bluuebunny/crossref_metadata_2025 huggingface dataset:
Research on the spin Hall effect of light for nonlinear multilayer dielectrics and its bistable and nonreciprocal features
Authors: Wang Pengxiang , Wang Qianyu , Peng Hongmei , Zhang Dan , Zhang Haifeng
Published: January 2021

In this paper, by utilizing the transfer matrix method, a structure composed of one-dimensional (1D) periodic multilayer dielectrics, InSb, and nonlinear material is proposed to investigate the behavior of the spin Hall effect of light (SHEL) and its nonreciprocity and bistable features. The results demonstrate that, as the light intensity increases, the reflection coefficients under both TM and TE waves have a bistable phenomenon, and the points of both horizontal and vertical displacements are consistent with the regions where reflection is close to 0. Furthermore, to make our study complete, the thicknesses of the nonlinear and InSb layers are adjusted to study the effects on the performance of SHEL, and it can be found that, with the escalation of the thicknesses of the nonlinear and InSb layers, all the points of displacements are shifting to the direction of the angle. Besides, all parameters demonstrate the phenomenon of nonreciprocity. This research supplies meaningful guidelines for some optical instruments, such as light intensity sensors.
Measurement of therapeutic 12C beam in a water phantom using CR-39
Authors: Yang Shiyan , Zhao Jingfang , Zhuo Weihai , Shen Hao , Chen Bo
Published: January 2021

The motivation for this study was to explore a new method to test the particle spatial distribution for a therapeutic carbon beam. CR-39 plastic nuclear track detectors were irradiated to a 276.5 MeV u−1 mono-energy carbon beam at the heavy ion facility in the Shanghai Proton and Heavy Ion Center. The spatial distribution of the primary carbon beam and secondary fragments in a water phantom were systematically analyzed both in the transverse direction (perpendicular to the projection direction of the primary beam) and at different depths in the longitudinal direction (along the projection direction of the primary beam) with measured tracks on the CR-39 detectors. Meanwhile, the theoretically spatial distribution and linear energy transfer (LET) spectra of the primary beam and secondary fragments were calculated using the Monte Carlo (MC) toolkit Geant4. The results showed that the CR-39 detectors are capable of providing high lateral resolution of carbon ion at different depths. In the range of the primary carbon beam, the beam width simulated with MC is in good agreement with that of experimental measurement. The track size registered in the CR-39 has a good correlation with the particle LET. These findings indicate that the CR-39 can be used for measuring both the particle flux and its spatial distribution of carbon ions.
A technique for measurement of a prism apex angle by optical angle sensors with a reference artefact
Authors: Shimizu Yuki , Ma Xu , Matsukuma Hiraku , Gao Wei
Published: January 2021

A new technique for measurement of the apex angle of a right-angle prism is proposed. A reference artefact is newly employed as the datum for angle measurement, and the apex angle of a target prism is measured by detecting its deviation from that of the reference artefact by using a pair of optical angle sensors. At first, the principle of the apex angle measurement with the reference artefact and the optical angle sensors are addressed. After that, an optical angle sensor capable of evaluating various sizes of right-angle prisms over a large measurement range is designed and developed. A two-dimensional position-sensitive detector is employed as the photodetector for the optical angle sensor so that a high resolution and a wide measurement range can be achieved simultaneously. To avoid the influence of the interference between a directly-reflected beam and an internally-reflected beam when measuring a face of a right-angle prism, the optical setup is designed to have a laser beam that is made incident to a measurement surface with an oblique incidence. After the design and development of the optical angle sensor, the measurement system has been developed and some basic experiments are carried out to evaluate the basic performance of the developed optical angle sensor. The feasibility of the proposed technique of the prism apex angle measurement is also demonstrated through experiments and theoretical measurement uncertainty analysis based on GUM.
Two-dimensional ScN with high carrier mobility and unexpected mechanical properties
Authors: Liang Dongmei , Jing Tao , Deng Mingsen , Cai Shaohong
Published: January 2021

Two-dimensional (2D) semiconductors with desirable bandgaps and high carrier mobility have great potential in electronic and optoelectronic applications. In the present work, 2D M-ScN, H-ScN, and O-ScN are predicted by the swarm-intelligent global structure search method. The low formation energies and high dynamical and thermal stabilities indicate the high feasibility of experimental synthesis of these ScN monolayers. The electronic structure calculations reveal that M-ScN and O-ScN are both direct bandgap semiconductors with the bandgaps of 1.39 and 2.14 eV, respectively, while H-ScN has a large indirect bandgap of 3.21 eV. In addition, both M-ScN and H-ScN exhibit ultra-high electron mobilities (3.09 × 104 cm2 V−1 s−1 and 1.22 × 104 cm2 V−1 s−1, respectively). More notably, O-ScN is found to be a promising 2D auxetic and ferroelastic material. The values of negative Possion’s ratios and reversible strain of this monolayer are predicted to be −0.27% and 15%, respectively.
Calculating the duration of various physical phenomena using basic mathematical tools
Authors: Kontomaris S V , Malamou A
Published: January 2021

