bluuebunny/crossref_metadata_2025 huggingface dataset:
Visible light modulator by sputter-deposited lithium niobate
Authors: Fukuzawa Hideaki , Yoshinari Jiro , Hara Hiroki , Sasaki Kenji , Take Hiroshi , Yoshida Makoto , Shimura Atsuhi , Kikukawa Takashi
Published: June 2022

Thin-film lithium niobate (LN) modulators have significant potential for ultra-high-speed optical communications. Although a significant cost reduction of the modulator is needed to satisfy the growing demands of huge data communications, all the existing studies of thin-film LN modulators were fabricated using the adhesion process of bulk LN to a substrate, and it severely constrains the use case of LN modulators. In order to overcome this critical issue, we have deposited thin-film LN (006) directly on a Al2O3 sapphire (001) substrate and fabricated LN modulators by using the wafer process. Furthermore, previous studies have been largely limited to the use of infrared light (typical wavelengths λ = 1550 nm), which also constrains half-wave voltage and interaction electrode length (Vπ · L) required for modulation. Small Vπ · L is essentially important not only for small die size with lower cost but also for small voltage operation by using a complementary metal oxide semiconductor. Here, we demonstrate the modulation of red (λ = 637 nm), green (λ = 520 nm), and blue (λ = 473 nm) visible light using sputter-deposited thin-film LN; the product of the half-wave voltage and interaction electrode length (Vπ · L) was 1.9, 1.4, and 1.2 V cm, respectively: it decreased with the decreasing wavelength. Thus, LN modulators can be adopted for emerging applications of visible light communications, and wafer-level fabrication using sputter-deposited thin-film LN provides opportunities for future mass production with a much lower fabrication cost.
Discovery of interpretable structural model errors by combining Bayesian sparse regression and data assimilation: A chaotic Kuramoto–Sivashinsky test case
Authors: Mojgani Rambod , Chattopadhyay Ashesh , Hassanzadeh Pedram
Published: June 2022

Models of many engineering and natural systems are imperfect. The discrepancy between the mathematical representations of a true physical system and its imperfect model is called the model error. These model errors can lead to substantial differences between the numerical solutions of the model and the state of the system, particularly in those involving nonlinear, multi-scale phenomena. Thus, there is increasing interest in reducing model errors, particularly by leveraging the rapidly growing observational data to understand their physics and sources. Here, we introduce a framework named MEDIDA: Model Error Discovery with Interpretability and Data Assimilation. MEDIDA only requires a working numerical solver of the model and a small number of noise-free or noisy sporadic observations of the system. In MEDIDA, first, the model error is estimated from differences between the observed states and model-predicted states (the latter are obtained from a number of one-time-step numerical integrations from the previous observed states). If observations are noisy, a data assimilation technique, such as the ensemble Kalman filter, is employed to provide the analysis state of the system, which is then used to estimate the model error. Finally, an equation-discovery technique, here the relevance vector machine, a sparsity-promoting Bayesian method, is used to identify an interpretable, parsimonious, and closed-form representation of the model error. Using the chaotic Kuramoto–Sivashinsky system as the test case, we demonstrate the excellent performance of MEDIDA in discovering different types of structural/parametric model errors, representing different types of missing physics, using noise-free and noisy observations.
Enhanced second harmonic Hall resistance in in-plane synthetic antiferromagnets
Authors: Zhu Libai , Xu Xiaoguang , Zhang Tanzhao , Wang Mengxi , Meng Kangkang , Wu Yong , Chen Jikun , Jiang Yong
Published: June 2022

Synthetic antiferromagnet (SyAF) has been demonstrated to be an ideal candidate for spin–orbit torque (SOT) based spintronic devices. However, the detailed mechanism needs to be clarified due to the coexistence of multiple effects. This paper studies SOT and the thermoelectric effect in SyAF of Pt/Co/Ru/Co/Pt by harmonic Hall resistance measurements. Different from the traditional Co/Pt bilayers, the second harmonic Hall resistance signals of the SyAF-based devices are obviously enhanced under a large external magnetic field (Bext), which is caused by the antiferromagnetic exchange coupling fields weakening the influence of Bext. By fitting the Hall resistance curves, the field-like torque is demonstrated to be the main contribution to the Hall resistance. Interestingly, both the SOT effective fields are greatly enhanced for antiparallel alignment. This study separates the contributions of SOT and the thermoelectric effect in the SyAF structures and enables the design of the spintronic devices with stability under a large magnetic field.
L21 ordering of Co2FeSn thin films promoted by high-temperature annealing
Authors: Fujiwara Kohei , Shibata Koya , Nishimura Shunsuke , Shiogai Junichi , Tsukazaki Atsushi
Published: June 2022

We report the effect of annealing on the crystalline ordering and physical properties in thin films of a nodal line semimetal candidate L21-type Co2FeSn. The Co–Fe–Sn films with a composition of Co:Fe:Sn ∼ 2:1:1 were deposited on MgO(001) substrates at a substrate temperature of 150 °C by radio-frequency magnetron sputtering. The as-deposited film showed x-ray diffraction patterns corresponding to the B2 ordering. Annealing at 600 and 700 °C after the deposition resulted in the appearance of the (111) diffraction peak, which is characteristic of the L21 ordering. Although anomalous Hall conductivity and transverse thermoelectric conductivity decreased from those of the as-deposited film with the annealing-induced L21 ordering, the low anomalous Hall conductivity of the 700 °C-annealed film was consistent with the theoretically estimated low value. These results show the significant influence of crystalline ordering on the electrical and thermoelectric transport properties. The annealing process is beneficial for studying the exotic physics arising from topological band features in the L21-ordered Co2FeSn thin films.
Probabilistic description for quasiparticle heat transport in one-dimensional nanostructures
Authors: Amrit J. , Medintseva T. , Nemchenko K. , Vikhtinskaya T.
Published: June 2022

