bluuebunny/crossref_metadata_2025 huggingface dataset:
Numerical investigation on effect of air vent on air supply
Authors: Song Kai , Wei Wangru , Wu Shiqiang , Zhang Luchen , Yang Zhengli
Published: August 2022

An improper design of an air vent will not only cause waste of resources but also seriously threaten the safety of the spillway tunnel. The present study analyzes the effects of the area and position of the air vent on the air supply, using the volume of fluid method with the k–ε turbulence model. The air speed in the air vent will decrease with an increase in the area, but the quantity of air supplied will increase. When the area of air vents is equal to the tunnel residual, the air supply capacity of the air vent reaches the maximum. A relationship between the quantity of air supplied and the area of the air vent is put forward, and the error with the prototype observation result is about 10%. The distribution of negative pressure in the tunnel may be improved by arranging the air vent in a proper position; the quantity of air supplied also decreases as the distance between the air vent and the pressurized conduit increases. In general, it is more advantageous to position the air vent upstream. These results provide a reference for the air ventilation design in hydraulic engineering.
Analysis of core asymmetries in inertial confinement fusion implosions using three-dimensional hot-spot reconstruction
Authors: Woo K. M. , Betti R. , Thomas C. A. , Stoeckl C. , Churnetski K. , Forrest C. J. , Mohamed Z. L. , Zirps B. , Regan S. P. , Collins T. J. B. , Theobald W. , Shah R. C. , Mannion O. M. , Patel D. , Cao D. , Knauer J. P. , Glebov V. Yu. , Goncharov V. N. , Radha P. B. , Rinderknecht H. G. , Epstein R. , Gopalaswamy V. , Marshall F. J. , Ivancic S. T. , Campbell E. M.
Published: August 2022

Three-dimensional effects play a crucial role during the hot-spot formation in inertial confinement fusion (ICF) implosions. A data analysis technique for 3D hot-spot reconstruction from experimental observables has been developed to characterize the effects of low modes on 3D hot-spot formations. In nuclear measurements, the effective flow direction, governed by the maximum eigenvalue in the velocity variance of apparent ion temperatures, has been found to agree with the measured hot-spot flows for implosions dominated by mode ℓ=1. Asymmetries in areal-density (ρR) measurements were found to be characterized by a unique cosine variation along the hot-spot flow axis. In x-ray images, a 3D hot-spot x-ray emission tomography method was developed to reconstruct the 3D hot-spot plasma emissivity using a generalized spherical-harmonic Gaussian function. The gradient-descent algorithm was used to optimize the mapping between the projections from the 3D hot-spot emission model and the measured x-ray images along multiple views. This work establishes a platform to analyze 3D low-mode core asymmetries in ICF.
Review of Real Numbers
Authors: Pereyra Nicolas A.
Published: August 2022

In this chapter, we will construct the set of real numbers from the set of rational numbers through equivalence classes. We will discuss convergent rational number sequences and some of their properties that can be applied in the study of real numbers. We will review the isomorphism between fractional real numbers and rational numbers. We will review the general properties of real number operations: addition, subtraction, negative operator, identity operator, multiplication, division, and exponentiation with integer exponents, root of order n of real numbers, and inequalities. For more detailed and thorough discussions of real numbers, the author directs the reader toward the book Real and Complex Numbers for Physicists.
Exponentiation of Real Numbers with Rational Number Exponents
Authors: Pereyra Nicolas A.
Published: August 2022

In this chapter, we will present some initial notes and derive additional properties of the exponentiation of nonnegative real numbers with Integer exponents (extending the properties presented in Sec. 4.6). We will then introduce the exponentiation of real numbers with rational number exponents. We will derive general properties of the exponentiation of real numbers with rational number exponents.
Real Number Sequences and Limits
Authors: Pereyra Nicolas A.
Published: August 2022

The exponential function “exp (x) = ex” and its corresponding inverse function the natural logarithmic function “ln(x)” are found throughout physics. The exponential function may be defined as the real number “e” to the power of the argument (the real number x). We are then lead to defining the exponentiation operation of a real number base to the power of a real number exponent (in addition to defining the number e). In turn, the exponentiation operation of a real number base to the power of a real number exponent may be defined, and its properties are derived from the exponentiation operation of a real number base to the power of a rational number exponent (discussed in Chap. 5) and from real number sequences and their properties.

In this chapter, we will discuss real number sequences and some of their general properties that we will be applying to the definition of the exponentiation operation of a real number to the power of a real number exponent, which, in turn, will lead us to the exponential function.
Exponentiation of Real Numbers with Real Number Exponents
Authors: Pereyra Nicolas A.
Published: August 2022

In this chapter, we will derive some additional mathematical properties that will allow us to appropriately define the exponentiation of a real number base to the power of a real number exponent. We will then derive general properties of the exponentiation operation of real numbers with real number exponents.
Elements of Geometry
Authors: Pereyra Nicolas A.
Published: August 2022

