-elites, often whites, but not others. One of racism’s economic consequences is that it systematically produces affordability crises for market participants on the wrong side of the color line. Drawing on the literature of published studies on white suburbanization combined with historical evidence on the Community Reinvestment movement, this article illustrates the contrasting affordability politics in the homeowner and renter markets, which are divergent both in racial composition and in terms of their affordability to people without wealth. Ultimately, this article explains how and why marginalized groups undertake efforts to politically reconfigure the way markets work from the ground up, albeit through necessarily strained and improvisational means: as in community groups’ appropriation of tax shelters to finance affordable rental housing production, marking a precursor to policies subsequently adopted by mainstream officials and legislators.
Dose dependence of susceptibility and transmission for an Argentinean West Nile virus strain in local Culex pipiens quinquefasciatus (Diptera: Culicidae)
Authors: Giayetto Octavio , Beranek Mauricio D , Nazar Franco N , Diaz Adrián
Published: December 2020

Background

West Nile virus (WNV) activity has been documented in the central region of Argentina since 2005, but its maintenance network has not been elucidated yet.

Methods

We evaluated the susceptibility to WNV oral infection and transmission in a Culex pipiens quinquefasciatus mosquito population by means of a dose-dependent vector competence assay. Mosquitoes were orally infected with five different viral loads and evaluated for viral infection, dissemination and transmission.

Results

The evaluated population was susceptible to WNV oral infection. Disseminated infections were detected in all the viral doses but transmission was only detected in the higher doses (6 and 7 log10 plaque-forming units/ml). A linear relationship between doses and transmission rates could be established.

Conclusions

A minimum transmission threshold suggests that the Cu. p. quinquefasciatus from Argentina could acquire WNV infection from local urban birds and transmit the virus.