Within the framework of the theory of random walks, we present an analytical study of one-dimensional ballistic flux of quasiparticles in the presence of scattering centers (SCs) such as defects or dopants. An explicit analytical expression is derived for the quasiparticle flux and the associated heat flux carried by phonons as a function of the number of SCs and the probabilities of (i) forward and backward scattering at SCs and (ii) absorption of quasiparticles by the SCs and in the conductor between SCs. The practical application of our model to one-dimensional nanostructures and to quasi-one-dimensional heat-conducting systems such as linear polycrystals is discussed. Various limiting cases are also considered. We demonstrate that our model is in excellent agreement with experimental data on the thermal conductance of Si nanowires having geometrically modified S-shaped extremities that act as SCs to the phonon flux.
Implementation of rapid microwave sintering using a 24 GHz gyrotron system
Authors: Egorov S. V. , Eremeev A. G. , Kholoptsev V. V. , Plotnikov I. V. , Rybakov K. I. , Sorokin A. A.
Published: June 2022

Rapid microwave sintering of different oxide ceramics with heating rates up to 300 °C/min and zero hold time has been implemented using a 24 GHz gyrotron-based system for high-temperature processing of materials. The design of the system, principle of operation, and process control are described. Particular attention is given to the design of thermal insulation assemblies and the implementation of temperature measurement in an environment with intense electromagnetic fields. A description of an optical system for dilatometry and temperature measurement is presented. The interrelation between the automatically regulated output power of the gyrotron and the microwave power absorbed volumetrically in the sample is analyzed on the basis of energy balance considerations. The analysis is illustrated by considering examples of rapid sintering processes with ZnO-based and BaTiO3 ceramic samples making use of direct and susceptor-assisted microwave heating. It is demonstrated that an increase in the volumetrically absorbed power leads to the development of a controlled thermal instability, which results in a lower temperature of the densification onset.
Tutorial: Piezoelectric and magnetoelectric N/MEMS—Materials, devices, and applications
Authors: Will-Cole A. R. , Hassanien Ahmed E. , Calisgan Sila Deniz , Jeong Min-Gyo , Liang Xianfeng , Kang Sungho , Rajaram Vageeswar , Martos-Repath Isabel , Chen Huaihao , Risso Antea , Qian Zhenyun , Seyed Abrishami Seyed Mahdi , Lobandi Nader , Rinaldi Matteo , Gong Songbin , Sun Nian X.
Published: June 2022

Nano- and micro-electromechanical systems (N/MEMSs) are traditionally based on electrostatic or piezoelectric coupling, which couples electrical and mechanical energy through acoustic resonator structures. Most recently, N/MEMS devices based on magnetoelectrics are gaining much attention. Unlike electrostatic or piezoelectric N/MEMS that rely on an AC electric field or voltage excitation, magnetoelecric N/MEMS rely on the electromechanical resonance of a magnetostrictive/piezoelectric bilayer heterostructure exhibiting a strong strain-mediated magnetoelectric coupling under the excitation of a magnetic field and/or electric field. As a consequence, magnetoelectric N/MEMS enable unprecedented new applications, ranging from magnetoelectric sensors, ultra-compact magnetoelectric antennas, etc. This Tutorial will first outline the fundamental principles of piezoelectric materials, resonator design, specifically different acoustic modes, and piezoelectric-based N/MEMS applications, i.e., radio frequency front end filters and infrared radiation sensors. We will then provide an overview of magnetoelectric materials and N/MEMS focusing on the governing physics of the magnetoelectric effect, magnetic material properties for achieving high magnetoelectric coupling, state-of-the-art magnetoelectric N/MEMS devices, and their respective applications.
Unraveling multi-state molecular dynamics in single-molecule FRET experiments. II. Quantitative analysis of multi-state kinetic networks
Authors: Opanasyuk Oleg , Barth Anders , Peulen Thomas-Otavio , Felekyan Suren , Kalinin Stanislav , Sanabria Hugo , Seidel Claus A. M.
Published: June 2022