Trigonometric functions are fundamental in physics and found throughout physics. Trigonometric functions, in turn, may be defined through the “trigonometric circle” in analytic planar geometry. Analytic planar geometry is the study of planar geometry through the application of coordinate systems. Planar geometry is the study of geometry when only points and geometric figures in a given plane are considered.We are, thus, led to discuss geometry. Geometry is the study of points and sets of points. In this book, a set of points will be referred to as a geometric figure. For example, as we will discuss below, a square can be seen as the union of four segments (its four sides), where each of the four segments, in turn, is sets of points. Thus, a square can be seen as a set of points and, therefore, a square is a “geometric figure.” In this chapter, we will introduce the axioms and axiomatic definitions of geometry used in this book.
Elements of Analytic Planar Geometry
Authors: Pereyra Nicolas A.
Published: August 2022

Trigonometric functions are fundamental in physics and found throughout physics. Trigonometric functions, in turn, may be defined through the “Trigonometric Circle” in analytic planar geometry. We are thus led to discuss analytic planar geometry.

Analytic Planar Geometry is the study of planar geometry through coordinate systems. In a plane, a coordinate system is a relation between points P in the plane and ordered pairs of real numbers (R1,R2) such that each ordered pair of real numbers represents a single point, and each point is represented by at least one ordered pair of real numbers.

Through Analytic Planar Geometry, Planar Geometry problems can be analyzed through the properties of real numbers and real number equations (rather than directly through the properties of geometric points). Also, through Analytic Planar Geometry, real number equations can, in turn, be analyzed through the properties of geometric points in Planar Geometry.
Historical persistence and isolation by distance of
Authors: Millar Melissa A. , Binks Rachel M. , Tapper Sarah-Louise , Macdonald Bronwyn M. , McArthur Shelley L. , Hankinson Margaret , Coates David J. , van Leeuwen Stephen , Byrne Margaret
Published: August 2022

Context Empirical studies of intraspecific genetic diversity and population structure can inform the evolutionary and demographic history of individual species and of landscapes at the bioregional level. Aims We aimed to assess intraspecific genetic variation at macroevolutionary and microevolutionary temporal scales for Mirbelia viminalis, a key species present on the Hamersley Range in the ancient and highly diverse landscape of the Pilbara bioregion of northwest Western Australia. Methods We sampled extant populations and assessed diversity and structure using sequences (chloroplast DNA, 1759 base pairs) and microsatellite markers (nuclear DNA, 15 loci) data. Key results Significant phylogeographic structure and a lack of historical demographic signals of population contraction or expansion suggest historical population persistence. Moderate chloroplast haplotype diversity (h = 15) and moderate divergence among extant haplotypes indicates a degree of historical connectivity via seed dispersal across central populations on the Hamersley Range. Levels of nuclear genetic diversity were low to moderate (allelic richness = 3.554, expected heterozygosity = 0.489, observed heterozygosity = 0.462) and depauperate compared to another member of the Mirbelia genus present further south in the Midwest region. Nuclear diversity revealed a strong signal of isolation by distance with localised admixture among populations and some contemporary genetic clustering along a north-west to south-east transect of the Hamersley Range. Conclusions Low nuclear genetic diversity may be related to recent reductions in population size for M. viminalis. Historical population persistence with few barriers to dispersal other than geographic distance may be common for members of the Fabaceae across the Hamersley Range.
Fact-checking on compound verbs in English
Authors: Bagasheva Alexandra , Fernández-Domínguez Jesús
Published: August 2022

The creation of compound verbs remains among the most contested phenomena of English word formation and the studies targeting these units have normally portrayed them as inconsistent or almost anomalous. This perception, together with the heterogeneous origins and the contested status of compound verbs, might explain why two central questions remain unanswered: (i) are these genuine compounds? and (ii) how can they be analyzed in a uniform manner? This paper tackles English verbal compounding with two hypotheses in mind: (i) that it is crucial to differentiate between a product- and a process-oriented approach to the phenomenon, and (ii) that a paradigm-based analysis acknowledging the role of analogy and the weight of metonymy proves highly beneficial.
Derivational paradigms
Authors: Mattiello Elisa
Published: August 2022

This chapter investigates a set of ten English combining forms attested in the
Oxford English Dictionary
between 1980 and 1997 and discusses the suitability of paradigms for the conceptualisation of analogy-based combining-form combinations. In this chapter, the focus is on the secreted type of combining forms, which involve both abbreviation and secretion, as in initial Franken- (from Frankenstein, in Frankenfood) or final -erati (from literati, in glitterati), respectively used to refer to ‘genetically modified –’ and ‘a prominent or elite group related to –’. Using a corpus-based approach, the chapter shows that secreted combining forms offer word-formation paradigms that apply to series of similar words in the lexicon and are applicable to other new words which are at the basis of English vocabulary expansion.
Derivational paradigms in ELT textbooks
Authors: Gráf Tomáš , Vašků Kateřina
Published: August 2022