A significant approach that should be followed by physics teachers at the secondary education level in order to enhance students’ understanding is to highlight the generality of the mathematical procedures that describe different physical phenomena. In this paper, the common procedure that is used to calculate the duration of various physical phenomena is presented. Examples from different scientific areas, from mechanics to circuit analysis and from nuclear physics to medicine are examined. In the presented examples, the magnitude of interest is always directly proportional to its rate of change. By ‘grouping’ physical phenomena that can be described using the same mathematical tools, the students’ interest is enhanced and their physics perception is increased towards a deep understanding of the scientific methodology.
Teaching optics as inquiry under lockdown: how we transformed a teaching-learning sequence from face-to-face to distance teaching
Authors: Carli Marta , Fontolan Maria Rosa , Pantano Ornella
Published: January 2021

We describe the design and implementation of a teaching-learning sequence that was started before the lockdown and was then transformed for distance teaching. A backward design approach was adopted in order to identify clear learning outcomes. The activities were outlined according to an inquiry-based learning paradigm, referring to research-based models. We discuss how these elements were relevant when redesigning the activities for distance teaching. In particular, we describe how we modified an ‘application experiment’ (measuring the thickness of a human hair) using a video-based activity, highlighting how this activity was designed in order to meet the original goals and outcomes. The results of the teacher’s assessment and the students’ self-evaluation suggest that the approach was meaningful and effective, and that the experience can provide useful hints also for teaching under regular conditions.
Nonlinear electric response of chiral topological superconductors
Authors: Lee Minchul , Lόpez Rosa
Published: January 2021

We investigate, in the non-equilibrium Keldysh frame, a topological resistor–capacitor (RC) circuit consisting of a quantum dot coupled to a Majorana edge mode formed around a chiral topological superconductor. We implement both the adiabatic approximation and the numerical exact calculations to find out the unique non-equilibrium features of the electric response of the dissipative Majorana channel. First, the dependence of the dissipation on the frequency Ω of the ac driving on the dot is found to be greatly different whether the time-dependent dot level crosses the Fermi level or not during the driving. In the latter case, the relaxation resistance R
q, the measure of the dissipation, obeys R
q ∝ Ω2 for small frequencies, and in the former case, R
q ∝ Ω−1/3 diverges as Ω → 0. In the former case, a universal scaling law for the dissipative part of the ac power is observed and attributed to the δ-peak in the dot density of states due to a uncoupled dot Majorana mode at the dot resonance condition. We compare the ac power, current, and the relaxation resistance between Majorana and trivial Dirac channels and clarify the Majorana nature in the dissipation.
Understanding charge transfer on the clinically used conical Utah electrode array: charge storage capacity, electrochemical impedance spectroscopy and effective electrode area
Authors: Harris Alexander R
Published: January 2021

Objective. The Utah electrode is used for pre/clinical studies on neural recording and stimulation. Anecdotal and empirical reports on their performance have been made, resulting in variable testing methods. An in depth investigation was performed to understand the electrochemical behaviour and charge transfer mechanisms occurring on these clinically important electrodes. The impact of electrode geometry and material on performance was determined. Approach. Platinum and iridium electrodes were assessed by cyclic voltammetry and electrochemical impedance spectroscopy. The effective electrode area was measured by reduction of Ru(NH3)6
3+. Main results. Pristine Utah electrodes have little to no oxide present and the surface roughness is less than the diffusion length of Ru(NH3)6
3+ during voltammetry, which was ∼30 µm. Pristine iridium electrodes pass charge through capacitance and oxide formation. Hydride and anion adsorption occurs on the platinum electrode. Anodic current oxidises both metal surfaces, altering the charge transfer mechanisms at the electrode-solution interface. Charge storage capacity depends on measurement technique and electrode structure, this simplified number ignores more detailed information on charge transfer mechanisms that can be obtained from cyclic voltammetry. Electrode oxidation increases pseudocapacitance, reducing impedance. Charge transfer was non-homogeneous, most likely due to the electrode geometry enhancing charge density at the electrode tip and base. Oxidation of the electrode surface enhanced charge transfer inhomogeneity. The effective electrode area could be measured by reduction of Ru(NH3)6
3+ and calculated with a finite cone geometry. Significance. Increasing electrode pseudocapacitance, demonstrated by metal oxidation, reduces impedance. Increasing electrode capacitance offers a potential route to reducing thermal noise and increasing signal-to-noise ratio of neural recording. The effective electrode area of conical electrodes can be measured. The charge density of the conical electrode was greater than expected compared to a planar disc electrode, indicating modification of electrode geometry can increase an electrodes safe charge injection capacity. in vivo electrochemical measurements often do not include sufficient details to understand the electrode behaviour. Electrode oxidation most likely accounts for a significant amount of variation in previously published Utah electrode impedance data.
Response of thermal and fast-ion transport to beam ion population, rotation and T
e/T
i in the DIII-D steady state hybrid scenario
Authors: Thome K.E. , Du X.D. , Grierson B.A. , Kramer G.J. , Petty C.C. , Holland C. , Knolker M. , McKee G.R. , McClenaghan J. , Pace D.C. , Rhodes T.L. , Smith S.P. , Sung C. , Turco F. , Van Zeeland M.A. , Zeng L. , Zhu Y.B.
Published: January 2021