Single-molecule Förster Resonance Energy Transfer (smFRET) experiments are ideally suited to resolve the structural dynamics of biomolecules. A significant challenge to date is capturing and quantifying the exchange between multiple conformational states, mainly when these dynamics occur on the sub-millisecond timescale. Many methods for quantitative analysis are challenged if more than two states are involved, and the appropriate choice of the number of states in the kinetic network is difficult. An additional complication arises if dynamically active molecules coexist with pseudo-static molecules in similar conformational states with undistinguishable Förster Resonance Energy Transfer (FRET) efficiencies. To address these problems, we developed a quantitative integrative analysis framework that combines the information from FRET-lines that relate average fluorescence lifetimes and intensities in two-dimensional burst frequency histograms, fluorescence decays obtained by time-correlated single-photon-counting, photon distribution analysis of the intensities, and fluorescence correlation spectroscopy. Individually, these methodologies provide ambiguous results for the characterization of dynamics in complex kinetic networks. However, the global analysis approach enables accurate determination of the number of states, their kinetic connectivity, the transition rate constants, and species fractions. To challenge the potential of smFRET experiments for studying multi-state kinetic networks, we apply our integrative framework using a set of synthetic data for three-state systems with different kinetic connectivity and exchange rates. Our methodology paves the way toward an integrated analysis of multiparameter smFRET experiments that spans all dimensions of the experimental data. Finally, we propose a workflow for the analysis and show examples that demonstrate the usefulness of this toolkit for dynamic structural biology.
Control of supersonic compression corner flow using a plasma actuator
Authors: Chen Zongnan , Hao Jiaao , Wen Chih-Yung
Published: June 2022

The control performance of a pulsed nanosecond dielectric barrier discharge (NSDBD) plasma actuator with varying pulse voltages and locations on a supersonic compression corner is studied using experiments and numerical simulations. The compression corner with a flat plate length of 60 mm and a ramp angle of 10° under laminar flow separation is experimentally investigated in a Ludwieg wind tunnel under a unit Reynolds number of 7.8 × 106 m−1 and Mach number of 4. The plasma actuators are placed either upstream or downstream of the separation point, extending in the spanwise direction. The Schlieren technique is used to visualize the shock wave interaction and estimate the propagation speed of the induced shock by the plasma actuator. For the numerical simulations, a one-zone inhomogeneous phenomenological plasma model is adopted to predict key discharge parameters and simulate the fast-heating region. The results show that the reduction of separation bubble length is up to 17% and 45%, respectively, in the cases of upstream and downstream of the separation point under a high applied voltage of 50 kV. The evolution of the flow structures is examined to reveal the underlying control mechanism. The results indicate that the high-speed external fluid is entrained into the original separation region after NSDBD activation upstream of the separation point, resulting in flow reattachment upstream of the corner. The entrained fluid with high momentum compels the main separation to move downstream, accompanied by the fragmentation of the original shear layer. Furthermore, the suppression of the separation region is more effective when the plasma actuator is installed close to the separation region and in the first 200 μs during one pulse, providing a good suggestion for the actuation frequency and installed location.
Coexistence of ferroelectricity and ferromagnetism in Ni-doped Al0.7Sc0.3N thin films
Authors: Liu Zhengyuan , Luo Bingcheng , Hou Boyu
Published: June 2022

Development of multiferroic materials with the capability of compatibility with the current semiconductor technology is of interest for practical applications. Recent experimental discovery of robust ferroelectricity in CMOS-compatible III-nitrides offers an alluring opportunity to construct multiferroic nitrides through chemical-doping engineering. We here reported the coexistence of ferroelectricity and ferromagnetism in Ni-doped Al0.7Sc0.3N thin films. It is found that apart from the promising ferroelectric properties, including a square-like polarization–electric field (P–E) hysteresis loop with a large coercive field (∼3 MV/cm) and high remanent polarizations (∼100 μC/cm2), the films also exhibit room-temperature ferromagnetism, with a saturation magnetization of ∼8 emu/cm3. Additionally, the magneto-dielectric effect has also been experimentally confirmed. Our work provides a reference for subsequent research on nitride multiferroic materials and related applications.
Computational modeling of drug dissolution in the human stomach: Effects of posture and gastroparesis on drug bioavailability
Authors: Lee J. H. , Kuhar S. , Seo J.-H. , Pasricha P. J. , Mittal R.
Published: June 2022

The oral route is the most common choice for drug administration because of several advantages, such as convenience, low cost, and high patient compliance, and the demand and investment in research and development for oral drugs continue to grow. The rate of dissolution and gastric emptying of the dissolved active pharmaceutical ingredient (API) into the duodenum is modulated by gastric motility, physical properties of the pill, and the contents of the stomach, but current in vitro procedures for assessing dissolution of oral drugs are limited in their ability to recapitulate this process. This is particularly relevant for disease conditions, such as gastroparesis, that alter the anatomy and/or physiology of the stomach. In silico models of gastric biomechanics offer the potential for overcoming these limitations of existing methods. In the current study, we employ a biomimetic in silico simulator based on the realistic anatomy and morphology of the stomach (referred to as “StomachSim”) to investigate and quantify the effect of body posture and stomach motility on drug bioavailability. The simulations show that changes in posture can potentially have a significant (up to 83%) effect on the emptying rate of the API into the duodenum. Similarly, a reduction in antral contractility associated with gastroparesis can also be found to significantly reduce the dissolution of the pill as well as emptying of the API into the duodenum. The simulations show that for an equivalent motility index, the reduction in gastric emptying due to neuropathic gastroparesis is larger by a factor of about five compared to myopathic gastroparesis.
Acoustic resonant imaging technique for visualizing the acoustic properties and thickness of polymer film on substrate
Authors: Kim Hyelin , Tohmyoh Hironori
Published: June 2022