Developing morphological awareness is an effective learning strategy which can simplify learning L2 vocabulary. The present chapter explores how far morphological-awareness activities are represented in over 100 international ELT coursebooks, 10 teacher training manuals and 17 practice books. The results show the coverage is rather low and unsystematic except in specialist manuals for vocabulary teaching and vocabulary practice books. Even in them the quality varies. Materials mostly focus on affixation and are not based on research findings. Attention should be paid to presenting teachers and teacher-trainees with more information on teaching derivational paradigms, and to introducing existing research and reliable materials which contain quality exercises and explicit information for students as well as ideas for classroom use.
Encoding and decoding communications based on perfect vector optical vortex arrays
Authors: Long Zixu , Hu Huajie , Ma Xin , Tai Yuping , Li Xinzhong
Published: August 2022

We proposed the perfect vector optical vortex arrays (PVOVAs) for encoding and decoding communications, including the 2 × 2, 1 × 4, 4 × 4, and 2 × 4 array forms, which were generated with the coaxial superposition of two vector optical vortex arrays with left- and right-handed circular polarization. The polarization order and state of each vector element could be modulated independently by adjusting the corresponding topological charges and additional phases, θn
. By attaching code information to these vector elements with different states of polarization, the hexadecimal code elements, including 0 to F, were represented. Therefore, PVOVAs consisting of multiple vector elements can transmit encoding information and be decoded as original information in the receiving end. The school badge grayscale image, with a size of 64 × 64 pixels, was transmitted using the encoding and decoding communication via PVOVAs, and the received restored image had a reliable accuracy. This study proves PVOVAs have flexible spatial structure and controllable states of polarization, and it expands the application of vector optical fields in optical encoding and decoding communication.
SiGeSn quantum well for photonics integrated circuits on Si photonics platform: a review
Authors: Olorunsola Oluwatobi , Said Abdulla , Ojo Solomon , Stanchu Hryhorii , Abernathy Grey , Amoah Sylvester , Saha Samir , Wangila Emmanuel , Grant Joshua , Acharya Sudip , Miller Lucas , Rosler Kyle , Jheng Yue-Tong , Chang Guo-En , Li Baohua , Salamo Gregory , Yu Shui-Qing , Du Wei
Published: August 2022

Recent studies of SiGeSn materials and optoelectronic devices hold great promise for photonics integrated circuits (PICs) on Si platform featuring scalable, cost-effective, and power-efficient. Thanks to the breakthrough of low temperature material growth techniques, device-quality level materials have been grown, following by the demonstration of light-emitting diodes, photodetectors, and optically pumped and electrically injected band-to-band lasers. While the exciting developments in bulk devices were reported, the quantum wells (QWs) have been investigated targeting the dramatically improved and/or novel device performance via variety of quantum confinement effects. In this review, we summarize the recent progress on development of SiGeSn QWs, including the fundamental optical and transition studies and optoelectronic device applications. The inspirational results reveal the possibility of all-group-IV PICs with photonics and electronics monolithically integrated on a single-chip.
Simultaneous measurements of atmospheric pressure at multiple locations and their distribution via website
Authors: Kojima Momoko , Kobata Tokihiko
Published: August 2022

Atmospheric pressure measurements have been performed in many places and fields. In recent years, traceability and reliability of the measured values are required in various applications, or even a simple pressure measurement sometimes needs the verification with a certain uncertainty. To meet these requirements, we developed a system to distribute the real-time values of atmospheric pressure traceable to the national pressure standards via a website. The pressure values are measured at several locations in a target site and users can easily obtain measured and estimated values at their locations, even if they are in a different building or on a different floor from the measurement location. To estimate the atmospheric pressure at unmeasured locations within the target site, the estimation of the head correction at each location was carefully validated by the results of simultaneous measurements at multiple locations. Then the uncertainty of the estimated value is evaluated to be approximately 10 Pa under relatively mild weather.
Fast and one-step synthesis of small ZnO nano-tetrapods Using CO2 laser in ambient air: physical properties
Authors: Riahimadvar Mohamad Sadegh , Tajaldini Mehdi
Published: August 2022

In this study, a simple laser ablation method was developed to synthesize small nano-tetrapods as a fast and one-step process. The used laser was a CO2 laser with 10.6 μm of wavelength with proper thermal penetration depth for performing the ZnO tetrapods in the interaction with Zn target in ambient air. The samples were produced in two different morphologies: nanorods and nano-tetrapods, in two states. The optical, structural, and morphological properties were studied by performing room-temperature scanning electron microscopy (FESEM), dynamic light scattering (DLS), x-ray diffraction (XRD), photoluminescence (PL), and UV-visible analysis. The FESEM analysis shows that the diameters of the produced ZnO nano-tetrapods are approximately 10–13 nm by arm length of about 250 nm with excellent morphologies. The XRD results indicated that the nanoparticles are in phase with pure ZnO and both morphologies have the Hexagonal wurtzite. Two high peaks in the PL spectrum were observed on UV and visible spectrums, a peak in the red wavelength was demonstrated that has been rarely found for ZnO nanostructures and show the capability of produced particle to use in lightning industry. UV–vis spectral of dispersed particles in deionized water determined that nanorods and nano-tetrapods have peaks at 374 nm and 370 nm, respectively. The spectrums showed produced nanostructures have a broad absorption band from ultra-violet to visible regions, leading the decreases the absorption when the wavelength increases slowly to the visible spectrum, that show capability to apply in photocatalytic processes. Therefore, results show the capability of the introduced method to access two different morphologies of ZnO and significantly the nano-tetrapods structure with well physical and morphological properties.
Constraining a possible time-variation of the speed of light along with the fine-structure constant using strong gravitational lensing and Type Ia supernovae observations
Authors: Colaço L.R. , Landau S.J. , Gonzalez J.E. , Spinelly J. , Santos G.L.F.
Published: August 2022