The thermal and fast-ion transport properties of DIII-D steady-state hybrid discharges with normalized beta β
N ≳ 3 are studied at low injected torque and an increased electron to ion temperature ratio T
e/T
i. Linear stability analysis performed with the TGLF turbulent code indicates that a high-k mode is usually dominant at smaller radii, whereas a low-k mode is usually dominant at larger radii in these plasmas. A reduction in the net injected torque from 8.6 to 4.3 N-m leads to reduced E × B shear and hence, an enhanced turbulence that was observed on the Doppler backscattering diagnostic and was also computed with TGLF. As T
e/T
i in the core was increased from 0.57 to 0.66 by adding electron cyclotron current drive (ECCD) to these plasmas, higher levels of transport are observed with increased high-k modes indicated by TGLF. The fast-ion transport level varied over an order of magnitude in these discharges depending on whether Alfvén eigenmodes, fishbones, or no instabilities were observed. Hybrid plasmas with fishbones have decreased fast-ion transport, compared to plasmas with Alfvén eigenmodes, since they are resonant with a smaller portion of phase space and their resonance is farther from the wall. This reduction in fast-ion transport with ECCD mitigates the increase in turbulent transport, resulting in higher performance than expected during strong electron heating. Similarly, the lowest fast-ion transport was observed in the low torque plasma, which also led to better than expected performance at this torque value. The thermal and fast-ion transport changes observed as the torque/rotation and T
e/T
i are varied indicate possible methods for transferring this scenario to a reactor.
Infinite system of random walkers: winners and losers
Authors: Krapivsky P L
Published: January 2021

We study an infinite system of particles initially occupying a half-line y ⩽ 0 and undergoing random walks on the entire line. The right-most particle is called a leader. Surprisingly, every particle except the original leader may never achieve the leadership throughout the evolution. For the equidistant initial configuration, the kth particle attains the leadership with probability e−2
k
−1(ln  k)−1/2 when k ≫ 1. This decay law provides a quantitative measure of the correlation between earlier misfortune proportional to the label k and eternal failure. We also show that the winner defined as the first walker overtaking the initial leader has label k ≫ 1 with probability decaying as

exp

−

1

2

(

ln

k

)

2

.
Spatial coherence effects in second-harmonic generation of scalar light fields
Authors: Pesonen Henri , Halder Atri , Huusko Juha-Matti , Friberg Ari T , Setälä Tero , Turunen Jari
Published: January 2021

We consider the spectral spatial coherence characteristics of scalar light fields in second-harmonic generation in an optically non-linear medium. Specifically, we take the fundamental-frequency (incident) field to be a Gaussian Schell-model (GSM) beam with variable peak spectral density and different coherence properties. We show that with increasing intensity the overall degree of coherence of both the fundamental and the second-harmonic field in general decreases on passage through the non-linear medium. In addition, the spectral density distributions and the two-point degree of coherence may, for both beams, deviate significantly from those of the GSM, especially at high intensities. Propagation in the non-linear medium is numerically analyzed with the Runge–Kutta and the beam-propagation methods, of which the latter is found to be considerably faster. The results of this work provide means to synthesize, via non-linear material interaction, random optical beams with desired coherence characteristics.
Effect of multiwalled carbon nanotube diameter on mechanical behavior and fracture toughness of epoxy nanocomposites
Authors: Xu Ting , Qi Zehao , Tan Yefa , Tian Jin , Li Xiaotun
Published: January 2021

Epoxy nanocomposites reinforced by multiwalled carbon nanotubes (MWCNT) with different diameters were prepared. The effect of MWCNT diameter on mechanical and fracture properties of epoxy nanocomposites were investigated. The results show that the MWCNT diameter has an important influence on its dispersion performance. As the MWCNT diameter increases, the dispersion performance becomes better. The reinforcing effect of MWCNTs on epoxy resins (EP) is affected by the combination of factors including the diameter and the additive amount of MWCNTs as well as its dispersion. At low additive amount of MWCNTs (≤0.3 wt%), the reinforcing effect of MWCNTs with smaller diameter is better. However, as the additive amount of MWCNTs increases (≥0.5 wt%), the reinforcing effect of MWCNTs with larger diameters becomes more significant. MWCNTs with diameter of 25 nm (MWCNT-25) have the best reinforcing effect when the additive amount is 0.5 wt%, and the tensile strength and elastic modulus of the MWCNT-25/EP composites are increased by 11.5% and 8.3% than those of EP, respectively. The fracture toughness of the composites shows a tendency to increase first and then decrease with the increase of MWCNT diameter. The main reason of this tendency is that the main failure mode of MWCNTs gradually changes from fracture to pull-out with the increase of MWCNT diameter. The optimal MWCNT diameter is 25 nm, reaching the best toughening effect (KIC and GIC are increased by 38.8% and 80.9% than those of EP, respectively) at the additive amount of 0.7 wt%.
Effect of samarium on the high temperature tensile properties and fracture behaviors of Al–Zn–Mg–Cu–Zr alloy
Authors: Zhai Fenglong , Wang Liping , Gao Xin , Zhao Sicong , Feng Yicheng , Ma Tao , Fan Rui
Published: January 2021

The Al-6.7Zn-2.6Mg-2.0Cu-0.1Zr alloy is modified by Sm for the purpose of improving its mechanical properties at high temperatures. According to the results, the as-cast structure can be refined through 0.3% Sm modification treatment, and finer precipitates can be obtained after aging. In the meantime, with the addition of Sm, a new high melting point Al10Cu7Sm2 phase is formed, the initial decomposition temperature of the alloy is raised, and the thermal stability is enhanced. As indicated by the tensile test results at room temperature and high temperatures, the strength of the modified sample was improved compared with the unmodified alloy. According to fracture surface analysis, ductile fracture conforms to the fracture characteristic exhibited by the modified alloy at room temperature and high temperatures. The improvement on high temperature strength of the modified alloy is attributed largely to a combination of grain refinement, precipitation strengthening and heat resistant phase to grain boundary pinning.
Biosynthesized TiO2 nanoparticles and their applications for the treatment of pediatric acute leukemia
Authors: Xiaoshang Gao , Murakonda Gopi Krishna , Jarubula Ramu , Zhao Shushu
Published: January 2021