This paper proposes an acoustic resonant imaging technique for visualizing the acoustic properties and thickness of a polymer film on a substrate. When ultrasound passes through a thin layer, transmission and reflection coefficients of sound pressure attain their extreme values at the resonant frequency. By obtaining the area information of the extreme value and resonant frequency and matching them with a theoretical model, the acoustic properties and thicknesses of a polymer film on a substrate can be visualized. Herein, this technique was applied to a photoresist film coated on a Si wafer, and in addition to visualizing fluctuations in film thickness, the differences in the film hardness that may have occurred during the curing process were successfully detected as the differences in the acoustic impedance of the film. The acoustic resonant imaging technique was successfully used to determine the frequency dependence of both the transmission and reflection coefficients.
Diversity of states in a chiral magnet nanocylinder
Authors: Savchenko Andrii S. , Zheng Fengshan , Kiselev Nikolai S. , Yang Luyan , Rybakov Filipp N. , Blügel Stefan , Dunin-Borkowski Rafal E.
Published: June 2022

The diversity of three-dimensional magnetic states in a FeGe nanocylinder is studied using micromagnetic simulations and off-axis electron holography in the transmission electron microscope. In particular, we report the observation of a dipole string—a spin texture composed of two coupled Bloch points—which becomes stable under geometrical confinement. Quantitative agreement is obtained between experimental and theoretical phase shift images by taking into account the presence of a damaged layer on the surface of the nanocylinder. The theoretical model is based on the assumption that the damaged surface layer, which results from focused ion beam milling during sample preparation, has similar magnetic properties to those of an amorphous FeGe alloy. The results highlight the importance of considering the magnetic properties of the surface layers of such nanoscale samples, which influence their magnetic states.
A mixing timescale model for differential mixing in transported probability density function simulations of turbulent non-premixed flames
Authors: Wei Jieli , Su Xingyu , Wang Xiao , Zhou Hua , Hawkes Evatt R. , Ren Zhuyin
Published: June 2022

The modeling of scalar mixing timescale remains a primary challenge in the transported probability density function (TPDF) method. The variation of scalar mixing timescale among species, i.e., differential mixing, results from the difference in molecular diffusivity and reaction-induced scalar gradient. Nevertheless, the vast majority of TPDF studies on turbulent non-premixed flames simply apply a single mixing timescale determined by the mixture fraction. In this work, a reaction-induced differential mixing timescale (RIDM) model for the mixing timescale of individual species in turbulent non-premixed flames is proposed. The key idea of the RIDM model is to approximate the relative magnitude of the species dissipation rates by using their values in laminar flamelets. A direct numerical simulation dataset of a temporally evolving non-premixed ethylene flame is employed to thoroughly evaluate the model performance via a priori and a posteriori tests. Results show that specifying a single mixing timescale for all species results in a poor prediction of the species dissipation rate and thus the failure to predict the overall combustion process. By accounting for the difference in molecular diffusivity, a slightly better prediction can be obtained, but the improvement is very limited, illustrating that simply modeling the difference due to molecular diffusivities for differential mixing is not sufficient. In comparison, the RIDM model exhibits superior performance in both a priori and a posteriori tests. Moreover, all the components of the RIDM model are readily available in the TPDF method, making the RIDM model a promising candidate employed in practice.
Computational studies of structural, energetic, and electronic properties of pure Pt and Mo and mixed Pt/Mo clusters: Comparative analysis of characteristics and trends
Authors: Sumer Aslihan , Jellinek Julius
Published: June 2022

The added technological potential of bimetallic clusters and nanoparticles, as compared to their pure (i.e., one-component) counterparts, stems from the ability to further fine-tune their properties and, consequently, functionalities through a simultaneous use of the “knobs” of size and composition. The practical realization of this potential can be greatly advanced by the knowledge of the correlations and relationships between the various characteristics of bimetallic nanosystems on the one hand and those of their pure counterparts as well as pure constituent components on the other hand. Here, we present results of a density functional theory based study of pure Ptn and Mon clusters aimed at revisiting and exploring further their structural, electronic, and energetic properties. These are then used as a basis for analysis and characterization of the results of calculations on two-component Ptn-mMom clusters. The analysis also includes establishing relationships between the properties of the Ptn-mMom clusters and those of their Ptn-m and Mom components. One of the particularly intriguing findings suggested by the calculated data is a linear dependence of the average binding energy per atom in sets of Ptn-mMom clusters that have the same fixed number m of Mo atoms and different number n-m of Pt atoms on the fractional content (n-m)/n of Pt atoms. We derive an analytical model that establishes the fundamental basis for this linearity and expresses its parameters—the m-dependent slope and intercept—in terms of characteristic properties of the constituent components, such as the average binding energy per atom of Mom and the average per-atom adsorption energy of the Pt atoms on Mom. The conditions of validity and degree of robustness of this model and of the linear relationship predicted by it are discussed.
Retromer dysfunction in amyotrophic lateral sclerosis
Authors: Pérez-Torres Eduardo J. , Utkina-Sosunova Irina , Mishra Vartika , Barbuti Peter , De Planell-Saguer Mariangels , Dermentzaki Georgia , Geiger Heather , Basile Anna O. , Robine Nicolas , Fagegaltier Delphine , Politi Kristin A. , Rinchetti Paola , Jackson-Lewis Vernice ,   NYGC ALS Consortium, Harms Matthew , Phatnani Hemali , Lotti Francesco , Przedborski Serge , Phatnani Hemali , Kwan Justin , Sareen Dhruv , Broach James R. , Simmons Zachary , Arcila-Londono Ximena , Lee Edward B. , Van Deerlin Vivianna M. , Shneider Neil A. , Fraenkel Ernest , Ostrow Lyle W. , Baas Frank , Zaitlen Noah , Berry James D. , Malaspina Andrea , Fratta Pietro , Cox Gregory A. , Thompson Leslie M. , Finkbeiner Steve , Dardiotis Efthimios , Miller Timothy M. , Chandran Siddharthan , Pal Suvankar , Hornstein Eran , MacGowan Daniel J. , Heiman-Patterson Terry , Hammell Molly G. , Patsopoulos Nikolaos A. , Butovsky Oleg , Dubnau Joshua , Nath Avindra , Bowser Robert , Harms Matthew , Aronica Eleonora , Poss Mary , Phillips-Cremins Jennifer , Crary John , Atassi Nazem , Lange Dale J. , Adams Darius J. , Stefanis Leonidas , Gotkine Marc , Baloh Robert H. , Babu Suma , Raj Towfique , Paganoni Sabrina , Shalem Ophir , Smith Colin , Zhang Bin , Harris Brent , Broce Iris , Drory Vivian , Ravits John , McMillan Corey , Menon Vilas , Wu Lani , Altschuler Steven , Lerner Yossef , Sattler Rita , Van Keuren-Jensen Kendall , Rozenblatt-Rosen Orit , Lindblad-Toh Kerstin , Nicholson Katharine , Gregersen Peter , Lee Jeong-Ho , Therapeutics Maze , Squibb Bristol-Myers , Pfizer  , Kokos Sulev , Muljo Stephen , Traynor Bryan J.
Published: June 2022