The possible time variation of the fundamental constants of nature has been an active subject of research since the large-number hypothesis was proposed by Dirac. In this paper, we propose a new method to investigate a possible time variation of the speed of light (c) along with the fine-structure constant (α) using Strong Gravitational Lensing (SGL) and Type Ia Supernovae (SNe Ia) observations. We assume a general approach to describe the mass distribution of lens-type galaxies, the one in favor of the power-law index model (PLAW). We also consider the runaway dilaton model to describe a possible time-variation of α. In order to explore the results deeply, we split the SGL sample into five sub-samples according to the lens stellar velocity dispersion and three sub-samples according to lens redshift. The results suggest that it is reasonable to treat the systems separately, but no strong indication of varying c was found.
Tuning infrared absorption in hyperbolic polaritons coated silk fibril composite
Authors: Shi Lihong , Peng Jiebin
Published: August 2022

Advanced textiles for thermal management give rise to many functional applications and unveil a new frontier for the study of human thermal comfort. Manipulating the coated quasi-particles between the composite components offers a platform to study the advanced thermoregulatory textiles. Here, we propose that coating the hyperbolic polariton can be an effective tool to tune infrared absorption in hexagonal boron nitride-coated silk composite. Remarkably, we achieve significant tuning of the infrared absorption efficiency of silk fibrils through the designed hexagonal boron nitride film. The underlying mechanism is related to resonance coupling between hyperbolic phonon polaritons. We find a notably high infrared absorption efficiency, nearly 3 orders larger than that without hBN coating, which can be achieved in our composite system. Our results indicate the promising future of advanced polariton-coated textiles and open a pathway to guide the artificial-intelligence design of advanced functional textiles.
Transmission-type reconfigurable metasurface for linear-to-circular and linear-to-linear polarization conversions
Authors: Wang Ping , Wang Yu , Yan Zhongming , Zhou Hongcheng
Published: August 2022

We present a transmission-type polarization conversion metamaterial (PCM) whose functions can be dynamically switched among the linear-to-circular (LTC) and linear-to-linear (LTL) polarization conversions. The proposed PCM consists of a grating, a polarization conversion surface and a reconfigurable polarization selective surface incorporated with PIN diodes. By changing the states of diodes, the PCM can achieve the reconfigurable manipulations for incident waves. The Fabry–Pérot (F–P) resonances excited by the PCM contribute to the polarization conversions, as is illustrated. Moreover, through establishing the F–P-like cavity model and analyzing the electric field components of the transmitted waves, the conditions for realizing LTC polarization conversion are revealed, which can guide the construction of PCM. The prototype of PCM is fabricated and measured, which can achieve LTC and LTL polarization conversions within 3.31–3.56 GHz and 2.76–4.24 GHz, respectively, the polarization conversion ratios of two functions are higher than 0.95. The measurement results are in agreement with the simulation data.
Solid-to-molecular-orientational-hexatic melting induced by local environment determined defect proliferations
Authors: Hou Zhanglin , Wang Jieli , Zeng Ying , Zhao Zhiyuan , Huang Xing , Zhao Kun , Ye Fangfu
Published: August 2022

Two-dimensional (2D) melting is a fundamental research topic in condensed matter physics, which can also provide guidance on fabricating new functional materials. Nevertheless, our understanding of 2D melting is still far from being complete due to existence of possible complicate transition mechanisms and absence of effective analysis methods. Here, using Monte Carlo simulations, we investigate 2D melting of 60° rhombs which melt from two different surface-fully-coverable crystals, a complex hexagonal crystal (cHX) whose primitive cell contains three rhombs, and a simple rhombic crystal (RB) whose primitive cell contains one rhomb. The melting of both crystals shows a sequence of solid, hexatic in molecular orientation (Hmo), and isotropic phases which obey the Berezinskii–Kosterlitz–Thouless–Halperin–Nelson–Young (BKTHNY) theory. However, local polymorphic configuration (LPC) based analysis reveals different melting mechanisms: the cHX–Hmo transition is driven by the proliferation of point-like defects during which defect-associated LPCs are generated sequentially, whereas the RB–Hmo transition is driven by line defects where defect-associated LPCs are generated simultaneously. These differences result in the observed different solid–Hmo transition points which are ϕ
A = 0.812 for the cHX–Hmo and ϕ
A = 0.828 for the RB–Hmo. Our work will shed light on the initial-crystal-dependence of 2D melting behavior.
RNAGCN: RNA tertiary structure assessment with a graph convolutional network
Authors: Deng Chengwei , Tang Yunxin , Zhang Jian , Li Wenfei , Wang Jun , Wang Wei
Published: August 2022