The current study demonstrates the efficiency of Salvia Spinosa (S. Spinosa) leaf extract in the biofabrication of Titanium dioxide nanoparticles (TiO2 NPs). An easy and green method was used to synthesize TiO2 NPs, which involves the addition of Titanium hydroxide [Ti(OH)2] solution and the leaf extract of S. Spinosa, followed by stirring results in the formation of a light green dispersion of TiO2 NPs. Characterization of the formed TiO2 NPs was performed using the spectroscopic techniques such as FTIR, XRD, EDS, SAED and TEM. The formation of polydisperse TiO2 NPs with a mean particle size of 23 nm was revealed by TEM analysis. The biomolecules that are possibly involved in reducing TiO2 ions are shown in the FTIR spectrum of the S. Spinosa plant leaf extract. Zeta potential results have confirmed the extreme negative charge of 19 mV for the formed TiO2 NPs. The crystalline structure of the fabricated NPs was revealed by the analysis of XRD. In addition, the cytotoxicity results have confirmed that the cytotoxicity against acute lymphoblastic leukemia (Molt-4) cells depends on the dose, further signifying their potential for the advance of new materials and techniques for pediatric leukemia treatment.
From molecular quantum electrodynamics at finite temperatures to nuclear magnetic resonance
Authors: Them Kolja
Published: January 2021

The algebraic reformulation of molecular Quantum Electrodynamics (mQED) at finite temperatures is applied to Nuclear Magnetic Resonance (NMR) in order to provide a foundation for the reconstruction of much more detailed molecular structures, than possible with current methods. Conventional NMR theories are directly related to the effective spin model, which idealizes nuclei as fixed points in a lattice

Z

3

. However, the delocalization of spins due to the thermal energy is more realistically described by the amplitude square of the nuclear wave function ∣Ψ
β
(X)∣2 with

X
∈

R

3
n

, instead of fixed points in

Z

3

. In addition, the phenomenological integration of thermalization only allows an investigation of the molecular structure based on the position of the punctiform center of an NMR signal, but not based on the width and shape of NMR signals. Hence, a lot information on molecular structures remain hidden in experimental NMR data. In this document it is shown how ∣Ψ
β
(X)∣2,

X
∈

R

3
n

can be reconstructed from NMR data. To this end, it is shown how NMR spectra can be calculated directly from mQED at finite temperatures without involving the effective description. The new method connects all data points—the positions, widths, heights and shapes—of NMR signals directly with the molecular structure, which allows more detailed investigations of the underlying system. Furthermore, it is shown that the presented method corrects wrong predictions of the effective spin model. The fundamental problem of performing numerical calculations with the infinite-dimensional radiation field is solved by using a purified representation of a KMS state on a W
*-algebra. It is outlined that the presented method can be applied to any molecular system whose electronic ground state can be calculated using a common quantum chemical method. Therefore, the presented method can replace the effective description which forms the basis for NMR theory since 1950.
Multidimensional analysis of excitonic spectra of monolayers of tungsten disulphide: toward computer-aided identification of structural and environmental perturbations of 2D materials
Authors: Kolesnichenko Pavel V , Zhang Qianhui , Zheng Changxi , Fuhrer Michael S , Davis Jeffrey A
Published: January 2021

Despite 2D materials holding great promise for a broad range of applications, the proliferation of devices and their fulfillment of real-life demands are still far from being realized. Experimentally obtainable samples commonly experience a wide range of perturbations (ripples and wrinkles, point and line defects, grain boundaries, strain field, doping, water intercalation, oxidation, edge reconstructions) significantly deviating the properties from idealistic models. These perturbations, in general, can be entangled or occur in groups with each group forming a complex perturbation making the interpretations of observable physical properties and the disentanglement of simultaneously acting effects a highly non-trivial task even for an experienced researcher. Here we generalise statistical correlation analysis of excitonic spectra of monolayer WS2, acquired by hyperspectral absorption and photoluminescence imaging, to a multidimensional case, and examine multidimensional correlations via unsupervised machine learning algorithms. Using principal component analysis we are able to identify four dominant components that are correlated with tensile strain, disorder induced by adsorption or intercalation of environmental molecules, multi-layer regions and charge doping, respectively. This approach has the potential to determine the local environment of WS2 monolayers or other 2D materials from simple optical measurements, and paves the way toward advanced, machine-aided, characterization of monolayer matter.
Thermal properties of ethylene glycol-carbon based nano-fluids
Authors: Bansal Arti , Sharma Gyan Prakash , Agarwal Ravi , Singh Ramvir
Published: January 2021