Retromer is a heteropentameric complex that plays a specialized role in endosomal protein sorting and trafficking. Here, we report a reduction in the retromer proteins—vacuolar protein sorting 35 (VPS35), VPS26A, and VPS29—in patients with amyotrophic lateral sclerosis (ALS) and in the ALS model provided by transgenic (Tg) mice expressing the mutant superoxide dismutase-1 G93A. These changes are accompanied by a reduction of levels of the α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor subunit GluA1, a proxy of retromer function, in spinal cords from Tg SOD1
G93A
mice. Correction of the retromer deficit by a viral vector expressing
VPS35
exacerbates the paralytic phenotype in Tg SOD1
G93A
mice. Conversely, lowering
Vps35
levels in Tg SOD1
G93A
mice ameliorates the disease phenotype. In light of these findings, we propose that mild alterations in retromer inversely modulate neurodegeneration propensity in ALS.
CLIL in the 21st Century
Authors: Dalton-Puffer Christiane , Hüttner Julia , Llinares Ana
Published: June 2022

This article traces the historical phases in the conceptualisation of and research on
Content-and-language-Integrated Learning in Europe since the 1990s. Following upon early programmatic statements, the first wave
of CLIL research concentrated on language learning outcomes. In a second wave, the focus was on descriptions of practice and
studies of participant perspectives. More recently, studies have focused on the unique character of CLIL as an educational
approach in its own right, not simply as a context of foreign language teaching. The crucial content-language interface is being
addressed in research focusing on language and literacy in content curricula and classroom practices. A new CLIL research focus is
the development of pedagogical practice through theory-based interventions. In line with the UN sustainable development goal of
Quality Education, we identify equity and team work as future challenges and argue that CLIL could be a catalyst for a more
collaborative and multidisciplinary approach in education.
Turbulence, Atmosphere and Climate Dynamics
Authors: Mokhov I I , Chkhetiani O G , Repina I A
Published: June 2022

The conference "Turbulence, Atmosphere and Climate Dynamics" dedicated to the memory of the Alexander M. Obukhov was held in Moscow from November 10 to 12, 2020. The topics of the conference covered the following scientific areas: turbulence; geophysical hydrodynamics; atmospheric and climate system dynamics; physics and composition of the atmosphere; air-sea interaction; wave propagation. The conference showed a high scientific level of almost all the presentations. Studies of turbulent, climatic and atmospheric processes are traditionally conducted in our country at the highest level, as evidenced by the publication in high-ranking scientific journals and the active participation of Russian scientists in international programs.

List of Program committee, Organizing committee are avilable in this pdf.
Estimating the parameters of wind turbulence from spectra of radial velocity measured by a pulsed Doppler lidar
Authors: Banakh V A , Smalikho I N
Published: June 2022

The paper proposes the method for estimating the turbulence energy dissipation rate and the variance of the vertical component of the wind velocity vector from the spectral density of radial velocity measured by a pulsed coherent Doppler lidar. The method takes into account the averaging of the radial velocity over the probing volume. It is shown that neglecting the spatial averaging leads to the understating the dissipation rate.
Influence of aerosols on the meteorological regime of Northern Eurasia according to COSMO-Ru Model
Authors: Poliukhov A A , Blinov D V
Published: June 2022