RNAs play crucial and versatile roles in cellular biochemical reactions. Since experimental approaches of determining their three-dimensional (3D) structures are costly and less efficient, it is greatly advantageous to develop computational methods to predict RNA 3D structures. For these methods, designing a model or scoring function for structure quality assessment is an essential step but this step poses challenges. In this study, we designed and trained a deep learning model to tackle this problem. The model was based on a graph convolutional network (GCN) and named RNAGCN. The model provided a natural way of representing RNA structures, avoided complex algorithms to preserve atomic rotational equivalence, and was capable of extracting features automatically out of structural patterns. Testing results on two datasets convincingly demonstrated that RNAGCN performs similarly to or better than four leading scoring functions. Our approach provides an alternative way of RNA tertiary structure assessment and may facilitate RNA structure predictions. RNAGCN can be downloaded from https://gitee.com/dcw-RNAGCN/rnagcn.
Optical and electrical properties of BaSnO3 and In2O3 mixed transparent conductive films deposited by filtered cathodic vacuum arc technique at room temperature
Authors: Yao Jian-Ke , Zhong Wen-Sen
Published: August 2022

For the crystalline temperature of BaSnO3 (BTO) was above 650 °C, the transparent conductive BTO-based films were always deposited above this temperature on epitaxy substrates by pulsed laser deposition or molecular beam epitaxy till now which limited there application in low temperature device process. In the article, the microstructure, optical and electrical of BTO and In2O3 mixed transparent conductive BaInSnO
x
(BITO) film deposited by filtered cathodic vacuum arc technique (FCVA) on glass substrate at room temperature were firstly reported. The BITO film with thickness of 300 nm had mainly In2O3 polycrystalline phase, and minor polycrystalline BTO phase with (001), (011), (111), (002), (222) crystal faces which were first deposited at room temperature on amorphous glass. The transmittance was 70%–80% in the visible light region with linear refractive index of 1.94 and extinction coefficient of 0.004 at 550-nm wavelength. The basic optical properties included the real and imaginary parts, high frequency dielectric constants, the absorption coefficient, the Urbach energy, the indirect and direct band gaps, the oscillator and dispersion energies, the static refractive index and dielectric constant, the average oscillator wavelength, oscillator length strength, the linear and the third-order nonlinear optical susceptibilities, and the nonlinear refractive index were all calculated. The film was the n-type conductor with sheet resistance of 704.7 Ω/□, resistivity of 0.02 Ω ⋅cm, mobility of 18.9 cm2/V⋅s, and carrier electron concentration of 1.6 × 1019 cm−3 at room temperature. The results suggested that the BITO film deposited by FCVA had potential application in transparent conductive films-based low temperature device process.
Thickness effect on solar-blind photoelectric properties of ultrathin β-Ga2O3 films prepared by atomic layer deposition
Authors: Wang Shao-Qing , Cheng Ni-Ni , Wang Hai-An , Jia Yi-Fan , Lu Qin , Ning Jing , Hao Yue , Liu Xiang-Tai , Chen Hai-Feng
Published: August 2022

The β-Ga2O3 films with different thicknesses are prepared by an atomic layer deposition system. The influence of film thickness on the crystal quality is obvious, indicating that the thicker films perform better crystal quality, which is verified from x-ray diffraction (XRD) and scanning electron microscope (SEM) results. The Ga2O3-based solar blind photodetectors with different thicknesses are fabricated and studied. The experimental results show that the responsivity of the photodetectors increases exponentially with the increase of the film thickness. The photodetectors with inter-fingered structure based on 900 growth cycles β-Ga2O3 active layers (corresponding film thickness of 58 nm) exhibit the best performances including a low dark current of 134 fA, photo-to-dark current ratio of 1.5 × 107, photoresponsivity of 1.56 A/W, detectivity of 2.77 × 1014 Jones, and external quantum efficiency of 764.49% at a bias voltage of 10 V under 254-nm DUV illumination. The photoresponse rejection ratio (R
254/R
365) is up to 1.86 × 105. In addition, we find that the photoelectric characteristics also depend on the finger spacing of the MSM structure. As the finger spacing decreases from 50 μm to 10 μm, the photoresponsivity, detectivity, and external quantum efficiency increase significantly.
Speculations on the W-mass measurement at CDF*
Authors: Gu Jiayin , Liu Zhen , Ma Teng , Shu Jing
Published: August 2022

The W mass determination at the Tevatron CDF experiment reported a deviation from the SM expectation at the 7σ level. We discuss a few possible interpretations and their collider implications. We perform electroweak global fits under various frameworks and assumptions. We consider three types of electroweak global fits in the effective-field-theory framework: the S-T, S-T-

, and eight-parameter flavor-universal one. We discuss the amounts of tensions between different

measurements reflected in these fits and the corresponding shifts in central values of these parameters. With these electroweak fit pictures in hand, we present a few different classes of models and discuss their compatibility with these results. We find that while explaining the

discrepancy, the single gauge boson extensions face strong LHC direct search constraints unless the

is fermiophobic (leptophobic), which can be realized if extra vector fermions (leptons) mix with the SM fermions (leptons). Vector-like top partners can partially generate the needed shift to the electroweak observables. The compatibility with the top squark is also studied in detail. We find that the non-degenerate top squark soft masses enhance the needed operator coefficients, enabling an allowed explanation compatible with current LHC measurements. Overall, more theoretical and experimental developments are highly in demand to reveal the physics behind this discrepancy.
Numerical investigation of the information complexity in Lorenz system based on Shannon entropy
Authors: Zhang Sen , Jia Tao
Published: August 2022