We present results of thermal conductivity, thermal diffusivity, and specific heat of Ethylene Glycol (EG)-Carbon nano-fluids obtained using Thermal Constants Analyser (TPS 2200). A two-step method including a magnetic stirrer and an ultrasonic device was used to prepare stable EG-Carbon nano-fluids. Carbon nanoparticles were dispersed slowly in EG with different concentrations of 1 wt%, 2 wt%, 3 wt%, and 4 wt%. Thermal coefficients of the prepared nano-fluids at each concentration were measured at temperatures 10, 20, 30, 40, 50, and 60 °C. The percentage increment in thermal conductivity increases with concentration, as is evident from the observed increments of 20% and 31% for 1 wt% and 4 wt% concentration at 10 ℃, respectively. The highest increase in thermal diffusivity of about 32% was observed when the loading of carbon nanoparticles was increased from 1 wt% to 4 wt% at 10 °C. On the other hand, the same increment in concentration at 10 °C led to a decrease of 15% in specific heat.
First-principles explorations on P8 and N2 assembled nanowire and nanosheet
Authors: Dong Yinan , Wang Shukai , Yu Chunbo , Li Fengyu , Gong Jian , Zhao Jijun
Published: January 2021

‘Bottom-up’ method is a powerful approach to design nanomaterials with desired properties. The bottle neck of being oxidized of phosphorous structures may be conquered by cluster assembling method. Here, we used P8 and N2 as assembling units to construct one-dimensional (1D) nanowire (NW) and two-dimensional (2D) nanosheet (NS), the stability, electronic and magnetic properties of these assembled nanomaterials are investigated using density functional theory (DFT) calculations. The assembled 1D-P8N2 NW and 2D-P8N4 NS are identified to possess good stability, as demonstrated by their high cohesive energies, positive phonon dispersions, and structural integrity through molecular dynamics simulations at 300 and 500 K. Moreover, they also exhibit good anti-oxidization property. The 2D-P8N4 NS is a direct bandgap semiconductor with the HSE06 gap of 2.61 eV, and shows appropriate band-edge aliments and moderate carrier mobility for photocatalyzing water splitting. The 1D-P8N2 NW is an indirect bandgap semiconductor, and Mn doping could convert it into a dilute magnetic semiconductor (DMS) with one Dirac cone in the spin-up channel, while the vdW-type sheet composed of Mn1@1D-P8N2 NWs is a ferromagnetic metal. Our theoretical study is helpful to design stable phosphorus-based nanomaterials with diverse properties and potential applications.
DeepSurf: a surface-based deep learning approach for the prediction of ligand binding sites on proteins
Authors: Mylonas Stelios K , Axenopoulos Apostolos , Daras Petros
Published: January 2021

Motivation

The knowledge of potentially druggable binding sites on proteins is an important preliminary step toward the discovery of novel drugs. The computational prediction of such areas can be boosted by following the recent major advances in the deep learning field and by exploiting the increasing availability of proper data.

Results

In this article, a novel computational method for the prediction of potential binding sites is proposed, called DeepSurf. DeepSurf combines a surface-based representation, where a number of 3D voxelized grids are placed on the protein’s surface, with state-of-the-art deep learning architectures. After being trained on the large database of scPDB, DeepSurf demonstrates superior results on three diverse testing datasets, by surpassing all its main deep learning-based competitors, while attaining competitive performance to a set of traditional non-data-driven approaches.

Availability and implementation

The source code of the method along with trained models are freely available at https://github.com/stemylonas/DeepSurf.git.

Supplementary information

Supplementary data are available at Bioinformatics online.
SinEx DB 2.0 update 2020: database for eukaryotic single-exon coding sequences
Authors: Jorquera R , González C , Clausen P T L C , Petersen B , Holmes D S
Published: January 2021

Single-exon coding sequences (CDSs), also known as ‘single-exon genes’ (SEGs), are defined as nuclear, protein-coding genes that lack introns in their CDSs. They have been studied not only to determine their origin and evolution but also because their expression has been linked to several types of human cancers and neurological/developmental disorders, and many exhibit tissue-specific transcription. We developed SinEx DB that houses DNA and protein sequence information of SEGs from 10 mammalian genomes including human. SinEx DB includes their functional predictions (KOG (euKaryotic Orthologous Groups)) and the relative distribution of these functions within species. Here, we report SinEx 2.0, a major update of SinEx DB that includes information of the occurrence, distribution and functional prediction of SEGs from 60 completely sequenced eukaryotic genomes, representing animals, fungi, protists and plants. The information is stored in a relational database built with MySQL Server 5.7, and the complete dataset of SEG sequences and their GO (Gene Ontology) functional assignations are available for downloading. SinEx DB 2.0 was built with a novel pipeline that helps disambiguate single-exon isoforms from SEGs. SinEx DB 2.0 is the largest available database for SEGs and provides a rich source of information for advancing our understanding of the evolution, function of SEGs and their associations with disorders including cancers and neurological and developmental diseases.

Database URL: http://v2.sinex.cl/
Bidirectional endovascular treatment for axillary artery injury secondary to proximal humerus fracture: a case report
Authors: Kanda Daisuke , Imagama Itsumi , Imoto Yutaka , Ohishi Mitsuru
Published: January 2021

Background

Axillary artery injury secondary to proximal humerus fracture is a rare but serious complication. The management of this injury has traditionally involved surgical treatment.