We provided the estimation of the aerosols effect at the surface and at the top of the atmosphere, as well as on the sensible and latent heat flux for the Northern Eurasia using the MACv2 aerosol climatology. The numerical experiments were performed with the COSMO-Ru model for the January and July in 2017. It is found that the aerosol radiation effect on the surface can reach -50 W/m2. At the same time, it is shown that the net shortwave radiation increase does not unequivocally leads to the air temperature at two meters increase. We revealed that the temperature at 2 meters decreases on -0.5±0.1 degrees per 100 W/m2 in the clear sky condition for Mediterranean, Red, Black and Caspian seas areas. The temperature sensitivity is positive and equals 0.9±0.3 degrees per 100 W/m2 for Middle East and southern Europe and 1.7±0.7 degrees per 100 W/m2 for northern Africa.
Three decades of remote sensing of NO2 vertical distribution and column content at the A. M. Obukhov Institute of Atmospheric Physics
Authors: Gruzdev A N , Elokhov A S
Published: June 2022

The paper reviews the results of 30-year spectrometric measurements of vertical distribution and column content of NO2 at the Zvenigorod Scientific Station (ZSS) of the A. M. Obukhov Institute of Atmospheric Physics and presents analysis of NO2 long-term trends and interannual variations. The station is located in the western Moscow region. It is part of the Network for the Detection of Atmospheric Composition Change (NDACC). Measurements are done in the morning and evening twilight by zenith-scattered visible solar radiation. Vertical NO2 profiles are retrieved and column NO2 contents are calculated by profile integration. Long term trends and inter-annual variations of NO2 are analysed by multivariate regression method taking into account autocorrelation of data in a wide range of time scales. Seasonally dependent estimates of NO2 trends and interannual variations due to the quasi-biennial oscillation, El Nino–Southern oscillation, North Atlantic Oscillation, and the 11-year solar cycle are obtained. Most pronounced (in per cent units) trends and circulation and solar cycle effects are peculiar to the winter–spring period of the year. Mutual influence is assessed between the estimates of the trend and the solar cycle effect in stratospheric NO2.
Temporal variations of downward solar radiation, aerosol optical thickness and cloudiness over North of the European part of Russia based on surface data records (during 40 years)
Authors: Plakhina I N , Repina I A , Makhotkina E L
Published: June 2022

The results of the analysis of temporal changes in the aerosol optical thickness of the atmosphere, the factor of turbidity, cloudiness and incoming solar radiation near the Earth's surface in the north of the European Territory of Russia (ETR) based on observations of the Roshydromet actinometric network for 1976—2014 are presented. Trends of synchronous changes in the above parameters have been revealed, both for the entire observation period and in the post-volcanic period (1995—2014). Under conditions of the aerosol optical thickness (AOT) decreasing (an increasing of the transparency of the atmosphere) for average cloudiness, a neutral time dependence of the incoming radiation is observed. Comparison with the results at actinometric stations in the south of ETR was carried out.
Study of biogas utilization as waste-to-energy plant and transport modelling of iron (Fe), lead (Pb) and copper (CU) in leachate at Muara Fajar landfill Pekanbaru
Authors: Yuvendius H , Zondra E , Zainuri  , Sari V I
Published: June 2022

Daily activities such as household, restaurants, markets and others especially in Pekanbaru city will produce waste. Waste produced is both organic and inorganic. A biogas utilization study has been conducted at the Muara Fajar landfill and 888.6 kW potential electricity has been obtained. Each landfill will produce leachate containing metals such as iron (Fe), lead (Pb), copper (Cu) and others. The level of metal toxicity will increasingly pollute the environment. Using the PHREEQC Interactive version 3.0.6.7757 modeling of these contaminants, it can be predicted the transport of the elements and at the same time reduce the risk of soil and water pollution. Modeling with parameter condition of the presence of dolomite show that concentration of Ca, Mg and Na metal decreased, while Cu metal showed a significant increase in the 10th to 50th years and stable at Cu concentration 1.4 mg/L. Lead (Pb) also increased from the 20th to 60th year and stable at Pb concentration 0.25 mg/L. In conditions without dolomite, concentration of iron (Fe) increase in the 15th year namely 0.175 mg/L and constant for the following year while Ca, Na and K have decreased to reach zero concentration.
The Utilization of Three-Dimensional Printing in Creating a Surgical Instrument: An Areola Cookie Cutter
Authors: Burhamah Waleed , Alshawaf Solaiman M , Alwazzan Sabika , AlYouha Sarah , Al-Sabah Salman
Published: June 2022

Three-dimensional (3D) printing is a rapidly evolving technology with many applications in the medical field. It involves printing solid objects from a digital file. In this paper, we describe our experience with the use of 3D printing in creating an areola cookie cutter that is compatible with sterilization. The objective of this study is to explore accurate and cost-effective methods of producing patient-specific areola cookie cutters. Auto computer-aided design (CAD) 3D software was used to design a digital model that was subsequently converted to a standard tessellation language (STL) file. The models were printed with the Formlabs Form 3+ SLA printer (Somerville, MA) using a resin material. Washing and curing were then performed followed by autoclave sterilization of the models. A total of 3 areola cookie cutters were created, each with different sizes (33, 38, and 42 mm) using resin material (Formlabs BioMed Clear Resin; Somerville, MA). All 3 models were able to withstand autoclave sterilization. The use of 3D printing has proven to be a valuable tool in Plastic surgery. We describe our experience of designing and producing an areola cookie cutter using a 3D printer; our model is compatible with the process of sterilization. We emphasize the advantages of a quick production time and accuracy in design.
The Cdc25/Ras/cAMP-dependent protein kinase A signaling pathway regulates proline utilization in wine yeast Saccharomyces cerevisiae under a wine fermentation model
Authors: Nishimura Akira , Ichikawa Kazuki , Nakazawa Hayate , Tanahashi Ryoya , Morita Fumika , Sitepu Irnayuli , Boundy-Mills Kyria , Fox Glen , Takagi Hiroshi
Published: June 2022