To quantify the information embedded in the Lorenz system, the Shannon entropies (also named information entropies) of the convection rate, the horizontal temperature variation, and the vertical temperature variation are calculated under the conditions of different values of the three parameters which are proportional to Prandtl number, Rayleigh number, and the liquid layer dimension respectively. Generalized autoregressive conditional heteroskedasticity models are employed to represent the change of the Shannon entropies with that of the three parameters.
Upscaling xylem phenology: sample size matters
Authors: Silvestro Roberto , Sylvain Jean-Daniel , Drolet Guillaume , Buttò Valentina , Auger Isabelle , Mencuccini Maurizio , Rossi Sergio
Published: August 2022

Background and Aims

Upscaling carbon allocation requires knowledge of the variability at the scales at which data are collected and applied. Trees exhibit different growth rates and timings of wood formation. However, the factors explaining these differences remain undetermined, making samplings and estimations of the growth dynamics a complicated task, habitually based on technical rather than statistical reasons. This study explored the variability in xylem phenology among 159 balsam firs [Abies balsamea (L.) Mill.].

Methods

Wood microcores were collected weekly from April to October 2018 in a natural stand in Quebec, Canada, to detect cambial activity and wood formation timings. We tested spatial autocorrelation, tree size and cell production rates as explanatory variables of xylem phenology. We assessed sample size and margin of error for wood phenology assessment at different confidence levels.

Key Results

Xylem formation lasted between 40 and 110 d, producing between 12 and 93 cells. No effect of spatial proximity or size of individuals was detected on the timings of xylem phenology. Trees with larger cell production rates showed a longer growing season, starting xylem differentiation earlier and ending later. A sample size of 23 trees produced estimates of xylem phenology at a confidence level of 95 % with a margin of error of 1 week.

Conclusions

This study highlighted the high variability in the timings of wood formation among trees within an area of 1 km2. The correlation between the number of new xylem cells and the growing season length suggests a close connection between the processes of wood formation and carbon sequestration. However, the causes of the observed differences in xylem phenology remain partially unresolved. We point out the need to carefully consider sample size when assessing xylem phenology to explore the reasons underlying this variability and to allow reliable upscaling of carbon allocation in forests.
FastMix: a versatile data integration pipeline for cell type-specific biomarker inference
Authors: Zhang Yun , Sun Hao , Mandava Aishwarya , Aevermann Brian D , Kollmann Tobias R , Scheuermann Richard H , Qiu Xing , Qian Yu
Published: August 2022

Motivation

Flow cytometry (FCM) and transcription profiling are the two widely used assays in translational immunology research. However, there is no data integration pipeline for analyzing these two types of assays together with experiment variables for biomarker inference. Current FCM data analysis mainly relies on subjective manual gating analysis, which is difficult to be directly integrated with other automated computational methods. Existing deconvolutional analysis of bulk transcriptomics relies on predefined marker genes in the transcriptomics data, which are unavailable for novel cell types and does not utilize the FCM data that provide canonical phenotypic definitions of the cell types.

Results

We developed a novel analytics pipeline—FastMix—for computational immunology, which integrates flow cytometry, bulk transcriptomics and clinical covariates for identifying cell type-specific gene expression signatures and biomarker genes. FastMix addresses the ‘large p, small n’ problem in the gene expression and flow cytometry integration analysis via a linear mixed effects model (LMER) for both cross-sectional and longitudinal studies. Its novel moment-based estimator not only reduces bias in parameter estimation but also is more efficient than iterative optimization. The FastMix pipeline also includes a cutting-edge flow cytometry data analysis method—DAFi—for identifying cell populations of interest and their characteristics. Simulation studies showed that FastMix produced smaller type I/II errors than competing methods. Validation using real data of two vaccine studies showed that FastMix identified a consistent set of signature genes as in independent single-cell RNA-seq analysis, producing additional interesting findings.

Availability and implementation

Source code of FastMix is publicly available at https://github.com/terrysun0302/FastMix.

Supplementary information

Supplementary data are available at Bioinformatics online.
Functional and structural features of L2/3 pyramidal cells continuously covary with pial depth in mouse visual cortex
Authors: Weiler Simon , Guggiana Nilo Drago , Bonhoeffer Tobias , Hübener Mark , Rose Tobias , Scheuss Volker
Published: August 2022