Case summary

A 66-year-old female with gait disturbance slipped and fell off her wheelchair at home. She presented to a local hospital with right shoulder pain and was subsequently urgently transferred to our hospital by helicopter because of suspicion of axillary artery injury. Computed tomography angiography revealed disruption of the right axillary artery. We decided to perform endovascular treatment instead of surgical treatment for axillary artery injury. However, since endovascular treatment via the right femoral artery was impossible, we performed bidirectional (right femoral and right brachial artery approaches) endovascular treatment. We expanded the occluded lesion using a 3.5 mm × 40 mm sized balloon and placed a 5.0 mm × 50 mm stent graft (Gore® Viabahn®) across the lesion. The final subclavian injection confirmed that distal flow to the brachial artery was preserved and that there was no leakage of contrast medium from the axillary artery.

Discussion

We performed endovascular treatment for axillary artery injury secondary to proximal humerus fracture. Although surgical repair is typically performed for this kind of injury, our experience suggests that endovascular treatment might be an option in patients with axillary artery injury.
Genomic Evidence of an Ancient East Asian Divergence Event in Wild Saccharomyces cerevisiae
Authors: Bendixsen Devin P , Gettle Noah , Gilchrist Ciaran , Zhang Zebin , Stelkens Rike
Published: January 2021

Comparative genome analyses have suggested East Asia to be the cradle of the domesticated microbe Brewer’s yeast (Saccharomyces cerevisiae), used in the food and biotechnology industry worldwide. Here, we provide seven new, high-quality long-read genomes of nondomesticated yeast strains isolated from primeval forests and other natural environments in China and Taiwan. In a comprehensive analysis of our new genome assemblies, along with other long-read Saccharomycetes genomes available, we show that the newly sequenced East Asian strains are among the closest living relatives of the ancestors of the global diversity of Brewer’s yeast, confirming predictions made from short-read genomic data. Three of these strains (termed the East Asian Clade IX Complex here) share a recent ancestry and evolutionary history suggesting an early divergence from other S. cerevisiae strains before the larger radiation of the species, and prior to its domestication. Our genomic analyses reveal that the wild East Asian strains contain elevated levels of structural variations. The new genomic resources provided here contribute to our understanding of the natural diversity of S. cerevisiae, expand the intraspecific genetic variation found in this heavily domesticated microbe, and provide a foundation for understanding its origin and global colonization history.
NATURALLY OCCURRING ENZYME ACTIVITY VARIATION IN DROSOPHILA MELANOGASTER. I. SOURCES OF VARIATION FOR 23 ENZYMES
Authors: Laurie-Ahlberg C C , Wilton A N , Curtsinger J W , Emigh T H
Published: January 2021

The genetic component of variation of enzyme activity levels in Drosophila melanogaster was investigated by using 48 second- and 48 third-chromosome isogenic substitution lines derived from natural populations. The results confirm those of our earlier experiments with the same lines and extend them to a number of additional enzymes. All 23 enzymes show a significant genetic component to the variation in one or both sets of lines and only a small part of this variation is accounted for by variation among the lines in the amount of tissue per fly. The magnitude of line effects is, in most cases, considerably larger than the magnitude of environmental and measurement error effects, and the line effects are approximately continuous in distribution. Variation in the geographic origin and karyotype of the chromosomes generally does not contribute to the line component of variation, but allozymes provide an important source of variation for a few of the enzymes. Many of the enzymes show evidence for variation of activity modifiers that are not linked to the structural locus of the enzyme.
STUDIES ON THE SEX-SPECIFIC LETHALS OF DROSOPHILA MELANOGASTER. IV. GYNANDROMORPH ANALYSIS OF THREE MALE-SPECIFIC LETHALS, mle, msl-2
27 AND mle(3)132
Authors: Uenoyama T , Uchida S , Fukunaga A , Oishi K
Published: January 2021

Mutants at three male-specific lethal loci of Drosophila melanogaster (mle, msl-2  27 and mle(3)132) were examined by gynandromorph analysis. In all cases only a very few gynandromorphs with small X/O patches appeared. Most of these small X/O patches were in the abdomen, and the structures in these X/O regions were reduced in size. These results indicate that the primary effects of these mutants are not on any particular organs or tissues, but rather on individual cells. mle and msl-2 have been shown by Belote and Lucchesi (1980a) to be defective in dosage compensation in X/Y males. We suggest that this dosage-compensation defect results in the expression of Minute-like phenotypes in X/O cells, and hence results in the death of X/O males and flies with large X/O tissue areas.
IDENTIFICATION OF A GENE REGULATING THE TISSUE EXPRESSION OF A PHOSPHOGLUCOMUTASE LOCUS IN RAINBOW TROUT
Authors: Allendorf Fred W , Knudsen Kathy L , Phelps Stevan R
Published: January 2021

Nine percent of the rainbow trout (Salmo gairdneri) from a hatchery source have a greater than 100-fold increase in expression of a phosphoglucomutase (PGM) locus, Pgm1, in the liver but have normal expression of this locus in other tissues. The results of genetic crosses are consistent with a single regulatory gene with additive inheritance being responsible for the differences in the amount of PGM activity in the liver.—The allele responsible for the expression of Pgm1 in the liver is apparently a recent mutation. This is supported by its restricted distribution in rainbow trout and the absence of liver Pgm1 expression in closely related species. This genetic system is valuable for future analysis of the control of gene expression and in determining the relative evolutionary importance of genetic variation at structural and regulatory genes.
ESSENTIAL GENES AND DEFICIENCIES IN THE UNC-22 IV REGION OF CAENORHABDITIS ELEGANS
Authors: Rogalski Teresa M , Moerman Donald G , Baillie David L
Published: January 2021