Proline is a predominant amino acid in grape must, but it is poorly utilized by the yeast Saccharomyces cerevisiae in wine-making processes. This sometimes leads to a nitrogen deficiency during fermentation and proline accumulation in wine. In this study, we clarified that a glucose response is involved in an inhibitory mechanism of proline utilization in yeast. Our genetic screen showed that strains with a loss-of-function mutation on the CDC25 gene can utilize proline even under fermentation conditions. Cdc25 is a regulator of the glucose response consisting of the Ras/cAMP-dependent protein kinase A (PKA) pathway. Moreover, we found that activation of the Ras/PKA pathway is necessary for the inhibitory mechanism of proline utilization. The present data revealed that crosstalk exists between the carbon and proline metabolisms. Our study could hold promise for the development of wine yeast strains that can efficiently assimilate proline during the fermentation processes.
Batch alignment via retention orders for preprocessing large-scale multi-batch LC-MS experiments
Authors: Malinka František , Zareie Ashkan , Prochazka Jan , Sedlacek Radislav , Novosadova Vendula
Published: June 2022

Motivation

Meticulous selection of chromatographic peak detection parameters and algorithms is a crucial step in preprocessing liquid chromatography–mass spectrometry (LC-MS) data. However, as mass-to-charge ratio and retention time shifts are larger between batches than within batches, finding apt parameters for all samples of a large-scale multi-batch experiment with the aim of minimizing information loss becomes a challenging task. Preprocessing independent batches individually can curtail said problems but requires a method for aligning and combining them for further downstream analysis.

Results

We present two methods for aligning and combining individually preprocessed batches in multi-batch LC-MS experiments. Our developed methods were tested on six sets of simulated and six sets of real datasets. Furthermore, by estimating the probabilities of peak insertion, deletion and swap between batches in authentic datasets, we demonstrate that retention order swaps are not rare in untargeted LC-MS data.

Availability and implementation

kmersAlignment and rtcorrectedAlignment algorithms are made available as an R package with raw data at https://metabocombiner.img.cas.cz

Supplementary information

Supplementary data are available at Bioinformatics online.
The Practical Haplotype Graph, a platform for storing and using pangenomes for imputation
Authors: Bradbury P J , Casstevens T , Jensen S E , Johnson L C , Miller Z R , Monier B , Romay M C , Song B , Buckler E S
Published: June 2022

Motivation

Pangenomes provide novel insights for population and quantitative genetics, genomics and breeding not available from studying a single reference genome. Instead, a species is better represented by a pangenome or collection of genomes. Unfortunately, managing and using pangenomes for genomically diverse species is computationally and practically challenging. We developed a trellis graph representation anchored to the reference genome that represents most pangenomes well and can be used to impute complete genomes from low density sequence or variant data.

Results

The Practical Haplotype Graph (PHG) is a pangenome pipeline, database (PostGRES & SQLite), data model (Java, Kotlin or R) and Breeding API (BrAPI) web service. The PHG has already been able to accurately represent diversity in four major crops including maize, one of the most genomically diverse species, with up to 1000-fold data compression. Using simulated data, we show that, at even 0.1× coverage, with appropriate reads and sequence alignment, imputation results in extremely accurate haplotype reconstruction. The PHG is a platform and environment for the understanding and application of genomic diversity.

Availability and implementation

All resources listed here are freely available. The PHG Docker used to generate the simulation results is https://hub.docker.com/ as maizegenetics/phg:0.0.27. PHG source code is at https://bitbucket.org/bucklerlab/practicalhaplotypegraph/src/master/. The code used for the analysis of simulated data is at https://bitbucket.org/bucklerlab/phg-manuscript/src/master/. The PHG database of NAM parent haplotypes is in the CyVerse data store (https://de.cyverse.org/de/) and named/iplant/home/shared/panzea/panGenome/PHG_db_maize/phg_v5Assemblies_20200608.db.

Supplementary information

Supplementary data are available at Bioinformatics online.
EasyGDB: a low-maintenance and highly customizable system to develop genomics portals
Authors: Fernandez-Pozo Noe , Bombarely Aureliano
Published: June 2022

EasyGDB is an easy-to-implement low-maintenance tool developed to create genomic data management web platforms. It can be used for any species, group of species, or multiple genome or annotation versions. EasyGDB provides a framework to develop a web portal that includes the general information about species, projects and members, and bioinformatics tools such as file downloads, BLAST, genome browser, annotation search, gene expression visualization, annotation and sequence download, and gene ids and orthologs lookup. The code of EasyGDB facilitates data maintenance and update for non-experienced bioinformaticians, using BLAST databases to store and retrieve sequence data in gene annotation pages and bioinformatics tools, and JSON files to customize metadata. EasyGDB is a highly customizable tool. Any section and tool can be enabled or disabled like a switch through a single configuration file. This tool aims to simplify the development of genomics portals in non-model species, providing a modern web style with embedded interactive bioinformatics tools to cover all the common needs derived from genomics projects.