Pyramidal cells of neocortical layer 2/3 (L2/3 PyrCs) integrate signals from numerous brain areas and project throughout the neocortex. These PyrCs show pial depth-dependent functional and structural specializations, indicating participation in different functional microcircuits. However, whether these depth-dependent differences result from separable PyrC subtypes or whether their features display a continuum correlated with pial depth is unknown. Here, we assessed the stimulus selectivity, electrophysiological properties, dendritic morphology, and excitatory and inhibitory connectivity across the depth of L2/3 in the binocular visual cortex of mice. We find that the apical, but not the basal dendritic tree structure, varies with pial depth, which is accompanied by variation in subthreshold electrophysiological properties. Lower L2/3 PyrCs receive increased input from L4, while upper L2/3 PyrCs receive a larger proportion of intralaminar input. In vivo calcium imaging revealed a systematic change in visual responsiveness, with deeper PyrCs showing more robust responses than superficial PyrCs. Furthermore, deeper PyrCs are more driven by contralateral than ipsilateral eye stimulation. Importantly, the property value transitions are gradual, and L2/3 PyrCs do not display discrete subtypes based on these parameters. Therefore, L2/3 PyrCs’ multiple functional and structural properties systematically correlate with their depth, forming a continuum rather than discrete subtypes.
Monovalent Rotavirus Vaccine Efficacy Against Different Rotavirus Genotypes: A Pooled Analysis of Phase II and III Trial Data
Authors: Amin Avnika B , Tate Jacqueline E , Waller Lance A , Lash Timothy L , Lopman Benjamin A
Published: August 2022

Background

Rotavirus vaccine performance appears worse in countries with high rotavirus genotype diversity. Evidence suggests diminished vaccine efficacy (VE) against G2P[4], which is heterotypic with existing monovalent rotavirus vaccine formulations. Most studies assessing genotype-specific VE have been underpowered and inconclusive.

Methods

We pooled individual-level data from 10 Phase II and III clinical trials of rotavirus vaccine containing G1 and P[8] antigens (RV1) conducted between 2000 and 2012. We estimated VE against both any-severity and severe (Vesikari score ≥11) rotavirus gastroenteritis (RVGE) using binomial and multinomial logistic regression models for non-specific VE against any RVGE, genotype-specific VE, and RV1-typic VE against genotypes homotypic, partially heterotypic, or fully heterotypic with RV1 antigens. We adjusted models for concomitant oral poliovirus and RV1 vaccination and the country's designated child mortality stratum.

Results

Analysis included 87 644 infants from 22 countries in the Americas, Europe, Africa, and Asia. For VE against severe RVGE, non-specific VE was 91% (95% confidence interval [CI]: 87–94%). Genotype-specific VE ranged from 96% (95% CI: 89–98%) against G1P[8] to 71% (43–85%) against G2P[4]. RV1-typic VE was 92% (95% CI: 84–96%) against partially heterotypic genotypes but 83% (67–91%) against fully heterotypic genotypes. For VE against any-severity RVGE, non-specific VE was 82% (95% CI: 75–87%). Genotype-specific VE ranged from 94% (95% CI: 86–97%) against G1P[8] to 63% (41–77%) against G2P[4]. RV1-typic VE was 83% (95% CI: 72–90%) against partially heterotypic genotypes but 63% (40–77%) against fully heterotypic genotypes.

Conclusions

RV1 VE is comparatively diminished against fully heterotypic genotypes including G2P[4].
Establishment of a nomogram for predicting prolonged mechanical ventilation in cardiovascular surgery patients
Authors: Meng Yunjiao , Gu Haoye , Qian Xuan , Wu Honglei , Liu Yanmei , Ji Peipei , Xu Yanghui
Published: August 2022

Aims

This study aimed to develop a nomogram model for predicting prolonged mechanical ventilation (PMV) in patients undergoing cardiovascular surgery.

Methods and results

In total, 693 patients undergoing cardiovascular surgery at an Affiliated Hospital of Nantong University between January 2018 and June 2020 were studied. Postoperative PMV was required in 147 patients (21.2%). Logistic regression analysis showed that delirium [odds ratio (OR), 3.063; 95% confidence interval (CI), 1.991–4.713; P < 0.001], intraoperative blood transfusion (OR, 2.489; 95% CI, 1.565–3.960; P < 0.001), obesity (OR, 2.789; 95% CI, 1.543–5.040; P = 0.001), postoperative serum creatinine level (mmol/L; OR, 1.012; 95% CI, 1.007–1.017; P < 0.001), postoperative serum albumin level (g/L; OR, 0.937; 95% CI, 0.902–0.973; P = 0.001), and postoperative total bilirubin level (μmol/L; OR, 1.020; 95% CI, 1.005–1.034; P = 0.008) were independent risk factors for PMV. The area under the receiver operating characteristic curve for our nomogram was found to be 0.770 (95% CI, 0.727–0.813). The goodness-of-fit test indicated that the model fitted the data well (χ2 = 12.480, P = 0.131). After the model was internally validated, the calibration plot demonstrated good performance of the nomogram, as supported by the Harrell concordance index of 0.760. Decision curve analysis demonstrated that the nomogram was clinically useful in identifying patients at risk for PMV.