Five formaldehyde-induced deficiencies that uncover unc-22 IV, a gene affecting muscle structure in the nematode Caenorhabditis elegans were isolated and positioned. The largest deficiency, sDf2, extends in both directions from unc-22 and is approximately 1.0-2.0 map units in length. The other four deficiencies, sDf7, sDf8, sDf9 and sDf10, are all smaller than sDf2 and are located within the region uncovered by this deficiency. Thirty-seven ethyl methanesulfonate-induced lethal and sterile mutations linked to unc-22 were isolated and tested for complementation with sDf2. Nineteen lethal mutations failed to complement sDf2. Sixteen of these were further positioned by recombination mapping and also by deficiency mapping with sDf7, sDf8, sDf9 and sDf10. These sixteen mutations define 11 new essential genes in this region. Eight of the genes lie in a 0.9-map unit interval to the left of unc-22, whereas the three remaining genes lie in a region of about 0.2 map units to the right of unc-22. We believe that two of the essential genes identified in this study, let-56 and let-52, are the adjacent genes on either side of unc-22. The lethal mutations exhibit a wide range of terminal phenotypes: from first stage larva to sterile adult.
IDENTIFICATION OF BRAIN SITES CONTROLLING FEMALE RECEPTIVITY IN MOSAICS OF DROSOPHILA MELANOGASTER
Authors: Tompkins Laurie , Hall Jeffrey C
Published: January 2021

We have identified cells in the brain of Drosophila melanogaster that are required to be of female genotype for receptivity to copulation with males. To do this, we determined experimental conditions in which female flies virtually always copulate, then measured the minimum amount of male courtship that is required to stimulate females to indicate their receptivity to copulation. We then observed gynandromorphs with female genitalia to determine whether the sex mosaics elicited at least the minimum amount of courtship and, if so, whether they copulated. By analyzing these gynandromorphs, in which the genotype of external and internal tissues could be ascertained, we were able to identify a group of cells in the dorsal anterior brain that, when bilaterally female, is necessary and sufficient for receptivity to copulation. This group of cells is anatomically distinct from those that are required to be of male genotype for the performance of courtship behaviors.
GLUCOCORTICOID-INDUCED CLEFT PALATE IN THE MOUSE: TWO MAJOR HISTOCOMPATIBILITY COMPLEX, H-2, LOCI WITH DIFFERENT MECHANISMS
Authors: Bonner Joseph J , Tyan Marvin L
Published: January 2021

Isolated cleft palate is induced in the progeny of pregnant mice that are given glucocorticoids. The incidence varies among inbred strains and with dose and stage of gestation when the drug is given. One chromosomal region responsible for strain-associated differences in sensitivity is the major histocompatibility complex, H-2. H-2a is associated with susceptibility, H-2b with resistance. There appear to be both maternal and embryonic genetic factors affecting the sensitivity to glucocorticoids. In experiments reported here congenic strains of mice with H-2a, H-2d and H-2k haplotypes on a C57BL/10 genomic background were used. This allowed the determination of the effect on sensitivity by two H-2 subregions; the subregions are H-2K to I-E and I-C to H-2D. Methods included dose-response analysis and reciprocal cross analysis using dexamethasone given on day 12 of pregnancy. Results show that each subregion affects the strain's sensitivity to dexamethasone-induced cleft palate. The regression coefficients for B10.A-H-2a (45.4 ± 4.13) were different from those for B10.BR-H-2k (67.2 ± 10.8) and B10.D2-H-2d (70.5 ± 9.74). The estimated mean arcsine% cleft palate at 160 mg/kg was different for each strain: B10.A-H-2a, 53.1 ± 2.19; B10.BR-H-2k, 33.1 ± 2.27; B10.D2-H-2d, 25.0 ± 2.75. Different patterns of change in sensitivity were observed among the reciprocal crosses. In summary, the H-2K to I-E subregion seemed to influence both maternal and embryonic factors, whereas only embryonic factors were influenced by the I-C to H-2D subregion. These data suggest that the mechanisms affecting glucocorticoid sensitivity which are genetically encoded within each H-2 subregion are different, and there is an interaction between the alleles. The mode of interaction can be either complementation or epistasis.
MITOCHONDRIAL FOUR-POINT CROSSES IN ASPERGILLUS NIDULANS: MAPPING OF A SUPPRESSOR OF A MITOCHONDRIALLY INHERITED COLD-SENSITIVE MUTATION
Authors: Waring Richard B , Scazzocchio Claudio
Published: January 2021

Four-point mitochondrial crosses were conducted in heterokaryons of Aspergillus nidulans. The mutations used were (oliA1), conferring resistance to oligomycin, (camA112), conferring resistance to chloramphenicol; (cs-67), conferring cold-sensitivity, and (sumD16), a suppressor of (cs-67). Initially, the crosses were conducted by observing the segregation of extranuclear markers in heterokaryotic sectors emerging from the original point of heterokaryosis. This showed that (camA112), (cs-67) and (sumD16) were linked but were probably all unlinked to (oliA1). Second, four-point crosses were conducted using a double marker selection technique, in which (camA112) and (oliA1) were always set in repulsion and the frequency of the phenotypes produced by the segregation of the mutant and wild-type alleles of (cs-67) and (sumD) were observed in (camA112 oliA1) recombinants. From these results we concluded that (camA112), (cs-67) and (sumD16) were linked and probably mapped in the order given. It was observed that the two nuclear types of conidia from a heterokaryon often had a dissimilar frequency distribution of the segregants of a mitochondrial cross.
ANALYSIS OF THE COVARIANCE STRUCTURE OF DIGITAL RIDGE COUNTS IN THE OFFSPRING OF MONOZYGOTIC TWINS
Authors: Cantor Rita M , Nance Walter E , Eaves Lindon J , Winter Phyllis M , Blanchard Marsha M
Published: January 2021