Availability and implementation

The code and manual to use EasyGDB can be found at https://github.com/noefp/easy_gdb.
XSI—a genotype compression tool for compressive genomics in large biobanks
Authors: Wertenbroek Rick , Rubinacci Simone , Xenarios Ioannis , Thoma Yann , Delaneau Olivier
Published: June 2022

Motivation

Generation of genotype data has been growing exponentially over the last decade. With the large size of recent datasets comes a storage and computational burden with ever increasing costs. To reduce this burden, we propose XSI, a file format with reduced storage footprint that also allows computation on the compressed data and we show how this can improve future analyses.

Results

We show that xSqueezeIt (XSI) allows for a file size reduction of 4-20× compared with compressed BCF and demonstrate its potential for ‘compressive genomics’ on the UK Biobank whole-genome sequencing genotypes with 8× faster loading times, 5× faster run of homozygozity computation, 30× faster dot products computation and 280× faster allele counts.

Availability and implementation

The XSI file format specifications, API and command line tool are released under open-source (MIT) license and are available at https://github.com/rwk-unil/xSqueezeIt

Supplementary information

Supplementary data are available at Bioinformatics online.
MIAMI: mutual information-based analysis of multiplex imaging data
Authors: Seal Souvik , Ghosh Debashis
Published: June 2022

Motivation

Studying the interaction or co-expression of the proteins or markers in the tumor microenvironment of cancer subjects can be crucial in the assessment of risks, such as death or recurrence. In the conventional approach, the cells need to be declared positive or negative for a marker based on its intensity. For multiple markers, manual thresholds are required for all the markers, which can become cumbersome. The performance of the subsequent analysis relies heavily on this step and thus suffers from subjectivity and lacks robustness.

Results

We present a new method where different marker intensities are viewed as dependent random variables, and the mutual information (MI) between them is considered to be a metric of co-expression. Estimation of the joint density, as required in the traditional form of MI, becomes increasingly challenging as the number of markers increases. We consider an alternative formulation of MI which is conceptually similar but has an efficient estimation technique for which we develop a new generalization. With the proposed method, we analyzed a lung cancer dataset finding the co-expression of the markers, HLA-DR and CK to be associated with survival. We also analyzed a triple negative breast cancer dataset finding the co-expression of the immuno-regulatory proteins, PD1, PD-L1, Lag3 and IDO, to be associated with disease recurrence. We demonstrated the robustness of our method through different simulation studies.

Availability and implementation

The associated R package can be found here, https://github.com/sealx017/MIAMI.

Supplementary information

Supplementary data are available at Bioinformatics online.
Deep learning models for RNA secondary structure prediction (probably) do not generalize across families
Authors: Szikszai Marcell , Wise Michael , Datta Amitava , Ward Max , Mathews David H
Published: June 2022

Motivation

The secondary structure of RNA is of importance to its function. Over the last few years, several papers attempted to use machine learning to improve de novo RNA secondary structure prediction. Many of these papers report impressive results for intra-family predictions but seldom address the much more difficult (and practical) inter-family problem.

Results

We demonstrate that it is nearly trivial with convolutional neural networks to generate pseudo-free energy changes, modelled after structure mapping data that improve the accuracy of structure prediction for intra-family cases. We propose a more rigorous method for inter-family cross-validation that can be used to assess the performance of learning-based models. Using this method, we further demonstrate that intra-family performance is insufficient proof of generalization despite the widespread assumption in the literature and provide strong evidence that many existing learning-based models have not generalized inter-family.

Availability and implementation

Source code and data are available at https://github.com/marcellszi/dl-rna.

Supplementary information

Supplementary data are available at Bioinformatics online.
The anaphase-promoting complex/cyclosome co-activator, Cdh1, is a novel target of human papillomavirus 16 E7 oncoprotein in cervical oncogenesis
Authors: Jaiswal Neha , Nandi Deeptashree , Cheema Pradeep Singh , Nag Alo
Published: June 2022

The transforming properties of the high-risk human papillomavirus (HPV) E7 oncoprotein are indispensable for driving the virus life cycle and pathogenesis. Besides inactivation of the retinoblastoma family of tumor suppressors as part of its oncogenic endeavors, E7-mediated perturbations of eminent cell cycle regulators, checkpoint proteins and proto-oncogenes are considered to be the tricks of its transformative traits. However, many such critical interactions are still unknown. In the present study, we have identified the anaphase-promoting complex/cyclosome (APC) co-activator, Cdh1, as a novel interacting partner and a degradation target of E7. We found that HPV16 E7-induced inactivation of Cdh1 promoted abnormal accumulation of multiple Cdh1 substrates. Such a mode of deregulation possibly contributes to HPV-mediated cervical oncogenesis. Our mapping studies recognized the C-terminal zinc-finger motif of E7 to associate with Cdh1 and interfere with the timely degradation of FoxM1, a bona fide Cdh1 substrate and a potent oncogene. Importantly, the E7 mutant with impaired interaction with Cdh1 exhibited defects in its ability for overriding typical cell cycle transition and oncogenic transformation, thereby validating the functional and pathological significance of the E7-Cdh1 axis during cervical carcinoma progression. Altogether, the findings from our study discover a unique nexus between E7 and APC/C-Cdh1, thereby adding to our understanding of the mechanism of E7-induced carcinogenesis and provide a promising target for the management of cervical carcinoma.