Conclusion

We established a new nomogram model that may provide an individual prediction of PMV. This model may provide nurses, social workers, physicians, and administrators with an accurate and objective assessment tool to identify patients at high risk for PMV after cardiovascular surgery.
The attitudes and expectation of caregivers of febrile child receiving medical services: a multicenter survey in Thailand
Authors: Chulapornsiri Chalie , Pradermdussadeeporn Ekachai , Pongpittayut Sorawit , Sutthithumthaworn Amphairat , Chulapornsiri Chatchai , Aninlabon Witsanu , Wisassittichok Meechokchai , Maitongngam Kritpisut , Subchartanan Jarujan , Suteerojntrakool Orapa , Tempark Therdpong , Bongsebandhu-phubhakdi Chansuda
Published: August 2022

Background

Most caregivers may visit pediatric outpatient clinics with high concern of fever and improper antipyretic use. However, studies of concern about fever in Asian countries are still limited.

Objectives

This study aimed to explore caregivers’ attitudes, management of their child’s fever, factors associated with their high concern, and expectation from medical services.

Methods

A cross-sectional 26-item self-administered questionnaire was used to survey caregivers of 1-month to 15-year-old febrile infants/children/teenagers visiting outpatient clinics in 9 government hospitals from July 2018 to August 2019.

Results

One thousand two hundred and six caregivers (67% response rate) completed self-administered questionnaire. The median age of the caregivers and the pediatric patients were 34 years (interquartile range [IQR] 28–40) and 3.3 years (IQR 1.8–6.1), respectively. Approximately 70% of them believed that fever could harm a child, resulting in brain damage or death. Also, 2% managed high doses of acetaminophen and overdosed the child. The high level of concern was significantly associated with acetaminophen overdose (P < 0.001, Kruskal–Wallis test). Caregivers of nonhealth care providers and children’s history of febrile seizure were factors related to higher score of concern. Most caregivers expected definite diagnosis (70.7%), antipyretic drugs (67.4%), and blood tests (48.9%).

Conclusion

Caregivers’ high concern of fever existed in Thailand. This may lead to unnecessary high doses of antipyretics. In clinical practice, the high concern of fever is a challenge for caregivers and pediatric health care providers. A better understanding of fever and its consequence should be advocated for proper management of the child’s fever.
The evolution and role of the periplasmic asparaginase Asp3 in yeast
Authors: Coral-Medina Angela , Fenton Darren A , Varela Javier , Baranov Pavel V , Camarasa Carole , Morrissey John P
Published: August 2022

The study of nitrogen assimilation in yeast is of interest from genetic, evolutionary, and biotechnological perspectives. Over the course of evolution, yeasts have developed sophisticated control mechanisms to regulate nitrogen metabolism, with domesticated lineages sometimes displaying particular specialisation. The focus of this study was on assimilation of asparagine, which is a significant nutritional source for some alcoholic fermentations. We were particularly interested in ASP3, which encodes a periplasmic asparaginase and that was proposed to have been acquired relatively recently in S. cerevisiae by horizontal gene transfer. We examined 1680 S. cerevisiae genome assemblies to evaluate the distribution and evolutionary trajectory of ASP3. Our findings suggest an alternative hypothesis that ASP3 is an ancient Saccharomyces gene that has generally been lost over the course of evolution but has been retained in certain fermentative environments. As asparagine is the major nitrogen source in apple juice, we explored whether the presence of ASP3 would confer a growth advantage. Interestingly, we found that although ASP3 enhances growth when asparagine is the sole nitrogen source, the same effect is not seen in apple juice. These data indicate that growth in pure culture may not reflect the original selective environment for ASP3+ strains and highlight the role that complex regulation may play in optimising nitrogen assimilation in yeasts.
Short-interval traffic lines: versatile tools for genetic analysis in Arabidopsis thaliana
Authors: Poethig R Scott , Cullina William L , Doody Erin , Floyd Taré , Fouracre Jim P , Hu Tieqiang , Xu Mingli , Zhao Jianfei
Published: August 2022

Traffic lines are transgenic stocks of Arabidopsis thaliana that contain a pair of linked seed-specific eGFP and DsRed markers. These stocks were originally developed for the purpose of studying recombination, but can also be used to follow the inheritance of unmarked chromosomes placed in trans to the marked chromosome. They are particularly useful for this latter purpose if the distance between markers is short, making double recombination within this interval relatively rare. We generated 163 traffic lines that cover the Arabidopsis genome in overlapping intervals of approximately 1.2 Mb (6.9 cM). These stocks make it possible to predict the genotype of a plant based on its seed fluorescence (or lack thereof) and facilitate many experiments in genetic analysis that are difficult, tedious, or expensive to perform using current techniques. Here, we show how these lines enable a phenotypic analysis of alleles with weak or variable phenotypes, genetic mapping of novel mutations, introducing transgenes into a lethal or sterile genetic background, and separating closely linked mutations.
German Princes in the Prussian Army: Political Patronage and Family Networks under Frederick II, 1740–1786
Authors: Winkel Carmen
Published: August 2022

Drawing primarily on Frederick II of Prussia’s correspondence, which was filtered through his cabinet secretaries, this article explores how the king used his army in constructing patronage networks that reached beyond the limits of Brandenburg-Prussia. He not only appointed members of German families as officers but also expected them to train with and command their men. Frederick II’s army was certainly a vital means of exercising power, but it also proved a viable tool for integrating and discipling client families within the Holy Roman Empire.