Improved methods for analysis of covariance structures now permit the rigorous testing of multivariate genetic hypotheses. Using Jöreskog's Lisrel IV computer program we have conducted a confirmatory factor analysis of dermal ridge counts on the individual fingers of 509 offspring of 107 monozygotic twin pairs. Prior to the initiation of the model-fitting procedure, the sex-adjusted ridge counts for the offspring of male and female twins were partitioned by a multivariate nested analysis of variance yielding five 10 ×10 variance-covariance matrices containing a total of 275 distinctly observed parameters with which to estimate latent sources of genetic and environmental variation and test hypotheses about the factor structure of those latent causes. To provide an adequate explanation for the observed patterns of covariation, it was necessary to include additive genetic, random environmental, epistatic and maternal effects in the model and a structure for the additive genetic effects which included a general factor and allowed for hand assymmetry and finger symmetry. The results illustrate the value of these methods for the analysis of interrelated metric traits.
A TAXONOMIC APPROACH TO EVALUATION OF THE CHARGE STATE MODEL USING TWELVE SPECIES OF SEA ANEMONE
Authors: McCommas Steven A
Published: January 2021

The charge-state model of electrophoretic variation was tested by comparing the distances between nearest electromorphs of five enzyme loci within polymorphic species and among pooled species of sea anemone. If the charge-state model is generally true, and in particular if it allows linear distance between electromorphs to be used as a measure of genetic distance, then electromorphs of different species should be on the same "mobility ladder". Therefore, distances between adjacent electromorphs should be approximately equal for the two sets of comparisons. It was found that distances between adjacent electromorphs for each locus were significantly smaller for the pooled comparisons than within polymorphic species. Thus, it was concluded that much of the variation detected among different species does not conform to the charge-state model, and therefore that distance between electromorphs per se would not be a good measure of genetic distance. However, the charge-state model does appear to adequately account for most of the variation existing as common polymorphisms within species, or between very closely related species. Possible reasons for this apparent difference in the nature of the variation seen within and among species are discussed.
EFFECTS OF THE SEX RATIO ORGANISM ON IN VITRO DIFFERENTIATION OF DROSOPHILA EMBRYONIC CELLS
Authors: Koana Takao , Miyake Tadashi
Published: January 2021

Effects of Sex Ratio Organism (SRO) on the development of embryonic cells of Drosophila melanogaster were studied in vitro. The single embryo culture technique and a histochemical staining method were employed to distinguish male embryo cultures from female ones. SRO-infected Zwn females were crossed to wild-type males, and their embryos were separately dissociated and cultured in vitro. Cell growth and differentiation in each culture were examined by phase contrast microscopy and described both qualitatively and quantitatively. Neurons, imaginal disk cells and plasmatocyte-like cells barely differentiated in male (Zwn/Y) cultures, whereas muscle and fatbody cells were not so severely affected. These symptoms were generally specific to male cultures. Female (Zwn/+) cultures were relatively normal. These observations are consistent with the results of mosaic analysis. The susceptibility of cells to SRO is discussed in relation to the dose of X chromosome in the cells.
THE MOLECULAR BASIS OF GENETIC DIVERSITY AMONG CYTOPLASMS OF TRITICUM AND AEGILOPS SPECIES. II. ON THE ORIGIN OF POLYPLOID WHEAT CYTOPLASMS AS SUGGESTED BY CHLOROPLAST DNA RESTRICTION FRAGMENT PATTERNS
Authors: Tsunewaki Koichiro , Ogihara Yasunari
Published: January 2021

In attempts to identify the phylogenetic donors of cytoplasm to Emmer-Dinkel and Timopheevi groups of wheat (Triticum), and the Aegilops kotschyi-Ae. variabilis complex, the restriction fragment patterns of chloroplast DNAs of representative species were compared with those of their putative diploid ancestors. The following seven restriction enzymes were used; BamHI, EcoRI, HindIII, KpnI, PstI, SmaI and XhoI. The restriction fragment patterns of an Emmer and a Dinkel (common) wheat were identical with those of Ae. longissima, and different from those of Ae. aucheri, Ae. bicornis, Ae. searsii, Ae. sharonensis, Ae. speltoides, and T. urartu by 4 to 12 fragments. The restriction fragment patterns of a Timopheevi wheat were identical with those of Ae. aucheri, and different from those of all other diploids by four to nine fragments. The restriction fragment patterns of Ae. variabilis were identical to those of Ae. bicornis and Ae. searsii, and different from those of all other species. Thus, we have concluded that Ae. longissima, Ae. aucheri and Ae. bicornis (or Ae. searsii) were the cytoplasm donors to the Emmer-Dinkel and the Timopheevi groups, and the Ae. kotschyi-Ae. variabilis complex, respectively. A diphyletic origin of Emmer and Timopheevi groups is supported by the present results.